Slicer Wiki - User contributions [en]

Slicer3:3.6 Final Issues

2011-01-11T19:19:00Z

Vrnova: /* DONE: Issues fixed for inclusion in Slicer 3.6.3 */

==TODO: Issues to fix for the 3.6.3 patch release==
* Adjust the appearance of slices in 3D view [http://www.na-mic.org/Bug/view.php?id=1061 1061]
* Resample widget does not work properly in linked mode.
* Integrate SPECTRE plugin as an extension (Nicole)
* Model Maker naming bug [http://www.na-mic.org/Bug/view.php?id=1043 1043]
* CompareView issue [http://na-mic.org/Mantis/view.php?id=936 936] (Jim)
* Maybe add DICOM support for XNAT xcat import. (Wendy)
* Integrate Endoscopic layout. (Wendy)
* Slice view toggles [http://www.na-mic.org/Bug/view.php?id=1003 1003] (Nicole)
* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.3 (Steve)
* Data loading and FetchMI:
** http://na-mic.org/Mantis/view.php?id=1029 (working on the leaks)
** http://na-mic.org/Mantis/view.php?id=1028 (partly fixed: slicer will not try to load zero-length downloads. no checksum yet.)
** http://na-mic.org/Mantis/view.php?id=1027 (fixed)
** http://na-mic.org/Mantis/view.php?id=983 (fixed)
* BRAINSResample is not available as a shared library (C++ symbol name in .so) (Jim) [http://www.na-mic.org/Bug/view.php?id=941 941]
* Remove bugs and simplify user interface of Extension manager: (Steve)
** uninstall does not work
** "Download /install" and "Uninstall" button should be removed and be executed via next button to keep philosophy of workflow wizard
* Generate Robust MRI brain registration for EMSegmenter (Dominik)
* Clean up code for creating DataIO manager in Slicer (Wendy,Steve ?) [http://na-mic.org/Mantis/view.php?id=1033 1033]
** Move vtkEMSegmentLogic::AddDataIOFromScene to base code and replace in Slicer3.cxx corresponding code with function call
** commandlines currently cannot execute links to files with http address
* 4D Image: origin is not consistent with "Add volume" loaded data [http://www.na-mic.org/Bug/view.php?id=1000 1000] (Steve, Andrey, Junichi)
* CompareView + side-by-sideLightbox + Widescreen CompareView problems [http://www.na-mic.org/Bug/view.php?id=995 995] (Jim)
* Display a warning message during installation on Windows if VC redistributable package is not installed (fix committed to the trunk by partyd on October 29, 2010)
* fix 3 view layout with endoscopy, external, and volume rendering view in distinct viewers to support Jay's programmaticly defined use-case (Steve) (not all functionality will be exposed in the GUI).
** switching layouts loses observers on scene
** no way to filter display of models or volume rendering in different viewers
* Expose step size parameter for Endoscopy (Steve)
* Warning and block when file type is changed using filename field in the Save dialog [http://www.na-mic.org/Bug/view.php?id=1064 1064]
* Loading *.mask files via 'Add Data' doesn't work [http://na-mic.org/Mantis/view.php?id=1067 1067]
* Model Hierarchy issues [http://www.na-mic.org/Bug/view.php?id=961 961] (Alex)
=== DONE: Issues fixed for inclusion in Slicer 3.6.3 ===
* Warning on unsaved data on scene close and exit (Alex)
* Status of fade slider is not captured by scenesnapshot (Alexy).
* Models Display UI cleanup (Alex)
* models under transforms do not move after save/load scene [http://www.na-mic.org/Bug/view.php?id=1058 1058] (Alex)
* multiple fiber tubes rendering performance (Alex)
* Slicer crash related to fiducials/MRML [http://www.na-mic.org/Bug/view.php?id=1042 1042] (Alex)
* Fixes to Camera/View handling (Alex & Wendy)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [[http://na-mic.org/Mantis/view.php?id=1036 1036], etc. (Alex)
* Modify ProstateNav so that it does not get recompiled all the time. Fixed in rev [http://viewvc.slicer.org/viewcvs.cgi?rev=15446&sortby=rev&sortdir=down&view=rev 15446], now only one file is recompiled. (Andras)
* Fixed BSplineDeformableRegistration (Fast non-rigid registration) CLI module to work correctly with rotated images (with direction cosines different from identity matrix) (Andras)
* Fix for vtkITKBSpline transform save with scene snapshot [http://www.na-mic.org/Bug/view.php?id=1050] (Steve)
* Fix for passing parameters to command line modules from Luca
* Fix to CropVolume module to correctly propagate the name for the output volume (Andrey)
* FastMarching crashes when applied two two different volumes one after another [http://www.na-mic.org/Bug/view.php?id=1057 1057] (Andrey)
* ChangeTracker deformable metric did not work because demons binary was not properly installed (Andrey)
* Setup node selector in LabelStatistics to allow label maps only (Andrey)
* CropVolume would not work anymore after scene is closed (Andrey)
* While in the volume rendering module, the render speed is slow while looking at a composited cross section. [http://www.na-mic.org/Bug/view.php?id=1052 1052]

==TODO: Issues to fix for the 3.6.2 patch release Oct 22/10==

* Create extensions for all versions of Slicer for the release (Steve)

=== DONE: Issues fixed for inclusion in Slicer 3.6.2 ===
* Merge "reference" volume attribute feature into CommandLineModule (Andrey)
* 3D Viewer does not update when slice model is visible and dragging the Fg/Bg slider [http://www.na-mic.org/Bug/view.php?id=1019 1019] (Alex)
* N4 module bug in histogram sharpening parameter passing (Andrey)
* Updated versions of BRAINS tools (Hans)
* Detection of some BRAINS modules (e.g. BRAINSResample) (Steve)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [http://na-mic.org/Mantis/view.php?id=1032 1032]
* Import does not correctly update reference [http://www.na-mic.org/Bug/view.php?id=1010 1010] (Alex)
* Changing names of volume nodes is not propagated to GUI [http://www.na-mic.org/Bug/view.php?id=1012 1012] (Steve)
* Editor tweaks:
** add search to the color selector box - color list dynamically filtered when typing in search box
** pick a new default size for the color selector box (or perhaps have it remember the last size/location picked by the user) - color box remembers size selected by user
** give the color box a 'recently used' section - most recently used colors are now added at top of list for easy access
** rename 'check points' to 'undo/redo'
** implement compression (to vtk stencils) for label maps in the undo/redo stack (update: vtk stencils only represent a single value so they won't work for a multi-value labelmap - looking for alternatives). Done: implemented using new vtkImageStash class that uses ZLib to compress scalar image data. Also allows for compression in background thread so it does not get in the way of interactive use.
* Failed memory allocation dialog box (Steve) - in slicer3 trunk
* 3D Viewer disappears [http://www.na-mic.org/Bug/view.php?id=1004 1004] (Alex)
* in the editor module compress saved label maps into stencils (Steve)
* Side-by-side and Widescreen compare view linking problems appear fixed.
* Ron requests default for crosshair to be navigator OFF
* Import of XNAT xcat files not working [http://www.na-mic.org/Bug/view.php?id=996 996] (Works for nrrd, not dicom. Release note added.)
* FetchMi does not store path names correctly [http://www.na-mic.org/Bug/view.php?id=993 (was listed as 998, but refers to duplicate bug 993] which appears to be fixed now.
* FetchMI problems mentioned here [http://www.na-mic.org/Bug/view.php?id=998 998] and here [http://na-mic.org/Mantis/view.php?id=955 955] are due to (1) no or loss of network connection or (2) a full cache. (Wendy) added tests for network and server availability in fetchmi and for a full cache before attempting to transact with services.
* FetchMI segfaults when uploading mrml file [http://www.na-mic.org/Bug/view.php?id=1011 1011] (Wendy: this problem is due to having no cache space. Clear the cache and make sure your filesystem has enough free space to play with, then the upload works.)
* CompareView issue [http://na-mic.org/Mantis/view.php?id=929 929] (Jim)
* Display tab in the volumes module should be open by default [http://www.na-mic.org/Bug/view.php?id=1001 1001]
* in the editor module replace the words "Check Points" with the word "Undo" (Steve)
* CompareView + Crosshairs issue [http://na-mic.org/Mantis/view.php?id=928 928] (Jim)
* Cannot change the window/level on color-by-orientation dti volumes (Alex [http://na-mic.org/Mantis/view.php?id=988]).
* Ron's requested changes to the volume rendering transfer function (email from 8/20) (Alex->Steve: implemented and checked in trunk for testing):
**add thumbnails to show effect of the transfer functions,
**remove unneeded ones, correct a typo.
**Materials are in drop box in Ronsexamples in a zipped folder called Transferfunctions.
* [http://na-mic.org/Mantis/view.php?id=971 971] Scene import does not work correctly (Alex: fixed on the trunk, Slicer3.6, SLicer4)
* Fiber bundle display GUI issue (Alex) [http://www.na-mic.org/Bug/view.php?id=994] '''NOTE: there is a MRML scene compatibility issue, see comments in [http://www.na-mic.org/Bug/view.php?id=994] '''
* Color-orientation display for DTI volumes crashes Slicer when trying to save scene [http://na-mic.org/Mantis/view.php?id=976 976] (Alex)
* Diffusion Tensor Glyphs not showing (Demian)
* Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)
* Make shift-leftbutton-drag be shift for slice viewers (Steve) (Committed to trunk -sending a binary to Ron for testing)
* volume rendering: sampling rate and a few other tweaks (Yanling)
* CompareView issues [http://na-mic.org/Mantis/view.php?id=927 927]
* Bug when volume rendering volumes with smooth gradients [http://viewvc.slicer.org/viewcvs.cgi?rev=14752&view=rev][http://viewvc.slicer.org/viewcvs.cgi?rev=14751&view=rev] (Steve)
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
* Loading a scene that contains a fiducial seeding node breaks fiducial seeding if the node points to an invalid fiducial node (Nicole)
* missing quick timeout if connection to web resource is blocked [http://na-mic.org/Mantis/view.php?id=969 969]
* [http://na-mic.org/Mantis/view.php?id=954 954] EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build
* [http://na-mic.org/Mantis/view.php?id=948 948] + [http://na-mic.org/Mantis/view.php?id=958 958] Segfault during segmentation when saving intermediate results
* [http://na-mic.org/Mantis/view.php?id=970 970] EMSegmentMRMMLanager cannot handle two taks
* [http://na-mic.org/Mantis/view.php?id=973 973] MRML file does not read nrrd files correctly when the files are located in different directory
* Ordering of the series by number in DICOM browser [http://na-mic.org/Mantis/view.php?id=965 965] (Steve)
* Create robust pipeline for 3D MRI brain images [http://na-mic.org/Mantis/view.php?id=972 972] (Kilian)
* It seems that the camera does not transform correctly under transform node (Steve). [http://na-mic.org/Mantis/view.php?id=957 957] fixed and checked in.
* Reading fiducial lists with .txt extensions. [http://www.na-mic.org/Bug/view.php?id=991 991] (Nicole)
* add the --tmpdir option to the start up allowing one to specify slicers temporary directory (Dominique)
* Fix the leaks in the nightly tests [http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=731096] (Dominique)
* Issue [http://na-mic.org/Mantis/view.php?id=968 968]: LD_LIBRARY_PATH screwewd up when no network connection (Steve with Kilian)
* Relative paths in volume storage nodes [http://www.na-mic.org/Bug/view.php?id=993 993] (Nicole)
* [https://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:GPURayCaster#Open_Issues VTK GPU Ray Cast issues] (Julien)
** Flickering has not been improved since 3.6.1.
** Crash on MAC: the 2 Apple bug reports from Francois Bertel and James Barabas are still open (rank #1). Apple didn't contact them.
* Change names of the grow cut gesture volume nodes to be consistent with the naming conventions of label map (Harini)
* Grow Cut: Change the gesture volume node to be displayed on the foreground and the segmented label volume node to be displayed on the label layer of the slice views (Harini)
* Grow Cut: Modify the opacities of the label layer and the foreground layer to overlay the user input gestures, the resulting segmentation on the image background (Harini)
* Grow Cut: Modify user interface for setting inputs to the Grow Cut algorithm (Harini)
* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.2 (Steve)
* [[Slicer3:Editor_Tuning_3.6.2|Several tweaks to the Editor Module]] (Steve)
* Resolve EMSegmenter related bug in connection with BRAINSFit [http://na-mic.org/Mantis/view.php?id=1025 1025] (Dominique)
* Resolved GetReferenceSubScene bugs: [http://na-mic.org/Mantis/view.php?id=1023 1023], [http://na-mic.org/Mantis/view.php?id=1031 1031], [http://na-mic.org/Mantis/view.php?id=1031 1034], [http://na-mic.org/Mantis/view.php?id=1035 1035]

