Slicer Wiki - User contributions [en]

Documentation/4.0/SlicerApplication/StereoViewing

2011-11-26T14:02:40Z

Clisle: /* Purpose */

{{documentation/{{documentation/version}}/slicerapplication-header}}


='''CURRENTLY UNDER DEVELOPMENT'''=
[[image:Slicer4StereoPanel-2011-11.png|left|The Stereo Viewing Icon]]

=Purpose=

Slicer has the capability to display data in the 3D Viewer stereoscopically in a number of fashions including Red/Blue, Anaglyphic, Interlaced. These rendering modes are automatically enabled.

The final mode, called ActiveStereo or CrystalEyes mode, requires special display hardware and is not enabled by default. You have to start Slicer from command line and use the --stereo flag when using the ActiveStereo mode. ActiveStereo mode is currently under development.

=Stereo Modes Explained=

The first two algorithms require only 3D glasses, not any special computer hardware configurations. The last two algorithms require special stereo-ready display systems:

'''Red/Blue''' - For use with red/blue glasses commonly available in magazines or on the internet (see http://www.3dglassesdirect.com) The scene is drawn twice (once in each color from the location of each eye). Using the glasses separates the views and recreates perspective. There is some "bleedthrough" of the images to the opposite eye, but users can generally see depth using this algorithm. The drawback to this algorithm is the natural color of objects is lost due to the red & blue only rendering.

'''[http://en.wikipedia.org/wiki/Anaglyph_image Analglyph]''' - This algorithm uses the same glasses as the red/blue algorithm but preserves much of the natural color of rendered objects. In general, this preserves the colors in the rendered scene, but adds depth. Some "bleedthrough" still occurs between the eyes, but there are less visual artifacts compared with the red/blue algorithm.

'''Interlaced''' - In this algorithm the pixel lines from each eye are intermixed as the picture is rendered from top to bottom. With an ordinary monitor the lines will seem "jaggy" because we are observing the left and right eye's version of the scene superimposed. However, a stereo image results when interlaced signals are fed to a specially-configured stereo monitor or stereo display panel. The Hyundai S465D is one example of a panel with a vertical interlaced rendering mode.

'''CrystalEyes''' - This stereo mode is named after the famous, legacy glasses now sold by RealD (please see the products at the following website: http://www.reald.com/Content/Crystal-Eyes-5.aspx ). This mode is also sometimes called '''"active stereo"''' or '''"frame sequential stereo"'''. In this mode, successive video frames alternate between the left and right eyes as time progresses. A pair of special goggles or a special display route the signals to one eye or the other in quick succession. As long as the framerate is fast enough so the user doesn't see excessive flicker, this is a convincing rendering approach. However, this algorithm makes the most demands on the computing and display systems of all stereo options. Only some GPUs can produce active stereo, as support for OpenGL quad-buffered stereo mode is required. CrystalEyes rendering with 3D Slicer has been tested successfully on NVIDIA FX 1500, FX 4600, and FX 5600 GPUs, though these are not the only GPUs which are capable of frame sequential stereo.The display device (panel, projector, CRT, etc.) attached to the workstation must also be able to handle frame sequential stereo modes as well. Not all display devices support this rendering mode.

For this stereo mode to work it is necessary to start Slicer4 from the command line and using the --stereo option (i.e. open a shell, cd into the folder containing the slicer executable and type ./Slicer --stereo). This is only required for CrystalEyes mode. This option instructs 3D Slicer to configure a window using OpenGL Quad-buffered stereo. If you have troubles with this mode, be sure you are using current drivers for the GPU .

