Slicer Wiki - User contributions [en]

Documentation

2017-05-02T11:05:17Z

Finetjul: /* Slicer 4 */

__NOTOC__

{{Infobox
|name = 3D Slicer {{documentation/version}}
|above = 3D Slicer
|abovestyle =

|image = [[File:3DSlicer41Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]
|imagestyle =
|headerstyle = background:#E7DCC3;
|labelstyle =
|datastyle =

|header1 = Description
|label1 =
|data1 =
|header2 =
|label2 =
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.
|header3 =
|label3 =
|data3 = Free and extensible open source package.
|header4 =
|label4 = Multi-platform
|data4 = Linux, MacOSX, Windows
|header5 =
|label5 = Version
|data5 = {{documentation/currentversion}}
|header6 =
|label6 = License
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]
}}

== Slicer 4 ==
* [[Documentation/Nightly|Nightly]]

* [[Documentation/4.6|4.6]] / [[Documentation/4.6/ReleaseNotes|Release notes]] / [[Documentation/4.6/Announcements | Announcement]] / [[Documentation/4.6/Acknowledgments | Acknowledgments]]
* [[Documentation/4.5|4.5]] / [[Documentation/4.5/ReleaseNotes|Release notes]] / [[Documentation/4.5/Announcements | Announcement]] / [[Documentation/4.5/Acknowledgments | Acknowledgments]]
* [[Documentation/4.4|4.4]] / [[Documentation/4.4/ReleaseNotes|Release notes]] / [[Documentation/4.4/Announcements | Announcement]] / [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/4.3|4.3]] / [[Documentation/4.3/ReleaseNotes|Release notes]] / [[Documentation/4.3/Announcements | Announcement]] / [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/4.2|4.2]] / [[Documentation/4.2/ReleaseNotes|Release notes]] / [[Documentation/4.2/Announcements | Announcement]] / [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/4.1|4.1]] / [[Documentation/4.1/ReleaseNotes|Release notes]] / [[Documentation/4.1/Announcements | Announcement]] / [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]
* [[Documentation/4.0|4.0]] / [[Documentation/4.0/ReleaseNotes|Release notes]] / [[Documentation/4.0/Announcements | Announcement]] / [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4 Acknowledgments]

Acknowledgments are now reported separately for each version.


== Slicer 3 ==
* [[Documentation/3.6|3.6]] / [[Documentation/3.6/ReleaseNotes|Release notes]] / [[Announcements:Slicer3.6 | Announcement]]
* [[Documentation/3.5|3.5]]
* [[Documentation/3.4|3.4]] / [[Documentation/3.4/ReleaseNotes|Release notes]] / [[Announcements:Slicer3.4 | Announcement]]
* [[Documentation/3.2|3.2]] / [[Documentation/3.2/ReleaseNotes|Release notes]]
The community contributing to Slicer 3 is acknowledged [http://www.slicer.org/pages/Acknowledgments#Acknowledgments_Slicer3 here]

== Slicer 2 ==
* [[Slicer:Slicer2.7_Getting_Started|2.7]] / [[Slicer:Slicer2.7_Release_Notes|Release notes]]
* [[Slicer:Slicer2.6_Getting_Started|2.6]] / [[Slicer:Slicer2.6_Release_Notes|Release notes]]
* [[Slicer:Slicer2.5_Getting_Started|2.5]] / [[Slicer:Slicer2.5_Release_Notes|Release notes]]
* [[Slicer:Slicer2.4_Getting_Started|2.4]] / [[Slicer:Slicer2.4_Release_Notes|Release notes]]
The community contributing to Slicer 2 is acknowledged [http://www.slicer.org/pages/Acknowledgments#Slicer2:_Individual.2FGroup_Contributors here]

== Slicer 1 ==
* [http://www.slicer.org/archives/download/index.html 1.3] / [http://massmail.spl.harvard.edu/public-archives/slicer-users/2002/000145.html Announcement]

<hr>
<center>[[Image:Slicer4Announcement-HiRes.png|350px]]</center>

Documentation/Nightly/Modules/Editor/WatershedFromMarkers

2017-03-27T15:01:49Z

Finetjul:

<noinclude>{{documentation/versioncheck}}</noinclude>
{{ambox
| type = protection
| image = [[File:InProgress.png|40px|alt=Work in progress]]
| text = WARNING: This module is Work in Progress, which means:
* the functionality provided by this module may change drastically in the future releases of 3D Slicer
* the scenes containing data types specific to this module may not be readable by the future versions of Slicer
* the functionality and user interface may change at any time
* some functionality may not work as intended
* testing and documentation is limited
}}


{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
{{documentation/{{documentation/version}}/module-introduction-row}}
: '''Author(s)/Contributor(s):''' Bradley Lowekamp (MSC/NLM), Steve Pieper(Isomics Inc.) 
: '''Acknowledgements:''' This work is supported by NLM, and the Slicer Community. 
: '''Contact:''' Bradley Lowekamp, <email>blowekamp@mail.nih.gov</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|nlm}}|{{collaborator|longname|nlm}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
Watershed from Markers is an edge based editing tool that detects edges and fills in a specific area based on the given outlines created in the label map. It is an effective way to segment features with robust outlines more efficiently.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
{|
|[[Image:step1_grayscale.png|thumb|Step 1: Tumor Gray Scale]]
|[[Image:step2_originallabel.png|thumb|Step 2: Original Label Map]]
|[[Image:step3_watershed.png|thumb|Step 3: Label Map after Watershed]]
|[[Image:step4_changelabelmap.png|thumb|Step 4: Label Map after Change Label effect]]
|[[Image:step5_leakedpixels.png|thumb|Step 5: Leaked Pixels]]
|[[Image:step6_finallabel.png|thumb|Step 6: Final Label Map]]
|}
# Use MRBrain Tumor Time Point 1 from Slicer's [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]]. Scroll through the data and find a feature of interest, for example the tumor.
# With the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool, create an original label map as the input for the Watershed from Markers tool. Using one color, paint the tumor precisely. Watershed from Markers is an edge based algorithm and labeling pixels outside of the tumor outline will result in an inaccurate label map. In another color, outline the tumor and fill in part of the background. This can be done for one slide or multiple slides in which the tumor is visible. Labeling more slides will result in a more accurate watershed.
# After the Watershed from Markers is applied, the tumor will be represented by one color and the background will be represented by another color.
# Using the [[Documentation/{{documentation/version}}/Modules/Editor#Change Label|Change Label]] effect, change the background color to black.
# Once the background label has been changed, look through each slice for leaked pixels.
# To fix leaked pixels, use the [[Documentation/{{documentation/version}}/Modules/Editor#Paint|Paint]] tool to erase extra pixels from the label map. Another way to edit your label map is to apply the [[Documentation/{{documentation/version}}/Modules/Editor#Undo/Redo|Undo/Redo]] tools. Using the undo, the watershed can be undone and the original label map can be edited. The redo tool can reapply an updated version of the Watershed from Markers effect. After looking through each slice for leaked pixels, the label map should accurately represent your tumor.


{{documentation/{{documentation/version}}/module-section|Tutorials}}
N/A


{{documentation/{{documentation/version}}/module-section|References}}
N/A


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
{{documentation/{{documentation/version}}/module-developerinfo}}

Documentation:Nightly:Registration:RegistrationLibrary:RegLib C03

2016-07-01T15:15:25Z

Finetjul: /* Procedure */ Update parameter names to Slicer 4.4

[[Documentation/Nightly/Registration/RegistrationLibrary|Back to Registration Library]] 
= Slicer Registration Library Case #3: Diffusion Weighted Image Volume: align with structural reference MRI=
== Input ==
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C03_thumb1.png|150px|left|this is the fixed T2 reference image. All images are aligned into this space]]
|[[Image:RegArrow_NonRigid.png|100px|left]]
|[[Image:RegLib_C03_thumb2.png|150px|left|this is the DTI Baseline scan, to be registered with the T2]]
|[[Image:RegLib_C03_thumb3.png|150px|left|this is the DTI tensor image, in the same orientation as the DTI Baseline]]
|-
|fixed image 1/target T2
|
|moving image 2a DTI baseline
|moving image 2b DTI tensor
|}

== Description ==
This is a simple case of diffusion MRI. Goal is to align the Diffusion Tensor Image (DTI) with the structural reference T2 scan that provides accuracte anatomical reference. 
'''Approach''': we compute the registration transform using a scalar DTI_baseline scan and then apply this transform to the DTI tensor image. Because reorienting tensor data requires a different form of resampling, we must use a dedicated module for this purpose. Because DTI acquisitions tend to contain strong geometric distortions, we apply a nonrigid transform to the DTI, which makes resampling necessary.

== Modules used ==
*[[Documentation/Nightly/Modules/BRAINSFit| ''General Registration (BRAINS)'']]
*[[Documentation/Nightly/Modules/ResampleDTI|''Resample DTI Volume'']]

== Alternate Versions ==
*this example covers the most basic form of directly registering a DTI + baseline to a T2. There is another (more advanced) version that show how to address additional issues of a strong initial rotation and strong voxel-anisotropy for the raw DWI image acquired:
*[http://na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C03 for the Slicer '''4.1''' version of this case see here]
*[http://na-mic.org/Wiki/index.php/Projects:RegistrationLibrary:RegLib_C03_v3 for the Slicer '''3.6.3''' version of this case see here]

== Download (from NAMIC MIDAS) ==
''Why 2 sets of files? The "input data" mrb includes only the unregistered data to try the method yourself from start to finish. The full dataset includes intermediate files and results (transforms, resampled images etc.). If you use the full dataset we recommend to choose different names for the images/results you create yourself to distinguish the old data from the new one you generated yourself. ''
*[http://slicer.kitware.com/midas3/download/?items=95490 '''RegLib_C03.mrb''': input data only, use this to run the tutorial from the start (Slicer mrb file. 50 MB). ]
*[http://slicer.kitware.com/midas3/download/?items=95491 '''RegLib_C03_full.mrb''': includes raw data + all solutions and intermediate files, use to browse/verify (Slicer mrb file. 108 MB). ]

== Keywords ==
MRI, brain, head, intra-subject, DTI, DWI

== Video Screencasts ==
#[[Media:RegLib_C03_m01_RegisterDTI.mov|Movie/screencast showing registration+resampling for Case #03]]

== Procedure ==
This assumes you have the following: 1) a T2 reference image, 2) a DTI baseline image and 3) the DTI volume (both obtained from the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Modules/DiffusionTensorEstimation Diffusion Tensor Estimation module]). If you do not have a baseline image, generate a scalar Trace image from the DTI, using the ''Diffusion Tensor Scalar Measurements'' module:
#'''Compute Registration''': open the [[Documentation/Nightly/Modules/BRAINSFit|''General Registration (BRAINS)'' module]]
##''Input Images: Fixed Image Volume'': T2
##''Input Images: Moving Image Volume'': DTI_baseline
##''Output Settings'':
###''Slicer BSpline Transform'' (create new transform, rename to: "Xf1_DTbase-T2_BSpline")
###''Slicer Linear Transform'' none
###''Output Image Volume'' (create new volume, rename to: "DTIbaseline_Xf1"
##''Registration Phases'': select/check ''Rigid'' , ''Rigid+Scale'', ''Affine'', ''BSpline''
##''Main Parameters'':
###increase ''Percentage of Samples'' to 0.006
###set ''B-Spline Grid Size'' to 7,7,5 (we have lower resolution in the IS-direction (z), hence we set a smaller (5) grid size there)
##Leave all other settings at default
##click: ''Apply''; runtime < 1 min.
#'''Resample DTI:''' We have now computed the registration transform, but the output volume produced above is a registered version of the baseline, which we need for validation only. To get the actual DTI registered we now apply this transform to the tensor image.
##Open the [[Documentation/Nightly/Modules/ResampleDTIVolume|''Resample DTI Volume'']] module (found under: All Modules) (Do not resample a tensor image with other modules, this one must be used to correctly transform the tensor data)
###''Input Volume'': select DTI
###''Output Volume'': select ''create new Diffusion Tensor Volume'',and rename it to ''DTI_Xf1''
###''Reference Volume'': select ''T2''
###''Transform Parameters'': select transform node "Xf1_DTI-T2_BSpline", for ''Deformation Field'': none ; '''check the ''displacement'' checkbox'''
###Leave all other settings at defaults
###Click Apply; runtime ~ 2 min.
##set ''T2'' as background and new ''DTI_Xf1'' volume as foreground
##fade between back- and foreground to see DTI overlay onto the T2 image. Note that you can also fade via holding the OPTION+CMD keys (mac) + dragging left mouse.

==Registration Results==

{|cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C03_baseline_unregistered.gif|300px]] ||baseline & T2 before registration (click to enlarge)
|-
|[[Image:RegLib_C03_baseline_registered.gif|300px]]||baseline to T2 after affine+nonrigid alignment (click to enlarge)
|-
|[[Image:RegLib_C03_DTI_registered.gif|300px]]||DTI and T2 before & after registration (click to enlarge)
|}

== Discussion: Key Strategies ==
*the strong EPI-based distortions of the DTI image make nonrigid registration necessary
*initial alignment & overlap is sufficient so that no "initialization" methods are necessary and registration can succeed without.
*contrast & initial pose are similar enough for registration to succeed without any masking. However the DTI estimation procedure '''does''' provide an optional mask that is usually very helpful in registering cases with more "distracting" image content.
*the DTI in this example is isotropic and hence can be resampled directly. If the DTI contains strong anisotropy of ratios 1:3 or greater, reorienting the DTI can lead to strong artifacts (e.g. in axial direction appear as blue cast in the color orientation view). In that case it is necessary to resample the DWI in the original orientation to an isotropic size before reorienting. It may also be advisable to first reorient the DWI and perform the DTI estimation afterwards.
=== Acknowledgments ===

Documentation/Nightly/Developers/Build Instructions/Prerequisites/Qt

2015-09-13T19:35:53Z

Finetjul: /* Qt 4.8.6 / VS2012 */ Add VS2013 patch

<noinclude>{{documentation/versioncheck}}</noinclude>
= Binary vs build-from-source ? =

If you build Slicer on ...

== Linux ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

== Mac ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

* To use QtCreator and the Slicer designer plugins, a possible option is to build QtCreator against the installed Qt libraries. See [http://slicer-devel.65872.n3.nabble.com/Using-Qt-Creator-with-Slicer4-On-Mac-OS-X-Multiple-Qt-libs-loaded-tp4026660p4026690.html discussion on the mailing list].

== Windows ==

=== Debug (32 and 64-bit) or Release (64-bit) ===

* Normally you should plan to build Qt from source to have complete control over the process. See [https://github.com/jcfr/qt-easy-build one-liner build command] or more detailed [[#Build_instructions]]

* You may find that the '''unsigned''' binary downloads from this site are usable: http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2008/

* '''Details''': Using the Qt Designer on Windows requires that the Slicer plugins are [http://doc.trolltech.com/4.6/deployment-plugins.html#debugging-plugins|compiled in the same mode as Qt]. If Qt was compiled in Release mode (default), Slicer would have to be compiled in Release mode as well. However if Qt is compiled in Debug mode only, Slicer has to be compiled in Debug too. When Qt is in "Release and Debug" mode only the Release version of Designer.exe is generated, Slicer would have to be compiled in Release. So for developers, the Debug mode is recommended, this is why we detail the compilation of Qt below.

=== Release (32-bit) ===

* Using [[#Download_links|binary]] works great for 32-bit Release build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

 

= Download Qt: Source and Binaries =

== Download links ==

The following table list the link allowing to download either the '''recommended''' source code or binary of Qt.

{| border="1" style="margin-left: 20px;"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="1" rowspan="2"|Linux
!colspan="2"|Mac
!colspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="1"|SnowLeopard
!colspan="1"|Lion, Mountain Lion
!colspan="1"|VS2008
!colspan="1"|VS2010
|- bgcolor="#FFFFCC"
!|64bits
!|64bits
!|64bits
!|64bits
!|64bits
|-
! bgcolor="#FFFFCC" | Qt source link
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/archive/qt/4.7/qt-everywhere-opensource-src-4.7.4.tar.gz 4.7.4]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|-
! bgcolor="#FFFFCC" | Qt binary link
|align="center" colspan="1"| (src or apt-get package) 
|align="center" colspan="1"| [http://packages.kitware.com/download/item/3736/qt-mac-opensource-4.7.4.dmg 4.7.4] [http://packages.kitware.com/download/item/3739/qt-mac-opensource-4.7.4-debug-libs.dmg 4.7.4 (optional: debug libs)]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1.dmg 4.8.6] [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1-debug-libs.dmg 4.8.6 (optional: debug libs)]

|align="center" colspan="1"| [http://sourceforge.net/projects/qt64ng/files/qt/x86-64/4.8.6/msvc2008/qt-4.8.6-x64-msvc2008.exe/download 4.8.6 (unsigned installer)]
|align="center" colspan="1"| [http://sourceforge.net/projects/qt64ng/files/qt/x86-64/4.8.6/msvc2010/qt-4.8.6-x64-msvc2010.exe/download 4.8.6 (unsigned installer)]
|}



== Qt version specific issues ==

* Issues for Qt < 4.7.4 are not reported

=== All ===
* NA

=== Linux ===

* NA

=== Mac ===
* Problem building Qt on MacOSX 10.9. See https://bugreports.qt-project.org/browse/QTBUG-32237


=== Windows ===

* NA

== How to change the minimum required version ? ==

* This applied only for Slicer < [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22466 r22466].

* It's indeed possible to use a different version, just be aware that moving forward in time, things may not work as expected. Even worse Slicer may simply fail to compile.

* By configuring Slicer using <code>-DSlicer_REQUIRED_QT_VERSION:STRING=4.7.0</code>, you will be able to change the minimum required version.

* See [https://github.com/Slicer/Slicer/commit/898bb14e 898bb14e], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19698 r19698], [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/008130.html Mailing list]

 

= Build instructions =
 
{{mbox
| text = Please, make sure that your IDE/compiler is '''properly installed''' and that all associated '''ServicePack''' are also installed. See [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites|Prerequisites]].
}}
 

== Linux ==

See [[Documentation/Nightly/Developers/Build_Instructions#Linux]]






== Mac ==

Similar to Linux configuration. Note that <code>-arch x86_64</code> has been added.

For earlier versions of Xcode and Mac OS X
{{pre2|scroll|
mkdir qt-everywhere-opensource-build-4.7.4
tar xvfz qt-everywhere-opensource-src-4.7.4.tar.gz
cd qt-everywhere-opensource-src-4.7.4
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -webkit -arch x86_64 -nomake examples -nomake demos -sdk /Developer/SDKs/MacOSX10.5.sdk
make -j8
make install
}}

On the latest Xcode versions (4.3) and Lion (10.7) the Developer directories have moved. The command is now:

{{pre2|scroll|
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -arch x86_64 -nomake examples -nomake demos -webkit -sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk
}}

* Consider reading: http://doc.qt.nokia.com/4.7/developing-on-mac.html)

* Note:
** If building against SDK 10.6 or 10.7, you will probably get link errors similar to what's described in [https://trac.macports.org/ticket/30346] and [http://qt-project.org/forums/viewthread/15933]. Solution is provided here [https://bugreports.qt-project.org/browse/QTBUG-24361 here].

== Windows ==

* Use a windows extracter to unzip the [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites/Qt#Download_links|Qt archive]], don't use cygwin unzip it.

=== Qt 4.7.4 / VS2008 ===

* Rename the folder into for example <code>qt-4.7.4-64-vs2008-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.7.4-32-vs2008-deb</code>

* Launch the msvc2008 command prompt 
** 32-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 Command Prompt"
** 64-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 x64 Win64 Command Prompt"


* Configure
** For debug: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -debug -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -release -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2008</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.
** Note: According to [http://qt.nokia.com/doc/4.7/supported-platforms.html] Qt does not support msvc2008 on windows xp. However, running <code>configure.exe</code> with no <code>-platform</code> argument seems to work. If you run configure with the <code>-platform</code> argument first by mistake, and if <code>configure -clean</code> doesn't work, then you may need to start from a fresh extraction from the .zip archive before running <code>configure.exe</code> again with no <code>-platform</code>, unless you can run <code>nmake</code> with the config clean target.

* Build using <code>nmake</code>
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart nmake. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.5 / VS2010 ===

* Rename the folder into for example <code>qt-4.8.5-64-vs2010-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.5-32-vs2010-deb</code>

* Launch the msvc2010 command prompt 
** 32-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 Command Prompt"
** 64-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 x64 Win64 Command Prompt"


*Download pearl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

*Download jom and create a new folder into for example <code>jom</code>.
**Add this new folder into the path (system properties)

* Configure
** For debug: <code>configure.exe -platform win32-msvc2010 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2010 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2010</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>jom -jn</code>
**Note: n is the number of cores of your CPU, so adapt it.
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart jom. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.6 / VS2012 ===

* Make sure your Visual Studio 2012 is patched with the latest patch (e.g. [http://www.microsoft.com/en-us/download/confirmation.aspx?id=39305 patch 4]).

* Download the [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip source archive], extract and rename the folder into for example <code>qt-4.8.6-64-vs2012-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.6-32-vs2010-deb</code>

* Replace the webkit src\3rdparty\webkit\Source\JavaScriptCore\wtf\hashset.h file with this [https://bitbucket.org/Vertexwahn/bluego/src/56dbe84212222ec6954d8d327a5e443106bcc447/deploy/BlueGo0.0.4/qt4.8.3vs2012patch/HashSet.h?at=default file]
* For VS2013, replace the MathExtras.h file [http://code.qt.io/cgit/qt/qt.git/commit/src/3rdparty/webkit/Source/JavaScriptCore/wtf/MathExtras.h?id=b05d05fd9ce2aeedfaf805a7ed9007a93c902bc9]
* Launch the msvc2012 command prompt 
** 32-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x86 Command Prompt"
** 64-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x64 Win64 Command Prompt"


* If you want openssl support (optional):
** Download perl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

* Configure
** For debug: <code>configure.exe -platform win32-msvc2012 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2012 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2012</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>nmake</code>
** Alternatively you can use jom (much faster)
*** Download jom and create a new folder into for example <code>jom</code>.
*** Add this new folder into the path (system properties)
*** Build using <code>jom -jn</code>
**** Note: n is the number of cores of your CPU, so adapt it.

Documentation/Nightly/Developers/Tutorials/Troubleshooting

2015-01-23T10:34:57Z

Finetjul: Add VTK object visibility troubleshooting

<noinclude>{{documentation/versioncheck}}</noinclude>
Here are some tips to narrow down various issues such as crash, or memory leaks

=Disable features=
Try running Slicer with as few features as possible:
* Disable Slicer options via the command line
*: <pre>$ ./Slicer --no-splash --ignore-slicerrc --disable-cli-module --disable-loadable-module --disable-scriptedmodule</pre>
** Look at all the possible options
**: <pre>$ ./Slicer --help</pre>
* Disable ITK plugins
*: CLI modules silently load the ITK plugins in lib/Slicer-{{documentation/currentversion}}/ITKFactories. These plugins are used to share the volumes between Slicer and the ITK filter without having to copy them on disk.
** rename lib/Slicer-{{documentation/currentversion}}/ITKFactories into lib/Slicer-{{documentation/currentversion}}/ITKFactories-disabled
* Disable Qt plugins
** rename lib/Slicer-{{documentation/currentversion}}/iconengine into lib/Slicer-{{documentation/currentversion}}/iconengine-disabled

=Track memory leaks=
<ol>
<li> Turn ON the VTK_DEBUG_LEAKS CMake variable and build Slicer</li>
<li> Create a test that reproduces the memory leak systematically </li>
After execution, the memory leaks are printed automatically by VTK on the standard output:
224: vtkDebugLeaks has detected LEAKS!
224: Class "vtkProperty2D" has 60 instances still around.
...
Alternatively, you can simply run Slicer instead of a custom test.