==DONE: Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm==

* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex).
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)
* Updated meshing module (Curt) - checked in trunk for [http://www.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010|tutorial contest]; needs merge to branch if all is well.
* "Change island" effect of Editor is not functioning when the Scope is set to "all"
* Scene save/restore crash for dti tutorial (Steve/Alex). [http://viewvc.slicer.org/viewcvs.cgi?rev=14416&view=rev] and [http://viewvc.slicer.org/viewcvs.cgi?rev=14415&view=rev]
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve) - in trunk, need to move to branch
* KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 [http://na-mic.org/Mantis/view.php?id=886 bug 886] (Steve)
* Tractography display modes issue with Data module (FiberBundles have 3 display nodes but the Data tree has only one eye icon). (Alex) (Steve disabled the eye icon for in the Data tree for any displayable with more than one display node)
* Fix for crash after Save Island operation on windows (Steve) [http://viewvc.slicer.org/viewcvs.cgi?rev=14505&view=rev]
* EMSegment command line works now with BRAINS (Kilian)
* Removed KWWidgets that do not work under Windows (Kilian)
* fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)
* fixed editor error dialog when editing on rotated volumes with some geometries (Steve [http://viewvc.slicer.org/viewcvs.cgi?rev=14668&view=rev], [http://viewvc.slicer.org/viewcvs.cgi?rev=14667&view=rev])
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)

==3.6 Release issues==
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:

'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]'''

*VTK GPU ray-cast clipping issue
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]
**90% of the flickering when the camera is inside the volume is removed
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)

*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).

Done:
* Remove unused color and glyph options from fiber bundle display (Alex)
* fiducial behavior
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)
** saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch
** tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!
** done for 2d, Andras has tested it and says it's fine
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)
*getting BRAINS tests to pass (Hans is working on it)
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).
* are there extra pick operations going on? There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. ''could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same''
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''
** should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. ''Not a good idea to change behavior at this point''
* roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)
* view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now!
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:
**for Output DTI volume: DTI Volume
**for Output Baseline Volume: Baseline DTI Volume
**for Otsu Threshold Mask: Otsu Threshold Label Volume
*new default color table (Nicole and Mike)
** Mike working on creating a LUT from <strike>[[CCA:Atlases:Florins_2010_Hierarchy|this hierarchy]]</strike> [[CCA:Atlases:Florins_2010_Hierarchy_Short|this subset]], by Jun 7
** Steve and Nicole to meet June 9 to integrate default editor color table
** Jun 10: checked in new color files, one from [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]], and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)

Issues that cannot be fixed (or aren't crucial to fix) should be listed in [[Release-notes-3.6| the slicer 3.6 release notes]].

Slicer3:3.6 Final Issues

2011-01-11T19:18:39Z

Vrnova: /* TODO: Issues to fix for the 3.6.3 patch release */

==TODO: Issues to fix for the 3.6.3 patch release==
* Adjust the appearance of slices in 3D view [http://www.na-mic.org/Bug/view.php?id=1061 1061]
* Resample widget does not work properly in linked mode.
* Integrate SPECTRE plugin as an extension (Nicole)
* Model Maker naming bug [http://www.na-mic.org/Bug/view.php?id=1043 1043]
* CompareView issue [http://na-mic.org/Mantis/view.php?id=936 936] (Jim)
* Maybe add DICOM support for XNAT xcat import. (Wendy)
* Integrate Endoscopic layout. (Wendy)
* Slice view toggles [http://www.na-mic.org/Bug/view.php?id=1003 1003] (Nicole)
* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.3 (Steve)
* Data loading and FetchMI:
** http://na-mic.org/Mantis/view.php?id=1029 (working on the leaks)
** http://na-mic.org/Mantis/view.php?id=1028 (partly fixed: slicer will not try to load zero-length downloads. no checksum yet.)
** http://na-mic.org/Mantis/view.php?id=1027 (fixed)
** http://na-mic.org/Mantis/view.php?id=983 (fixed)
* BRAINSResample is not available as a shared library (C++ symbol name in .so) (Jim) [http://www.na-mic.org/Bug/view.php?id=941 941]
* Remove bugs and simplify user interface of Extension manager: (Steve)
** uninstall does not work
** "Download /install" and "Uninstall" button should be removed and be executed via next button to keep philosophy of workflow wizard
* Generate Robust MRI brain registration for EMSegmenter (Dominik)
* Clean up code for creating DataIO manager in Slicer (Wendy,Steve ?) [http://na-mic.org/Mantis/view.php?id=1033 1033]
** Move vtkEMSegmentLogic::AddDataIOFromScene to base code and replace in Slicer3.cxx corresponding code with function call
** commandlines currently cannot execute links to files with http address
* 4D Image: origin is not consistent with "Add volume" loaded data [http://www.na-mic.org/Bug/view.php?id=1000 1000] (Steve, Andrey, Junichi)
* CompareView + side-by-sideLightbox + Widescreen CompareView problems [http://www.na-mic.org/Bug/view.php?id=995 995] (Jim)
* Display a warning message during installation on Windows if VC redistributable package is not installed (fix committed to the trunk by partyd on October 29, 2010)
* fix 3 view layout with endoscopy, external, and volume rendering view in distinct viewers to support Jay's programmaticly defined use-case (Steve) (not all functionality will be exposed in the GUI).
** switching layouts loses observers on scene
** no way to filter display of models or volume rendering in different viewers
* Expose step size parameter for Endoscopy (Steve)
* Warning and block when file type is changed using filename field in the Save dialog [http://www.na-mic.org/Bug/view.php?id=1064 1064]
* Loading *.mask files via 'Add Data' doesn't work [http://na-mic.org/Mantis/view.php?id=1067 1067]
* Model Hierarchy issues [http://www.na-mic.org/Bug/view.php?id=961 961] (Alex)
=== DONE: Issues fixed for inclusion in Slicer 3.6.3 ===
* Warning on unsaved data on scene close and exit (Alex)
* Status of fade slider is not captured by scenesnapshot (Alexy).
* Models Display UI cleanup (Alex)
* models under transforms do not move after save/load scene [http://www.na-mic.org/Bug/view.php?id=1058 1058] (Alex)
* multiple fiber tubes rendering performance (Alex)
* Slicer crash related to fiducials/MRML [http://www.na-mic.org/Bug/view.php?id=1042 1042] (Alex)
* Fixes to Camera/View handling (Alex & Wendy)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [[http://na-mic.org/Mantis/view.php?id=1036 1036], etc. (Alex)
* Modify ProstateNav so that it does not get recompiled all the time. Fixed in rev [http://viewvc.slicer.org/viewcvs.cgi?rev=15446&sortby=rev&sortdir=down&view=rev 15446], now only one file is recompiled. (Andras)
* Fixed BSplineDeformableRegistration (Fast non-rigid registration) CLI module to work correctly with rotated images (with direction cosines different from identity matrix) (Andras)
* Fix for vtkITKBSpline transform save with scene snapshot [http://www.na-mic.org/Bug/view.php?id=1050] (Steve)
* Fix for passing parameters to command line modules from Luca
* Fix to CropVolume module to correctly propagate the name for the output volume (Andrey)
* FastMarching crashes when applied two two different volumes one after another [http://www.na-mic.org/Bug/view.php?id=1057 1057] (Andrey)
* ChangeTracker deformable metric did not work because demons binary was not properly installed (Andrey)
* Setup node selector in LabelStatistics to allow label maps only (Andrey)
* CropVolume would not work anymore after scene is closed (Andrey)