{{warning}}See http://www.slicer.org/slicerWiki/index.php/Modules:StereoViewing-3.6


{{documentation/{{documentation/version}}/slicerapplication-footer}}

Slicer3::Eclipse

2010-10-15T14:32:02Z

Clisle: /* Note to Snow Leopard users */

=Howto Setup Eclipse – Slicer3 Development Environment:=

First download your Eclipse version (e.g. from http://eclipse.org/downloads/ )

This description is based on Eclipse Helios:
eclipse-cpp-helios-linux-gtk.tar.gz

After checking out the sources and building 3D Slicer

CASE: the classic way (Slicer 3.6)
svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-6 Slicer3

./Slicer3/Scripts/getbuildtest.tcl

you will find 3 folders in your directory
Slicer3 (3D Slicer source)
Slicer3-lib (Dependencies source+binary)
Slicer3-build (3D Slicer binary)

Go to the 3D Slicer binary directory and generate your eclipse project files

cd Slicer3-build
cmake -G"Eclipse CDT4 - Unix Makefiles" -D CMAKE_BUILD_TYPE=Debug ../Slicer3

CASE: using Superbuild (Slicer 4.0)
svn co http://svn.slicer.org/Slicer4/trunk Slicer4

mkdir Slicer4-SuperBuild
cd Slicer4-SuperBuild
cmake -DSlicer_USE_KWWIDGETS:BOOL=OFF -DSlicer_USE_PYTHON:BOOL=OFF -DSlicer_USE_QT:BOOL=ON -DSlicer_USE_PYTHONQT:BOOL=OFF ../Slicer4/SuperBuild
make
cd ..

You will find 2+1 folders in your directory
Slicer4 (3D Slicer source)
Slicer4-SuperBuild (Dependencies source+binary)
Slicer4-SuperBuild/Slicer-build (3D Slicer binary)

Go to the 3D Slicer binary directory and generate your eclipse project files

cd Slicer4-SuperBuild/Slicer-build
cmake -G"Eclipse CDT4 - Unix Makefiles" -D CMAKE_BUILD_TYPE=Debug ../../Slicer4

You will get 2 files
Slicer3-build/.project
Slicer3-build/.cproject

Import the created project file into Eclipse

1. Import project using Menu File->Import
2. Select General->Existing projects into workspace:
3. Browse where your build tree is and select the root build tree directory. Keep "Copy projects into workspace" unchecked.
4. Click "Finish"
You get a fully functional eclipse project

* Add a -j<cores> to your make command (Properties->C/C++MakeProject)
* Under "Window->Preferences->General->Editors->Text Editors" please check "Insert spaces for tabs"

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment (Eclipse 3.5)=

<gallery>
Image:Slicer-editing-in-eclipse.png‎|A Slicer editing session in Eclipse 3.5 (Gallileo).
</gallery>

==Installing Eclipse:==
These instructions have been tested with Eclipse editions including "Ganymede" (3.4), "Galileo" (3.5), and "Helios" (3.6), but this should work with any Eclipse Version 3.3 or higher. The easiest way to get started is to select an eclipse distribution which already includes CDT, the C++ development tools, integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse by executing ./eclipse from the base directory of your eclipse installation.

==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/Users/dot/Projects/slicers/trunk-012210" contains the Slicer3* directories. So we could go into /Users/dot/Projects/slicers/trunk-012210/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/Users/dot/Projects/slicers/trunk-012210/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

[[Image:Eclipse-create-project.png|Create Project]]

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C Users/dot/Projects/slicers/trunk-012210/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

[[Image:Eclipse-build-ops.png|Eclipse Build Options Dialog]]

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

== Continuing with Debugging under Eclipse==
At this point, you should be able to build Slicer using Eclipse and run Slicer from inside Eclipse. If you want to debug Slicer interactively under Eclipse, there is a bit more configuration to perform. Please continue with the debugging instructions found below.

=Debugging with Eclipse Instructions=
There are a few key things about interactive debugging under Eclipse that once are done right, then it just works:

# build Slicer totally first the normal way, either with cmake or getbuildtest.tcl.
# Create the project in Eclipse by referring to the makefile and entering an external make command line

Assuming that Slicer is building under Eclipse, we'll take off from this point on:

==Understanding Slicer's startup process==
The executable ./Slicer3-build/Slicer3 is not the real program, instead it is just a "launcher". This executable sets up a bunch of paths and environment variables, then launches the real executable. The "real" Slicer3 program is stored in: ./Slicer3-build/bin/Slicer3-real. So when we are asking Eclipse to run Slicer under the debugger, we really want Eclipse to startup and attach to an instance of "Slicer3-real".