<li>Find what specific instance of a class (here vtkProperty2D) leaks.</li>
If the class is instantiated a large amount of time, it is hard to know what instance is leaking. By making verbose the constructor and destructor of the faulty class, you can infer which instance is leaking. Below are 2 techniques to print whenever the con/destructors are called:
<ol>
<li>By recompiling VTK</li>
You can edit the constructor and destructor of the class (here vtkProperty2D::vtkProperty2D() and vtkProperty2D::~vtkProperty2D())
vtkProperty2D::vtkProperty2D()
{
...
static int count = 0;
std::cout << "CREATE vtkProperty2D instance #" << count++ << " " << this << std::endl;
}

vtkProperty2D::~vtkProperty2D()
{
...
static int count = 0;
std::cout << "DELETE vtkProperty2D instance #" << count++ << " " << this << std::endl;
}
Don't forget to rebuild VTK if the class is from VTK (no need to build Slicer inner build)
After running the test, you should see outputs similar to
...
CREATE vtkProperty2D instance #0 0x0123456
...
CREATE vtkProperty2D instance #1 0x01234E5
...
DELETE vtkProperty2D instance #0 0x0123456
...
DELETE vtkProperty2D instance #1 0x01234E5
...
CREATE vtkProperty2D instance #2 0x0123A23
...
CREATE vtkProperty2D instance #3 0x0124312
...
Copy/paste the listing in a text editor and ensure that for each CREATE of a pointer (e.g. 0x0123456) it exists a DELETE. If there isn't, you found what instance is leaking. Note the instance # (here instance #2 and #3)

<li>Without recompiling any library but using the debugger</li>
Any debugger with advanced breakpoint controls should work.
* With Visual Studio
<ol>
<li>Set breakpoints in the class constructor and destructor methods.</li>
<li>Right click on the breakpoint, select "When Hit..." and "Print a message" with "Function: $FUNCTION {this}". Make sure the "Continue execution" checkbox is selected.
<li>Execute the test or Slicer</li>
<li>Open the "Output" tab and copy paste the contents into an advanced file editor (not Visual Studio)</li>
</ol>
* With GDB
<ol>
<li>Start gdb</li>
Using the launcher
$ ./Slicer --gdb
Or sometimes the following works as well
$ gdb ./bin/SlicerApp-real
<li>Place breakpoints in the functions</li>
(gdb) break vtkProperty2D::vtkProperty2D()
(gdb) break vtkProperty2D::~vtkProperty2D()
gdb will stop in those methods each time the program steps into. It will then print a line such as:
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x123456789) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
<li>Automatically continue execution after each break</li>
(gdb) commands 1
> continue
> end
(gdb) commands 2
> continue
> end
<li> Start the execution and copy paste the logs printed by gdb into an advanced file editor (e.g. emacs)</li>
(gdb) run
</ol>

After running the test(by recompiling or with debugger), you should see outputs similar to
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
37 vtkProperty2D::vtkProperty2D()
...
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
37 vtkProperty2D::vtkProperty2D()
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
37 vtkProperty2D::vtkProperty2D()
...

In an text editor, cleanup the logs by keeping only the "Breakpoint*" lines:
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37

Save a copy of this file, and make the destructor lines similar to the constructor ones (using Replace tools):
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22

Sort the file to make the constructor and destructor lines next to each other(emacs: M-x sort-lines, Notepad++: TextFX/TextFX Tools/Sort lines case sensitive):
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22

Find the line that is not duplicated:
* Using Notepad++ (version >=6):
** Open the search dialog
** Find what: "^(.*?)$\s+?^(?=.*^\1$)", Replace with: "dup ", toggle "Regular expression"
** Replace All
** The line without the "dup" prefix is the line we are looking for
* Using emacs:
** C-M-%
** Replace regexp: $.*$<type C-q C-j>\1
** with: dup<type C-q C-j>

Extract the instance address from the line: e.g. 0x0124312

From the original logs, keep only the Constructor lines:
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22

Search into the original saved file what line the address is: e.g. 4

</ol>

<li>Find the leaking instance at run-time</li>
Run the test with the [[Documentation/4.0/Developers/Tutorials/Debug_Instructions|debugger]], set a breakpoint in the class constructor and ignore the break as many time as the instance number (say it's 2):
* GDB
(gdb) break vtkProperty2D::vtkProperty2D()
Breakpoint 1 at 0x5b22d0e55d04296: file vtkProperty2D.cxx, line 22
(gdb) ignore 1 2
(gdb) run
When the debugger stops, check the call stack:
(gdb) backtrace
*Visual Studio
**Set a breakpoint in vtkProperty2D::vtkProperty2D()
**Right click on the breakpoint and select HitCount, select "break when the hit count is equal to" and type '2'
**Start the application
By analyzing the trace, you should be able to find the faulty instance.

<li> Analyze the code to see where the leak could be</li>
Here is a listing of the most common mistakes
* this->MyXXX = vtkXXX::New();
** Is there a matching this->MyXXX->Delete() ?
** Are you sure <code>this->MyXXX</code> is <code>0</code> before being assigned a new pointer ? If not, then you need to add
if (this->MyXXX != 0)
{
this->MyXXX->Delete();
this->MyXXX = 0;
}
this->MyXXX = vtkXXX::New();
</ol>
{{ombox
|type=content
|text=To reduce memory leaks, use the following tools:
* <code>vtkNew<vtkXXX> myXXX;</code>
* <code>vtkSmartPointer<vtkXXX> myXXX = vtkSmartPointer<vtkXXX>::New()</code>
* <code>vtkSmartPointer<vtkXXX> myXXX; myXXX.TakeReference(this->CreateObjAndCallerOwnsReference())</code>.
}}

==Other resources==
* [[Slicer3:VTK_Leak_Debugging|Slicer3 VTK leak debugging]]
* [[Strategies_for_Writing_and_Debugging_Code_in_Slicer_3|Strategies for Writing and Debugging Code in Slicer3]]

=Track a crash while accessing already deleted object pointer=
If the application crashes by accessing an invalid pointer. The goal here is to find when (and why) the pointer is deleted before it is accessed .
<ol>
<li>Before the crash, print the value of the pointer:</li>
Add before the crash (i.e. <code>this->MyObject->update()</code>)
std::cout << ">>>>>Object pointer: " << this->MyObject << std::endl;
<li>Add a counter in the destructor:</li>
Add in the object destructor (it can be in the base class (vtkObject or vtkMRMLNode) if you don't know the type):
static int count = 0;
std::cout << "#######Object Destructed: " << this << " " << count++ << std::endl;
<li>Run the application and make it crash.</li>
<li>In the logs you shall see something like that:</li>
#######Object Destructed: 0x12345678 0
#######Object Destructed: 0x12345679 1
#######Object Destructed: 0x12345680 2
>>>>>Object Pointer: 0x12345660
>>>>>Object Pointer: 0x12345661
>>>>>Object Pointer: 0x12345662
#######Object Destructed: 0x12345660 3
#######Object Destructed: 0x12345661 4
#######Object Destructed: 0x12345662 5
#######Object Destructed: 0x12345663 6
>>>>>Object Pointer: 0x12345670
>>>>>Object Pointer: 0x12345671
>>>>>Object Pointer: 0x12345672
#######Object Destructed: 0x12345660 7
#######Object Destructed: 0x12345661 8
#######Object Destructed: 0x12345662 9
>>>>>Object Pointer: '''0x12345663'''
Segfault
<li> Search in the logs when the pointer before crash has been deleted. Set a conditional breakpoint in the debugger:</li>
(gdb) break MyObj.cxx:103 if count == 6
or
(gdb) break MyObj.cxx:103
(gdb) ignore 1 5
or if you don't want to use a debugger, you can make it crash the 6th time:
assert(count != 6);
<li> Analyze the backtrace to understand why the pointer has been deleted without letting know the object that tries to access it.</li>
</ol>

= Why is my VTK actor/widget not visible ?=
* Add a breakpoint in RenderOpaqueGeometry() check if it is called. If not, then:
** Check its vtkProp::Visibility value.
*** For vtkWidgets, it is the visibility of the representation.
** Check its GetBounds() method. If they are outside the camera frustrum, the object won't be rendered.
*** For vtkWidgets, it is the bounds of the representation.

=Console output on Windows=
On Windows, the application is built with no console output. A workaround for this issue is described in the following bug reports:
* http://www.na-mic.org/Bug/view.php?id=2376
* http://www.na-mic.org/Bug/view.php?id=2917
To add console output, you need to compile Slicer application with Slicer_BUILD_WIN32_CONSOLE set to ON at the configure time (uninitialized/OFF by default).

Documentation/Nightly/Developers/FAQ/Debugging

2015-01-23T10:31:27Z

Finetjul: /* Developer FAQ: {{{1}}} */

<noinclude>{{documentation/versioncheck}}</noinclude>
<noinclude>__TOC__
={{#titleparts: {{PAGENAME}} | | -1 }}=</noinclude><includeonly>
='''Developer FAQ: {{{1}}}'''=
</includeonly>

== How to print QString using GDB ? ==

See http://silmor.de/qtstuff.printqstring.php

== More troubleshooting questions ? ==

See [[Documentation/{{documentation/currentversion}}/Developers/Tutorials/Troubleshooting|Troubleshooting]]

User:Finetjul

2014-08-26T21:28:55Z

Finetjul: /* To do after release */

=To do after release=
*"Edit properties..." should open module and select node
** Dbl click in Data module should open module, not rename
*Check order of unload with ITKv4: MRML plugin shall unload before VTK and even more before ITK
** Breakpoint in a destructor of static variable in mrml plugin and vtk ?
*Add unit test to vtkMRMLStorableNode/StorableNode and make it faster (e.g. ProcessMRMLNodeEvent)
*Review SaveDataBundle dialog, write a custom "save dialog"
*qMRMLSliceControllerWidget::setSliceViewName, setSliceViewLabel and setSliceViewColor must be set automatically from qMRMLSliceControlllerWidget::setSlisetMRMLSliceNode
** To confirm with Jim.
** See qMRMLLayoutManager::createSliceWidget and qMRMLSliceControllerWidget::setSliceViewLabel
* Add option in qMRMLNodeComboBox to "renameAtCreation" mrml nodes. Can be useful for CLI modules.
* Default opacity when selecting a foreground volume is 0%, should be 50%
* Review vtkMRMLVolumeRenderingDisplayNode::Copy(), it should do StartModify() and EndModify() instead
* vtkMRML::CopyWithSingleModifiedEvent should do StartModify and EndModify() instead (dito for CopyWithSceneWithSingleModifiedEvent)
* Singleton node vtkMRMLLayoutNode has an ID of vtkMRMLLayoutNodevtkMRMLLayoutNode
* Uniformize StartModify()/EndModify()
** Can vtkMRMLDoubleArrayStorageNode::ReadDataInternal use StartModify()/EndModify()?
** vtkMRMLAnnotationBidimensionalDisplayableManager: Why notify scene ? bidimensionalNode->GetScene()->InvokeEvent(vtkCommand::ModifiedEvent, bidimensionalNode);
** vtkMRMLAnnotationStorageNode::ReadAnnotation : Need to fire events ?
** vtkMRMLAnnotationNode::Initialize(), vtkMRMLAnnotationLinesNode::Initialize(), vtkMRMLAnnotationControlPointsNode::Initialize()
** vtkSlicerTractographyFiducialSeedingLogic::CreateTracts()
** Unique class between vtkMRMLNode and vtkMRMLAbstractLogic ?
** Done: MRMLIDImageIO::Write() ?
* check if vtkMRMLNode::SceneRootDir is needed
* Remove all margins in all modules (including wizards).
** Also set WindowTitle in all the modules (including wizards)

=What am I working on?=
* Various mantis issues
** [http://na-mic.org/Mantis/view.php?id=2125 2125], [http://na-mic.org/Mantis/view.php?id=2093 2093], [http://www.na-mic.org/Bug/view.php?id=1938 1938]

=On hold =

=What's coming next?=
* Usability of Slicer
# Sense of dimension: [http://www.na-mic.org/Bug/view.php?id=1694 1694], [http://www.na-mic.org/Bug/view.php?id=1300 1300]
# Multiple digit value change using the keyboard in numerical input widgets
# Add mouse gesture support for numeric input components
# Fix keyboard input in popup spinbox on Linux and Mac OS X
# Apply range popup to all sliders
# Add mechanism to register and save custom layouts
# Add tool to pop out cluttered item list or tree views
# Add support to nested custom styles
# Add support for custom color palette theme
# Bonus: Multi Volume Rendering support (improve refresh -> done)
* Mantis issues: [http://www.na-mic.org/Bug/view.php?id=1996 1996], [http://www.na-mic.org/Bug/view.php?id=1962 1962], [http://na-mic.org/Mantis/view.php?id=1917 1917], [http://na-mic.org/Mantis/view.php?id=1588 1588],[http://www.na-mic.org/Bug/view.php?id=1805 1805]...
* [http://www.na-mic.org/Bug/view.php?id=2185 Support Volume Rendering extensions]

=Done=
*Back faces of models should be visible by default (see http://www.na-mic.org/Bug/view.php?id=1798 )
*VTK callback speed-up (in VTK 6.0, to be merged on Slicer/VTK)
*Long MHD filename: http://na-mic.org/Mantis/view.php?id=1900
*[http://na-mic.org/Mantis/view.php?id=2179 3D interaction with keyboard]
* Usability of Slicer
# Save Data Dialog redesign: [http://www.na-mic.org/Bug/view.php?id=2098 2098], [http://www.na-mic.org/Bug/view.php?id=2082 2082], [http://www.na-mic.org/Bug/view.php?id=986 986], [http://www.na-mic.org/Bug/view.php?id=1866 1866], [http://www.na-mic.org/Bug/view.php?id=1825 1825], [http://www.na-mic.org/Bug/view.php?id=1459 1459], [http://www.na-mic.org/Bug/view.php?id=2023 2023], [http://www.na-mic.org/Bug/view.php?id=1740 1740], [http://www.na-mic.org/Bug/view.php?id=2097 2097], [http://www.na-mic.org/Bug/view.php?id=1817 1817]
* Numpad key support for 3D view ([http://na-mic.org/Mantis/view.php?id=2179 2179])
* Volume Rendering support for extra mappers ([http://na-mic.org/Mantis/view.php?id=2185 2185])
* Default layout should be 4up.
* Features: 1870
* Bugs: 1980, 2010, 2038, 2066
* Scene file loading options ([http://na-mic.org/Mantis/view.php?id=1952 1952])
* Cleanup qMRMLTransformsSlider, restored unit tests
* Skullstripper extension for Slicer4.1QtTesting package
* Failing tests (due to GetAttribute() returning 0)
* CTK Layout flickering ([http://na-mic.org/Mantis/view.php?id=2073 Grid layout regression])
* Volume Rendering supports color transfer function
* Scene view speed-up
* QtTesting integration
* Crash when restoring sceneview

User:Finetjul

2014-08-26T21:20:01Z

Finetjul: /* To do after release */

=To do after release=
*"Edit properties..." should open module and select node
** Dbl click in Data module should open module, not rename
*Check order of unload with ITKv4: MRML plugin shall unload before VTK and even more before ITK
** Breakpoint in a destructor of static variable in mrml plugin and vtk ?
*Add unit test to vtkMRMLStorableNode/StorableNode and make it faster (e.g. ProcessMRMLNodeEvent)
*Review SaveDataBundle dialog, write a custom "save dialog"
*qMRMLSliceControllerWidget::setSliceViewName, setSliceViewLabel and setSliceViewColor must be set automatically from qMRMLSliceControlllerWidget::setSlisetMRMLSliceNode
** To confirm with Jim.
** See qMRMLLayoutManager::createSliceWidget and qMRMLSliceControllerWidget::setSliceViewLabel
* Add option in qMRMLNodeComboBox to "renameAtCreation" mrml nodes. Can be useful for CLI modules.
* Default opacity when selecting a foreground volume is 0%, should be 50%
* Review vtkMRMLVolumeRenderingDisplayNode::Copy(), it should do StartModify() and EndModify() instead
* vtkMRML::CopyWithSingleModifiedEvent should do StartModify and EndModify() instead (dito for CopyWithSceneWithSingleModifiedEvent)
* Singleton node vtkMRMLLayoutNode has an ID of vtkMRMLLayoutNodevtkMRMLLayoutNode
* Uniformize StartModify()/EndModify()
** Can vtkMRMLDoubleArrayStorageNode::ReadDataInternal use StartModify()/EndModify()?
** vtkMRMLAnnotationBidimensionalDisplayableManager: Why notify scene ? bidimensionalNode->GetScene()->InvokeEvent(vtkCommand::ModifiedEvent, bidimensionalNode);
** vtkMRMLAnnotationStorageNode::ReadAnnotation : Need to fire events ?
** vtkMRMLAnnotationNode::Initialize(), vtkMRMLAnnotationLinesNode::Initialize(), vtkMRMLAnnotationControlPointsNode::Initialize()
** vtkSlicerTractographyFiducialSeedingLogic::CreateTracts()
** Unique class between vtkMRMLNode and vtkMRMLAbstractLogic ?
** Done: MRMLIDImageIO::Write() ?
* check if vtkMRMLNode::SceneRootDir is needed
* Remove all margins in all modules (including wizard)

=What am I working on?=
* Various mantis issues
** [http://na-mic.org/Mantis/view.php?id=2125 2125], [http://na-mic.org/Mantis/view.php?id=2093 2093], [http://www.na-mic.org/Bug/view.php?id=1938 1938]

=On hold =

=What's coming next?=
* Usability of Slicer
# Sense of dimension: [http://www.na-mic.org/Bug/view.php?id=1694 1694], [http://www.na-mic.org/Bug/view.php?id=1300 1300]
# Multiple digit value change using the keyboard in numerical input widgets
# Add mouse gesture support for numeric input components
# Fix keyboard input in popup spinbox on Linux and Mac OS X
# Apply range popup to all sliders
# Add mechanism to register and save custom layouts
# Add tool to pop out cluttered item list or tree views
# Add support to nested custom styles
# Add support for custom color palette theme
# Bonus: Multi Volume Rendering support (improve refresh -> done)
* Mantis issues: [http://www.na-mic.org/Bug/view.php?id=1996 1996], [http://www.na-mic.org/Bug/view.php?id=1962 1962], [http://na-mic.org/Mantis/view.php?id=1917 1917], [http://na-mic.org/Mantis/view.php?id=1588 1588],[http://www.na-mic.org/Bug/view.php?id=1805 1805]...
* [http://www.na-mic.org/Bug/view.php?id=2185 Support Volume Rendering extensions]

=Done=
*Back faces of models should be visible by default (see http://www.na-mic.org/Bug/view.php?id=1798 )
*VTK callback speed-up (in VTK 6.0, to be merged on Slicer/VTK)
*Long MHD filename: http://na-mic.org/Mantis/view.php?id=1900
*[http://na-mic.org/Mantis/view.php?id=2179 3D interaction with keyboard]
* Usability of Slicer
# Save Data Dialog redesign: [http://www.na-mic.org/Bug/view.php?id=2098 2098], [http://www.na-mic.org/Bug/view.php?id=2082 2082], [http://www.na-mic.org/Bug/view.php?id=986 986], [http://www.na-mic.org/Bug/view.php?id=1866 1866], [http://www.na-mic.org/Bug/view.php?id=1825 1825], [http://www.na-mic.org/Bug/view.php?id=1459 1459], [http://www.na-mic.org/Bug/view.php?id=2023 2023], [http://www.na-mic.org/Bug/view.php?id=1740 1740], [http://www.na-mic.org/Bug/view.php?id=2097 2097], [http://www.na-mic.org/Bug/view.php?id=1817 1817]
* Numpad key support for 3D view ([http://na-mic.org/Mantis/view.php?id=2179 2179])
* Volume Rendering support for extra mappers ([http://na-mic.org/Mantis/view.php?id=2185 2185])
* Default layout should be 4up.
* Features: 1870
* Bugs: 1980, 2010, 2038, 2066
* Scene file loading options ([http://na-mic.org/Mantis/view.php?id=1952 1952])
* Cleanup qMRMLTransformsSlider, restored unit tests
* Skullstripper extension for Slicer4.1QtTesting package
* Failing tests (due to GetAttribute() returning 0)
* CTK Layout flickering ([http://na-mic.org/Mantis/view.php?id=2073 Grid layout regression])
* Volume Rendering supports color transfer function
* Scene view speed-up
* QtTesting integration
* Crash when restoring sceneview

Documentation/Nightly/Developers/ModuleWizard

2014-08-26T20:49:59Z

Finetjul: /* Step by Step */

<noinclude>{{documentation/versioncheck}}</noinclude>

{{ambox
| type = warning
| text = '''Deprecated'''This page describes a utility which has been deprecated. If you are using Slicer 4.4 or later, it is recommended to use the [[Documentation/{{documentation/version}}/Developers/ExtensionWizard|Extension Wizard]] instead.
}}

 

== Background ==

Slicer modules typically consist of several files of various types, such as CMake files, source files, and binary files.

In many cases, the names of the files and the names of text strings inside the files are related and need to be in sync in order for things to compile.

Also, it is not uncommon to want to use one module as the starting point for implementing similar functionality.

For development, we suggest starting with the structure of an Extension that can contains one or more modules. The [[Documentation/{{documentation/version}}/Developers/Modules|modules]] can be of different types, such as python scripted module or pure C++ modules or a combination.

The ModuleWizard will do most of the copying and renaming for you, but you will also need to manually configure some steps (specifically, you need to edit the CMakeLists.txt file when you add a module to an extension).

== Terminology ==

* The ''template'' is a directory containing a slicer module
* The ''templateKey'' is a text string, typically the name of the module, that is used in both filename and identifiers inside the module.
* The ''target'' is a directory where you want the new module to be placed
* The ''moduleName'' is the string that you want to use in place of the ''templateKey''

== Usage ==

ModuleWizard [--template <dir>] [--templateKey <key>] [--target <dir>] <moduleName>
--template default ./Extensions/Testing/LoadableExtensionTemplate
--templateKey default is dirname of template
--target default ./Modules/Loadable/<moduleName>

== Step by Step ==

The idea of the wizard is to create a new self-contained directory that is a working module from the slicer perspective. This means that for C++ extensions, you only need to compile the extension and it will work with slicer. For scripted (python) extensions, you don't even need to compile.

Running this wizard will create the module in the specified target directory and will give it the name you specify on the command line.

On Windows, you can execute the wizard by running the command as a parameter of python:
../Slicer-Superbuild/python-install/bin/python.exe ./Utilities/Scripts/ModuleWizard.py --template [...]

=== Creating an Extension ===

For example, running this command:

./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/ScriptedLoadableExtensionTemplate --target ../MyExtension MyExtension

should be done from within the slicer source directory, so that the <code>ModuleWizard.py</code> script is found, and so that the template path points to the correct spot. This command relies on your machine having an installed python interpreter to run the wizard (any version of python should work, you don't need to use the one that gets built with slicer).

This command will create a new directory parallel to the Slicer source directory, in this case called MyExtension.

The resulting extension will include a sample module in a directory called "ScriptedLoadableModuleTemplate" -- ''you should delete this directory since we will replace it in the next step.''

Edit the MyExtension/CMakeLists.txt file to customize it for your work. For example, list yourself and your colleagues as contributors and add the proper links to your project pages and icons. You should also make a custom icon for extension, that will represent it in the ExtensionManager.

=== Adding a Module ===

Instead of the generic module, we'll want a new one with a custom name, you can use the ModuleWizard again to rename the file and the contents from the template:

./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/ScriptedLoadableExtensionTemplate/ScriptedLoadableModuleTemplate --target ../MyExtension/MyScriptedModule MyScriptedModule

Now you will need to edit the ../MyExtension/CMakeLists.txt and change the following line:

add_subdirectory(ScriptedLoadableModuleTemplate)

to read:

add_subdirectory(MyScriptedModule)

Since we used the ScriptedLoadableExtensionTemplate, the only thing we need to do is set the additional module path to point to the full path to MyExtension/MyScriptedModule in the [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings|Application Settings]] dialog.