==TODO: Issues to fix for the 3.6.2 patch release Oct 22/10==

* Create extensions for all versions of Slicer for the release (Steve)

=== DONE: Issues fixed for inclusion in Slicer 3.6.2 ===
* Merge "reference" volume attribute feature into CommandLineModule (Andrey)
* 3D Viewer does not update when slice model is visible and dragging the Fg/Bg slider [http://www.na-mic.org/Bug/view.php?id=1019 1019] (Alex)
* N4 module bug in histogram sharpening parameter passing (Andrey)
* Updated versions of BRAINS tools (Hans)
* Detection of some BRAINS modules (e.g. BRAINSResample) (Steve)
* Resolve bugs concerning vtkMRMLScene::GetReferencedSubScene [http://na-mic.org/Mantis/view.php?id=1032 1032]
* Import does not correctly update reference [http://www.na-mic.org/Bug/view.php?id=1010 1010] (Alex)
* Changing names of volume nodes is not propagated to GUI [http://www.na-mic.org/Bug/view.php?id=1012 1012] (Steve)
* Editor tweaks:
** add search to the color selector box - color list dynamically filtered when typing in search box
** pick a new default size for the color selector box (or perhaps have it remember the last size/location picked by the user) - color box remembers size selected by user
** give the color box a 'recently used' section - most recently used colors are now added at top of list for easy access
** rename 'check points' to 'undo/redo'
** implement compression (to vtk stencils) for label maps in the undo/redo stack (update: vtk stencils only represent a single value so they won't work for a multi-value labelmap - looking for alternatives). Done: implemented using new vtkImageStash class that uses ZLib to compress scalar image data. Also allows for compression in background thread so it does not get in the way of interactive use.
* Failed memory allocation dialog box (Steve) - in slicer3 trunk
* 3D Viewer disappears [http://www.na-mic.org/Bug/view.php?id=1004 1004] (Alex)
* in the editor module compress saved label maps into stencils (Steve)
* Side-by-side and Widescreen compare view linking problems appear fixed.
* Ron requests default for crosshair to be navigator OFF
* Import of XNAT xcat files not working [http://www.na-mic.org/Bug/view.php?id=996 996] (Works for nrrd, not dicom. Release note added.)
* FetchMi does not store path names correctly [http://www.na-mic.org/Bug/view.php?id=993 (was listed as 998, but refers to duplicate bug 993] which appears to be fixed now.
* FetchMI problems mentioned here [http://www.na-mic.org/Bug/view.php?id=998 998] and here [http://na-mic.org/Mantis/view.php?id=955 955] are due to (1) no or loss of network connection or (2) a full cache. (Wendy) added tests for network and server availability in fetchmi and for a full cache before attempting to transact with services.
* FetchMI segfaults when uploading mrml file [http://www.na-mic.org/Bug/view.php?id=1011 1011] (Wendy: this problem is due to having no cache space. Clear the cache and make sure your filesystem has enough free space to play with, then the upload works.)
* CompareView issue [http://na-mic.org/Mantis/view.php?id=929 929] (Jim)
* Display tab in the volumes module should be open by default [http://www.na-mic.org/Bug/view.php?id=1001 1001]
* in the editor module replace the words "Check Points" with the word "Undo" (Steve)
* CompareView + Crosshairs issue [http://na-mic.org/Mantis/view.php?id=928 928] (Jim)
* Cannot change the window/level on color-by-orientation dti volumes (Alex [http://na-mic.org/Mantis/view.php?id=988]).
* Ron's requested changes to the volume rendering transfer function (email from 8/20) (Alex->Steve: implemented and checked in trunk for testing):
**add thumbnails to show effect of the transfer functions,
**remove unneeded ones, correct a typo.
**Materials are in drop box in Ronsexamples in a zipped folder called Transferfunctions.
* [http://na-mic.org/Mantis/view.php?id=971 971] Scene import does not work correctly (Alex: fixed on the trunk, Slicer3.6, SLicer4)
* Fiber bundle display GUI issue (Alex) [http://www.na-mic.org/Bug/view.php?id=994] '''NOTE: there is a MRML scene compatibility issue, see comments in [http://www.na-mic.org/Bug/view.php?id=994] '''
* Color-orientation display for DTI volumes crashes Slicer when trying to save scene [http://na-mic.org/Mantis/view.php?id=976 976] (Alex)
* Diffusion Tensor Glyphs not showing (Demian)
* Diffusion Tensor Tractography having a strange no-tracking through high FA areas case (Demian)
* Make shift-leftbutton-drag be shift for slice viewers (Steve) (Committed to trunk -sending a binary to Ron for testing)
* volume rendering: sampling rate and a few other tweaks (Yanling)
* CompareView issues [http://na-mic.org/Mantis/view.php?id=927 927]
* Bug when volume rendering volumes with smooth gradients [http://viewvc.slicer.org/viewcvs.cgi?rev=14752&view=rev][http://viewvc.slicer.org/viewcvs.cgi?rev=14751&view=rev] (Steve)
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
* Loading a scene that contains a fiducial seeding node breaks fiducial seeding if the node points to an invalid fiducial node (Nicole)
* missing quick timeout if connection to web resource is blocked [http://na-mic.org/Mantis/view.php?id=969 969]
* [http://na-mic.org/Mantis/view.php?id=954 954] EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build
* [http://na-mic.org/Mantis/view.php?id=948 948] + [http://na-mic.org/Mantis/view.php?id=958 958] Segfault during segmentation when saving intermediate results
* [http://na-mic.org/Mantis/view.php?id=970 970] EMSegmentMRMMLanager cannot handle two taks
* [http://na-mic.org/Mantis/view.php?id=973 973] MRML file does not read nrrd files correctly when the files are located in different directory
* Ordering of the series by number in DICOM browser [http://na-mic.org/Mantis/view.php?id=965 965] (Steve)
* Create robust pipeline for 3D MRI brain images [http://na-mic.org/Mantis/view.php?id=972 972] (Kilian)
* It seems that the camera does not transform correctly under transform node (Steve). [http://na-mic.org/Mantis/view.php?id=957 957] fixed and checked in.
* Reading fiducial lists with .txt extensions. [http://www.na-mic.org/Bug/view.php?id=991 991] (Nicole)
* add the --tmpdir option to the start up allowing one to specify slicers temporary directory (Dominique)
* Fix the leaks in the nightly tests [http://www.cdash.org/CDash/viewTest.php?onlyfailed&buildid=731096] (Dominique)
* Issue [http://na-mic.org/Mantis/view.php?id=968 968]: LD_LIBRARY_PATH screwewd up when no network connection (Steve with Kilian)
* Relative paths in volume storage nodes [http://www.na-mic.org/Bug/view.php?id=993 993] (Nicole)
* [https://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:GPURayCaster#Open_Issues VTK GPU Ray Cast issues] (Julien)
** Flickering has not been improved since 3.6.1.
** Crash on MAC: the 2 Apple bug reports from Francois Bertel and James Barabas are still open (rank #1). Apple didn't contact them.
* Change names of the grow cut gesture volume nodes to be consistent with the naming conventions of label map (Harini)
* Grow Cut: Change the gesture volume node to be displayed on the foreground and the segmented label volume node to be displayed on the label layer of the slice views (Harini)
* Grow Cut: Modify the opacities of the label layer and the foreground layer to overlay the user input gestures, the resulting segmentation on the image background (Harini)
* Grow Cut: Modify user interface for setting inputs to the Grow Cut algorithm (Harini)
* [[Slicer3:ChangingVersionsCheckList | update to version]] 3.6.2 (Steve)
* [[Slicer3:Editor_Tuning_3.6.2|Several tweaks to the Editor Module]] (Steve)
* Resolve EMSegmenter related bug in connection with BRAINSFit [http://na-mic.org/Mantis/view.php?id=1025 1025] (Dominique)
* Resolved GetReferenceSubScene bugs: [http://na-mic.org/Mantis/view.php?id=1023 1023], [http://na-mic.org/Mantis/view.php?id=1031 1031], [http://na-mic.org/Mantis/view.php?id=1031 1034], [http://na-mic.org/Mantis/view.php?id=1035 1035]