'''Step 1:''' There is a script in ./Slicer3-build/bin/Slicer3SetupPaths.sh or ./Slicer3-build/bin/Slicer3SetupPaths.csh which sets up the same paths as the launcher. If we run this script in a shell window (on Mac or Linux), then run eclipse from the same shell, we will have the environment defined. This is how to try it the first few times, but there is a cleaner way we will try after we know debugging is working. So if you are on either a Mac or Linux, open a shell and source this setup script, please.

Then in the same shell, start eclipse. It will be something like this:

#% source ./Slicer3-build/bin/Slicer3SetupPaths.sh
#% ~/Desktop/eclipse/eclipse &

'''Step 2:''' Then in the Eclipse window, open the Project/Properties by right-clicking on the Project Explorer entry for your Slicer build. Then select the "Run/Debug Settings" entry. We want to set the executable to point to "Slicer3-real" instead of "Slicer3". This plus running the script in the shell Eclipse was started from *may* be enough to get the debugger started on Slicer.

If you are using a Mac, shared library loading can be slow and gdb can timeout during Slicer's loading process. I have not had this problem on Linux and can't comment on Windows since I have not tried it in under Windows. It was helpful on Mac under Leopard and Snow Leopard to increase the default timeout allowed by Eclipse if your Mac needs a bit more time to get everything initialized when first beginning a debugging session.

== Note to Snow Leopard users ==
In the Summer of 2010, we found moving to Snow Leopard caused debugging to stop working. The newest (nightly build) of Eclipse was needed to get breakpoints to actually force the program to stop again. Debugging worked without tweaking Eclipse for systems running Tiger and Leopard. However, the 64-bit only mode of Snow Leopard meant a 64-bit Eclipse is needed for debugging. It is expected that these issues will be resolved in the release version of Eclipse 3.6 (Helios). Do remember that debugging only works using a 64-bit version of Eclipse on Snow Leopard (because the build is now a 64-bit build.)

Also, there is a known bug where Eclipse/GDB cannot insert breakpoints into the code is they were defined before program execution began, so the debugger doesn't stop when it comes across a previously-defined breakpoint. For now, the work-around for this is to invoke Slicer, so the Slicer GUI is constructed. Then once execution has started, use the Eclipse interface to set the desired breakpoints and continue with the debugging. This will work for debugging cases not involved in the initial GUI construction.

=Old description from 2008=
==PreRequirements for compiling Slicer3:==
# [http://www.cmake.org/ CMake (2.4.1 or later)]
# [http://www.tcl.tk/ Tcl/Tk (8.4 or later)]
# [http://sourceforge.net/projects/incrtcl/ incrTcl (3.2.1)]
# [http://www.vtk.org/ VTK 5.0]
# [http://www.itk.org/ ITK 2.8]
# [http://www.kwwidgets.org/ KWWidgets CVS head]
==Installing Eclipse:==
I installed Eclipse 3.3 M4, but this should also be applicable with Eclipse Versions under this. Download Eclipse from www.eclipse.org and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
To get Eclipse handling these big source packages in a good manner it is good to tweak a little the properties of the eclipse startup. First it is very advisable to use Eclipse with JRE 1.5. Download it from [http://java.sun.com/javase/downloads/index.jsp] and put it in your project folder (or elsewhere). In addition I increased the size of the memory Java can use with the lower bound switch -Xms and the upper bound -Xmx.

So my Eclispe command looks like this: ./eclipse -Xms64m – Xmx512m -vm /<path to your jre base-directory>/bin/java

Because sun only offers a java JRE for AMDX64 and not for Xeon CPU's it is also possible to use the JRE from BEA [http://commerce.bea.com/products/weblogicjrockit/accept_terms50.jsp?DL=www_JRockit_5_d2d&WT.ac=DL_www_JRockit_5_d2d jorckit].
This should be faster but also a little less stable (I didn't feel that something was unstable!)

==Modules for Eclipse you need:==
Before integrate the source-code into Eclipse we need two separate modules.
# CDT – C++ Environment: [http://www.eclipse.org/cdt/downloads.php http://www.eclipse.org/cdt/downloads.php]
# SubClipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

I use right now [http://download.eclipse.org/tools/cdt/builds/4.0.0/index.html CDT 4.0 - nightly build] which is much more feature rich then 3.1.
On the other Hand this is still under development and though not stable in any situation.