Then when you restart slicer, you should select your module using in the [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Module_Selection_.26_Navigation|Module Navigation]] interface.

=== Adding More Modules ===

Note that you can repeat the steps for adding modules so that your extension can contain many modules of different types. Just run the ModuleWizard with the path to the appropriate template, and add the directory to the CMakeLists.txt.

== Examples ==

To create a [[Documentation/{{documentation/version}}/Developers/Modules#Command_Line_Interface_.28CLI.29|CLI]] Extension:

./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate --target ../MyExtension/MyCLIModule MyCLIModule

where <code>MyFooExtension</code> is the name of your extension

To create a [[Documentation/{{documentation/version}}/Developers/Tutorials/CreateLoadableModule|Loadable]] Module:

./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/LoadableExtensionTemplate/LoadableModuleTemplate --target ../MyExtension/MyLoadableModule MyLoadableModule

To create a [[Documentation/{{documentation/version}}/Developers/Modules#Scripted_Modules|Scripted Loadable]] Module:

./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/ScriptedLoadableExtensionTemplate/ScriptedLoadableModuleTemplate --target ../MyExtension/MyScriptedModule MyScriptedModule

To create an [[Documentation/{{documentation/version}}/Developers/EditorExtension|EditorEffect]] Extension
./Utilities/Scripts/ModuleWizard.py --template ./Extensions/Testing/EditorExtensionTemplate/EditorEffectTemplate --target ../MyExtension/MyEditorEffect MyEditorEffect

For reference, an extension directory that results from the steps above can be found [https://github.com/pieper/MyExtension in this git repository].

=== Creating and Testing a Loadable Module ===

The following code can be run from the SuperBuild directory (mac and linux):

<pre>
NEWMODULE=NewModule
SLICERSUPERBUILD=`pwd`

../Slicer/Utilities/Scripts/ModuleWizard.py --template ../Slicer/Extensions/Testing/LoadableExtensionTemplate --target /tmp/${NEWMODULE} ${NEWMODULE}
mkdir /tmp/${NEWMODULE}-build
(cd /tmp/${NEWMODULE}-build; cmake /tmp/${NEWMODULE} -DSlicer_DIR:PATH=${SLICERSUPERBUILD}/Slicer-build; make)
./Slicer-build/Slicer --additional-module-paths /tmp/${NEWMODULE}-build/lib/Slicer-4.2/qt-loadable-modules

</pre>

After running this command, Slicer will start, and you will find the default LoadableModuleTempate in the modules menu under Examples. In the python interpreter, you can access the wrapped logic with:

logic = slicer.modules.loadablemoduletemplate.logic()

From here, you can add additional methods to the logic and develop the GUI.

''Note: use the latest version of CMake (2.8.11) on mac''

Documentation/Nightly/Developers/Build Instructions/Prerequisites/Qt

2014-08-25T13:54:24Z

Finetjul: /* Qt 4.8.6 / VS2012 */

<noinclude>{{documentation/versioncheck}}</noinclude>
= Binary vs build-from-source ? =

If you build Slicer on ...

== Linux ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

== Mac ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

* To use QtCreator and the Slicer designer plugins, a possible option is to build QtCreator against the installed Qt libraries. See [http://slicer-devel.65872.n3.nabble.com/Using-Qt-Creator-with-Slicer4-On-Mac-OS-X-Multiple-Qt-libs-loaded-tp4026660p4026690.html discussion on the mailing list].

== Windows ==

=== Debug (32 and 64-bit) or Release (64-bit) ===

* Normally you should plan to build Qt from source to have complete control over the process. See [https://github.com/jcfr/qt-easy-build one-liner build command] or more detailed [[#Build_instructions]]

* You may find that the '''unsigned''' binary downloads from this site are usable: http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2008/

* '''Details''': Using the Qt Designer on Windows requires that the Slicer plugins are [http://doc.trolltech.com/4.6/deployment-plugins.html#debugging-plugins|compiled in the same mode as Qt]. If Qt was compiled in Release mode (default), Slicer would have to be compiled in Release mode as well. However if Qt is compiled in Debug mode only, Slicer has to be compiled in Debug too. When Qt is in "Release and Debug" mode only the Release version of Designer.exe is generated, Slicer would have to be compiled in Release. So for developers, the Debug mode is recommended, this is why we detail the compilation of Qt below.

=== Release (32-bit) ===

* Using [[#Download_links|binary]] works great for 32-bit Release build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

 

= Download Qt: Source and Binaries =

== Download links ==

The following table list the link allowing to download either the '''recommended''' source code or binary of Qt.

{| border="1" style="margin-left: 20px;"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="1" rowspan="2"|Linux
!colspan="2"|Mac
!colspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="1"|SnowLeopard
!colspan="1"|Lion, Mountain Lion
!colspan="1"|VS2008
!colspan="1"|VS2010
|- bgcolor="#FFFFCC"
!|64bits
!|64bits
!|64bits
!|64bits
!|64bits
|-
! bgcolor="#FFFFCC" | Qt source link
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/archive/qt/4.7/qt-everywhere-opensource-src-4.7.4.tar.gz 4.7.4]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|-
! bgcolor="#FFFFCC" | Qt binary link
|align="center" colspan="1"| (src or apt-get package) 
|align="center" colspan="1"| [http://packages.kitware.com/download/item/3736/qt-mac-opensource-4.7.4.dmg 4.7.4] [http://packages.kitware.com/download/item/3739/qt-mac-opensource-4.7.4-debug-libs.dmg 4.7.4 (optional: debug libs)]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1.dmg 4.8.6] [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1-debug-libs.dmg 4.8.6 (optional: debug libs)]

|align="center" colspan="1"| [http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2008/ 4.8.5 (unsigned installer)]
|align="center" colspan="1"| [http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2010/ 4.8.5 (unsigned installer)]
|}



== Qt version specific issues ==

* Issues for Qt < 4.7.4 are not reported

=== All ===
* NA

=== Linux ===

* NA

=== Mac ===
* Problem building Qt on MacOSX 10.9. See https://bugreports.qt-project.org/browse/QTBUG-32237


=== Windows ===

* NA

== How to change the minimum required version ? ==

* This applied only for Slicer < [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22466 r22466].

* It's indeed possible to use a different version, just be aware that moving forward in time, things may not work as expected. Even worse Slicer may simply fail to compile.

* By configuring Slicer using <code>-DSlicer_REQUIRED_QT_VERSION:STRING=4.7.0</code>, you will be able to change the minimum required version.

* See [https://github.com/Slicer/Slicer/commit/898bb14e 898bb14e], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19698 r19698], [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/008130.html Mailing list]

 

= Build instructions =
 
{{mbox
| text = Please, make sure that your IDE/compiler is '''properly installed''' and that all associated '''ServicePack''' are also installed. See [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites|Prerequisites]].
}}
 

== Linux ==

See [[Documentation/Nightly/Developers/Build_Instructions#Linux]]






== Mac ==

Similar to Linux configuration. Note that <code>-arch x86_64</code> has been added.

For earlier versions of Xcode and Mac OS X
{{pre2|scroll|
mkdir qt-everywhere-opensource-build-4.7.4
tar xvfz qt-everywhere-opensource-src-4.7.4.tar.gz
cd qt-everywhere-opensource-src-4.7.4
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -webkit -arch x86_64 -nomake examples -nomake demos -sdk /Developer/SDKs/MacOSX10.5.sdk
make -j8
make install
}}

On the latest Xcode versions (4.3) and Lion (10.7) the Developer directories have moved. The command is now:

{{pre2|scroll|
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -arch x86_64 -nomake examples -nomake demos -webkit -sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk
}}

* Consider reading: http://doc.qt.nokia.com/4.7/developing-on-mac.html)

* Note:
** If building against SDK 10.6 or 10.7, you will probably get link errors similar to what's described in [https://trac.macports.org/ticket/30346] and [http://qt-project.org/forums/viewthread/15933]. Solution is provided here [https://bugreports.qt-project.org/browse/QTBUG-24361 here].

== Windows ==

* Use a windows extracter to unzip the [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites/Qt#Download_links|Qt archive]], don't use cygwin unzip it.

=== Qt 4.7.4 / VS2008 ===

* Rename the folder into for example <code>qt-4.7.4-64-vs2008-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.7.4-32-vs2008-deb</code>

* Launch the msvc2008 command prompt 
** 32-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 Command Prompt"
** 64-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 x64 Win64 Command Prompt"


* Configure
** For debug: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -debug -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -release -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2008</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.
** Note: According to [http://qt.nokia.com/doc/4.7/supported-platforms.html] Qt does not support msvc2008 on windows xp. However, running <code>configure.exe</code> with no <code>-platform</code> argument seems to work. If you run configure with the <code>-platform</code> argument first by mistake, and if <code>configure -clean</code> doesn't work, then you may need to start from a fresh extraction from the .zip archive before running <code>configure.exe</code> again with no <code>-platform</code>, unless you can run <code>nmake</code> with the config clean target.

* Build using <code>nmake</code>
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart nmake. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.5 / VS2010 ===

* Rename the folder into for example <code>qt-4.8.5-64-vs2010-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.5-32-vs2010-deb</code>

* Launch the msvc2010 command prompt 
** 32-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 Command Prompt"
** 64-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 x64 Win64 Command Prompt"


*Download pearl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

*Download jom and create a new folder into for example <code>jom</code>.
**Add this new folder into the path (system properties)

* Configure
** For debug: <code>configure.exe -platform win32-msvc2010 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2010 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2010</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>jom -jn</code>
**Note: n is the number of cores of your CPU, so adapt it.
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart jom. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.6 / VS2012 ===

* Make sure your Visual Studio 2012 is patched with the latest patch (e.g. [http://www.microsoft.com/en-us/download/confirmation.aspx?id=39305 patch 4]).

* Download the [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip source archive], extract and rename the folder into for example <code>qt-4.8.6-64-vs2012-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.6-32-vs2010-deb</code>

* Replace the webkit src\3rdparty\webkit\Source\JavaScriptCore\wtf\hashset.h file with this [https://bitbucket.org/Vertexwahn/bluego/src/56dbe84212222ec6954d8d327a5e443106bcc447/deploy/BlueGo0.0.4/qt4.8.3vs2012patch/HashSet.h?at=default file]

* Launch the msvc2012 command prompt 
** 32-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x86 Command Prompt"
** 64-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x64 Win64 Command Prompt"


* If you want openssl support (optional):
** Download perl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

* Configure
** For debug: <code>configure.exe -platform win32-msvc2012 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2012 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2010</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>nmake</code>
** Alternatively you can use jom (much faster)
*** Download jom and create a new folder into for example <code>jom</code>.
*** Add this new folder into the path (system properties)
*** Build using <code>jom -jn</code>
**** Note: n is the number of cores of your CPU, so adapt it.

Documentation/Nightly/Developers/Build Instructions/Prerequisites/Qt

2014-08-25T13:54:05Z

Finetjul: /* Qt 4.8.6 / VS2012 */

<noinclude>{{documentation/versioncheck}}</noinclude>
= Binary vs build-from-source ? =

If you build Slicer on ...

== Linux ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

== Mac ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

* To use QtCreator and the Slicer designer plugins, a possible option is to build QtCreator against the installed Qt libraries. See [http://slicer-devel.65872.n3.nabble.com/Using-Qt-Creator-with-Slicer4-On-Mac-OS-X-Multiple-Qt-libs-loaded-tp4026660p4026690.html discussion on the mailing list].

== Windows ==

=== Debug (32 and 64-bit) or Release (64-bit) ===

* Normally you should plan to build Qt from source to have complete control over the process. See [https://github.com/jcfr/qt-easy-build one-liner build command] or more detailed [[#Build_instructions]]

* You may find that the '''unsigned''' binary downloads from this site are usable: http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2008/

* '''Details''': Using the Qt Designer on Windows requires that the Slicer plugins are [http://doc.trolltech.com/4.6/deployment-plugins.html#debugging-plugins|compiled in the same mode as Qt]. If Qt was compiled in Release mode (default), Slicer would have to be compiled in Release mode as well. However if Qt is compiled in Debug mode only, Slicer has to be compiled in Debug too. When Qt is in "Release and Debug" mode only the Release version of Designer.exe is generated, Slicer would have to be compiled in Release. So for developers, the Debug mode is recommended, this is why we detail the compilation of Qt below.

=== Release (32-bit) ===

* Using [[#Download_links|binary]] works great for 32-bit Release build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

 

= Download Qt: Source and Binaries =

== Download links ==

The following table list the link allowing to download either the '''recommended''' source code or binary of Qt.

{| border="1" style="margin-left: 20px;"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="1" rowspan="2"|Linux
!colspan="2"|Mac
!colspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="1"|SnowLeopard
!colspan="1"|Lion, Mountain Lion
!colspan="1"|VS2008
!colspan="1"|VS2010
|- bgcolor="#FFFFCC"
!|64bits
!|64bits
!|64bits
!|64bits
!|64bits
|-
! bgcolor="#FFFFCC" | Qt source link
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/archive/qt/4.7/qt-everywhere-opensource-src-4.7.4.tar.gz 4.7.4]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|-
! bgcolor="#FFFFCC" | Qt binary link
|align="center" colspan="1"| (src or apt-get package) 
|align="center" colspan="1"| [http://packages.kitware.com/download/item/3736/qt-mac-opensource-4.7.4.dmg 4.7.4] [http://packages.kitware.com/download/item/3739/qt-mac-opensource-4.7.4-debug-libs.dmg 4.7.4 (optional: debug libs)]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1.dmg 4.8.6] [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1-debug-libs.dmg 4.8.6 (optional: debug libs)]

|align="center" colspan="1"| [http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2008/ 4.8.5 (unsigned installer)]
|align="center" colspan="1"| [http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2010/ 4.8.5 (unsigned installer)]
|}



== Qt version specific issues ==

* Issues for Qt < 4.7.4 are not reported

=== All ===
* NA

=== Linux ===

* NA

=== Mac ===
* Problem building Qt on MacOSX 10.9. See https://bugreports.qt-project.org/browse/QTBUG-32237


=== Windows ===

* NA

== How to change the minimum required version ? ==

* This applied only for Slicer < [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22466 r22466].

* It's indeed possible to use a different version, just be aware that moving forward in time, things may not work as expected. Even worse Slicer may simply fail to compile.

* By configuring Slicer using <code>-DSlicer_REQUIRED_QT_VERSION:STRING=4.7.0</code>, you will be able to change the minimum required version.

* See [https://github.com/Slicer/Slicer/commit/898bb14e 898bb14e], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19698 r19698], [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/008130.html Mailing list]

 

= Build instructions =
 
{{mbox
| text = Please, make sure that your IDE/compiler is '''properly installed''' and that all associated '''ServicePack''' are also installed. See [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites|Prerequisites]].
}}
 

== Linux ==

See [[Documentation/Nightly/Developers/Build_Instructions#Linux]]






== Mac ==

Similar to Linux configuration. Note that <code>-arch x86_64</code> has been added.

For earlier versions of Xcode and Mac OS X
{{pre2|scroll|
mkdir qt-everywhere-opensource-build-4.7.4
tar xvfz qt-everywhere-opensource-src-4.7.4.tar.gz
cd qt-everywhere-opensource-src-4.7.4
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -webkit -arch x86_64 -nomake examples -nomake demos -sdk /Developer/SDKs/MacOSX10.5.sdk
make -j8
make install
}}

On the latest Xcode versions (4.3) and Lion (10.7) the Developer directories have moved. The command is now:

{{pre2|scroll|
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -arch x86_64 -nomake examples -nomake demos -webkit -sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk
}}

* Consider reading: http://doc.qt.nokia.com/4.7/developing-on-mac.html)

* Note:
** If building against SDK 10.6 or 10.7, you will probably get link errors similar to what's described in [https://trac.macports.org/ticket/30346] and [http://qt-project.org/forums/viewthread/15933]. Solution is provided here [https://bugreports.qt-project.org/browse/QTBUG-24361 here].

== Windows ==

* Use a windows extracter to unzip the [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites/Qt#Download_links|Qt archive]], don't use cygwin unzip it.

=== Qt 4.7.4 / VS2008 ===

* Rename the folder into for example <code>qt-4.7.4-64-vs2008-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.7.4-32-vs2008-deb</code>

* Launch the msvc2008 command prompt 
** 32-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 Command Prompt"
** 64-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 x64 Win64 Command Prompt"


* Configure
** For debug: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -debug -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -release -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2008</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.
** Note: According to [http://qt.nokia.com/doc/4.7/supported-platforms.html] Qt does not support msvc2008 on windows xp. However, running <code>configure.exe</code> with no <code>-platform</code> argument seems to work. If you run configure with the <code>-platform</code> argument first by mistake, and if <code>configure -clean</code> doesn't work, then you may need to start from a fresh extraction from the .zip archive before running <code>configure.exe</code> again with no <code>-platform</code>, unless you can run <code>nmake</code> with the config clean target.

* Build using <code>nmake</code>
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart nmake. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.5 / VS2010 ===

* Rename the folder into for example <code>qt-4.8.5-64-vs2010-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.5-32-vs2010-deb</code>

* Launch the msvc2010 command prompt 
** 32-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 Command Prompt"
** 64-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 x64 Win64 Command Prompt"


*Download pearl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

*Download jom and create a new folder into for example <code>jom</code>.
**Add this new folder into the path (system properties)

* Configure
** For debug: <code>configure.exe -platform win32-msvc2010 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2010 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2010</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>jom -jn</code>
**Note: n is the number of cores of your CPU, so adapt it.
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart jom. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.6 / VS2012 ===

* Make sure your Visual Studio 2012 is patched with the latest patch (e.g. [http://www.microsoft.com/en-us/download/confirmation.aspx?id=39305 patch 4]).

* Download the [source archive http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip], extract and rename the folder into for example <code>qt-4.8.6-64-vs2012-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.6-32-vs2010-deb</code>

* Replace the webkit src\3rdparty\webkit\Source\JavaScriptCore\wtf\hashset.h file with this [https://bitbucket.org/Vertexwahn/bluego/src/56dbe84212222ec6954d8d327a5e443106bcc447/deploy/BlueGo0.0.4/qt4.8.3vs2012patch/HashSet.h?at=default file]

* Launch the msvc2012 command prompt 
** 32-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x86 Command Prompt"
** 64-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x64 Win64 Command Prompt"


* If you want openssl support (optional):
** Download perl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

* Configure
** For debug: <code>configure.exe -platform win32-msvc2012 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2012 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2010</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>nmake</code>
** Alternatively you can use jom (much faster)
*** Download jom and create a new folder into for example <code>jom</code>.
*** Add this new folder into the path (system properties)
*** Build using <code>jom -jn</code>
**** Note: n is the number of cores of your CPU, so adapt it.

Documentation/Nightly/Developers/Build Instructions/Prerequisites/Qt

2014-08-25T13:53:21Z

Finetjul: /* Qt 4.8.6 / VS2012 */

<noinclude>{{documentation/versioncheck}}</noinclude>
= Binary vs build-from-source ? =

If you build Slicer on ...

== Linux ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

== Mac ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

* To use QtCreator and the Slicer designer plugins, a possible option is to build QtCreator against the installed Qt libraries. See [http://slicer-devel.65872.n3.nabble.com/Using-Qt-Creator-with-Slicer4-On-Mac-OS-X-Multiple-Qt-libs-loaded-tp4026660p4026690.html discussion on the mailing list].

== Windows ==

=== Debug (32 and 64-bit) or Release (64-bit) ===

* Normally you should plan to build Qt from source to have complete control over the process. See [https://github.com/jcfr/qt-easy-build one-liner build command] or more detailed [[#Build_instructions]]

* You may find that the '''unsigned''' binary downloads from this site are usable: http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2008/

* '''Details''': Using the Qt Designer on Windows requires that the Slicer plugins are [http://doc.trolltech.com/4.6/deployment-plugins.html#debugging-plugins|compiled in the same mode as Qt]. If Qt was compiled in Release mode (default), Slicer would have to be compiled in Release mode as well. However if Qt is compiled in Debug mode only, Slicer has to be compiled in Debug too. When Qt is in "Release and Debug" mode only the Release version of Designer.exe is generated, Slicer would have to be compiled in Release. So for developers, the Debug mode is recommended, this is why we detail the compilation of Qt below.

=== Release (32-bit) ===

* Using [[#Download_links|binary]] works great for 32-bit Release build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

 

= Download Qt: Source and Binaries =

== Download links ==

The following table list the link allowing to download either the '''recommended''' source code or binary of Qt.

{| border="1" style="margin-left: 20px;"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="1" rowspan="2"|Linux
!colspan="2"|Mac
!colspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="1"|SnowLeopard
!colspan="1"|Lion, Mountain Lion
!colspan="1"|VS2008
!colspan="1"|VS2010
|- bgcolor="#FFFFCC"
!|64bits
!|64bits
!|64bits
!|64bits
!|64bits
|-
! bgcolor="#FFFFCC" | Qt source link
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/archive/qt/4.7/qt-everywhere-opensource-src-4.7.4.tar.gz 4.7.4]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|-
! bgcolor="#FFFFCC" | Qt binary link
|align="center" colspan="1"| (src or apt-get package) 
|align="center" colspan="1"| [http://packages.kitware.com/download/item/3736/qt-mac-opensource-4.7.4.dmg 4.7.4] [http://packages.kitware.com/download/item/3739/qt-mac-opensource-4.7.4-debug-libs.dmg 4.7.4 (optional: debug libs)]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1.dmg 4.8.6] [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1-debug-libs.dmg 4.8.6 (optional: debug libs)]

|align="center" colspan="1"| [http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2008/ 4.8.5 (unsigned installer)]
|align="center" colspan="1"| [http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2010/ 4.8.5 (unsigned installer)]
|}



== Qt version specific issues ==

* Issues for Qt < 4.7.4 are not reported

=== All ===
* NA

=== Linux ===

* NA

=== Mac ===
* Problem building Qt on MacOSX 10.9. See https://bugreports.qt-project.org/browse/QTBUG-32237


=== Windows ===

* NA

== How to change the minimum required version ? ==

* This applied only for Slicer < [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22466 r22466].

* It's indeed possible to use a different version, just be aware that moving forward in time, things may not work as expected. Even worse Slicer may simply fail to compile.

* By configuring Slicer using <code>-DSlicer_REQUIRED_QT_VERSION:STRING=4.7.0</code>, you will be able to change the minimum required version.

* See [https://github.com/Slicer/Slicer/commit/898bb14e 898bb14e], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19698 r19698], [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/008130.html Mailing list]

 

= Build instructions =
 
{{mbox
| text = Please, make sure that your IDE/compiler is '''properly installed''' and that all associated '''ServicePack''' are also installed. See [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites|Prerequisites]].
}}
 

== Linux ==

See [[Documentation/Nightly/Developers/Build_Instructions#Linux]]






== Mac ==

Similar to Linux configuration. Note that <code>-arch x86_64</code> has been added.

For earlier versions of Xcode and Mac OS X
{{pre2|scroll|
mkdir qt-everywhere-opensource-build-4.7.4
tar xvfz qt-everywhere-opensource-src-4.7.4.tar.gz
cd qt-everywhere-opensource-src-4.7.4
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -webkit -arch x86_64 -nomake examples -nomake demos -sdk /Developer/SDKs/MacOSX10.5.sdk
make -j8
make install
}}

On the latest Xcode versions (4.3) and Lion (10.7) the Developer directories have moved. The command is now:

{{pre2|scroll|
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -arch x86_64 -nomake examples -nomake demos -webkit -sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk
}}

* Consider reading: http://doc.qt.nokia.com/4.7/developing-on-mac.html)

* Note:
** If building against SDK 10.6 or 10.7, you will probably get link errors similar to what's described in [https://trac.macports.org/ticket/30346] and [http://qt-project.org/forums/viewthread/15933]. Solution is provided here [https://bugreports.qt-project.org/browse/QTBUG-24361 here].