==DONE: Issues included in 3.6.1 patch release - in Slicer-3-6 branch by 2010-08-03 6pm==

* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex).
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)
* Updated meshing module (Curt) - checked in trunk for [http://www.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010|tutorial contest]; needs merge to branch if all is well.
* "Change island" effect of Editor is not functioning when the Scope is set to "all"
* Scene save/restore crash for dti tutorial (Steve/Alex). [http://viewvc.slicer.org/viewcvs.cgi?rev=14416&view=rev] and [http://viewvc.slicer.org/viewcvs.cgi?rev=14415&view=rev]
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve) - in trunk, need to move to branch
* KWWidgets issue with "%" in file names produced by DICOM browser -- fixed in trunk, need to make sure propagated to 3.6 [http://na-mic.org/Mantis/view.php?id=886 bug 886] (Steve)
* Tractography display modes issue with Data module (FiberBundles have 3 display nodes but the Data tree has only one eye icon). (Alex) (Steve disabled the eye icon for in the Data tree for any displayable with more than one display node)
* Fix for crash after Save Island operation on windows (Steve) [http://viewvc.slicer.org/viewcvs.cgi?rev=14505&view=rev]
* EMSegment command line works now with BRAINS (Kilian)
* Removed KWWidgets that do not work under Windows (Kilian)
* fixed warning for some bad image spacing geometries http://www.na-mic.org/Bug/view.php?id=951 (Steve)
* fixed editor error dialog when editing on rotated volumes with some geometries (Steve [http://viewvc.slicer.org/viewcvs.cgi?rev=14668&view=rev], [http://viewvc.slicer.org/viewcvs.cgi?rev=14667&view=rev])
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)

==3.6 Release issues==
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:

'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]'''

*VTK GPU ray-cast clipping issue
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]
**90% of the flickering when the camera is inside the volume is removed
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)

*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).

Done:
* Remove unused color and glyph options from fiber bundle display (Alex)
* fiducial behavior
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)
** saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch
** tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!
** done for 2d, Andras has tested it and says it's fine
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)
*getting BRAINS tests to pass (Hans is working on it)
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).
* are there extra pick operations going on? There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. ''could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same''
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''
** should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. ''Not a good idea to change behavior at this point''
* roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)
* view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now!
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:
**for Output DTI volume: DTI Volume
**for Output Baseline Volume: Baseline DTI Volume
**for Otsu Threshold Mask: Otsu Threshold Label Volume
*new default color table (Nicole and Mike)
** Mike working on creating a LUT from <strike>[[CCA:Atlases:Florins_2010_Hierarchy|this hierarchy]]</strike> [[CCA:Atlases:Florins_2010_Hierarchy_Short|this subset]], by Jun 7
** Steve and Nicole to meet June 9 to integrate default editor color table
** Jun 10: checked in new color files, one from [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]], and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)

Issues that cannot be fixed (or aren't crucial to fix) should be listed in [[Release-notes-3.6| the slicer 3.6 release notes]].

Modules:VolumeRendering-Documentation-3.6

2010-07-26T15:28:58Z

Vrnova: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* '''Distance Color Blending in NCI GPU Ray Casting'''
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* '''Pausing VolumeRendering module in scene loading'''
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* '''Multi-Volume GPU Ray Casting'''
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|[[Image:PET-CT.gif|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* '''Dual 3D View mode'''
**The NCI GPU Ray casting does support the Dual 3D View mode.
**The VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* '''Volume-Following Mode'''
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Intro:
***VTK CPU raycasting can do both volume rendering and z-buffer compositing. The same is true for the VTK GRPU ray casting and the VTK OpenGL 3D Texture mapping methods, the latter sometimes produces a "rougher" looking image. The NCI GPU raycaster offers good quality and speed, but does not allow for z-buffer compositing. That means that the volume rendering cannot be combined with a triangulated surface model or a cross section in the 3D view.
*** In general you want dedicated GPUs with dedicated GPU memory, if using GPU accelerated methods. Computers that are labeled "gaming computers" will usually have the right type of hardware. Depending on the size of data that is rendered, you will need more GPU memory. If your data set is too large for your memory, performance will drop considerably. It might take some time before the rendering is shown.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** Dist. Color Blending: Enhancing depth info in volume rendering by darkening voxels based on their distance to user/camera. Voxels more far away will be darken more.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information in video card driver control panel on your computer.
** Quality Control: Defines mapper rendering behavior
*** Adaptive: Effect on all mappers. When user using mouse button to do interactions, all mappers automatically switch to the frame rate setting in '''Interactive Speed'''. After user release mouse button to finish interaction, all mappers switch back to highest quality rendering.
*** Maximum: Force highest quality rendering on all mappers except VTK OpenGL Texture Mapping
*** Fixed Framerate: Force mapper to user fixed frame rate setting in '''Interactive Speed'''. Effect on NCI mappers only.
*** Interactive Speed: defines the frame rate to be used during user interaction, for example, rotate the volume using mouse left button.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-07-26T15:28:03Z

Vrnova: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* '''Distance Color Blending in NCI GPU Ray Casting'''
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* '''Pausing VolumeRendering module in scene loading'''
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* '''Multi-Volume GPU Ray Casting'''
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|[[Image:PET-CT.gif|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* '''Dual 3D View mode'''
**The NCI GPU Ray casting does support the Dual 3D View mode.
**The VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* '''Volume-Following Mode'''
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Intro:
***VTK CPU raycasting can do both volume rendering and z-buffer compositing. The same is true for the VTK GRPU ray casting and the VTK OpenGL 3D Texture mapping methods, the latter sometimes produces a "rougher" looking image. The NCI GPU raycaster offers good quality and speed, but does not allow for z-buffer compositing. That means that the volume rendering cannot be combined with a triangulated surface model or a cross section in the 3D view.
*** In general you want dedicated GPUs with dedicated GPU memory, if using GPU accelerated methods. Computers that are labeled "gaming computers" will usually have the right type of hardware. Depending on the size of data that is rendered, you will need more GPU memory. If your data set is too large for your memory, performance will drop considerably. It might take some time before the rendering is shown.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** Dist. Color Blending: Enhancing depth info in volume rendering by darkening voxels far away from user/camera.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information in video card driver control panel on your computer.
** Quality Control: Defines mapper rendering behavior
*** Adaptive: Effect on all mappers. When user using mouse button to do interactions, all mappers automatically switch to the frame rate setting in '''Interactive Speed'''. After user release mouse button to finish interaction, all mappers switch back to highest quality rendering.
*** Maximum: Force highest quality rendering on all mappers except VTK OpenGL Texture Mapping
*** Fixed Framerate: Force mapper to user fixed frame rate setting in '''Interactive Speed'''. Effect on NCI mappers only.
*** Interactive Speed: defines the frame rate to be used during user interaction, for example, rotate the volume using mouse left button.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-07-26T15:26:24Z