== Windows ==

* Use a windows extracter to unzip the [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites/Qt#Download_links|Qt archive]], don't use cygwin unzip it.

=== Qt 4.7.4 / VS2008 ===

* Rename the folder into for example <code>qt-4.7.4-64-vs2008-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.7.4-32-vs2008-deb</code>

* Launch the msvc2008 command prompt 
** 32-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 Command Prompt"
** 64-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 x64 Win64 Command Prompt"


* Configure
** For debug: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -debug -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -release -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2008</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.
** Note: According to [http://qt.nokia.com/doc/4.7/supported-platforms.html] Qt does not support msvc2008 on windows xp. However, running <code>configure.exe</code> with no <code>-platform</code> argument seems to work. If you run configure with the <code>-platform</code> argument first by mistake, and if <code>configure -clean</code> doesn't work, then you may need to start from a fresh extraction from the .zip archive before running <code>configure.exe</code> again with no <code>-platform</code>, unless you can run <code>nmake</code> with the config clean target.

* Build using <code>nmake</code>
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart nmake. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.5 / VS2010 ===

* Rename the folder into for example <code>qt-4.8.5-64-vs2010-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.5-32-vs2010-deb</code>

* Launch the msvc2010 command prompt 
** 32-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 Command Prompt"
** 64-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 x64 Win64 Command Prompt"


*Download pearl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

*Download jom and create a new folder into for example <code>jom</code>.
**Add this new folder into the path (system properties)

* Configure
** For debug: <code>configure.exe -platform win32-msvc2010 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2010 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2010</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>jom -jn</code>
**Note: n is the number of cores of your CPU, so adapt it.
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart jom. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.6 / VS2012 ===

* Make sure your Visual Studio 2012 is patched with the latest patch (e.g. [http://www.microsoft.com/en-us/download/confirmation.aspx?id=39305 patch 4]).

* Download the source archive, extract and rename the folder into for example <code>qt-4.8.6-64-vs2012-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.6-32-vs2010-deb</code>

* Replace the webkit src\3rdparty\webkit\Source\JavaScriptCore\wtf\hashset.h file with this [https://bitbucket.org/Vertexwahn/bluego/src/56dbe84212222ec6954d8d327a5e443106bcc447/deploy/BlueGo0.0.4/qt4.8.3vs2012patch/HashSet.h?at=default file]

* Launch the msvc2012 command prompt 
** 32-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x86 Command Prompt"
** 64-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x64 Win64 Command Prompt"


* If you want openssl support (optional):
** Download perl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

* Configure
** For debug: <code>configure.exe -platform win32-msvc2012 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2012 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2010</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>nmake</code>
** Alternatively you can use jom (much faster)
*** Download jom and create a new folder into for example <code>jom</code>.
*** Add this new folder into the path (system properties)
*** Build using <code>jom -jn</code>
**** Note: n is the number of cores of your CPU, so adapt it.

Documentation/Nightly/Developers/Build Instructions/Prerequisites/Qt

2014-08-23T16:46:49Z

Finetjul: Add MSVC2012 with QT 4.8.6 building instructions

<noinclude>{{documentation/versioncheck}}</noinclude>
= Binary vs build-from-source ? =

If you build Slicer on ...

== Linux ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

== Mac ==

* Using [[#Download_links|binary]] works great for both '''Debug''' and '''Release''' build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

* To use QtCreator and the Slicer designer plugins, a possible option is to build QtCreator against the installed Qt libraries. See [http://slicer-devel.65872.n3.nabble.com/Using-Qt-Creator-with-Slicer4-On-Mac-OS-X-Multiple-Qt-libs-loaded-tp4026660p4026690.html discussion on the mailing list].

== Windows ==

=== Debug (32 and 64-bit) or Release (64-bit) ===

* Normally you should plan to build Qt from source to have complete control over the process. See [https://github.com/jcfr/qt-easy-build one-liner build command] or more detailed [[#Build_instructions]]

* You may find that the '''unsigned''' binary downloads from this site are usable: http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2008/

* '''Details''': Using the Qt Designer on Windows requires that the Slicer plugins are [http://doc.trolltech.com/4.6/deployment-plugins.html#debugging-plugins|compiled in the same mode as Qt]. If Qt was compiled in Release mode (default), Slicer would have to be compiled in Release mode as well. However if Qt is compiled in Debug mode only, Slicer has to be compiled in Debug too. When Qt is in "Release and Debug" mode only the Release version of Designer.exe is generated, Slicer would have to be compiled in Release. So for developers, the Debug mode is recommended, this is why we detail the compilation of Qt below.

=== Release (32-bit) ===

* Using [[#Download_links|binary]] works great for 32-bit Release build of Slicer. See [[#Download_links]] and [[#Installation_instruction]]

 

= Download Qt: Source and Binaries =

== Download links ==

The following table list the link allowing to download either the '''recommended''' source code or binary of Qt.

{| border="1" style="margin-left: 20px;"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="1" rowspan="2"|Linux
!colspan="2"|Mac
!colspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="1"|SnowLeopard
!colspan="1"|Lion, Mountain Lion
!colspan="1"|VS2008
!colspan="1"|VS2010
|- bgcolor="#FFFFCC"
!|64bits
!|64bits
!|64bits
!|64bits
!|64bits
|-
! bgcolor="#FFFFCC" | Qt source link
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/archive/qt/4.7/qt-everywhere-opensource-src-4.7.4.tar.gz 4.7.4]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.tar.gz 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-everywhere-opensource-src-4.8.6.zip 4.8.6]
|-
! bgcolor="#FFFFCC" | Qt binary link
|align="center" colspan="1"| (src or apt-get package) 
|align="center" colspan="1"| [http://packages.kitware.com/download/item/3736/qt-mac-opensource-4.7.4.dmg 4.7.4] [http://packages.kitware.com/download/item/3739/qt-mac-opensource-4.7.4-debug-libs.dmg 4.7.4 (optional: debug libs)]
|align="center" colspan="1"| [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1.dmg 4.8.6] [http://download.qt-project.org/official_releases/qt/4.8/4.8.6/qt-opensource-mac-4.8.6-1-debug-libs.dmg 4.8.6 (optional: debug libs)]

|align="center" colspan="1"| [http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2008/ 4.8.5 (unsigned installer)]
|align="center" colspan="1"| [http://sourceforge.net/projects/qtx64/files/qt-x64/4.8.5/msvc2010/ 4.8.5 (unsigned installer)]
|}



== Qt version specific issues ==

* Issues for Qt < 4.7.4 are not reported

=== All ===
* NA

=== Linux ===

* NA

=== Mac ===
* Problem building Qt on MacOSX 10.9. See https://bugreports.qt-project.org/browse/QTBUG-32237


=== Windows ===

* NA

== How to change the minimum required version ? ==

* This applied only for Slicer < [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=22466 r22466].

* It's indeed possible to use a different version, just be aware that moving forward in time, things may not work as expected. Even worse Slicer may simply fail to compile.

* By configuring Slicer using <code>-DSlicer_REQUIRED_QT_VERSION:STRING=4.7.0</code>, you will be able to change the minimum required version.

* See [https://github.com/Slicer/Slicer/commit/898bb14e 898bb14e], [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=19698 r19698], [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2012/008130.html Mailing list]

 

= Build instructions =
 
{{mbox
| text = Please, make sure that your IDE/compiler is '''properly installed''' and that all associated '''ServicePack''' are also installed. See [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites|Prerequisites]].
}}
 

== Linux ==

See [[Documentation/Nightly/Developers/Build_Instructions#Linux]]






== Mac ==

Similar to Linux configuration. Note that <code>-arch x86_64</code> has been added.

For earlier versions of Xcode and Mac OS X
{{pre2|scroll|
mkdir qt-everywhere-opensource-build-4.7.4
tar xvfz qt-everywhere-opensource-src-4.7.4.tar.gz
cd qt-everywhere-opensource-src-4.7.4
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -webkit -arch x86_64 -nomake examples -nomake demos -sdk /Developer/SDKs/MacOSX10.5.sdk
make -j8
make install
}}

On the latest Xcode versions (4.3) and Lion (10.7) the Developer directories have moved. The command is now:

{{pre2|scroll|
./configure -prefix ../qt-everywhere-opensource-build-4.7.4 -debug-and-release -opensource -confirm-license -no-qt3support -arch x86_64 -nomake examples -nomake demos -webkit -sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk
}}

* Consider reading: http://doc.qt.nokia.com/4.7/developing-on-mac.html)

* Note:
** If building against SDK 10.6 or 10.7, you will probably get link errors similar to what's described in [https://trac.macports.org/ticket/30346] and [http://qt-project.org/forums/viewthread/15933]. Solution is provided here [https://bugreports.qt-project.org/browse/QTBUG-24361 here].

== Windows ==

* Use a windows extracter to unzip the [[Documentation/{{documentation/version}}/Developers/Build_Instructions/Prerequisites/Qt#Download_links|Qt archive]], don't use cygwin unzip it.

=== Qt 4.7.4 / VS2008 ===

* Rename the folder into for example <code>qt-4.7.4-64-vs2008-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.7.4-32-vs2008-deb</code>

* Launch the msvc2008 command prompt 
** 32-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 Command Prompt"
** 64-bit build: Start menu -> MSVC08->Tools -> "Visual Studio 2008 x64 Win64 Command Prompt"


* Configure
** For debug: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -debug -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2008 -opensource -confirm-license -release -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2008</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.
** Note: According to [http://qt.nokia.com/doc/4.7/supported-platforms.html] Qt does not support msvc2008 on windows xp. However, running <code>configure.exe</code> with no <code>-platform</code> argument seems to work. If you run configure with the <code>-platform</code> argument first by mistake, and if <code>configure -clean</code> doesn't work, then you may need to start from a fresh extraction from the .zip archive before running <code>configure.exe</code> again with no <code>-platform</code>, unless you can run <code>nmake</code> with the config clean target.

* Build using <code>nmake</code>
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart nmake. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.5 / VS2010 ===

* Rename the folder into for example <code>qt-4.8.5-64-vs2010-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.5-32-vs2010-deb</code>

* Launch the msvc2010 command prompt 
** 32-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 Command Prompt"
** 64-bit build: Start menu -> MSVC10->Tools -> "Visual Studio 2010 x64 Win64 Command Prompt"


*Download pearl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

*Download jom and create a new folder into for example <code>jom</code>.
**Add this new folder into the path (system properties)

* Configure
** For debug: <code>configure.exe -platform win32-msvc2010 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2010 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2010</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>jom -jn</code>
**Note: n is the number of cores of your CPU, so adapt it.
** Note: building with webkit support requires that src/3rdparty/webkit/WebCore/tmp/moc/{debug,release}_shared/mocinclude.tmp be removed. else you will get linker errors like <code>QNetworkReplyHandler.obj : error LNK2001: unresolved external symbol "public: virtual struct QMetaObject const * __thiscall WebCore::FormDataIODevice::metaObject(void)const (?metaObject@FormDataIODevice@WebCore@@UBEPBUQMetaObject@@XZ)</code>
** Note: If you encounter the following error <code>api\qscriptextensionplugin.h(43): Error: Undefined interface,</code>, delete the files \src\script\tmp\moc\debug_shared\mocinclude.tmp and \src\script\tmp\moc\release_shared\mocinclude.tmp and restart jom. For more info, please see [http://bugreports.qt.nokia.com/browse/QTBUG-6470 QTBug 6470]].

=== Qt 4.8.6 / VS2012 ===

* Rename the folder into for example <code>qt-4.8.6-64-vs2012-rel</code>.
** Note: Each build of Qt should be done it its own folder !
** Note: A 32 bit debug build would be done in a folder named <code>qt-4.8.6-32-vs2010-deb</code>

* Replace the webkit src\3rdparty\webkit\Source\JavaScriptCore\wtf\hashset.h file with this [ https://bitbucket.org/Vertexwahn/bluego/src/56dbe84212222ec6954d8d327a5e443106bcc447/deploy/BlueGo0.0.4/qt4.8.3vs2012patch/HashSet.h?at=default file]

* Launch the msvc2012 command prompt 
** 32-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x86 Command Prompt"
** 64-bit build: Start menu -> MSVC12->Visual Studio Tools -> "VS2012 x64 Win64 Command Prompt"


* If you want openssl support:
** Download perl http://strawberryperl.com/ and create a new folder into for example <code>strawberry</code>.

* Configure
** For debug: <code>configure.exe -platform win32-msvc2012 -debug -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** For release: <code>configure.exe -platform win32-msvc2012 -release -opensource -confirm-license -webkit -nomake examples -nomake demos</code>
** Note: <code>win32-msvc2010</code> is used for both 32 and 64-bit.
** Note: The option <code>-prefix</code> doesn't work on Windows.

* Build using <code>nmake</code>
** Alternatively you can use jom (much faster)
*** Download jom and create a new folder into for example <code>jom</code>.
*** Add this new folder into the path (system properties)
*** Build using <code>jom -jn</code>
**** Note: n is the number of cores of your CPU, so adapt it.

Documentation/Nightly/Developers/Tutorials/Troubleshooting

2014-08-14T16:06:44Z

Finetjul: /* Track memory leaks */

<noinclude>{{documentation/versioncheck}}</noinclude>
Here are some tips to narrow down various issues such as crash, or memory leaks

=Disable features=
Try running Slicer with as few features as possible:
* Disable Slicer options via the command line
*: <pre>$ ./Slicer --no-splash --ignore-slicerrc --disable-cli-module --disable-loadable-module --disable-scriptedmodule</pre>
** Look at all the possible options
**: <pre>$ ./Slicer --help</pre>
* Disable ITK plugins
*: CLI modules silently load the ITK plugins in lib/Slicer-{{documentation/currentversion}}/ITKFactories. These plugins are used to share the volumes between Slicer and the ITK filter without having to copy them on disk.
** rename lib/Slicer-{{documentation/currentversion}}/ITKFactories into lib/Slicer-{{documentation/currentversion}}/ITKFactories-disabled
* Disable Qt plugins
** rename lib/Slicer-{{documentation/currentversion}}/iconengine into lib/Slicer-{{documentation/currentversion}}/iconengine-disabled

=Track memory leaks=
<ol>
<li> Turn ON the VTK_DEBUG_LEAKS CMake variable and build Slicer</li>
<li> Create a test that reproduces the memory leak systematically </li>
After execution, the memory leaks are printed automatically by VTK on the standard output:
224: vtkDebugLeaks has detected LEAKS!
224: Class "vtkProperty2D" has 60 instances still around.
...
Alternatively, you can simply run Slicer instead of a custom test.

<li>Find what specific instance of a class (here vtkProperty2D) leaks.</li>
If the class is instantiated a large amount of time, it is hard to know what instance is leaking. By making verbose the constructor and destructor of the faulty class, you can infer which instance is leaking. Below are 2 techniques to print whenever the con/destructors are called:
<ol>
<li>By recompiling VTK</li>
You can edit the constructor and destructor of the class (here vtkProperty2D::vtkProperty2D() and vtkProperty2D::~vtkProperty2D())
vtkProperty2D::vtkProperty2D()
{
...
static int count = 0;
std::cout << "CREATE vtkProperty2D instance #" << count++ << " " << this << std::endl;
}

vtkProperty2D::~vtkProperty2D()
{
...
static int count = 0;
std::cout << "DELETE vtkProperty2D instance #" << count++ << " " << this << std::endl;
}
Don't forget to rebuild VTK if the class is from VTK (no need to build Slicer inner build)
After running the test, you should see outputs similar to
...
CREATE vtkProperty2D instance #0 0x0123456
...
CREATE vtkProperty2D instance #1 0x01234E5
...
DELETE vtkProperty2D instance #0 0x0123456
...
DELETE vtkProperty2D instance #1 0x01234E5
...
CREATE vtkProperty2D instance #2 0x0123A23
...
CREATE vtkProperty2D instance #3 0x0124312
...
Copy/paste the listing in a text editor and ensure that for each CREATE of a pointer (e.g. 0x0123456) it exists a DELETE. If there isn't, you found what instance is leaking. Note the instance # (here instance #2 and #3)

<li>Without recompiling any library but using the debugger</li>
Any debugger with advanced breakpoint controls should work.
* With Visual Studio
<ol>
<li>Set breakpoints in the class constructor and destructor methods.</li>
<li>Right click on the breakpoint, select "When Hit..." and "Print a message" with "Function: $FUNCTION {this}". Make sure the "Continue execution" checkbox is selected.
<li>Execute the test or Slicer</li>
<li>Open the "Output" tab and copy paste the contents into an advanced file editor (not Visual Studio)</li>
</ol>
* With GDB
<ol>
<li>Start gdb</li>
Using the launcher
$ ./Slicer --gdb
Or sometimes the following works as well
$ gdb ./bin/SlicerApp-real
<li>Place breakpoints in the functions</li>
(gdb) break vtkProperty2D::vtkProperty2D()
(gdb) break vtkProperty2D::~vtkProperty2D()
gdb will stop in those methods each time the program steps into. It will then print a line such as:
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x123456789) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
<li>Automatically continue execution after each break</li>
(gdb) commands 1
> continue
> end
(gdb) commands 2
> continue
> end
<li> Start the execution and copy paste the logs printed by gdb into an advanced file editor (e.g. emacs)</li>
(gdb) run
</ol>

After running the test(by recompiling or with debugger), you should see outputs similar to
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
37 vtkProperty2D::vtkProperty2D()
...
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
37 vtkProperty2D::vtkProperty2D()
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
37 vtkProperty2D::vtkProperty2D()
...

In an text editor, cleanup the logs by keeping only the "Breakpoint*" lines:
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37

Save a copy of this file, and make the destructor lines similar to the constructor ones (using Replace tools):
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22

Sort the file to make the constructor and destructor lines next to each other(emacs: M-x sort-lines, Notepad++: TextFX/TextFX Tools/Sort lines case sensitive):
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22

Find the line that is not duplicated:
* Using Notepad++ (version >=6):
** Open the search dialog
** Find what: "^(.*?)$\s+?^(?=.*^\1$)", Replace with: "dup ", toggle "Regular expression"
** Replace All
** The line without the "dup" prefix is the line we are looking for
* Using emacs:
** C-M-%
** Replace regexp: $.*$<type C-q C-j>\1
** with: dup<type C-q C-j>

Extract the instance address from the line: e.g. 0x0124312

From the original logs, keep only the Constructor lines:
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22

Search into the original saved file what line the address is: e.g. 4

</ol>

<li>Find the leaking instance at run-time</li>
Run the test with the [[Documentation/4.0/Developers/Tutorials/Debug_Instructions|debugger]], set a breakpoint in the class constructor and ignore the break as many time as the instance number (say it's 2):
* GDB
(gdb) break vtkProperty2D::vtkProperty2D()
Breakpoint 1 at 0x5b22d0e55d04296: file vtkProperty2D.cxx, line 22
(gdb) ignore 1 2
(gdb) run
When the debugger stops, check the call stack:
(gdb) backtrace
*Visual Studio
**Set a breakpoint in vtkProperty2D::vtkProperty2D()
**Right click on the breakpoint and select HitCount, select "break when the hit count is equal to" and type '2'
**Start the application
By analyzing the trace, you should be able to find the faulty instance.

<li> Analyze the code to see where the leak could be</li>
Here is a listing of the most common mistakes
* this->MyXXX = vtkXXX::New();
** Is there a matching this->MyXXX->Delete() ?
** Are you sure <code>this->MyXXX</code> is <code>0</code> before being assigned a new pointer ? If not, then you need to add
if (this->MyXXX != 0)
{
this->MyXXX->Delete();
this->MyXXX = 0;
}
this->MyXXX = vtkXXX::New();
</ol>
{{ombox
|type=content
|text=To reduce memory leaks, use the following tools:
* <code>vtkNew<vtkXXX> myXXX;</code>
* <code>vtkSmartPointer<vtkXXX> myXXX = vtkSmartPointer<vtkXXX>::New()</code>
* <code>vtkSmartPointer<vtkXXX> myXXX; myXXX.TakeReference(this->CreateObjAndCallerOwnsReference())</code>.
}}

==Other resources==
* [[Slicer3:VTK_Leak_Debugging|Slicer3 VTK leak debugging]]
* [[Strategies_for_Writing_and_Debugging_Code_in_Slicer_3|Strategies for Writing and Debugging Code in Slicer3]]

=Track a crash while accessing already deleted object pointer=
If the application crashes by accessing an invalid pointer. The goal here is to find when (and why) the pointer is deleted before it is accessed .
<ol>
<li>Before the crash, print the value of the pointer:</li>
Add before the crash (i.e. <code>this->MyObject->update()</code>)
std::cout << ">>>>>Object pointer: " << this->MyObject << std::endl;
<li>Add a counter in the destructor:</li>
Add in the object destructor (it can be in the base class (vtkObject or vtkMRMLNode) if you don't know the type):
static int count = 0;
std::cout << "#######Object Destructed: " << this << " " << count++ << std::endl;
<li>Run the application and make it crash.</li>
<li>In the logs you shall see something like that:</li>
#######Object Destructed: 0x12345678 0
#######Object Destructed: 0x12345679 1
#######Object Destructed: 0x12345680 2
>>>>>Object Pointer: 0x12345660
>>>>>Object Pointer: 0x12345661
>>>>>Object Pointer: 0x12345662
#######Object Destructed: 0x12345660 3
#######Object Destructed: 0x12345661 4
#######Object Destructed: 0x12345662 5
#######Object Destructed: 0x12345663 6
>>>>>Object Pointer: 0x12345670
>>>>>Object Pointer: 0x12345671
>>>>>Object Pointer: 0x12345672
#######Object Destructed: 0x12345660 7
#######Object Destructed: 0x12345661 8
#######Object Destructed: 0x12345662 9
>>>>>Object Pointer: '''0x12345663'''
Segfault
<li> Search in the logs when the pointer before crash has been deleted. Set a conditional breakpoint in the debugger:</li>
(gdb) break MyObj.cxx:103 if count == 6
or
(gdb) break MyObj.cxx:103
(gdb) ignore 1 5
or if you don't want to use a debugger, you can make it crash the 6th time:
assert(count != 6);
<li> Analyze the backtrace to understand why the pointer has been deleted without letting know the object that tries to access it.</li>
</ol>

=Console output on Windows=
On Windows, the application is built with no console output. A workaround for this issue is described in the following bug reports:
* http://www.na-mic.org/Bug/view.php?id=2376
* http://www.na-mic.org/Bug/view.php?id=2917
To add console output, you need to compile Slicer application with Slicer_BUILD_WIN32_CONSOLE set to ON at the configure time (uninitialized/OFF by default).

Documentation/Nightly/Developers/Tutorials/Troubleshooting

2014-08-14T14:57:18Z

Finetjul: /* Track memory leaks */

<noinclude>{{documentation/versioncheck}}</noinclude>
Here are some tips to narrow down various issues such as crash, or memory leaks

=Disable features=
Try running Slicer with as few features as possible:
* Disable Slicer options via the command line
*: <pre>$ ./Slicer --no-splash --ignore-slicerrc --disable-cli-module --disable-loadable-module --disable-scriptedmodule</pre>
** Look at all the possible options
**: <pre>$ ./Slicer --help</pre>
* Disable ITK plugins
*: CLI modules silently load the ITK plugins in lib/Slicer-{{documentation/currentversion}}/ITKFactories. These plugins are used to share the volumes between Slicer and the ITK filter without having to copy them on disk.
** rename lib/Slicer-{{documentation/currentversion}}/ITKFactories into lib/Slicer-{{documentation/currentversion}}/ITKFactories-disabled
* Disable Qt plugins
** rename lib/Slicer-{{documentation/currentversion}}/iconengine into lib/Slicer-{{documentation/currentversion}}/iconengine-disabled

=Track memory leaks=
<ol>
<li> Turn ON the VTK_DEBUG_LEAKS CMake variable and build Slicer</li>
<li> Create a test that reproduces the memory leak systematically </li>
After execution, the memory leaks are printed automatically by VTK on the standard output:
224: vtkDebugLeaks has detected LEAKS!
224: Class "vtkProperty2D" has 60 instances still around.
...
Alternatively, you can simply run Slicer instead of a custom test.

<li>Find what specific instance of a class (here vtkProperty2D) leaks.</li>
If the class is instantiated a large amount of time, it is hard to know what instance is leaking. By making verbose the constructor and destructor of the faulty class, you can infer which instance is leaking. Below are 2 techniques to print whenever the con/destructors are called:
<ol>
<li>By recompiling VTK</li>
You can edit the constructor and destructor of the class (here vtkProperty2D::vtkProperty2D() and vtkProperty2D::~vtkProperty2D())
vtkProperty2D::vtkProperty2D()
{
...
static int count = 0;
std::cout << "CREATE vtkProperty2D instance #" << count++ << " " << this << std::endl;
}

vtkProperty2D::~vtkProperty2D()
{
...
static int count = 0;
std::cout << "DELETE vtkProperty2D instance #" << count++ << " " << this << std::endl;
}
Don't forget to rebuild VTK if the class is from VTK (no need to build Slicer inner build)
After running the test, you should see outputs similar to
...
CREATE vtkProperty2D instance #0 0x0123456
...
CREATE vtkProperty2D instance #1 0x01234E5
...
DELETE vtkProperty2D instance #0 0x0123456
...
DELETE vtkProperty2D instance #1 0x01234E5
...
CREATE vtkProperty2D instance #2 0x0123A23
...
CREATE vtkProperty2D instance #3 0x0124312
...
Copy/paste the listing in a text editor and ensure that for each CREATE of a pointer (e.g. 0x0123456) it exists a DELETE. If there isn't, you found what instance is leaking. Note the instance # (here instance #2 and #3)

<li>Without recompiling any library but using the debugger</li>
Any debugger with advanced breakpoint controls should work.
* With Visual Studio
<ol>
<li>Set breakpoints in the class constructor and destructor methods.</li>
<li>Right click on the breakpoint, select "When Hit..." and "Print a message" with "Function: $FUNCTION {this}". Make sure the "Continue execution" checkbox is selected.
<li>Execute the test or Slicer</li>
<li>Open the "Output" tab and copy paste the contents into an advanced file editor (not Visual Studio)</li>
</ol>
* With GDB
<ol>
<li>Start gdb</li>
Using the launcher
$ ./Slicer --gdb
Or sometimes the following works as well
$ gdb ./bin/SlicerApp-real
<li>Place breakpoints in the functions</li>
(gdb) break vtkProperty2D::vtkProperty2D()
(gdb) break vtkProperty2D::~vtkProperty2D()
gdb will stop in those methods each time the program steps into. It will then print a line such as:
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x123456789) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
<li>Automatically continue execution after each break</li>
(gdb) commands 1
> continue
> end
(gdb) commands 1
> continue
> end
<li> Start the execution and copy paste the logs printed by gdb into an advanced file editor (e.g. emacs)</li>
(gdb) run
</ol>

After running the test(by recompiling or with debugger), you should see outputs similar to
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
37 vtkProperty2D::vtkProperty2D()
...
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
37 vtkProperty2D::vtkProperty2D()
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
22 vtkProperty2D::vtkProperty2D()
...
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
37 vtkProperty2D::vtkProperty2D()
...

In an text editor, cleanup the logs by keeping only the "Breakpoint*" lines:
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 2, vtkProperty2D::~vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:37

Save a copy of this file, and make the destructor lines similar to the constructor ones (using Replace tools):
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22

Sort the file to make the constructor and destructor lines next to each other(emacs: M-x sort-lines, Notepad++: TextFX/TextFX Tools/Sort lines case sensitive):
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22

Find the line that is not duplicated:
* Using Notepad++ (version >=6):
** Open the search dialog
** Find what: "^(.*?)$\s+?^(?=.*^\1$)", Replace with: "dup ", toggle "Regular expression"
** Replace All
** The line without the "dup" prefix is the line we are looking for
* Using emacs:
** C-M-%
** Replace regexp: $.*$<type C-q C-j>\1
** with: dup<type C-q C-j>

Extract the instance address from the line: e.g. 0x0124312

From the original logs, keep only the Constructor lines:
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123456) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x01234E5) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0123A23) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22
Breakpoint 1, vtkProperty2D::vtkProperty2() (this=0x0124312) at /home/user/Slicer-superbuild/VTK/.../vtkProperty2D.cxx:22

Search into the original saved file what line the address is: e.g. 4

</ol>

<li>Find the leaking instance at run-time</li>
Run the test with the [[Documentation/4.0/Developers/Tutorials/Debug_Instructions|debugger]], set a breakpoint in the class constructor and ignore the break as many time as the instance number (say it's 2):
* GDB
(gdb) break vtkProperty2D::vtkProperty2D()
Breakpoint 1 at 0x5b22d0e55d04296: file vtkProperty2D.cxx, line 22
(gdb) ignore 1 2
(gdb) run
When the debugger stops, check the call stack:
(gdb) backtrace
*Visual Studio
**Set a breakpoint in vtkProperty2D::vtkProperty2D()
**Right click on the breakpoint and select HitCount, select "break when the hit count is equal to" and type '2'
**Start the application
By analyzing the trace, you should be able to find the faulty instance.

<li> Analyze the code to see where the leak could be</li>
Here is a listing of the most common mistakes
* this->MyXXX = vtkXXX::New();
** Is there a matching this->MyXXX->Delete() ?
** Are you sure <code>this->MyXXX</code> is <code>0</code> before being assigned a new pointer ? If not, then you need to add
if (this->MyXXX != 0)
{
this->MyXXX->Delete();
this->MyXXX = 0;
}
this->MyXXX = vtkXXX::New();
</ol>
{{ombox
|type=content
|text=To reduce memory leaks, use the following tools:
* <code>vtkNew<vtkXXX> myXXX;</code>
* <code>vtkSmartPointer<vtkXXX> myXXX = vtkSmartPointer<vtkXXX>::New()</code>
* <code>vtkSmartPointer<vtkXXX> myXXX; myXXX.TakeReference(this->CreateObjAndCallerOwnsReference())</code>.
}}

==Other resources==
* [[Slicer3:VTK_Leak_Debugging|Slicer3 VTK leak debugging]]
* [[Strategies_for_Writing_and_Debugging_Code_in_Slicer_3|Strategies for Writing and Debugging Code in Slicer3]]

=Track a crash while accessing already deleted object pointer=
If the application crashes by accessing an invalid pointer. The goal here is to find when (and why) the pointer is deleted before it is accessed .
<ol>
<li>Before the crash, print the value of the pointer:</li>
Add before the crash (i.e. <code>this->MyObject->update()</code>)
std::cout << ">>>>>Object pointer: " << this->MyObject << std::endl;
<li>Add a counter in the destructor:</li>
Add in the object destructor (it can be in the base class (vtkObject or vtkMRMLNode) if you don't know the type):
static int count = 0;
std::cout << "#######Object Destructed: " << this << " " << count++ << std::endl;
<li>Run the application and make it crash.</li>
<li>In the logs you shall see something like that:</li>
#######Object Destructed: 0x12345678 0
#######Object Destructed: 0x12345679 1
#######Object Destructed: 0x12345680 2
>>>>>Object Pointer: 0x12345660
>>>>>Object Pointer: 0x12345661
>>>>>Object Pointer: 0x12345662
#######Object Destructed: 0x12345660 3
#######Object Destructed: 0x12345661 4
#######Object Destructed: 0x12345662 5
#######Object Destructed: 0x12345663 6
>>>>>Object Pointer: 0x12345670
>>>>>Object Pointer: 0x12345671
>>>>>Object Pointer: 0x12345672
#######Object Destructed: 0x12345660 7
#######Object Destructed: 0x12345661 8
#######Object Destructed: 0x12345662 9
>>>>>Object Pointer: '''0x12345663'''
Segfault
<li> Search in the logs when the pointer before crash has been deleted. Set a conditional breakpoint in the debugger:</li>
(gdb) break MyObj.cxx:103 if count == 6
or
(gdb) break MyObj.cxx:103
(gdb) ignore 1 5
or if you don't want to use a debugger, you can make it crash the 6th time:
assert(count != 6);
<li> Analyze the backtrace to understand why the pointer has been deleted without letting know the object that tries to access it.</li>
</ol>

=Console output on Windows=
On Windows, the application is built with no console output. A workaround for this issue is described in the following bug reports:
* http://www.na-mic.org/Bug/view.php?id=2376
* http://www.na-mic.org/Bug/view.php?id=2917
To add console output, you need to compile Slicer application with Slicer_BUILD_WIN32_CONSOLE set to ON at the configure time (uninitialized/OFF by default).

Documentation/Nightly/Developers/IO

2014-08-01T11:26:32Z

Finetjul: /* How to register a dialog ? */

<noinclude>{{documentation/versioncheck}}</noinclude>
=Read=
[[Image:IOOverview.png|600px|center]]
== Main classes ==
* <code>vtkSlicerXYZNode</code> is a [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Libs/MRML/Core/vtkMRMLStorableNode.h?view=markup storable node] that represents the data from file (e.g. [[http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Libs/MRML/Core/vtkMRMLModelNode.h?view=markup vtkMRMLModelNode])
* <code>vtkSlicerXYZStorageNode</code> is the file reader. It populates the storable node using the method <code>vtkMRMLXYZStorageNode::ReadData(vtkMRMLStorableNode*,bool)</code>.
* <code>vtkSlicerXYZsLogic</code> is the MRML logic of the <code>XYZ</code> module. It exposes a convenient method <code>AddXYZ(const char* fileName, const char* nodeName=0);</code> that creates a MRML XYZ node (<code>vtkMRMLXYZNode</code>)and its associated storage node (<code>vtkMRMLXYZStorageNode</code>), add them into the scene, and call <code>vtkMRMLXYZStorageNode::ReadData(vtkMRMLStorableNode*,bool);</code> on the storage node to load the file. If the loading fails, it removes the previously created nodes from the scene.
* <code>qSlicerXYZsIO</code> is a plugin that is registered by modules into the <code>qSlicerCoreIOManager</code>. It is the interface between Qt and MRML logics. It internally calls <code>vtkSlicerXYZsLogic::AddXYZ</code>().
* <code>qSlicerXYZsIOOptionsWidget</code> is a widget that sets loading options that gets passed to the logic.
* <code>qSlicerCoreIOManager</code> is the central class where any IO operation must go through. qSlicerIOs can be registered using <code>qSlicerCoreIOManager::registerIO(qSlicerIO*)</code> and nodes can be loaded using <code>qSlicerCoreIOManager::loadNodes(...)</code>. It exposes a set of convenient methods such as "what reader must be used for what file".
* <code>qSlicerDataDialog</code> is the dialog that allows the user to select the files to load.

==How to add support for reading a new file format ?==
# Write method <code>vtkMRMLXYZStorageNode::ReadDataInternal(vtkMRMLStorableNode*, bool temporary);</code>
# Write method <code>vtkMRMLXYZsLogic::AddXYZ(const char* fileName, const char nodeName =0);</code>
# Write class <code>qSlicerXYZsIO</code>
# Optional: Write class <code>qSlicerXYZsIOOptionsWidget</code> if you want the user to optionally specify loading options.
# In <code>qSlicerXYZsModule::setup()</code>, instantiate and register <code>qSlicerXYZsIO</code> to <code>qSlicerCoreIOManager</code>
# Add file format to [Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|SupportedDataFormat] wiki page

== ModifiedSinceRead ==
In order to inform the user what data has been changed since it was last read, a ModifiedSinceRead mechanism is in place to track when was the file last read and when was the data last modified. If a modification happened , the storable node <code>vtkMRMLStorableNode::GetModifiedSinceRead()</code> must return true. If the data in the node is the same as in the file, then <code>vtkMRMLStorableNode::GetModifiedSinceRead()</code> must return false.

<code>vtkMRMLStorageNode</code> keeps track of when a file was last read or written (<code>vtkTimeStamp* vtkMRMLStorageNode::StoredTime</code>). <code>vtkMRMLStorableNode</code> keeps track of when the data was last modified (<code>vtkTimeStamp vtkMRMLStorableNode::StorableModifiedTime</code>). Anytime a <code>vtkMRMLStorableNode</code> property that is saved in file is modified, the <code>StorableModifiedTime</code> time stamp must be modified.

At exit time (<code>qSlicerMainWindow::closeEvent()</code>), <code>vtkMRMLStorableNode::GetModifiedSinceRead()</code> is called to check if the data in the node is the same as in the file or if it has been modified after the file was last read or written. It internally checks <code>vtkTimeStamp* vtkMRMLStorageNode::StoredTime</code> and <code>vtkTimeStamp vtkMRMLStorableNode::StorableModifiedTime</code>. If the data is more recent, then a message dialog is shown to the user telling him that some data is different from file; leaving without saving will loose the changes.

== Example ==
* Models
** [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Libs/MRML/Core/vtkMRMLModelNode.h?view=markup Libs/MRML/Core/vtkMRMLModelNode]
** [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Libs/MRML/Core/vtkMRMLModelStorageNode.h?view=markup Libs/MRML/Core/vtkMRMLModelStorageNode]
** [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Models/Logic/vtkSlicerModelsLogic.h?view=markup Modules/Loadable/Models/Logic/vtkSlicerModelsLogic]
** [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Models/qSlicerModelsIO.h?view=markup Modules/Loadable/Models/qSlicerModelsIO]
** [http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Models/qSlicerModelsModule.h?view=markup Modules/Loadable/Models/qSlicerModelsModule]

== How to load files programmatically ==
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
[http://slicer.org/doc/html/classqSlicerCoreIOManager.html qSlicerCoreIOManager]* coreIOManager = qSlicerCoreApplication::application()->coreIOManager();
qSlicerIO::IOProperties fileParameters;
fileParameters["filename"] = "/path/of/file.ext";
vtkMRMLNode* volumeNode = coreIOManager->[http://slicer.org/doc/html/classqSlicerCoreIOManager.html#a36a78dba553b52f395f997fe11aaff23 loadNodesAndGetFirst]("VolumeFile", parameters);
Works also with "ModelFile", "TransformFile", "SceneFile"...
| valign="top" |
>>> volumeNode = slicer.util.loadVolume('/path/of/file.ext')
It works also with loadModel, loadTransform, loadScene...
|}
Note that [[#IO_Dialogs|IO dialogs]] should be used as often as possible.

=Write=
The mechanism is similar to '''Read'''. <code>vtkMRMLXYZStorageNode::WriteDataInternal(...)</code> and <code>qSlicerXYZWriter</code> must implemented.

== How to save files programmatically ==
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
[http://slicer.org/doc/html/classqSlicerCoreIOManager.html qSlicerCoreIOManager]* coreIOManager = qSlicerCoreApplication::application()->coreIOManager();
qSlicerIO::IOProperties fileParameters;
fileParameters["nodeID"] = volumeNode->GetID();
fileParameters["fileName"] = "/path/of/file.ext";
coreIOManager->[http://slicer.org/doc/html/classqSlicerCoreIOManager.html#a1cd29140ded984afdd0f667064d38845 saveNodes]("VolumeFile", parameters);
Works also with "ModelFile", "TransformFile", "SceneFile"...
| valign="top" |
>>> slicer.util.saveNode(volumeNode, '/path/of/file.ext')
|}
Note that [[#IO_Dialogs|IO dialogs]] should be used as often as possible.

=IO Dialogs=
* <code>[http://slicer.org/doc/html/classqSlicerFileDialog.html qSlicerFileDialog]</code> is the base class to override a custom dialog.
* <code>[http://slicer.org/doc/html/classqSlicerStandardFileDialog.html qSlicerStandardFileDialog]</code> is a multi-purpose file dialog.
* <code>[http://slicer.org/doc/html/classqSlicerDataDialog.html qSlicerDataDialog.h]</code> is the default dialog to load files.
* <code>[http://slicer.org/doc/html/classqSlicerSaveDataDialog.html qSlicerSaveDataDialog]</code> is the default dialog to save files.

By default, all the IOs must be done through <code>qSlicerDataDialog</code> for reading files and <code>qSlicerSaveDataDialog</code> for writting files. However, due to historical reasons, it is possible to have custom dialogs for each node types.

It can be useful to create your own IO dialog to add custom behavior to the Slicer drag&drop default behavior.
== How to register a dialog ? ==
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
Register dialogs in qSlicerXYZModule::[http://slicer.org/doc/html/classqSlicerAbstractCoreModule.html#a9ad37e756338e7226f157b4eb54b9bcd setup()]:
[http://slicer.org/doc/html/classqSlicerIOManager.html qSlicerIOManager]* ioManager = qSlicerApplication::application()->ioManager();
ioManager->[http://slicer.org/doc/html/classqSlicerIOManager.html#ae47e9cf27f230335b865bce84a56e156 registerDialog](new qSlicerXYZDialog(this));
ioManager->[http://slicer.org/doc/html/classqSlicerIOManager.html#ae47e9cf27f230335b865bce84a56e156 registerDialog](new qSlicerSaveXYZDialog(this));
| valign="top" |
Declare an XYZFileDialog in your XYZ.py module file. It will be automatically registered. For example:
class XYZFileDialog:
def __init__(self, parent):
self.parent = parent
parent.fileType = 'XYZFile'
parent.description = 'XYZ'
parent.action = slicer.qSlicerFileDialog.Read
def isMimeDataAccepted(self):
accept = self.parent.mimeData().hasFormat("text/uri-list")
self.parent.acceptMimeData(accept)
def dropEvent(self):
self.parent.dropEvent().accept()
def execDialog(self):
print 'exec'
|}

== How to open a registered a dialog ? ==
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
[http://slicer.org/doc/html/classqSlicerIOManager.html qSlicerIOManager]* ioManager = qSlicerApplication::application()->ioManager();
ioManager->openDialog("VolumeFile", qSlicerFileDialog::Read, qSlicerIO::IOProperties());
| valign="top" |
io = slicer.app.ioManager()
params = {}
io.openDialog("VolumeFile", slicer.qSlicerFileDialog.Read, params)
And the special case for standard data file types:
slicer.util.openAddVolumeDialog()
|}

== How to order the list of drag&drop dialogs ?==
By controlling the order of module initialization. This is done by adding module dependencies. Make your module dependent of of the "Data" would make it initialize after the Data module that registers the "Any Data" dialogs:
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
QStringList qSlicerXYZModule::dependencies() const
{
QStringList moduleDependencies;
moduleDependencies << "Data";
return moduleDependencies;
}
| valign="top" |
def __init__(self, parent):
...
parent.dependencies = ["Data"] class XYZFileDialog:
...
|}

Documentation/Nightly/Developers/OpenIGTLinkIF

2014-06-26T14:27:39Z

Finetjul: Add link to github code

<noinclude>{{documentation/versioncheck}}</noinclude>
This page provides developer's information for 3D Slicer's OpenIGTLink IF module.

=Source code=
* Github: [https://github.com/openigtlink/OpenIGTLinkIF https://github.com/openigtlink/OpenIGTLinkIF]

=Creating external OpenIGTLink server/client software=
With the OpenIGTLink IF module, you can exchange various types of data (e.g. linear transforms and images) between 3D Slicer and external software over the local area network. We provide [http://www.na-mic.org/Wiki/index.php/OpenIGTLink/Library OpenIGTLink Library] to support OpenIGTLink-compatible software. Please refer the [http://www.na-mic.org/Wiki/index.php/OpenIGTLink/Library/Tutorial Tutorial].

=Controlling OpenIGTLink IF from Python module=
You can use the OpenIGTLink IF module's features from [[Slicer4:Python| 3D Slicer's Python interface]]. The features can be called from both Slicer Python Interactor (Python console) and Python module.

==Requirements==
*3D Slicer 4.2 nightly build (November 10, 2012 or later) available at [http://slicer.org http://slicer.org/] (4.2.0 release version has an issue in initialization of the OpenIGTLinkIF module. If you use this version, you need to open the OpenIGTLinkIF module, before using the Python interface)
*OpenIGTLink Simulators available in [http://wiki.slicer.org/slicerWiki/index.php/Modules:OpenIGTLinkIF-3.6-Simulators NA-MIC wiki] or the OpenIGTLink Library

==Creating an OpenIGTLink connector node from Python Interactor==

To establish an OpenIGTLink connection, first you need to create an OpenIGTLink connector node (vtkMRMLIGTLConnectorNode).
From Python Interactor:

>>> cnode = slicer.vtkMRMLIGTLConnectorNode()
>>> slicer.mrmlScene.AddNode(cnode)
(vtkMRMLIGTLConnectorNode)0x125e6ce10

You may name the connector as follows:
>>> cnode.SetName('Connector1')

If the connector node is properly added to the scene, you could see it in the Connector list in the OpenIGTLink IF module.

==Importing a linear transform to external software (3D Slicer as a client)==

Suppose the downloaded simulator files are in <working directory>.

First, launch the "TrackerServer" simulator from a terminal (or a command prompt on Windows) and ask to wait for a connection from the 3D Slicer at port # 18944. The frame rate for sending linear transforms is set to 10 frames/sec

$ cd <working directory>
$ ./TrackerServer 18944 10

Then open the Python Interactor and type in the following commands to configure the connector node as a client:

>>> cnode.SetTypeClient('localhost', 18944)
1

Make sure that cnode.SetTypeClient() function returns 1. Then, start the client by:

>>> cnode.Start()
1

If the connector node is successfully connected to the TrackerServer, you will start seeing 4x4 matrices printed on the terminal every 100 ms.
You could also confirm in the Transform module that those matrices are imported to a linear transform node in the scene. Open "Transform" module
and select "Tracker" from "Active Transform" menu.

==Exporting a linear transform to external software (3D Slicer as a client)==

Suppose the simulator files are in <working directory>.

First, launch the "ReceiveServer" simulator from the terminal (or the command prompt on Windows) and ask to wait for a connection from the 3D Slicer at port # 18944.

$ cd <working directory>
$ ./ReceiveServer 18944

Then open the Python Interactor and type in the following command to configure the connector node as a client:

>>> cnode.SetTypeClient('localhost', 18944)
1

Make sure that cnode.SetTypeClient() function returns 1. Then, start the client by:

>>> cnode.Start()
1

Now the connector is connected to the ReceiveServer. You can confirm it from the Connector list in the OpenIGTLink IF module. If it is connected, the "Status" of the connector must be "ON".

The next step is to create a linear transform node to export. You can create it from "Transform" module, or from the Python Interactor:

>>> tnode = slicer.vtkMRMLLinearTransformNode()
>>> slicer.mrmlScene.AddNode(tnode)
(vtkMRMLLinearTransformNode)0x125e6cf70
>>>

If you created the transform node from the Transform module, you need to get the node object in the Python Interactor. To do so, open "Data" module, click the "Display MRML ID's" under the "Nodes" interface, and check the node ID written on the right end of the "Nodes" interface. If the transform node is the first node you created after launching 3D Slicer, the node ID is usually "vtkMRMLLinearTransformNode4". You can obtain the node object in the Python Interactor by using GetNodeByID() function:

>>> tnode = slicer.mrmlScene.GetNodeByID('vtkMRMLLinearTransformNode4')

Now it's ready for the connector node to observe the transform node. Register the transform node to the connector as an outgoing data:

>>> cnode.RegisterOutgoingMRMLNode(tnode)
1
>>>

You may check from "I/O Configuration" in the OpenIGTLinkIF module if the linear transform node is registered as a OUTGOING node. (The linear transform node should be under "OUT" branch of the connector node.)