Vrnova: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* '''Distance Color Blending in NCI GPU Ray Casting'''
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* '''Pausing VolumeRendering module in scene loading'''
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* '''Multi-Volume GPU Ray Casting'''
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|[[Image:PET-CT.gif|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* '''Dual 3D View mode'''
**The NCI GPU Ray casting does support the Dual 3D View mode.
**The VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* '''Volume-Following Mode'''
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Intro:
***VTK CPU raycasting can do both volume rendering and z-buffer compositing. The same is true for the VTK GRPU ray casting and the VTK OpenGL 3D Texture mapping methods, the latter sometimes produces a "rougher" looking image. The NCI GPU raycaster offers good quality and speed, but does not allow for z-buffer compositing. That means that the volume rendering cannot be combined with a triangulated surface model or a cross section in the 3D view.
*** In general you want dedicated GPUs with dedicated GPU memory, if using GPU accelerated methods. Computers that are labeled "gaming computers" will usually have the right type of hardware. Depending on the size of data that is rendered, you will need more GPU memory. If your data set is too large for your memory, performance will drop considerably. It might take some time before the rendering is shown.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information in video card driver control panel on your computer.
** Quality Control: Defines mapper rendering behavior
*** Adaptive: Effect on all mappers. When user using mouse button to do interactions, all mappers automatically switch to the frame rate setting in '''Interactive Speed'''. After user release mouse button to finish interaction, all mappers switch back to highest quality rendering.
*** Maximum: Force highest quality rendering on all mappers except VTK OpenGL Texture Mapping
*** Fixed Framerate: Force mapper to user fixed frame rate setting in '''Interactive Speed'''. Effect on NCI mappers only.
*** Interactive Speed: defines the frame rate to be used during user interaction, for example, rotate the volume using mouse left button.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-07-25T20:43:26Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* '''Distance Color Blending in NCI GPU Ray Casting'''
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* '''Pausing VolumeRendering module in scene loading'''
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* '''Multi-Volume GPU Ray Casting'''
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|[[Image:PET-CT.gif|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* '''Dual 3D View mode'''
**The NCI GPU Ray casting does support the Dual 3D View mode.
**The VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* '''Volume-Following Mode'''
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Intro:
***VTK CPU raycasting can do both volume rendering and z-buffer compositing. The same is true for the VTK GRPU ray casting and the VTK OpenGL 3D Texture mapping methods, the latter sometimes produces a "rougher" looking image. The NCI GPU raycaster offers good quality and speed, but does not allow for z-buffer compositing. That means that the volume rendering cannot be combined with a triangulated surface model or a cross section in the 3D view.
*** In general you want dedicated GPUs with dedicated GPU memory, if using GPU accelerated methods. Computers that are labeled "gaming computers" will usually have the right type of hardware. Depending on the size of data that is rendered, you will need more GPU memory. If your data set is too large for your memory, performance will drop considerably. It might take some time before the rendering is shown.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Slicer3:3.6 Final Issues

2010-07-25T16:33:43Z

Vrnova: /* 3.6 Release issues */

==Issues to include in 3.6.1 patch release==

* Fixes for EMSegment command line working with BRAINS (Kilian)
* VTK GPU Ray Cast flashing (Julien)
* Picking NCI GPU Raycasting on machine that doesn't support it causes lockup (Yanling)
* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch
* Editor rounding issue [http://www.na-mic.org/Bug/view.php?id=932] (Steve)
* Snapshot issue [http://na-mic.org/Mantis/view.php?id=933] (Alex)

Done (in branches/Slicer-3-6 after June 10):
* check for duplicate filepaths when saving data (Alex) http://www.na-mic.org/Bug/view.php?id=925
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885: Changed Tracttography/LabelMapSeeding module: 1. added UseIndexSpace option for seeding placement. 2. Also found that IJK indexes used for traversing the label volume were floats. Changed them to doubles that may crate slightly different tracts, but it is less prone to error accumulation (Alex).
* Added multi-label selection to Tractography/ROISelect module (PNL request for Slicer2 compatibility, Alex)
* Added more scalar options to Diffusion Tensor Scalar Measurement module (PNL request for Slicer2 compatibility, Alex)
* [http://www.na-mic.org/Bug/view.php?id=871 fix] for Python programming tutorial (Steve, Luca)
* Fixes for color table preview icons showing up in node selectors (Wendy and Nicole)
** [http://viewvc.slicer.org/viewcvs.cgi?rev=13771&view=rev svn 1377]
* DicomToNrrd issues reported by AlexZ and Sylvain (Xiaodong)
* Crosshair traking modes (Jim); also see [http://na-mic.org/Mantis/view.php?id=861 bug #861]
* Wizard page transition error in ProstateNav. The issue was fixed by Haiying.
* OpenIGTLink reslice performance (Junichi) (fixed by Steve)
* Updated meshing module (Curt) - checked in trunk for [http://www.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010|tutorial contest]; needs merge to branch if all is well.

==3.6 Release issues==
Final punch list for [[Slicer3:3.6Release|slicer 3.6 release]]:

'''Finalized June 10 for 3.6 binaries and [[Announcements:Slicer3.6]]'''

*VTK GPU ray-cast clipping issue
**bug fix:[[http://na-mic.org/Mantis/view.php?id=800 Non axis aligned volumes]]
**bug fix:[[http://na-mic.org/Mantis/view.php?id=798#c1780 ROI on Non axis aligned volumes]]
**90% of the flickering when the camera is inside the volume is removed
*compare view + crosshair issue when loading a scene, the crosshair does not appear in all viewers until the slice location is changed, (Jim)

*Picking NCI GPU Raycasting on machine that doesn't support it causes lockup. Not able to reproduce the problem (Yanling).

Done:
* Remove unused color and glyph options from fiber bundle display (Alex)
* fiducial behavior
* fiducial behavior/3D viewer behavior: (Steve, Nicole, Wendy met Jun 7)
** saw one example of persistent place mode being stolen by pick mode. I think this has to do with inappropriate initialization of modes. It is possible for pick mode to take over until transient-pick mode is explicitly chosen. (FIXED)
** tractography updates not happening during drag - fixes checked into SlicerVTK and Slicer3 branch
** tractography updates slow when drag stops (Steve confirmed this was due to update only happening when mouse was moved after button released - made it seem extra slow)
**widget issues (Nicole putting fixes in [http://github.com/pieper/CTK SlicerVTK])
*making sure mouse-modes work same in 3D/2D (Wendy and Nicole) Let's call it DONE!
** done for 2d, Andras has tested it and says it's fine
*editor volume merge feature clarification (Steve meeting Sonia June 2, fixes committed June 3)
*getting BRAINS tests to pass (Hans is working on it)
*tracking down what is making that crash on Mac OsX when several PET volumes are loaded into Slicer (Wendy).
* are there extra pick operations going on? There seems to be a delay after clicking mouse before camera begins to rotate when large models are present in scene. ''could not replicate - tried 2.5 million triangle model on slicer and paraview and performance is the same''
* should picking of fiducials in 3D be disabled unless user explicitly chooses 'pick mode'? ''Not a good idea to change behavior at this point''
** should parallel behavior be implemented in 2D for consistency? Stevie votes no, Wendy votes yes. ''Not a good idea to change behavior at this point''
* roundtrip to xnat desktop --OK: confirmed that Ron was using dirty files in cache; checking 'always re-download' in the Cache and DataI/O Manager GUI caused fresh download and successful load into slicer. Sometimes, even when you delete cached files thru the GUI, some applicaiton is holding on to files still there and they don't get cleared out. I'm adding a little code to check for remaining files after a ClearCache() is called; if so, we'll warn user that not all files were removed, and to select 'always re-download' to ensure proper data loading.(Wendy)
* view control gui: (Wendy) this guy isn't always updating anymore. He may be a casualty of multiple view nodes in the scene. He was a casualty but is fixed now!
*The diffusion tensor estimation module is using defaults that are not good and partially incorrect. Can the defaults be as follows:
**for Output DTI volume: DTI Volume
**for Output Baseline Volume: Baseline DTI Volume
**for Otsu Threshold Mask: Otsu Threshold Label Volume
*new default color table (Nicole and Mike)
** Mike working on creating a LUT from <strike>[[CCA:Atlases:Florins_2010_Hierarchy|this hierarchy]]</strike> [[CCA:Atlases:Florins_2010_Hierarchy_Short|this subset]], by Jun 7
** Steve and Nicole to meet June 9 to integrate default editor color table
** Jun 10: checked in new color files, one from [[Slicer3:2010_GenericAnatomyColors|GenericAnatomyColors]], and one based on that but with names set to integer values and the color for 255 changed to blue. Wendy making new drop down menu icons.
*finishing up the DICOM file copy on remote upload, also close (Wendy) (DONE)

Issues that cannot be fixed (or aren't crucial to fix) should be listed in [[Release-notes-3.6| the slicer 3.6 release notes]].

Modules:VolumeRendering-Documentation-3.6

2010-06-06T02:13:25Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* '''Distance Color Blending in NCI GPU Ray Casting'''
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* '''Pausing VolumeRendering module in scene loading'''
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* '''Multi-Volume GPU Ray Casting'''
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|[[Image:PET-CT.gif|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* '''Dual 3D View mode'''
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* '''Volume-Following Mode'''
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-06-06T02:11:36Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* '''Distance Color Blending in NCI GPU Ray Casting'''
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* '''Pausing VolumeRendering module in scene loading'''
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* '''Multi-Volume GPU Ray Casting'''
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|[[Image:PET-CT.gif|thumb|320px|PET-CT Visualization]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* '''Dual 3D View mode'''
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* '''Volume-Following Mode'''
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

File:PET-CT.gif

2010-06-06T02:03:07Z

Vrnova: uploaded a new version of "File:PET-CT.gif": Reverted to version as of 01:52, 6 June 2010

File:PET-CT.gif

2010-06-06T02:01:05Z

Vrnova: uploaded a new version of "File:PET-CT.gif"

Modules:VolumeRendering-Documentation-3.6

2010-06-06T01:59:02Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* '''Distance Color Blending in NCI GPU Ray Casting'''
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* '''Pausing VolumeRendering module in scene loading'''
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* '''Multi-Volume GPU Ray Casting'''
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|[[Image:PET-CT.gif|PET-CT Visualization]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* '''Dual 3D View mode'''
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* '''Volume-Following Mode'''
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