Let's try updating the transform node. Open the "Transform" module, choose the linear transform node from "Active Transform" and drag any of translation/rotation sliders. While you are dragging those sliders, you will see 4x4 matrices are shown on the terminal that runs "ReceiveServer."

To close the connection, you may call:

>>> cnode.Stop()

=Extended Interface for External Software (Ideas)=
There has been discussion how to send extra data (data that are not defined as MRML nodes) to 3D Slicer through OpenIGTLink [http://massmail.spl.harvard.edu/public-archives/slicer-devel/2013/011903.html]. For example, some developers are interested in sending switch status for their tracking devices. Here are some notes and ideas

*Extra information in MRML scene
**Extra information can be stored in key/value array format as "attributes" in MRML nodes.
**Slicer developers use "ModuleName.attribute" as a key.
**With an MRML node, the OpenIGTLink IF module can notify other modules that the attribute has been updated through Event mechanism in 3D Slicer.
*Extra information in OpenIGTLink IF
**There is no mechanism to add any attribute information with existing data format. The challenge is to maintain the current rule (the message name and type corresponds to the MRML name and node type respectively), while handling the extra information using existing data types.
**The STRING type may be used to send key/attribute.
***PRO: Implementation is simple. It can be implemented without defining a new message type or changing the mechanism in the OpenIGTLinkIF module.
***CON: Cannot differentiate from STRING data, which will be stored in annotation node.
**Define COMMAND type in OpenIGTLink? A COMMAND message will not be converted to MRML node. It will be interpreted at the OpenIGTLinkIF module.
***PRO: This mechanism can be used for other purpose e.g. controlling 3D Slicer from external software by sending Python script.
***CON: The new message type is required.
**Use [http://openigtlink.org/protocols/v2_bind.html BIND] message. The BIND message bundles multiple OpenIGTLink messages into one message. If the module receives a BIND message, it converts the first element to an MRML node, and then coverts other elements (must be STRING type) to key/value and set in the MRML node converted from the first element.
***PRO: Does not need any change in the protocol.
***CON: The API becomes a bit complicated.

Documentation/Nightly/Announcements

2014-05-12T17:00:25Z

Finetjul: /* Slicer Highlights */

<noinclude>{{documentation/versioncheck}}</noinclude>
__NOTOC__

{|width="100%"
|align="center"|
[[image:Slicer4Announcement-HiRes.png|center|'''{{documentation/version}}''']]
|}

{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
|[[#Introduction|Introduction ]]
|[[#Our Philosophy| Our Philosophy ]]
|[[#Slicer Highlights|Slicer Highlights ]]
|[[#Slicer Extensions|Slicer Extensions]]
|[[#Other Improvements, Additions & Documentation| Other Improvements, Additions & Documentation]]
|}
=Introduction=

=Slicer Highlights=
* .mrb files
* data store module
* improved integration of non rigid deformations
* Transform visualizer
* Faster image stack (png, jpg, bmp, tiff...) loading



=Slicer Extensions=

= Looking at the Code Changes =

From a git checkout you can easily see the all the commits since the time of the 4.4.2 release:

git log --since="Sat Dec 8 03:32:53 2012"

To see a summary of your own commits, you could use something like:

git log --since="Sat Dec 8 03:32:53 2012" --oneline --author=pieper

see [https://www.kernel.org/pub/software/scm/git/docs/git-log.html the git log man page] for more options.

[[Release_Details#Slicer_{{documentation/version}}.0|Commit stats and full changelog]]

= Related Projects =
<gallery caption="" widths="250px" heights="150px" perrow="3">
</gallery>

Documentation/Nightly/Modules/VolumeRendering

2014-04-03T14:02:54Z

Finetjul: /* How Tos */ Add how to register a new volume rendering method

<noinclude>{{documentation/versioncheck}}</noinclude>

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}} }}
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-acknowledgements}}
: '''Contact:''' Julien Finet, <email>julien.finet@kitware.com</email> 
{{documentation/{{documentation/version}}/module-introduction-row}}
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|kitware}}|{{collaborator|longname|kitware}}
|{{collaborator|logo|isomics}}|{{collaborator|longname|isomics}}
|{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
|{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
}}
{{documentation/{{documentation/version}}/module-introduction-end}}


{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description}}
Only UNSIGNED CHAR images are supported for now. You can convert your images into UCHAR by using the [[Documentation/{{documentation/version}}/Modules/CastScalarVolume|Cast Scalar Volume]] module.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:Tumor-Volume-Rendering-PostGad-2011.png|Tumor post pad (preset: MR-Default)
Image:Modules-VolumeRendering-LabelMap.png|Segmented (labelmap) knee (interpolation: nearest neighbor, shading: off)
Image:QSlicerVolumeRendering-default.png|Default view of the module. Inputs and Advanced... are hidden by default
Image:VolumeRenderingSettings.png|Volume Rendering settings ''Edit -> Application Settings -> Volume Rendering settings''
</gallery>


{{documentation/{{documentation/version}}/module-section|Tutorials}}

Tutorial about [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering_Tutorials using the volume rendering module].

===Labelmap rendering===
[[File:Modules-VolumeRendering-LabelMap.png|right|500px]]
A labelmap is a volume, and as such it can be visualized using the Volume Rendering method. It can be an alternative from [[Documentation/{{documentation/version}}/Modules/ModelMaker|creating surface models]] from labelmap.
# First you need to load your labelmap.
## Make sure you check the "Labelmap" check box at load time.
## Make sure the labelmap is a Unsigned Char image, not Unsigned/Signed Short, Int or Long. If needed, you can [[Documentation/{{documentation/version}}/Modules/CastScalarVolume| cast]] the labelmap to UCHAR.
# Open the Volume Rendering module
## As usual, click on the eye to start the Volume Rendering.
# To turn off shading:
## go to Advanced../Volume Properties/Advanced group box and uncheck the "Shade" checkbox
# To turn on/off a specific label:
## Go to the Advanced.../Volume Properties/Scalar Opacity Mapping group box
## Toggle down the '>>' button to show the Opacity controls.
## Browse each label with the "Point:" spinbox. When the spinbox shows the current label value,
## Set the Opacity spinbox value to 0.0/1.0 to hide/show the label.

===Render 2 volumes in 2 views===
[[File:DualVR.png|right|500px]]
# [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Change layout]] into "Dual 3D"
# [[Documentation/{{documentation/version}}/SlicerApplication/LoadingData|Load]] your 2 volumes
# [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Module_Selection_.26_Navigation|Open]] Volume Rendering module
# For the first volume:
## Open the "Inputs" section
## Uncheck "View2" -> only "View1" is checked
## Don't click the "eye" icon yet.
# Select the 2nd volume
## Check "View2"
## Uncheck "View1" -> only "View2" is checked
## Click the eye icon for the VR to show up in View2
# Select the 1st volume
## Click the eye icon for the VR to show up in View1


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
[[File:VolumeRenderingPanel.png|right|]]
{{documentation/{{documentation/version}}/module-parametersdescription}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]]


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
===Limitations===
*To date, only 1 volume can be visible at a time. This happens because the current volume rendering displayable node is hidden when changing to a different volume node.
*Only UNSIGNED CHAR images are supported for now. You can convert your images into UCHAR by using the [[Documentation/{{documentation/version}}/Modules/CastScalarVolume|Cast Scalar Volume]] module.

===Key [[Documentation/{{documentation/version}}/Developers/MRML|nodes]] and classes===
* [http://slicer.org/doc/html/classvtkMRMLVolumeRenderingDisplayNode.html vtkMRMLVolumeRenderingDisplayNode] controls the volume rendering properties. Each volume rendering technique has its own subclass.
* [http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html vtkSlicerVolumeRenderingLogic] contains utility functions
* [http://slicer.org/doc/html/classvtkMRMLScalarVolumeNode.html vtkMRMLScalarVolumeNode] contains the volume itself
* [http://slicer.org/doc/html/classvtkMRMLVolumePropertyNode.html vtkMRMLVolumePropertyNode] points to the transfer functions
* [http://slicer.org/doc/html/classvtkMRMLAnnotationROINode.html vtkMRMLAnnotationROINode] controls the clipping planes
* [http://slicer.org/doc/html/classvtkMRMLVolumeRenderingDisplayableManager.html vtkMRMLVolumeRenderingDisplayableManager] adds the volume renderings into the views

===How Tos===
*How to programmatically volume render your volume node?
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
qSlicerAbstractCoreModule* volumeRenderingModule =
qSlicerCoreApplication::application()->moduleManager()->module("VolumeRendering");
vtkSlicerVolumeRenderingLogic* volumeRenderingLogic =
volumeRenderingModule ? vtkSlicerVolumeRenderingLogic::SafeDownCast(volumeRenderingModule->logic()) : 0;
vtkMRMLVolumeNode* volumeNode = mrmlScene->GetNodeByID('vtkMRMLScalarVolumeNode1');
if (volumeRenderingLogic)
{
vtkMRMLVolumeRenderingDisplayNode* displayNode =
volumeRenderingLogic->CreateVolumeRenderingDisplayNode();
mrmlScene->AddNode(displayNode);
displayNode->Delete();
volumeRenderingLogic->UpdateDisplayNodeFromVolumeNode(displayNode, volumeNode);
volumeNode->AddAndObserveDisplayNodeID(displayNode->GetID());
}
See [[Documentation/{{documentation/version}}/Developers/Tutorials/CreateLoadableModule#Dependency_between_modules|here]] for more about volume dependency.
| valign="top" |
>>> logic = slicer.modules.volumerendering.logic()
>>> volumeNode = slicer.mrmlScene.GetNodeByID('vtkMRMLScalarVolumeNode1')
>>> displayNode = logic.CreateVolumeRenderingDisplayNode()
>>> slicer.mrmlScene.AddNode(displayNode)
>>> displayNode.UnRegister(logic)
>>> logic.UpdateDisplayNodeFromVolumeNode(displayNode, volumeNode)
>>> volumeNode.AddAndObserveDisplayNodeID(displayNode.GetID())
|}

*How to programmatically apply a custom color/opacity transfer function?
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
vtkColorTransferFunction* colors = ...
vtkPiecewiseFunction* opacities = ...
vtkMRMLVolumeRenderingDisplayNode* displayNode = ...
vtkMRMLVolumePropertyNode* propertyNode = displayNode->GetVolumePropertyNode();
propertyNode->SetColor(colorTransferFunction);
propertyNode->SetScalarOpacity(opacities);
// optionally set the gradients opacities with SetGradientOpacity
The logic has utility functions to help you create those transfer functions:
volumeRenderingLogic->[http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#ab8dbda38ad81b39b445b01e1bf8c7a86 SetWindowLevelToVolumeProp](...)
volumeRenderingLogic->[http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a1dcbe614493f3cbb9aa50c68a64764ca SetThresholdToVolumeProp](...)
volumeRenderingLogic->[http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a359314889c2b386fd4c3ffe5414522da SetLabelMapToVolumeProp](...)
| valign="top" |
>>> propertyNode = displayNode.GetVolumePropertyNode()
>>> ...
|}

*How to programmatically limit volume rendering to a subset of the volume?
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
[http://slicer.org/doc/html/classvtkMRMLAnnotationROINode.html vtkMRMLAnnotationROINode]* roiNode =...
vtkMRMLVolumeRenderingDisplayNode* displayNode = ...
displayNode->SetAndObserveROINodeID(roiNode->GetID());
displayNode->SetCroppingEnabled(1);
| valign="top" |
>>> displayNode.SetAndObserveROINodeID(roiNode.GetID())
>>> displayNode.CroppingEnabled = 1
|}

*How to register a new Volume Rendering mapper?
You need to derive from [http://slicer.org/doc/html/classvtkMRMLVolumeRenderingDisplayNode.html vtkMRMLVolumeRenderingDisplayNode] and register your class within [http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html vtkSlicerVolumeRenderingLogic].

{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |

void qSlicerMyABCVolumeRenderingModule::setup()
{
vtkMRMLThreeDViewDisplayableManagerFactory::GetInstance()->
RegisterDisplayableManager("vtkMRMLMyABCVolumeRenderingDisplayableManager");

this->Superclass::setup();

qSlicerAbstractCoreModule* volumeRenderingModule =
qSlicerCoreApplication::application()->moduleManager()->module("VolumeRendering");
if (volumeRenderingModule)
{
vtkNew<vtkMRMLMyABCVolumeRenderingDisplayNode> displayNode;
vtkSlicerVolumeRenderingLogic* volumeRenderingLogic =
vtkSlicerVolumeRenderingLogic::SafeDownCast(volumeRenderingModule->logic());
volumeRenderingLogic->RegisterRenderingMethod(
"My ABC Volume Rendering", displayNode->GetClassName());
}
else
{
qWarning() << "Volume Rendering module is not found";
}
}
If you want to expose control widgets for your volume rendering method, then register your widget with [http://slicer.org/doc/html/classqSlicerVolumeRenderingModuleWidget.html#acd9cdb60f1fd260f3ebf74428bb7c45b addRenderingMethodWidget()]
|}


{{documentation/{{documentation/version}}/module-footer}}

Slicer4:QtPort/FunFacts

2014-01-28T14:55:04Z

Finetjul: /* Number of lines per author in Slicer 3 */

=Slicer 4 vs Slicer 3=
* Superbuild
** Slicer 3.6 (Mac Os X, 4 proc.)
*** real: 141m33.004s user: 118m2.658s sys:13m31.075s
** Slicer 4.0.1 (Mac Os X, 4 proc.)
*** real: 51m24.573s user: 159m38.262s sys: 21m41.498s
** Slicer 3.6 vs 4.0.1 is '''2.8x faster'''
* Lib
** Slicer3 MRML (gcc, 1 proc., Ubuntu 64b):
*** real: 4m50s user: 3m51s sys: 0m40s
** Slicer3 MRML (Visual Studio 2008, 1 proc., Release):
*** 6m20s
** Slicer4 MRML (gcc, 1 proc., Ubuntu 64b):
*** real: 2m11s user: 1m51s sys: 0m22s
** Slicer4 MRML (Visual Studio 2008, Release):
*** 4m40s
** Slicer 3.6 vs 4.0.1 is '''1.5x to 2x faster'''

=Number of lines per author in Slicer 2=
{|
!Slicer 2.4 - 2004-11-23
!Slicer 2.5 - 2005-05-23
!Slicer 2.6 - 2006-08-12
!Slicer 2.7 - 2007-04-20
|-
| valign="top" |
36691 nicole
24944 pieper
13836 mark
7999 odonnell
6693 samson
5948 gering
4430 hanifa
4411 halazar
4124 sylvain
3125 delfin
2390 tanacs
2053 meng
1680 pohl
1175 hliu
1166 ahans
967 alexy
856 joshea
652 hayes
375 krauth
366 wjp
319 peverett
301 kquintus
260 ctj
252 lorensen
212 karl
203 rjosest
96 eric
93 andyc
40 jjomier
14 haker
9 mikey
8 mathieu
1 frida
| valign="top"|
36840 nicole
28374 pieper
13836 mark
9432 odonnell
6707 samson
5711 gering
4430 hanifa
4415 halazar
4145 sylvain
3125 delfin
2390 tanacs
2053 meng
1909 pohl
1369 alexy
1175 hliu
1166 ahans
859 joshea
669 hayes
375 krauth
366 wjp
319 peverett
301 kquintus
260 ctj
252 lorensen
212 karl
203 rjosest
106 andyc
96 eric
40 jjomier
14 haker
9 mikey
8 mathieu
1 frida
| valign="top"|
45796 nicole
27332 pieper
13836 mark
8805 odonnell
6707 samson
5705 gering
4430 hanifa
4411 halazar
4145 sylvain
3125 delfin
2390 tanacs
2053 meng
1909 pohl
1369 alexy
1175 hliu
1166 ahans
856 joshea
659 hayes
442 andyc
375 krauth
366 wjp
319 peverett
301 kquintus
260 ctj
252 lorensen
212 karl
185 rjosest
96 eric
93 mathieu
40 jjomier
14 haker
9 mikey
1 frida
| valign="top"|
45913 nicole
28851 pieper
13836 mark
8805 odonnell
6707 samson
5705 gering
4430 hanifa
4411 halazar
4145 sylvain
3125 delfin
2390 tanacs
2053 meng
1909 pohl
1369 alexy
1175 hliu
1166 ahans
856 joshea
705 kquintus
659 hayes
442 andyc
375 krauth
366 wjp
319 peverett
294 mathieu
260 ctj
252 lorensen
212 karl
185 rjosest
96 eric
40 jjomier
14 haker
9 mikey
1 frida
|}

= Number of lines per author in Slicer 3=
{|
! Slicer 3.0 - 2008-02-13
! Slicer 3.2 - 2008-11-25
! Slicer 3.4 - 2010-03-23
! Slicer 3.6 - 2011-11-25
|-
| valign="top" |
27051 pieper
18619 lorensen
17500 wjp@bwh.harvard.edu
10751 naucoin
9037 davisb
6500 millerjv
6064 hliu
5771 rjosest
5184 blezek
4720 andy
3947 aylward
3001 kquintus
2288 vmagnotta
1392 alexy
1211 tringo
535 lauren
426 barre
275 mike
225 padfield
189 freudling
160 hayes
39 FeiZhao
35 jcross186
32 malaterre
20 tokuda
17 gcasey
11 taox
3 samset
2 zack.galbreath
2 rsierra
2 nobyhata
2 demian
1 yumin
| valign="top"|
29292 pieper
18283 lorensen
17930 wjp@bwh.harvard.edu
11279 naucoin
9944 aylward
9800 barre
8848 davisb
8089 millerjv
6322 blezek
5466 rjosest
5298 hliu
4550 andy
2843 kquintus
2147 vmagnotta
1340 lantiga
1332 tringo
1185 tgl
1156 alexy
475 kerstin
390 lauren
261 mike
217 padfield
195 hayes
70 freudling
35 taox
35 jcross186
17 tokuda
17 gcasey
15 malaterre
15 FeiZhao
8 hjohnson
3 samset
2 rsierra
2 bess
1 zack.galbreath
1 yumin
| valign="top"|
41211 pieper
38143 clisle
29839 hliu
22787 lorensen
18833 wjp@bwh.harvard.edu
11807 naucoin
11305 aylward
10070 millerjv
9901 pohl
9895 barre
7865 davisb
7494 jvs
5552 atriveg
4896 nicky
4738 blezek
4549 andy
3672 rjosest
2839 kquintus
2485 lantiga
1882 alexy
1309 tgl
1301 fedorov
1164 finetjul
1129 tringo
1058 sgerber
776 pkarasev3
769 ibanez
648 demian
338 kerstin
268 lauren
244 bess
205 padfield
198 hayes
73 hjohnson
69 freudling
46 vmagnotta
36 tokuda
33 jcross186
31 taox
17 gcasey
15 malaterre
15 FeiZhao
7 karthik
3 yumin
3 samset
3 mike
2 rsierra
1 domibel
| valign="top"|
48212 hjohnson
46278 pieper
38104 clisle
30247 hliu
25404 jcfr
23992 finetjul
21644 lorensen
21037 haehn
20548 wjp@bwh.harvard.edu
16284 jvs
15909 fedorov
11708 aylward
11092 millerjv
10805 naucoin
9987 barre
9534 casey.goodlett
8378 alexy
7589 pohl
6431 domibel
5796 sylvain
5545 atriveg
4603 blezek
4548 andy
3892 ibanez
3496 ygao
2836 kquintus
2829 tokuda
2252 lantiga
2168 nicky
1993 mscully
1573 vmagnotta
1447 partyd
1294 tgl
1137 pkarasev
855 demian
708 lauren
562 lassoan
421 rjosest
394 taox
332 kerstin
274 harveerar
242 bess
205 padfield
191 awiles
185 hayes
122 tringo
98 francois_budin
67 davisb
55 freudling
25 vrnova
24 jcross186
17 gcasey
13 FeiZhao
10 malaterre
7 karthik
3 samset
3 mike
2 yumin
2 rsierra
2 maddah
|}