File:PET-CT.gif

2010-06-06T01:52:57Z

Vrnova:

Modules:VolumeRendering-Documentation-3.6

2010-06-06T00:17:43Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* '''Distance Color Blending in NCI GPU Ray Casting'''
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* '''Pausing VolumeRendering module in scene loading'''
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* '''Multi-Volume GPU Ray Casting'''
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. GMOM rendering technique used for both bg and fg.]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* '''Dual 3D View mode'''
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* '''Volume-Following Mode'''
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-06-05T01:53:46Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* '''Distance Color Blending in NCI GPU Ray Casting'''
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* '''Pausing VolumeRendering module in scene loading'''
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* '''Multi-Volume GPU Ray Casting'''
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. ]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* '''Dual 3D View mode'''
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* '''Volume-Following Mode'''
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-06-05T01:52:57Z

Vrnova: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. ]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.'' Both bg and fg volumes need to have '''same data type'''. See above Use Case and Example section for details.
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-06-05T01:51:44Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer to crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. ]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-06-05T01:50:56Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg), GMOM (bg) + GMOM (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. ]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-06-05T01:45:19Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have '''same data type'''. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float. Using bg and fg volumes with different data type may cause Slicer crash.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. ]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-06-05T01:44:14Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

'''Important:''' when using Multi-Volume GPU Ray Casting, both bg and fg volume need to have the same data type. Please use Cast Image filter to cast image with smaller data type to larger data type. For example, if bg volume is short and fg volume is float, use Cast Image filter to cast bg volume to be float.
{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. ]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-06-04T19:55:27Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization. Gray scale colors are from PET volume. Non-Gray scale colors are from CT volume. ]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-06-04T14:31:02Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:PET-CT.png|thumb|320px|PET-CT Visualization]]
|}

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' ''Note: this is a newly added mode that should be considered experimental.'' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

File:PET-CT.png

2010-06-04T14:29:53Z

Vrnova:

Announcments-3.6-Team

2010-06-03T21:41:37Z

Vrnova:

Back to the [[Announcements:Slicer3.6|Slicer 3.6 announcement]]

Development of Slicer 3.6 has been supported through volunteer work and through a number of funding mechanisms and sources. Please see the [http://www.slicer.org/pages/Acknowledgments Slicer Acknowledgements] page.

Major contributors for the Slicer 3.6 release include (in alphabetic order):
* [http://www.orobix.com/luca Luca Antiga]: Python integration, CLI
* [http://www.spl.harvard.edu/pages/People/nicole Nicole Aucoin]: Software development, Fiducials, Informatics
* [http://kitware.com/company/team/aylward.html Stephen Aylward]: Registration, ITK
* [http://www.kitware.com/company/team/barre.html Sébastien Barré]: GUI, KWWidgets
* [http://www.niral.unc.edu/people Francois Budin]: Resampling of scalar images and DTI
* [http://www.kitware.com/company/team/fillion.html Jean-Christophe Fillion-Robin]: CTK, Qt
* [http://kitware.com/company/team/finet.html Julien Finet]: Volume rendering, CTK
* [http://kitware.com/company/team/galbreath.html Zack Galbreath]: CDash, Wiki, Sys Admin
* [http://www.kitware.com/company/team/goodlett.html Casey Goodlett]: Registration
* [http://www.spl.harvard.edu/~hayes Kathryn Hayes]: Release engineering, software development, quality assurance
* [http://www.kitware.com/company/team/hoffman.html Bill Hoffman]: CMake, CTest, CPack, Software Process
* [http://kitware.com/company/team/ibanez.html Luis Ibanez]: Registration, Segmentation, ITK, Software Process (Testing)
* [http://www.uiowa.edu Hans Johnson]: BRAINSFit, BRAINSDemonWarp, BRAINSResample, BRAINSROIAuto
* [http://kitware.com/company/team/jomier.html Julien Jomier]: MIDAS, CDash
* [http://www.spl.harvard.edu/~kikinis Ron Kikinis]: Principal Investigator, busboy
* [http://www.kitware.com/company/team/krishnan.html Karthik Krishnan]: 3D Widgets.
* [http://isp.ncifcrf.gov/abcc Yanling Liu]: Volume rendering.
* Mahnaz Maddah: EM Clustering of tractography
* [http://www.uiowa.edu Vincent Magnotta]: IA_FEM Mesh
* [http://wiki.na-mic.org/Wiki/index.php/User:Millerjv Jim Miller]: CLI, Registration, Lightbox, Compare View, Crosshairs
* [http://kitware.com/company/team/partyka.html Dave Partyka]: Cross-platform build and installation, CDash
* [http://www.spl.harvard.edu/~pieper Steve Pieper]: Chief architect, editor
* [http://www.spl.harvard.edu/pages/People/wjp Wendy Plesniak]: GUI, Informatics
* [http://www.csail.mit.edu/~pohl Kilian Pohl]: EMSegmenter
* [http://lmi.bwh.harvard.edu/~spujol/ Sonia Pujol]: Workshops, Tutorials, Testing
* [http://kitware.com/company/team/schroeder.html Will Schroeder]: VTK, 3D widgets
* Xiaodong Tao: Diffusion DICOM, Skull stripping, HAMMER, MS Lesion
* [http://www.niral.unc.edu/people Clement Vachet]: ARCTIC cortical thickness, Shape Analysis module
* [http://pnl.bwh.harvard.edu/people/profiles/wassermann.html Demian Wassermann]: Diffusion MRI modules, documentation.
* [http://lmi.bwh.harvard.edu/~westin Carl-Fredrik Westin]: Diffusion MRI overview
* Andrew Wiles: IGT tool selector, collect patient fiducials
* [http://www.spl.harvard.edu/~alexy Alex Yarmarkovich]: MRML, DTI modules, software development

Announcments-3.6-Team

2010-06-03T21:40:25Z

Vrnova:

Back to the [[Announcements:Slicer3.6|Slicer 3.6 announcement]]

Development of Slicer 3.6 has been supported through volunteer work and through a number of funding mechanisms and sources. Please see the [http://www.slicer.org/pages/Acknowledgments Slicer Acknowledgements] page.

Major contributors for the Slicer 3.6 release include (in alphabetic order):
* [http://www.orobix.com/luca Luca Antiga]: Python integration, CLI
* [http://www.spl.harvard.edu/pages/People/nicole Nicole Aucoin]: Software development, Fiducials, Informatics
* [http://kitware.com/company/team/aylward.html Stephen Aylward]: Registration, ITK
* [http://www.kitware.com/company/team/barre.html Sébastien Barré]: GUI, KWWidgets
* [http://www.niral.unc.edu/people Francois Budin]: Resampling of scalar images and DTI
* [http://www.kitware.com/company/team/fillion.html Jean-Christophe Fillion-Robin]: CTK, Qt
* [http://kitware.com/company/team/finet.html Julien Finet]: Volume rendering, CTK
* [http://kitware.com/company/team/galbreath.html Zack Galbreath]: CDash, Wiki, Sys Admin
* [http://www.kitware.com/company/team/goodlett.html Casey Goodlett]: Registration
* [http://www.spl.harvard.edu/~hayes Kathryn Hayes]: Release engineering, software development, quality assurance
* [http://www.kitware.com/company/team/hoffman.html Bill Hoffman]: CMake, CTest, CPack, Software Process
* [http://kitware.com/company/team/ibanez.html Luis Ibanez]: Registration, Segmentation, ITK, Software Process (Testing)
* [http://www.uiowa.edu Hans Johnson]: BRAINSFit, BRAINSDemonWarp, BRAINSResample, BRAINSROIAuto
* [http://kitware.com/company/team/jomier.html Julien Jomier]: MIDAS, CDash
* [http://www.spl.harvard.edu/~kikinis Ron Kikinis]: Principal Investigator, busboy
* [http://www.kitware.com/company/team/krishnan.html Karthik Krishnan]: 3D Widgets.
* [http://http://isp.ncifcrf.gov/abcc Yanling Liu]: Volume rendering.
* Mahnaz Maddah: EM Clustering of tractography
* [http://www.uiowa.edu Vincent Magnotta]: IA_FEM Mesh
* [http://wiki.na-mic.org/Wiki/index.php/User:Millerjv Jim Miller]: CLI, Registration, Lightbox, Compare View, Crosshairs
* [http://kitware.com/company/team/partyka.html Dave Partyka]: Cross-platform build and installation, CDash
* [http://www.spl.harvard.edu/~pieper Steve Pieper]: Chief architect, editor
* [http://www.spl.harvard.edu/pages/People/wjp Wendy Plesniak]: GUI, Informatics
* [http://www.csail.mit.edu/~pohl Kilian Pohl]: EMSegmenter
* [http://lmi.bwh.harvard.edu/~spujol/ Sonia Pujol]: Workshops, Tutorials, Testing
* [http://kitware.com/company/team/schroeder.html Will Schroeder]: VTK, 3D widgets
* Xiaodong Tao: Diffusion DICOM, Skull stripping, HAMMER, MS Lesion
* [http://www.niral.unc.edu/people Clement Vachet]: ARCTIC cortical thickness, Shape Analysis module
* [http://pnl.bwh.harvard.edu/people/profiles/wassermann.html Demian Wassermann]: Diffusion MRI modules, documentation.
* [http://lmi.bwh.harvard.edu/~westin Carl-Fredrik Westin]: Diffusion MRI overview
* Andrew Wiles: IGT tool selector, collect patient fiducials
* [http://www.spl.harvard.edu/~alexy Alex Yarmarkovich]: MRML, DTI modules, software development

Modules:VolumeRendering-Documentation-3.6

2010-05-24T17:29:23Z

Vrnova: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
*"Fit ROI to Volume" button is helpful when ROI default range is smaller than volume.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-05-24T17:17:51Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

The effect is available on Composite With Shading, Composite With Pseudo Shading, and Gradient Magnitude Opacity Modulation techniques.