=Number of lines per author in Slicer 4=
{|
! Slicer 4.0.0 - 2011 Nov 27
! Slicer 4.0.1 - 2012 Jan 06
! Slicer 4.1.0 - 2012 Apr 12
! Slicer 4.2.0 - 2012 Oct 31
! Slicer 4.3.0 - 2013 Sept 8
|-
| valign="top" |
57424 finetjul
48649 pieper
47795 jcfr
37846 clisle
26534 tokuda
19262 hjohnson
16278 jvs
12840 naucoin
9515 pohl
8739 fedorov
7868 aylward
7342 wjp@bwh.harvard.edu
7227 millerjv
6596 casey.goodlett
5995 lorensen
5503 blezek
4823 haehn
4427 alexy
4138 sylvain
3195 atriveg
2818 kquintus
2719 inorton
2377 demian
2310 barre
1926 lantiga
1840 nicky
1769 ygao
1449 ibanez
1372 vmagnotta
976 Michael.jeulinl
893 benjamin.long
672 hliu
587 pkarasev
570 rjosest
518 kedar_p
508 dpace
403 partyd
381 lauren
369 lassoan
352 zach.mullen
328 harveerar
313 ilknur.kabul
312 johan.andruejol
265 taox
244 kerstin
216 andy
175 bess
144 vrnova
143 awiles
122 tringo
85 tgl
64 domibel
50 freudling
49 padfield
47 taylor
25 jcross186
13 FeiZhao
9 hayes
9 davisb
7 karthik
3 malaterre
2 maddah
1 yumin
1 matthew.bowman
| valign="top"|
58209 finetjul
45473 jcfr
42133 pieper
19103 hjohnson
10814 naucoin
7853 aylward
7017 millerjv
6792 wjp@bwh.harvard.edu
6592 casey.goodlett
4760 haehn
4207 blezek
4146 fedorov
3978 lorensen
3969 sylvain
3664 alexy
3195 atriveg
2719 inorton
2238 demian
1769 ygao
1357 ibanez
1027 Michael.jeulinl
940 lantiga
930 benjamin.long
713 barre
584 pkarasev
570 rjosest
500 dpace
473 nicky
387 lauren
377 partyd
342 zach.mullen
328 harveerar
312 ilknur.kabul
311 johan.andruejol
256 taox
175 bess
133 kedar_p
122 vrnova
122 tringo
54 kerstin
49 padfield
47 taylor
26 tokuda
25 jcross186
25 hliu
23 andy
18 domibel
9 kquintus
7 karthik
7 hayes
3 malaterre
2 maddah
1 yumin
1 matthew.bowman
1 FeiZhao
| valign="top"|
63785 finetjul
52609 jcfr
35487 pieper
17980 hjohnson
10141 naucoin
9870 millerjv
7314 aylward
6866 wjp@bwh.harvard.edu
6471 casey.goodlett
4553 haehn
4151 fedorov
3969 sylvain
3804 alexy
3360 lorensen
3170 atriveg
2809 Michael.jeulinl
2618 inorton
2059 demian
1640 ygao
1188 ibanez
1159 vrnova
927 benjamin.long
624 barre
473 nicky
458 rjosest
413 dpace
358 partyd
342 lauren
299 ilknur.kabul
278 johan.andruejol
272 taox
261 zach.mullen
235 harveerar
175 bess
130 kedar_p
122 tringo
54 kerstin
49 padfield
36 taylor
36 joe.snyder
28 tokuda
25 jcross186
25 hliu
23 andy
16 domibel
9 kquintus
7 karthik
5 hayes
5 blezek
3 malaterre
2 pohl
2 maddah
1 yumin
1 matthew.bowman
1 FeiZhao
|valign="top"|
68905 finetjul
57186 jcfr
37747 pieper
18098 hjohnson
11068 millerjv
10133 naucoin
7311 aylward
7272 benjamin.long
6848 wjp@bwh.harvard.edu
6400 casey.goodlett
5317 alexy
4815 fedorov
4386 haehn
3947 sylvain
3342 lorensen
3169 atriveg
3024 Michael.jeulinl
2598 pinter
2482 inorton
2308 demian
2064 vrnova
1636 ygao
1153 ibanez
616 barre
507 sankhesh
473 nicky
457 rjosest
424 christopher.mullins
342 lauren
328 partyd
328 dpace
299 ilknur.kabul
278 johan.andruejol
263 taox
261 zach.mullen
222 ungi
175 bess
171 mccormic
130 kedar_p
122 tringo
74 harveerar
54 kerstin
49 padfield
42 joe.snyder
25 taylor
25 jcross186
25 hliu
24 tokuda
23 andy
16 domibel
9 kquintus
7 karthik
5 hayes
5 blezek
3 malaterre
1 yumin
1 pohl
1 matthew.bowman
1 maddah
1 lassoan
1 FeiZhao
|valign="top"|
75299 jcfr
69692 finetjul
22923 pieper
21919 hjohnson
19023 naucoin
10294 millerjv
7287 aylward
7145 benjamin.long
6335 casey.goodlett
5385 fedorov
5385 alexy
5171 wjp@bwh.harvard.edu
4856 johan.andruejol
4130 haehn
3941 sylvain
3323 lorensen
3166 atriveg
3082 demian
2908 Michael.jeulinl
2377 inorton
2028 vrnova
1951 pinter
1633 ygao
1188 nicky
1079 ibanez
916 sankhesh
522 barre
483 christopher.mullins
453 rjosest
342 lauren
310 partyd
305 dpace
278 ilknur.kabul
261 zach.mullen
238 taox
222 mccormic
192 ungi
175 bess
130 kedar_p
122 tringo
54 kerstin
49 padfield
42 joe.snyder
37 jamie.snape
25 taylor
22 andy
13 domibel
9 kquintus
7 harveerar
5 tokuda
5 blezek
4 hayes
3 pohl
3 malaterre
3 hliu
1 yumin
1 matthew.bowman
1 maddah
1 lassoan
|}
Script used to count (cvs):
find . -type f | egrep -v \.'png|gif|vtk|stl|jpeg|jpg|ico|nrrd|dcm|xml|gz|md5|nhdr|log|mrml|mha|s3ext|s4ext|raw|html|dox|mhd|pack|vtp|am|nii|JPG|exe|db|zip|svg|img|cache|kit|hdr' | grep -v CVS | grep -v weave | grep -v tclkit-darwin-univ | grep -v Slicer3Launchers | grep -v tclkits | xargs -n1 -d'\n' -i cvs annotate {} | perl -n -e '/\s\((.*?)\s[0-9]{2}/ && print "$1\n"' | sort -f | uniq -c -w3 | sort -r
Script used to count (svn):
find . -type f | egrep -v \.'png|gif|vtk|stl|jpeg|jpg|ico|nrrd|dcm|xml|gz|md5|nhdr|log|mrml|mha|s3ext|s4ext|raw|html|dox|mhd|pack|vtp|am|nii|JPG|exe|db|zip|svg|img|cache|kit|hdr' | grep -v ".svn" | grep -v weave | grep -v tclkit-darwin-univ | grep -v Slicer3Launchers | grep -v tclkits | xargs -n1 -d'\n' -i svn blame {} | perl -n -e '/\s*[\d]+\s+(.*?)\s.*/ && print "$1\n"' | sort -f | uniq -c -w3 | sort -r
Script used to count (git):
git ls-files | egrep -v \.'png|gif|vtk|stl|jpeg|jpg|ico|nrrd|dcm|xml|gz|md5|nhdr|log|mrml|mha|s3ext|s4ext|raw|html|dox|mhd|pack|vtp|am|nii|JPG|exe|db|zip|svg|img|cache|kit|hdr' | grep -v weave | grep -v tclkit-darwin-univ | grep -v Slicer3Launchers | grep -v tclkits | xargs -n1 -d'\n' -i git blame {} | perl -n -e '/\s\((.*?)\s[0-9]{4}/ && print "$1\n"' | sort -f | uniq -c -w3 | sort -r

Slicer4:QtPort/FunFacts

2014-01-28T14:29:05Z

Finetjul: /* Number of lines per author in Slicer 3 */

=Slicer 4 vs Slicer 3=
* Superbuild
** Slicer 3.6 (Mac Os X, 4 proc.)
*** real: 141m33.004s user: 118m2.658s sys:13m31.075s
** Slicer 4.0.1 (Mac Os X, 4 proc.)
*** real: 51m24.573s user: 159m38.262s sys: 21m41.498s
** Slicer 3.6 vs 4.0.1 is '''2.8x faster'''
* Lib
** Slicer3 MRML (gcc, 1 proc., Ubuntu 64b):
*** real: 4m50s user: 3m51s sys: 0m40s
** Slicer3 MRML (Visual Studio 2008, 1 proc., Release):
*** 6m20s
** Slicer4 MRML (gcc, 1 proc., Ubuntu 64b):
*** real: 2m11s user: 1m51s sys: 0m22s
** Slicer4 MRML (Visual Studio 2008, Release):
*** 4m40s
** Slicer 3.6 vs 4.0.1 is '''1.5x to 2x faster'''

=Number of lines per author in Slicer 2=
{|
!Slicer 2.4 - 2004-11-23
!Slicer 2.5 - 2005-05-23
!Slicer 2.6 - 2006-08-12
!Slicer 2.7 - 2007-04-20
|-
| valign="top" |
36691 nicole
24944 pieper
13836 mark
7999 odonnell
6693 samson
5948 gering
4430 hanifa
4411 halazar
4124 sylvain
3125 delfin
2390 tanacs
2053 meng
1680 pohl
1175 hliu
1166 ahans
967 alexy
856 joshea
652 hayes
375 krauth
366 wjp
319 peverett
301 kquintus
260 ctj
252 lorensen
212 karl
203 rjosest
96 eric
93 andyc
40 jjomier
14 haker
9 mikey
8 mathieu
1 frida
| valign="top"|
36840 nicole
28374 pieper
13836 mark
9432 odonnell
6707 samson
5711 gering
4430 hanifa
4415 halazar
4145 sylvain
3125 delfin
2390 tanacs
2053 meng
1909 pohl
1369 alexy
1175 hliu
1166 ahans
859 joshea
669 hayes
375 krauth
366 wjp
319 peverett
301 kquintus
260 ctj
252 lorensen
212 karl
203 rjosest
106 andyc
96 eric
40 jjomier
14 haker
9 mikey
8 mathieu
1 frida
| valign="top"|
45796 nicole
27332 pieper
13836 mark
8805 odonnell
6707 samson
5705 gering
4430 hanifa
4411 halazar
4145 sylvain
3125 delfin
2390 tanacs
2053 meng
1909 pohl
1369 alexy
1175 hliu
1166 ahans
856 joshea
659 hayes
442 andyc
375 krauth
366 wjp
319 peverett
301 kquintus
260 ctj
252 lorensen
212 karl
185 rjosest
96 eric
93 mathieu
40 jjomier
14 haker
9 mikey
1 frida
| valign="top"|
45913 nicole
28851 pieper
13836 mark
8805 odonnell
6707 samson
5705 gering
4430 hanifa
4411 halazar
4145 sylvain
3125 delfin
2390 tanacs
2053 meng
1909 pohl
1369 alexy
1175 hliu
1166 ahans
856 joshea
705 kquintus
659 hayes
442 andyc
375 krauth
366 wjp
319 peverett
294 mathieu
260 ctj
252 lorensen
212 karl
185 rjosest
96 eric
40 jjomier
14 haker
9 mikey
1 frida
|}

= Number of lines per author in Slicer 3=
{|
! Slicer 3.0 - 2008-02-13
! Slicer 3.2 - 2008-11-25
! Slicer 3.4 -
! Slicer 3.6 -
|-
| valign="top" |
27051 pieper
18619 lorensen
17500 wjp@bwh.harvard.edu
10751 naucoin
9037 davisb
6500 millerjv
6064 hliu
5771 rjosest
5184 blezek
4720 andy
3947 aylward
3001 kquintus
2288 vmagnotta
1392 alexy
1211 tringo
535 lauren
426 barre
275 mike
225 padfield
189 freudling
160 hayes
39 FeiZhao
35 jcross186
32 malaterre
20 tokuda
17 gcasey
11 taox
3 samset
2 zack.galbreath
2 rsierra
2 nobyhata
2 demian
1 yumin
| valign="top"|
29292 pieper
18283 lorensen
17930 wjp@bwh.harvard.edu
11279 naucoin
9944 aylward
9800 barre
8848 davisb
8089 millerjv
6322 blezek
5466 rjosest
5298 hliu
4550 andy
2843 kquintus
2147 vmagnotta
1340 lantiga
1332 tringo
1185 tgl
1156 alexy
475 kerstin
390 lauren
261 mike
217 padfield
195 hayes
70 freudling
35 taox
35 jcross186
17 tokuda
17 gcasey
15 malaterre
15 FeiZhao
8 hjohnson
3 samset
2 rsierra
2 bess
1 zack.galbreath
1 yumin
|}

=Number of lines per author in Slicer 4=
{|
! Slicer 4.0.0 - 2011 Nov 27
! Slicer 4.0.1 - 2012 Jan 06
! Slicer 4.1.0 - 2012 Apr 12
! Slicer 4.2.0 - 2012 Oct 31
! Slicer 4.3.0 - 2013 Sept 8
|-
| valign="top" |
57424 finetjul
48649 pieper
47795 jcfr
37846 clisle
26534 tokuda
19262 hjohnson
16278 jvs
12840 naucoin
9515 pohl
8739 fedorov
7868 aylward
7342 wjp@bwh.harvard.edu
7227 millerjv
6596 casey.goodlett
5995 lorensen
5503 blezek
4823 haehn
4427 alexy
4138 sylvain
3195 atriveg
2818 kquintus
2719 inorton
2377 demian
2310 barre
1926 lantiga
1840 nicky
1769 ygao
1449 ibanez
1372 vmagnotta
976 Michael.jeulinl
893 benjamin.long
672 hliu
587 pkarasev
570 rjosest
518 kedar_p
508 dpace
403 partyd
381 lauren
369 lassoan
352 zach.mullen
328 harveerar
313 ilknur.kabul
312 johan.andruejol
265 taox
244 kerstin
216 andy
175 bess
144 vrnova
143 awiles
122 tringo
85 tgl
64 domibel
50 freudling
49 padfield
47 taylor
25 jcross186
13 FeiZhao
9 hayes
9 davisb
7 karthik
3 malaterre
2 maddah
1 yumin
1 matthew.bowman
| valign="top"|
58209 finetjul
45473 jcfr
42133 pieper
19103 hjohnson
10814 naucoin
7853 aylward
7017 millerjv
6792 wjp@bwh.harvard.edu
6592 casey.goodlett
4760 haehn
4207 blezek
4146 fedorov
3978 lorensen
3969 sylvain
3664 alexy
3195 atriveg
2719 inorton
2238 demian
1769 ygao
1357 ibanez
1027 Michael.jeulinl
940 lantiga
930 benjamin.long
713 barre
584 pkarasev
570 rjosest
500 dpace
473 nicky
387 lauren
377 partyd
342 zach.mullen
328 harveerar
312 ilknur.kabul
311 johan.andruejol
256 taox
175 bess
133 kedar_p
122 vrnova
122 tringo
54 kerstin
49 padfield
47 taylor
26 tokuda
25 jcross186
25 hliu
23 andy
18 domibel
9 kquintus
7 karthik
7 hayes
3 malaterre
2 maddah
1 yumin
1 matthew.bowman
1 FeiZhao
| valign="top"|
63785 finetjul
52609 jcfr
35487 pieper
17980 hjohnson
10141 naucoin
9870 millerjv
7314 aylward
6866 wjp@bwh.harvard.edu
6471 casey.goodlett
4553 haehn
4151 fedorov
3969 sylvain
3804 alexy
3360 lorensen
3170 atriveg
2809 Michael.jeulinl
2618 inorton
2059 demian
1640 ygao
1188 ibanez
1159 vrnova
927 benjamin.long
624 barre
473 nicky
458 rjosest
413 dpace
358 partyd
342 lauren
299 ilknur.kabul
278 johan.andruejol
272 taox
261 zach.mullen
235 harveerar
175 bess
130 kedar_p
122 tringo
54 kerstin
49 padfield
36 taylor
36 joe.snyder
28 tokuda
25 jcross186
25 hliu
23 andy
16 domibel
9 kquintus
7 karthik
5 hayes
5 blezek
3 malaterre
2 pohl
2 maddah
1 yumin
1 matthew.bowman
1 FeiZhao
|valign="top"|
68905 finetjul
57186 jcfr
37747 pieper
18098 hjohnson
11068 millerjv
10133 naucoin
7311 aylward
7272 benjamin.long
6848 wjp@bwh.harvard.edu
6400 casey.goodlett
5317 alexy
4815 fedorov
4386 haehn
3947 sylvain
3342 lorensen
3169 atriveg
3024 Michael.jeulinl
2598 pinter
2482 inorton
2308 demian
2064 vrnova
1636 ygao
1153 ibanez
616 barre
507 sankhesh
473 nicky
457 rjosest
424 christopher.mullins
342 lauren
328 partyd
328 dpace
299 ilknur.kabul
278 johan.andruejol
263 taox
261 zach.mullen
222 ungi
175 bess
171 mccormic
130 kedar_p
122 tringo
74 harveerar
54 kerstin
49 padfield
42 joe.snyder
25 taylor
25 jcross186
25 hliu
24 tokuda
23 andy
16 domibel
9 kquintus
7 karthik
5 hayes
5 blezek
3 malaterre
1 yumin
1 pohl
1 matthew.bowman
1 maddah
1 lassoan
1 FeiZhao
|valign="top"|
75299 jcfr
69692 finetjul
22923 pieper
21919 hjohnson
19023 naucoin
10294 millerjv
7287 aylward
7145 benjamin.long
6335 casey.goodlett
5385 fedorov
5385 alexy
5171 wjp@bwh.harvard.edu
4856 johan.andruejol
4130 haehn
3941 sylvain
3323 lorensen
3166 atriveg
3082 demian
2908 Michael.jeulinl
2377 inorton
2028 vrnova
1951 pinter
1633 ygao
1188 nicky
1079 ibanez
916 sankhesh
522 barre
483 christopher.mullins
453 rjosest
342 lauren
310 partyd
305 dpace
278 ilknur.kabul
261 zach.mullen
238 taox
222 mccormic
192 ungi
175 bess
130 kedar_p
122 tringo
54 kerstin
49 padfield
42 joe.snyder
37 jamie.snape
25 taylor
22 andy
13 domibel
9 kquintus
7 harveerar
5 tokuda
5 blezek
4 hayes
3 pohl
3 malaterre
3 hliu
1 yumin
1 matthew.bowman
1 maddah
1 lassoan
|}
Script used to count (cvs):
find . -type f | egrep -v \.'png|gif|vtk|stl|jpeg|jpg|ico|nrrd|dcm|xml|gz|md5|nhdr|log|mrml|mha|s3ext|s4ext|raw|html|dox|mhd|pack|vtp|am|nii|JPG|exe|db|zip|svg|img|cache|kit|hdr' | grep -v CVS | grep -v weave | grep -v tclkit-darwin-univ | grep -v Slicer3Launchers | grep -v tclkits | xargs -n1 -d'\n' -i cvs annotate {} | perl -n -e '/\s\((.*?)\s[0-9]{2}/ && print "$1\n"' | sort -f | uniq -c -w3 | sort -r
Script used to count (svn):
find . -type f | egrep -v \.'png|gif|vtk|stl|jpeg|jpg|ico|nrrd|dcm|xml|gz|md5|nhdr|log|mrml|mha|s3ext|s4ext|raw|html|dox|mhd|pack|vtp|am|nii|JPG|exe|db|zip|svg|img|cache|kit|hdr' | grep -v ".svn" | grep -v weave | grep -v tclkit-darwin-univ | grep -v Slicer3Launchers | grep -v tclkits | xargs -n1 -d'\n' -i svn blame {} | perl -n -e '/\s*[\d]+\s+(.*?)\s.*/ && print "$1\n"' | sort -f | uniq -c -w3 | sort -r
Script used to count (git):
git ls-files | egrep -v \.'png|gif|vtk|stl|jpeg|jpg|ico|nrrd|dcm|xml|gz|md5|nhdr|log|mrml|mha|s3ext|s4ext|raw|html|dox|mhd|pack|vtp|am|nii|JPG|exe|db|zip|svg|img|cache|kit|hdr' | grep -v weave | grep -v tclkit-darwin-univ | grep -v Slicer3Launchers | grep -v tclkits | xargs -n1 -d'\n' -i git blame {} | perl -n -e '/\s\((.*?)\s[0-9]{4}/ && print "$1\n"' | sort -f | uniq -c -w3 | sort -r

Slicer4:QtPort/FunFacts

2014-01-28T14:23:44Z

Finetjul: /* Number of lines per author in Slicer 4 */

=Slicer 4 vs Slicer 3=
* Superbuild
** Slicer 3.6 (Mac Os X, 4 proc.)
*** real: 141m33.004s user: 118m2.658s sys:13m31.075s
** Slicer 4.0.1 (Mac Os X, 4 proc.)
*** real: 51m24.573s user: 159m38.262s sys: 21m41.498s
** Slicer 3.6 vs 4.0.1 is '''2.8x faster'''
* Lib
** Slicer3 MRML (gcc, 1 proc., Ubuntu 64b):
*** real: 4m50s user: 3m51s sys: 0m40s
** Slicer3 MRML (Visual Studio 2008, 1 proc., Release):
*** 6m20s
** Slicer4 MRML (gcc, 1 proc., Ubuntu 64b):
*** real: 2m11s user: 1m51s sys: 0m22s
** Slicer4 MRML (Visual Studio 2008, Release):
*** 4m40s
** Slicer 3.6 vs 4.0.1 is '''1.5x to 2x faster'''

=Number of lines per author in Slicer 2=
{|
!Slicer 2.4 - 2004-11-23
!Slicer 2.5 - 2005-05-23
!Slicer 2.6 - 2006-08-12
!Slicer 2.7 - 2007-04-20
|-
| valign="top" |
36691 nicole
24944 pieper
13836 mark
7999 odonnell
6693 samson
5948 gering
4430 hanifa
4411 halazar
4124 sylvain
3125 delfin
2390 tanacs
2053 meng
1680 pohl
1175 hliu
1166 ahans
967 alexy
856 joshea
652 hayes
375 krauth
366 wjp
319 peverett
301 kquintus
260 ctj
252 lorensen
212 karl
203 rjosest
96 eric
93 andyc
40 jjomier
14 haker
9 mikey
8 mathieu
1 frida
| valign="top"|
36840 nicole
28374 pieper
13836 mark
9432 odonnell
6707 samson
5711 gering
4430 hanifa
4415 halazar
4145 sylvain
3125 delfin
2390 tanacs
2053 meng
1909 pohl
1369 alexy
1175 hliu
1166 ahans
859 joshea
669 hayes
375 krauth
366 wjp
319 peverett
301 kquintus
260 ctj
252 lorensen
212 karl
203 rjosest
106 andyc
96 eric
40 jjomier
14 haker
9 mikey
8 mathieu
1 frida
| valign="top"|
45796 nicole
27332 pieper
13836 mark
8805 odonnell
6707 samson
5705 gering
4430 hanifa
4411 halazar
4145 sylvain
3125 delfin
2390 tanacs
2053 meng
1909 pohl
1369 alexy
1175 hliu
1166 ahans
856 joshea
659 hayes
442 andyc
375 krauth
366 wjp
319 peverett
301 kquintus
260 ctj
252 lorensen
212 karl
185 rjosest
96 eric
93 mathieu
40 jjomier
14 haker
9 mikey
1 frida
| valign="top"|
45913 nicole
28851 pieper
13836 mark
8805 odonnell
6707 samson
5705 gering
4430 hanifa
4411 halazar
4145 sylvain
3125 delfin
2390 tanacs
2053 meng
1909 pohl
1369 alexy
1175 hliu
1166 ahans
856 joshea
705 kquintus
659 hayes
442 andyc
375 krauth
366 wjp
319 peverett
294 mathieu
260 ctj
252 lorensen
212 karl
185 rjosest
96 eric
40 jjomier
14 haker
9 mikey
1 frida
|}

= Number of lines per author in Slicer 3=
{|
! Slicer 3.0 -
! Slicer 3.2 -
! Slicer 3.4 -
! Slicer 3.6 -
|-
| valign="top"
27051 pieper
18619 lorensen
17500 wjp@bwh.harvard.edu
10751 naucoin
9037 davisb
6500 millerjv
6064 hliu
5771 rjosest
5184 blezek
4720 andy
3947 aylward
3001 kquintus
2288 vmagnotta
1392 alexy
1211 tringo
535 lauren
426 barre
275 mike
225 padfield
189 freudling
160 hayes
39 FeiZhao
35 jcross186
32 malaterre
20 tokuda
17 gcasey
11 taox
3 samset
2 zack.galbreath
2 rsierra
2 nobyhata
2 demian
1 yumin
|}