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-05-24T16:12:27Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

Below are two images of the same volume with identical transfer functions. The first one is rendered with the feature off and the second one is rendered with the feature on. On the second image, darker voxels indicate these voxels are more far away from eye/camera.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-05-24T16:10:22Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera more darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

A "Dist. Color Blending" slider bar is available in NCI GPU Ray Casting parameter panel to adjust the effect. Higher value indicates stronger darkening effect. Setting the value to be 0 will turn off the effect.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-05-24T16:08:41Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera moare darker than voxels with shorter distance. The effect helps to reveal depth information in volume.

{|
|[[Image:DistColorBlendingOff.png|thumb|320px|Distance Color Blending Off]]
|[[Image:DistColorBlendingOn.png|thumb|320px|Distance Color Blending On]]
|}

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

File:DistColorBlendingOn.png

2010-05-24T16:07:10Z

Vrnova:

File:DistColorBlendingOff.png

2010-05-24T16:06:57Z

Vrnova:

Modules:VolumeRendering-Documentation-3.6

2010-05-24T16:06:38Z

Vrnova: /* Use Cases, Examples */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
*Origianl work: Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu), Steve Pieper, Isomics
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===
* Distance Color Blending in NCI GPU Ray Casting
Distance Color Blending will make voxels with longer distance to eye/camera moare darker than voxels with shorter distance. The effect helps to reveal depth information in volume.
* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). Please see [[Modules:VolumeRendering-Documentation-3.6-TransferFunctions|'''here''']] for a listing.
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-05-18T13:58:55Z

Vrnova: /* References */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
* Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu)
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). '''(VolView people credits?)'''
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===

Modules:VolumeRendering-Documentation-3.6

2010-05-18T13:58:29Z

Vrnova: /* Quick Tour of Features and Use */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
* Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu)
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

===Quick Tour of Features and Use===

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). '''(VolView people credits?)'''
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled for now. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and non-transparent triangulated surface model.
**** Method Configuration Panel:
***** Maximum Intensity Projection: turn on/off MIP rendering in VTK CPU Ray Casting.
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing with non-transparent polygon models only. This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
***** Technique: Two techniques available: Composite and MIP.
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slightly lower performance and slightly coarser appearance.
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
**** Method Configuration Panel:
***** Rendering Technique:
****** Composite With Shading: regular ray casting volume rendering with shading
****** Composite Psuedo Shading: slightly faster than regular composite
****** Maximum Intensity Projection:
****** Minimum Intensity Projection:
****** Gradient Magnitude Opacity Modulation: Enhances boundary in volume by multiplying gradient magnitude with voxel opacity
****** Illustrative Context Preserving Exploration: Automatic "open up" boundaries that are closer to viewer. Two parameters ICPE scale and ICPE smoothness controls "open up" depth and width.
***** ICPE Scale: parameter for Illustrative Context Preserving Exploration
***** ICPE Smoothness: parameter for Illustrative Context Preserving Exploration
***** Vol. Depth Peeling: Starting volume rendering once voxel with high intensity than the threshold value has been hit by viewing ray. Helps to reveal close objects with similar intensity.
*** '''NCI GPU Ray Casting (Multi-Volume):''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "NCI GPU Ray Casting (Multi-Volume)" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
***** Technique (Bg): rendering techniques for bg volume.
***** Technique (Fg): rendering techniques for fg volume.
***** Fusion: bg/fg blending method
***** Bg|Fg Ratio: blending weights for bg and fg volumes in.
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:VolumeRendering-Documentation-3.6

2010-05-18T13:47:23Z

Vrnova: /* Quick Tour of Features and Use */

Modules:VolumeRendering-Documentation-3.6

2010-05-18T13:38:49Z

Vrnova: /* Quick Tour of Features and Use */

Modules:VolumeRendering-Documentation-3.6

2010-05-18T13:27:29Z

Vrnova: /* Quick Tour of Features and Use */

Modules:VolumeRendering-Documentation-3.6

2010-05-18T13:09:38Z

Vrnova: /* Quick Tour of Features and Use */

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:38:34Z

Vrnova: /* Quick Tour of Features and Use */

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:38:03Z

Vrnova: /* Tutorials */

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:37:46Z

Vrnova: /* Notes from the Developer(s) */

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:37:38Z

Vrnova: /* Tests */

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:37:27Z

Vrnova: /* Known bugs */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
* Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu)
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). '''(VolView people credits?)'''
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and triangulated surface model. '''Do not use semi-transparent surface models (Yanling, is this true?).'''
**** Method Configuration Panel:
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing... etc. '''Do not use semi-transparent surface models (Yanling, is this true?).''' This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slicghtly lower performance and slightly coarser appearance.
**** Method Configuration Panel:
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
*** '''Multi-volume GPU Ray Caster:''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "GPU Ray Casting II" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:37:15Z

Vrnova: /* Source code & documentation */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
* Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu)
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). '''(VolView people credits?)'''
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and triangulated surface model. '''Do not use semi-transparent surface models (Yanling, is this true?).'''
**** Method Configuration Panel:
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing... etc. '''Do not use semi-transparent surface models (Yanling, is this true?).''' This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slicghtly lower performance and slightly coarser appearance.
**** Method Configuration Panel:
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
*** '''Multi-volume GPU Ray Caster:''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "GPU Ray Casting II" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:37:07Z

Vrnova: /* Source code & documentation */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
* Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu)
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). '''(VolView people credits?)'''
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and triangulated surface model. '''Do not use semi-transparent surface models (Yanling, is this true?).'''
**** Method Configuration Panel:
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing... etc. '''Do not use semi-transparent surface models (Yanling, is this true?).''' This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slicghtly lower performance and slightly coarser appearance.
**** Method Configuration Panel:
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
*** '''Multi-volume GPU Ray Caster:''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "GPU Ray Casting II" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:
http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:34:41Z

Vrnova: /* Dependencies */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
* Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu)
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). '''(VolView people credits?)'''
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and triangulated surface model. '''Do not use semi-transparent surface models (Yanling, is this true?).'''
**** Method Configuration Panel:
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing... etc. '''Do not use semi-transparent surface models (Yanling, is this true?).''' This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slicghtly lower performance and slightly coarser appearance.
**** Method Configuration Panel:
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
*** '''Multi-volume GPU Ray Caster:''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "GPU Ray Casting II" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

None.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:33:55Z

Vrnova: /* Source code & documentation */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
* Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu)
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). '''(VolView people credits?)'''
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and triangulated surface model. '''Do not use semi-transparent surface models (Yanling, is this true?).'''
**** Method Configuration Panel:
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing... etc. '''Do not use semi-transparent surface models (Yanling, is this true?).''' This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slicghtly lower performance and slightly coarser appearance.
**** Method Configuration Panel:
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
*** '''Multi-volume GPU Ray Caster:''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "GPU Ray Casting II" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/Modules/VolumeRendering/?rev=13274

Doxygen documentation:

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:32:45Z

Vrnova: /* Acknowledgment */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
* Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu)
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). '''(VolView people credits?)'''
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and triangulated surface model. '''Do not use semi-transparent surface models (Yanling, is this true?).'''
**** Method Configuration Panel:
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing... etc. '''Do not use semi-transparent surface models (Yanling, is this true?).''' This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slicghtly lower performance and slightly coarser appearance.
**** Method Configuration Panel:
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
*** '''Multi-volume GPU Ray Caster:''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "GPU Ray Casting II" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See http://www.slicer.org for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===
Publications related to this module go here. Links to pdfs would be useful.

Modules:VolumeRendering-Documentation-3.6

2010-05-13T21:32:31Z

Vrnova: /* Acknowledgment */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]

__NOTOC__
===Module Name===
Volume Rendering

{|
|[[Image:VolumeRenderingGMOM.png|thumb|280px|Gradient Magnitude Opacity Modulation]]
|[[Image:VolumeRenderingICPE.png|thumb|280px|Illustrative Context Preserving Exploration]]
|[[Image:CellMultiChannel.png|thumb|280px|Volume Rendering on Multi-Channel Confocal Microscopy Image]]
|}

== General Information ==
===Module Type & Category===

Type: Interactive

Category: Base

===Authors, Collaborators & Contact===
* Yanling Liu, SAIC-Frederick/NCI-Frederick, Alex Yarmarkovich, Isomics, SPL
* Andreas Freudling, Student Intern at SPL (freudling@bwh.harvard.edu)
* Contact: Yanling Liu, liuy5@mail.nih.gov, Alex Yarmarkovich, alexy@bwh.harvard.edu
* Some of the transfer functions were contributed by Kitware, Inc. (VolView)

===Module Description===
Provides interactive visualization of 3D image data. To learn about volume rendering start with [http://en.wikipedia.org/wiki/Volume_rendering Wikipedia].