=Number of lines per author in Slicer 4=
{|
! Slicer 4.0.0 - 2011 Nov 27
! Slicer 4.0.1 - 2012 Jan 06
! Slicer 4.1.0 - 2012 Apr 12
! Slicer 4.2.0 - 2012 Oct 31
! Slicer 4.3.0 - 2013 Sept 8
|-
| valign="top" |
57424 finetjul
48649 pieper
47795 jcfr
37846 clisle
26534 tokuda
19262 hjohnson
16278 jvs
12840 naucoin
9515 pohl
8739 fedorov
7868 aylward
7342 wjp@bwh.harvard.edu
7227 millerjv
6596 casey.goodlett
5995 lorensen
5503 blezek
4823 haehn
4427 alexy
4138 sylvain
3195 atriveg
2818 kquintus
2719 inorton
2377 demian
2310 barre
1926 lantiga
1840 nicky
1769 ygao
1449 ibanez
1372 vmagnotta
976 Michael.jeulinl
893 benjamin.long
672 hliu
587 pkarasev
570 rjosest
518 kedar_p
508 dpace
403 partyd
381 lauren
369 lassoan
352 zach.mullen
328 harveerar
313 ilknur.kabul
312 johan.andruejol
265 taox
244 kerstin
216 andy
175 bess
144 vrnova
143 awiles
122 tringo
85 tgl
64 domibel
50 freudling
49 padfield
47 taylor
25 jcross186
13 FeiZhao
9 hayes
9 davisb
7 karthik
3 malaterre
2 maddah
1 yumin
1 matthew.bowman
| valign="top"|
58209 finetjul
45473 jcfr
42133 pieper
19103 hjohnson
10814 naucoin
7853 aylward
7017 millerjv
6792 wjp@bwh.harvard.edu
6592 casey.goodlett
4760 haehn
4207 blezek
4146 fedorov
3978 lorensen
3969 sylvain
3664 alexy
3195 atriveg
2719 inorton
2238 demian
1769 ygao
1357 ibanez
1027 Michael.jeulinl
940 lantiga
930 benjamin.long
713 barre
584 pkarasev
570 rjosest
500 dpace
473 nicky
387 lauren
377 partyd
342 zach.mullen
328 harveerar
312 ilknur.kabul
311 johan.andruejol
256 taox
175 bess
133 kedar_p
122 vrnova
122 tringo
54 kerstin
49 padfield
47 taylor
26 tokuda
25 jcross186
25 hliu
23 andy
18 domibel
9 kquintus
7 karthik
7 hayes
3 malaterre
2 maddah
1 yumin
1 matthew.bowman
1 FeiZhao
| valign="top"|
63785 finetjul
52609 jcfr
35487 pieper
17980 hjohnson
10141 naucoin
9870 millerjv
7314 aylward
6866 wjp@bwh.harvard.edu
6471 casey.goodlett
4553 haehn
4151 fedorov
3969 sylvain
3804 alexy
3360 lorensen
3170 atriveg
2809 Michael.jeulinl
2618 inorton
2059 demian
1640 ygao
1188 ibanez
1159 vrnova
927 benjamin.long
624 barre
473 nicky
458 rjosest
413 dpace
358 partyd
342 lauren
299 ilknur.kabul
278 johan.andruejol
272 taox
261 zach.mullen
235 harveerar
175 bess
130 kedar_p
122 tringo
54 kerstin
49 padfield
36 taylor
36 joe.snyder
28 tokuda
25 jcross186
25 hliu
23 andy
16 domibel
9 kquintus
7 karthik
5 hayes
5 blezek
3 malaterre
2 pohl
2 maddah
1 yumin
1 matthew.bowman
1 FeiZhao
|valign="top"|
68905 finetjul
57186 jcfr
37747 pieper
18098 hjohnson
11068 millerjv
10133 naucoin
7311 aylward
7272 benjamin.long
6848 wjp@bwh.harvard.edu
6400 casey.goodlett
5317 alexy
4815 fedorov
4386 haehn
3947 sylvain
3342 lorensen
3169 atriveg
3024 Michael.jeulinl
2598 pinter
2482 inorton
2308 demian
2064 vrnova
1636 ygao
1153 ibanez
616 barre
507 sankhesh
473 nicky
457 rjosest
424 christopher.mullins
342 lauren
328 partyd
328 dpace
299 ilknur.kabul
278 johan.andruejol
263 taox
261 zach.mullen
222 ungi
175 bess
171 mccormic
130 kedar_p
122 tringo
74 harveerar
54 kerstin
49 padfield
42 joe.snyder
25 taylor
25 jcross186
25 hliu
24 tokuda
23 andy
16 domibel
9 kquintus
7 karthik
5 hayes
5 blezek
3 malaterre
1 yumin
1 pohl
1 matthew.bowman
1 maddah
1 lassoan
1 FeiZhao
|valign="top"|
75299 jcfr
69692 finetjul
22923 pieper
21919 hjohnson
19023 naucoin
10294 millerjv
7287 aylward
7145 benjamin.long
6335 casey.goodlett
5385 fedorov
5385 alexy
5171 wjp@bwh.harvard.edu
4856 johan.andruejol
4130 haehn
3941 sylvain
3323 lorensen
3166 atriveg
3082 demian
2908 Michael.jeulinl
2377 inorton
2028 vrnova
1951 pinter
1633 ygao
1188 nicky
1079 ibanez
916 sankhesh
522 barre
483 christopher.mullins
453 rjosest
342 lauren
310 partyd
305 dpace
278 ilknur.kabul
261 zach.mullen
238 taox
222 mccormic
192 ungi
175 bess
130 kedar_p
122 tringo
54 kerstin
49 padfield
42 joe.snyder
37 jamie.snape
25 taylor
22 andy
13 domibel
9 kquintus
7 harveerar
5 tokuda
5 blezek
4 hayes
3 pohl
3 malaterre
3 hliu
1 yumin
1 matthew.bowman
1 maddah
1 lassoan
|}
Script used to count (cvs):
find . -type f | egrep -v \.'png|gif|vtk|stl|jpeg|jpg|ico|nrrd|dcm|xml|gz|md5|nhdr|log|mrml|mha|s3ext|s4ext|raw|html|dox|mhd|pack|vtp|am|nii|JPG|exe|db|zip|svg|img|cache|kit|hdr' | grep -v CVS | grep -v weave | grep -v tclkit-darwin-univ | grep -v Slicer3Launchers | grep -v tclkits | xargs -n1 -d'\n' -i cvs annotate {} | perl -n -e '/\s\((.*?)\s[0-9]{2}/ && print "$1\n"' | sort -f | uniq -c -w3 | sort -r
Script used to count (svn):
find . -type f | egrep -v \.'png|gif|vtk|stl|jpeg|jpg|ico|nrrd|dcm|xml|gz|md5|nhdr|log|mrml|mha|s3ext|s4ext|raw|html|dox|mhd|pack|vtp|am|nii|JPG|exe|db|zip|svg|img|cache|kit|hdr' | grep -v ".svn" | grep -v weave | grep -v tclkit-darwin-univ | grep -v Slicer3Launchers | grep -v tclkits | xargs -n1 -d'\n' -i svn blame {} | perl -n -e '/\s*[\d]+\s+(.*?)\s.*/ && print "$1\n"' | sort -f | uniq -c -w3 | sort -r
Script used to count (git):
git ls-files | egrep -v \.'png|gif|vtk|stl|jpeg|jpg|ico|nrrd|dcm|xml|gz|md5|nhdr|log|mrml|mha|s3ext|s4ext|raw|html|dox|mhd|pack|vtp|am|nii|JPG|exe|db|zip|svg|img|cache|kit|hdr' | grep -v weave | grep -v tclkit-darwin-univ | grep -v Slicer3Launchers | grep -v tclkits | xargs -n1 -d'\n' -i git blame {} | perl -n -e '/\s\((.*?)\s[0-9]{4}/ && print "$1\n"' | sort -f | uniq -c -w3 | sort -r

Slicer4:QtPort/FunFacts

2014-01-28T14:22:06Z

2013-11-04T20:27:08Z

Finetjul: Add growcut link

Documentation/4.3/Modules/SimpleRegionGrowingSegmentation

2013-11-04T20:26:17Z

Finetjul: Add growcut link

Documentation/4.3/Modules/SimpleRegionGrowingSegmentation

2013-11-04T20:24:50Z

Finetjul: Link to RobustStatisticsSegmenter current version

Documentation/Nightly/Modules/SimpleRegionGrowingSegmentation

2013-11-04T20:24:16Z

Finetjul: Link to RobustStatisticsSegmenter current version

Documentation/4.3/ModulesMetadata

2013-10-15T20:14:50Z

Finetjul: Bump Data module revision to 4.3

<noinclude>{{documentation/versioncheck}}</noinclude>
<includeonly>
Name, XMLDescriptionURL
ACPCTransform, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ACPCTransform/ACPCTransform.xml?revision=19608&view=co
AddScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/AddScalarVolumes/AddScalarVolumes.xml?revision=19194&view=co
AffineRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/AffineRegistration/AffineRegistration.xml?revision=19194&view=co
Annotations, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Annotations/Documentation/Annotations.xml?revision=22424&view=co
BRAINSDemonWarp, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSDemonWarp/BRAINSDemonWarp.xml
BRAINSFit, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSFit/BRAINSFit.xml
BRAINSResample, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSResample/BRAINSResample.xml
BSplineDeformableRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/BSplineDeformableRegistration/BSplineDeformableRegistration.xml?revision=19194&view=co
BSplineToDeformationField, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/BSplineToDeformationField/BSplineToDeformationField.xml?revision=19194&view=co
Cameras, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Core/Cameras/Documentation/Cameras.xml?revision=19238&view=co
CastScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CastScalarVolume/CastScalarVolume.xml?revision=19608&view=co
CheckerBoardFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CheckerBoardFilter/CheckerBoardFilter.xml?revision=19170&view=co
CreateDICOMSeries, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CreateDICOMSeries/CreateDICOMSeries.xml?revision=19171&view=co
CurvatureAnisotropicDiffusion, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CurvatureAnisotropicDiffusion/CurvatureAnisotropicDiffusion.xml?revision=18864&view=co
Data, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Data/Documentation/Data.xml?revision=22613&view=co
DICOM, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/Scripts/DICOM.xml?revision=19903&view=co
DicomToNrrdConverter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DicomToNrrdConverter/DicomToNrrdConverter.xml?revision=19089&view=co
DiffusionTensorScalarMeasurements, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DiffusionTensorScalarMeasurements/DiffusionTensorScalarMeasurements.xml?revision=19172&view=co
DiffusionWeightedVolumeMasking, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DiffusionWeightedVolumeMasking/DiffusionWeightedVolumeMasking.xml?revision=19194&view=co
DTIExport, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DTIImportExport/DTIexport.xml?revision=19928&view=co
DTIImport, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DTIImportExport/DTIimport.xml?revision=19928&view=co
DWICompare, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DicomToNrrdConverter/ExtendedTesting/DWICompare.xml?revision=18864&view=co
DWIJointRicianLMMSEFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIJointRicianLMMSEFilter/DWIJointRicianLMMSEFilter.xml?revision=19197&view=co
DWIRicianLMMSEFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIRicianLMMSEFilter/DWIRicianLMMSEFilter.xml?revision=19197&view=co
DWIToDTIEstimation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIToDTIEstimation/DWIToDTIEstimation.xml?revision=19201&view=co
DWIUnbiasedNonLocalMeansFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIUnbiasedNonLocalMeansFilter/DWIUnbiasedNonLocalMeansFilter.xml?revision=19197&view=co
EMSegment_Command-line, http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co
Endoscopy, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/Scripts/Endoscopy.xml?revision=18864&view=co
EventBroker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Core/EventBroker/Documentation/EventBroker.xml?revision=19045&view=co
ExecutionModelTour, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExecutionModelTour/ExecutionModelTour.xml?revision=19194&view=co
ExpertAutomatedRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExpertAutomatedRegistration/ExpertAutomatedRegistration.xml?revision=19173&view=co
ExtractSkeleton, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExtractSkeleton/ExtractSkeleton.xml?revision=18864&view=co
FiducialRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/FiducialRegistration/FiducialRegistration.xml?revision=19173&view=co
ForegroundMasking, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSROIAuto/BRAINSROIAuto.xml
FreesurferSurfaceSectionExtraction, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/FreesurferSurfaceSectionExtraction/FreesurferSurfaceSectionExtraction.xml?revision=18864&view=co
GaussianBlurImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GaussianBlurImageFilter/GaussianBlurImageFilter.xml?revision=19194&view=co
GradientAnisotropicDiffusion, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GradientAnisotropicDiffusion/GradientAnisotropicDiffusion.xml?revision=18864&view=co
GrayscaleFillHoleImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleFillHoleImageFilter/GrayscaleFillHoleImageFilter.xml?revision=19194&view=co
GrayscaleGrindPeakImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleGrindPeakImageFilter/GrayscaleGrindPeakImageFilter.xml?revision=19194&view=co
GrayscaleModelMaker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleModelMaker/GrayscaleModelMaker.xml?revision=18864&view=co
HistogramMatching, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/HistogramMatching/HistogramMatching.xml?revision=18864&view=co
ImageLabelCombine, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ImageLabelCombine/ImageLabelCombine.xml?revision=18864&view=co
LabelMapSmoothing, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/LabelMapSmoothing/LabelMapSmoothing.xml?revision=18864&view=co
LinearRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/LinearRegistration/LinearRegistration.xml?revision=19194&view=co
Markups, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Markups/Documentation/Markups.xml?revision=22358&view=co
MaskScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MaskScalarVolume/MaskScalarVolume.xml?revision=19608&view=co
MatlabCommander, https://www.assembla.com/code/slicerrt/subversion/node/blob/trunk/MatlabBridge/src/MatlabCommander/MatlabCommander.xml?raw=1&rev=957
MedianImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MedianImageFilter/MedianImageFilter.xml?revision=19194&view=co
MergeModels, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MergeModels/MergeModels.xml?revision=19608&view=co
MeshContourSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MeshContourSegmentation/MeshContourSegmentation.xml?revision=19175&view=co
ModelMaker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ModelMaker/ModelMaker.xml?revision=19608&view=co
Models, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Models/Documentation/Models.xml?revision=21908&view=co
ModelToLabelMap, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ModelToLabelMap/ModelToLabelMap.xml?revision=22218&view=co
MRIBiasFieldCorrection, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MRIBiasFieldCorrection/MRIBiasFieldCorrection.xml?revision=18864&view=co
MultiplyScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MultiplyScalarVolumes/MultiplyScalarVolumes.xml?revision=19194&view=co
MultiResolutionAffineRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MultiResolutionAffineRegistration/MultiResolutionAffineRegistration.xml?revision=19194&view=co
N4ITKBiasFieldCorrection, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/N4ITKBiasFieldCorrection/N4ITKBiasFieldCorrection.xml?revision=18864&view=co
OrientScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OrientScalarVolume/OrientScalarVolume.xml?revision=19193&view=co
OtsuThresholdImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OtsuThresholdImageFilter/OtsuThresholdImageFilter.xml?revision=19194&view=co
OtsuThresholdSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OtsuThresholdSegmentation/OtsuThresholdSegmentation.xml?revision=18864&view=co
PETStandardUptakeValueComputation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/PETStandardUptakeValueComputation/PETStandardUptakeValueComputation.xml?revision=19608&view=co
ProbeVolumeWithModel, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ProbeVolumeWithModel/ProbeVolumeWithModel.xml?revision=19194&view=co
Reformat, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Reformat/Documentation/Reformat.xml?revision=19165&view=co
ResampleDTIVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleDTIVolume/ResampleDTIVolume.xml?revision=19197&view=co
ResampleScalarVectorDWIVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleScalarVectorDWIVolume/ResampleScalarVectorDWIVolume.xml?revision=19186&view=co
ResampleScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleScalarVolume/ResampleScalarVolume.xml?revision=19185&view=co
RigidRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/RigidRegistration/RigidRegistration.xml?revision=19194&view=co
RobustStatisticsSegmenter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/RobustStatisticsSegmenter/RobustStatisticsSegmenter.xml?revision=19198&view=co
SceneViews, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/SceneViews/Documentation/SceneViews.xml?revision=19608&view=co
SimpleRegionGrowingSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/SimpleRegionGrowingSegmentation/SimpleRegionGrowingSegmentation.xml?revision=22482&view=co
SubtractScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/SubtractScalarVolumes/SubtractScalarVolumes.xml?revision=19194&view=co
ThresholdScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ThresholdScalarVolume/ThresholdScalarVolume.xml?revision=19608&view=co
TractographyLabelMapSeeding, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/TractographyLabelMapSeeding/TractographyLabelMapSeeding.xml?revision=19194&view=co
Transforms, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Transforms/Documentation/Transforms.xml?revision=19899&view=co
ViewControllers, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/ViewControllers/Documentation/ViewControllers.xml?revision=18864&view=co
VolumeRendering, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/VolumeRendering/Documentation/VolumeRendering.xml?revision=19029&view=co
Volumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Volumes/Documentation/Volumes.xml?revision=18864&view=co
VotingBinaryHoleFillingImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/VotingBinaryHoleFillingImageFilter/VotingBinaryHoleFillingImageFilter.xml?revision=19194&view=co
</includeonly><noinclude>

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</noinclude>

Documentation/Nightly/ModulesMetadata

2013-10-15T20:11:09Z

Finetjul: Bump Data module revision to 4.3

<noinclude>{{documentation/versioncheck}}</noinclude>
<includeonly>
Name, XMLDescriptionURL
ACPCTransform, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ACPCTransform/ACPCTransform.xml?revision=19608&view=co
AddScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/AddScalarVolumes/AddScalarVolumes.xml?revision=19194&view=co
AffineRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/AffineRegistration/AffineRegistration.xml?revision=19194&view=co
Annotations, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Annotations/Documentation/Annotations.xml?revision=22424&view=co
BRAINSDemonWarp, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSDemonWarp/BRAINSDemonWarp.xml
BRAINSFit, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSFit/BRAINSFit.xml
BRAINSResample, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSResample/BRAINSResample.xml
BSplineDeformableRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/BSplineDeformableRegistration/BSplineDeformableRegistration.xml?revision=19194&view=co
BSplineToDeformationField, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/BSplineToDeformationField/BSplineToDeformationField.xml?revision=19194&view=co
Cameras, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Core/Cameras/Documentation/Cameras.xml?revision=19238&view=co
CastScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CastScalarVolume/CastScalarVolume.xml?revision=19608&view=co
CheckerBoardFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CheckerBoardFilter/CheckerBoardFilter.xml?revision=19170&view=co
CreateDICOMSeries, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CreateDICOMSeries/CreateDICOMSeries.xml?revision=19171&view=co
CurvatureAnisotropicDiffusion, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/CurvatureAnisotropicDiffusion/CurvatureAnisotropicDiffusion.xml?revision=18864&view=co
Data, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Data/Documentation/Data.xml?revision=22613&view=co
DICOM, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/Scripts/DICOM.xml?revision=19903&view=co
DicomToNrrdConverter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DicomToNrrdConverter/DicomToNrrdConverter.xml?revision=19089&view=co
DiffusionTensorScalarMeasurements, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DiffusionTensorScalarMeasurements/DiffusionTensorScalarMeasurements.xml?revision=19172&view=co
DiffusionWeightedVolumeMasking, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DiffusionWeightedVolumeMasking/DiffusionWeightedVolumeMasking.xml?revision=19194&view=co
DTIExport, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DTIImportExport/DTIexport.xml?revision=19928&view=co
DTIImport, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DTIImportExport/DTIimport.xml?revision=19928&view=co
DWICompare, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DicomToNrrdConverter/ExtendedTesting/DWICompare.xml?revision=18864&view=co
DWIJointRicianLMMSEFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIJointRicianLMMSEFilter/DWIJointRicianLMMSEFilter.xml?revision=19197&view=co
DWIRicianLMMSEFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIRicianLMMSEFilter/DWIRicianLMMSEFilter.xml?revision=19197&view=co
DWIToDTIEstimation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIToDTIEstimation/DWIToDTIEstimation.xml?revision=19201&view=co
DWIUnbiasedNonLocalMeansFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/DWIUnbiasedNonLocalMeansFilter/DWIUnbiasedNonLocalMeansFilter.xml?revision=19197&view=co
EMSegment_Command-line, http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co
Endoscopy, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Scripted/Scripts/Endoscopy.xml?revision=18864&view=co
EventBroker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Core/EventBroker/Documentation/EventBroker.xml?revision=19045&view=co
ExecutionModelTour, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExecutionModelTour/ExecutionModelTour.xml?revision=19194&view=co
ExpertAutomatedRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExpertAutomatedRegistration/ExpertAutomatedRegistration.xml?revision=19173&view=co
ExtractSkeleton, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ExtractSkeleton/ExtractSkeleton.xml?revision=18864&view=co
FiducialRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/FiducialRegistration/FiducialRegistration.xml?revision=19173&view=co
ForegroundMasking, https://raw.github.com/BRAINSia/BRAINSTools/master/BRAINSROIAuto/BRAINSROIAuto.xml
FreesurferSurfaceSectionExtraction, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/FreesurferSurfaceSectionExtraction/FreesurferSurfaceSectionExtraction.xml?revision=18864&view=co
GaussianBlurImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GaussianBlurImageFilter/GaussianBlurImageFilter.xml?revision=19194&view=co
GradientAnisotropicDiffusion, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GradientAnisotropicDiffusion/GradientAnisotropicDiffusion.xml?revision=18864&view=co
GrayscaleFillHoleImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleFillHoleImageFilter/GrayscaleFillHoleImageFilter.xml?revision=19194&view=co
GrayscaleGrindPeakImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleGrindPeakImageFilter/GrayscaleGrindPeakImageFilter.xml?revision=19194&view=co
GrayscaleModelMaker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/GrayscaleModelMaker/GrayscaleModelMaker.xml?revision=18864&view=co
HistogramMatching, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/HistogramMatching/HistogramMatching.xml?revision=18864&view=co
ImageLabelCombine, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ImageLabelCombine/ImageLabelCombine.xml?revision=18864&view=co
LabelMapSmoothing, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/LabelMapSmoothing/LabelMapSmoothing.xml?revision=18864&view=co
LinearRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/LinearRegistration/LinearRegistration.xml?revision=19194&view=co
Markups, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Markups/Documentation/Markups.xml?revision=22608&view=co
MaskScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MaskScalarVolume/MaskScalarVolume.xml?revision=19608&view=co
MatlabCommander, https://www.assembla.com/code/slicerrt/subversion/node/blob/trunk/MatlabBridge/src/MatlabCommander/MatlabCommander.xml?raw=1&rev=957
MedianImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MedianImageFilter/MedianImageFilter.xml?revision=19194&view=co
MergeModels, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MergeModels/MergeModels.xml?revision=19608&view=co
MeshContourSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MeshContourSegmentation/MeshContourSegmentation.xml?revision=19175&view=co
ModelMaker, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ModelMaker/ModelMaker.xml?revision=19608&view=co
Models, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Models/Documentation/Models.xml?revision=21908&view=co
ModelToLabelMap, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ModelToLabelMap/ModelToLabelMap.xml?revision=22218&view=co
MRIBiasFieldCorrection, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MRIBiasFieldCorrection/MRIBiasFieldCorrection.xml?revision=18864&view=co
MultiplyScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MultiplyScalarVolumes/MultiplyScalarVolumes.xml?revision=19194&view=co
MultiResolutionAffineRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/MultiResolutionAffineRegistration/MultiResolutionAffineRegistration.xml?revision=19194&view=co
N4ITKBiasFieldCorrection, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/N4ITKBiasFieldCorrection/N4ITKBiasFieldCorrection.xml?revision=18864&view=co
OrientScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OrientScalarVolume/OrientScalarVolume.xml?revision=19193&view=co
OtsuThresholdImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OtsuThresholdImageFilter/OtsuThresholdImageFilter.xml?revision=19194&view=co
OtsuThresholdSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/OtsuThresholdSegmentation/OtsuThresholdSegmentation.xml?revision=18864&view=co
PETStandardUptakeValueComputation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/PETStandardUptakeValueComputation/PETStandardUptakeValueComputation.xml?revision=19608&view=co
ProbeVolumeWithModel, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ProbeVolumeWithModel/ProbeVolumeWithModel.xml?revision=19194&view=co
Reformat, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Reformat/Documentation/Reformat.xml?revision=19165&view=co
ResampleDTIVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleDTIVolume/ResampleDTIVolume.xml?revision=19197&view=co
ResampleScalarVectorDWIVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleScalarVectorDWIVolume/ResampleScalarVectorDWIVolume.xml?revision=19186&view=co
ResampleScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ResampleScalarVolume/ResampleScalarVolume.xml?revision=19185&view=co
RigidRegistration, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/RigidRegistration/RigidRegistration.xml?revision=19194&view=co
RobustStatisticsSegmenter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/RobustStatisticsSegmenter/RobustStatisticsSegmenter.xml?revision=19198&view=co
SceneViews, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/SceneViews/Documentation/SceneViews.xml?revision=19608&view=co
SimpleRegionGrowingSegmentation, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/SimpleRegionGrowingSegmentation/SimpleRegionGrowingSegmentation.xml?revision=22482&view=co
SubtractScalarVolumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/SubtractScalarVolumes/SubtractScalarVolumes.xml?revision=19194&view=co
ThresholdScalarVolume, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/ThresholdScalarVolume/ThresholdScalarVolume.xml?revision=19608&view=co
TractographyLabelMapSeeding, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/TractographyLabelMapSeeding/TractographyLabelMapSeeding.xml?revision=19194&view=co
Transforms, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Transforms/Documentation/Transforms.xml?revision=19899&view=co
ViewControllers, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/ViewControllers/Documentation/ViewControllers.xml?revision=18864&view=co
VolumeRendering, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/VolumeRendering/Documentation/VolumeRendering.xml?revision=19029&view=co
Volumes, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/Loadable/Volumes/Documentation/Volumes.xml?revision=18864&view=co
VotingBinaryHoleFillingImageFilter, http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Modules/CLI/VotingBinaryHoleFillingImageFilter/VotingBinaryHoleFillingImageFilter.xml?revision=19194&view=co
</includeonly><noinclude>

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| type = warning
| text = To force MediaWiki to clear the cached version of a given page, or to force the page to be redisplayed from its source. Add '''?action=purge''' to the URL of the page you are viewing. For more details, click [http://www.mediawiki.org/wiki/Manual:Purge here].
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{{#get_web_data:
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