== Usage ==

===Use Cases, Examples===

* Pausing VolumeRendering module in scene loading
The VolumeRendering module can be paused in scene loading by un-checking the "Monitor Scene Loading Event" check button. Re-checking the check button will flush the paused pipeline and initialize the module using the loaded scene.

* Multi-Volume GPU Ray Casting
VolumeRendering module has the capability to blend two (bg and fg) volumes in one rendering pipeline. User may select different rendering technique for bg or fg volumes. Different blending options are also available.

Currently under development. Available rendering techniques: Composite (bg) + Composite (fg) + OR blending, Composite (bg) + Composite (fg) + AND blending, Composite (bg) + MIP (fg), MIP (bg) + MIP (fg).

{|
|[[Image:multi-vol-bg-composite.png|thumb|320px|Bg volume only (Composite)]]
|[[Image:multi-vol-bg-composite-fg-mip-alpha_blending.png|thumb|320px|Bg and Fg volume]]
|[[Image:multi-vol-fg-mip.png|thumb|320px|Fg volume only (MIP)]]
|}

* Dual 3D View mode
VTK GPU Ray Casting doesn't support the Dual 3D View mode.

{|
|[[Image:GPUraycastDual3Dview.png|thumb|320px|Gradient Magnitude Opacity Modulation in Dual 3D View mode (Single Volume GPU Ray Casting)]]
|}

* Volume-Following Mode
In Volume-Following mode, color and opacity transfer functions in the VolumeRendering module will follow window/level and threshold settings in the Volumes module for a uniform appearance on both slice view and 3D volume rendering view. To use, check VolumeRendering module -> Rendering panel -> Volume Property tab -> Follow Volumes Module check button.

In Volume-Following mode, window/level plus lookup table in Volumes module will be used to set colors in volume rendering. Threshold in Volumes module will be used to set opacity in volume rendering. Color and opacity transfer function editor also are disabled in Volume-Following mode because we are following volumes module now.

{|
|[[Image:Volumes_following.png|thumb|320px|Volume Rendering in Volume-Following Mode]]
|}

===Tutorials===

Links to tutorials explaining how to use this module:

* Tutorial 1
** Data Set 1

===Quick Tour of Features and Use===

A list panels in the interface, their features, what they mean, and how to use them. For instance:

{|
|
* '''Input panel:'''
** '''Monitor scene loading event''' If unchecked the Volume rendering module will not monitor scene loading event. If a scene contains volume rendering node and a very large dataset, loading this scene on machine without volume rendering capabilities, can cause errors (a crash or a frozen machine -- if the machine runs out of memory).
** '''Scenario''' A volume rendering scenario is defined by input set of bg, fg and label map volumes.
** '''ROI''' The single ROI node for the current scenario. The ROI can be defined using volume rendering and then used to crop a volume in the crop volume module. May be changed to one ROI per input(bg/fg/labelmap) instead of per scenario.
** '''Background Volume''' This specifies the default volume for volume rendering. Volume input, volume property, and presets for background.
*** Source: Background volume source.
*** Property: Volume Rendering Property Node: Volume rendering properties, such as color and opacity transfer functions are saved in the Volume Rendering Property Node.
*** Presets: Predefined transfer functions for convenience. Some are provided by Jim Miller, and the majority of them are transferred from VolView (Thank you very much). '''(VolView people credits?)'''
** '''Foreground Volume''' This is used only in experimental NCI GPU Ray Casting (which is one of the Rendering Methods in the Rendering Techniques Tab). Otherwise this volume is ignored. Volume input. volume property, and presets for foreground. Works only with the experimental NCI GPU Raycasting Multi-volume (experimental)
** '''Label Map''' This volume is experimental and disabled. Volume input, volume property, and presets for label map. 
|[[Image:3.6VolrendInputs.png|thumb|280px|User Interface]]
|-
|
'''Rendering panel:''' This panel is Dynamically generated panel when valid input is selected.
* '''Techniques TAB ''' Under the techniques tab, there are currently five rendering methods available. Each of these are described below.
** Rendering Method
*** '''VTK CPU Ray Casting:''' Uses the CPU for volume rendering, is parallelized and can take advantage of multi-core capabilities. Uses level-of-detail approach where low resolution is rendered while moving, and high resolution is rendered once motion ceases. Allows zbuffer compositing with texture map cross sections and triangulated surface model. '''Do not use semi-transparent surface models (Yanling, is this true?).'''
**** Method Configuration Panel:
*** '''VTK GPU Ray Casting:''' Uses GPU accelerated ray caster. Allows z-buffer compositing... etc. '''Do not use semi-transparent surface models (Yanling, is this true?).''' This is currently working on Linux and Win32, but not on Mac due to a bug in the OpenGL drivers.
**** Method Configuration Panel:
*** '''VTK OpenGL 3D Texture Mapping:''' Uses texture mapping approach to volume rendering compared to the two render methods above, it has slicghtly lower performance and slightly coarser appearance.
**** Method Configuration Panel:
*** '''NCI GPU Ray Casting:''' This is a GLSL-based ray caster with several experimental mapping techniques. No z-buffer compositing with polygon models. Good performance and quality. No hardware restrictions on this method.
*** '''Multi-volume GPU Ray Caster:''' This allows two volumes to be volume rendered and performs an alpha blend between the two volumes. This method requires enough graphics memory to hold all data, or a crash or frozen machine may occur. ''If you use this method, and select a foreground volume, you need to set the "Fg|Bg Ratio" slider in "GPU Ray Casting II" section to see the rendering of the foreground volume. By default, the foreground volume is completely transparent.''
**** Method Configuration Panel:
** GPU Memory Size: A user must hand-select the amount of graphics memory in your machine. The setting will be remembered for your next session. Find this information, (Alex, can fill in for each platform, or for some?)
** Expected Interactive Frame Rate: For VTK mappers, this slider forces faster render speeds at the expense of quality. For NCI mappers, this slider defines the rendering speed (No low-high quality rendering switching). This feature may be removed.
|[[Image:3.6VolrendRenderingTechniques.png|thumb|280px|User Interface]]
|-
|
'''Volume Property Tab'''
* Follow Volumes Module Option: When this is checked, you can use the window level and threshold settings and the Color LUT settings in the volumes module display section to manipulate a ramp-shaped transfer function.
* Use Thresholding Option: Basically this is a block filter with adjustable upper and lower thresholds in the transfer function. The opacity slider may be used to adjust the opacity of the pass band. Effects of this option can be seen below in the Scalar Opacity Mapping Transfer Function Editor.
*Volume Appearance Settings
**Interpolation: Linear or nearest neighbor. Usually, linear will produce more pleasing results.
**Material: A pop-up allows to determine the reflection properties for the rendered structures ("shiny" to "dull")
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its signal intensity value and opacity. 0 means transparent and 1 means opaque.
**Scalar Opacity Mapping: select a control point (click to create a new one) and change its color. Both Hue/Saturation and value can be selected
|[[Image:3.6VolrendRenderingVolumeProperty.png|thumb|280px|User Interface]]
|-
|
'''ROI Tab'''
*The ROI's are compatible with the crop volume module.
*Interactive cropping of the volume visualization. You can use either the sliders or click on the colorized spheres in the 3D view.
*ROI box can be made visible or invisible
*check box allows to apply to the visualization or not.
|[[Image:3.6VolrendRenderingROI.png|thumb|280px|User Interface]]
|-
|
'''Misc Tab'''
*Turn volume rendering visibility on or off
*Turn models on or off
*May need to be moved to main toolbar.
|[[Image:3.6VolrendRenderingMisc.png|thumb|280px|User Interface]]
|}

== Development ==

===Notes from the Developer(s)===

Algorithms used, library classes depended upon, use cases, etc.

===Dependencies===

Other modules or packages that are required for this module's use.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* MyModuleTest1 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest1.cxx]
* MyModuleTest2 [http://viewvc.slicer.org/viewcvs.cgi/trunk MyModuleTest2.cxx]

===Known bugs===

Links to known bugs in the Slicer3 bug tracker

* [http://www.na-mic.org/Bug/view.php?id=000 Bug 000: description]

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

===Source code & documentation===

Links to the module's source code:

Source code:
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.cxx ]
*[http://viewvc.slicer.org/viewcvs.cgi/trunk file.h ]

Doxygen documentation:
*[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classes.html class1]

== More Information ==

===Acknowledgment===
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a>http://www.slicer.org</a> for details. The VolumeRendering module is implemented by Yanling Liu, NCI-Frederick/SAIC-Frederick, Andreas Freudling, Student Intern at SPL, BWH (Ron Kikinis) and Alex Yarmarkovich, Isomics Inc. (Steve Pieper). Some of the transfer functions were contributed by Kitware, Inc. (VolView)".

===References===
Publications related to this module go here. Links to pdfs would be useful.