* To install these Modules, start Eclipse and go to Help->Software Updates->Find And Install
[[Image:Eclipse-Step1.png]]
* Click on “Search for new features to install” and then on “Next”:
[[Image:Eclipse-Step2.png]]
* Now click the “New Remote Site...” Button and insert the appropriate informations in the input fields.
* For CDT this should look like this:
[[Image:Eclipse-Step3.png]]
* For SubClipse:
[[Image:Eclipse-Step4.png]]
After adding these to module Site just click on the “Next” Button and Install both items.

You will be prompt to restart Eclipse. After the restart you're ready to get the sources into Eclipse.
==Creating Project and getting the Source-Code for it:==
Now that you have setup eclipse we can focus an getting the code and compile it. One of the disadvantages of eclipse is the inability to use Cmake and CmakeLists.txt files directly. So some manual configuration is still necessary. But hopefully the Eclipse on Linux Project will close this gap in the future. Go to the na-mic.org Slicer3-Development website and create for each listed application a new project in Eclipse. For CVS based projects create a new CVS-Checkout-Project and for SVN the SVN counterpart. Then to checkout the source select the branch or the head sources and create a “Standard C++ Makefile Project”. (right now it is recommend to use for tcl and tk the 8.4 branch, because till now VTK, KWWidgets and ITK are not modified to match tcl/tk 8.5) Configure all projects in the sequence as stated above. All projects besides Cmake, VTK, ITK, KWWidgets and Slicer3 itself are autoconf/ configure based application. For tcl/tk it is necessary to change the default source path to unix.
* Right-Click on the project folder
* click on properties (or just press Alt+Enter)
[[Image:Eclipse-Step5.png]]
* then at C/C++ Make Project
[[Image:Eclipse-Step6.png]]
* click on “Workspace...”
* select the unix folder from tcl or tk
[[Image:Eclipse-Step7.png]]
==Compile the projects:==
After successfully configuring all projects eclipse should start automatically building the application. If this is not the case, right click on project and select “Build Project” and see how the project is compiling.
==Download==
[[Media:Howto - Eclipse And Slicer3.pdf| How to Setup Eclipse – Slicer3 Development Environment]]

Slicer3::Eclipse

2010-10-15T14:27:50Z

Clisle: /* Understanding Slicer's startup process */

=Howto Setup Eclipse – Slicer3 Development Environment:=

First download your Eclipse version (e.g. from http://eclipse.org/downloads/ )

This description is based on Eclipse Helios:
eclipse-cpp-helios-linux-gtk.tar.gz

After checking out the sources and building 3D Slicer

CASE: the classic way (Slicer 3.6)
svn co http://svn.slicer.org/Slicer3/branches/Slicer-3-6 Slicer3

./Slicer3/Scripts/getbuildtest.tcl

you will find 3 folders in your directory
Slicer3 (3D Slicer source)
Slicer3-lib (Dependencies source+binary)
Slicer3-build (3D Slicer binary)

Go to the 3D Slicer binary directory and generate your eclipse project files

cd Slicer3-build
cmake -G"Eclipse CDT4 - Unix Makefiles" -D CMAKE_BUILD_TYPE=Debug ../Slicer3

CASE: using Superbuild (Slicer 4.0)
svn co http://svn.slicer.org/Slicer4/trunk Slicer4

mkdir Slicer4-SuperBuild
cd Slicer4-SuperBuild
cmake -DSlicer_USE_KWWIDGETS:BOOL=OFF -DSlicer_USE_PYTHON:BOOL=OFF -DSlicer_USE_QT:BOOL=ON -DSlicer_USE_PYTHONQT:BOOL=OFF ../Slicer4/SuperBuild
make
cd ..

You will find 2+1 folders in your directory
Slicer4 (3D Slicer source)
Slicer4-SuperBuild (Dependencies source+binary)
Slicer4-SuperBuild/Slicer-build (3D Slicer binary)

Go to the 3D Slicer binary directory and generate your eclipse project files

cd Slicer4-SuperBuild/Slicer-build
cmake -G"Eclipse CDT4 - Unix Makefiles" -D CMAKE_BUILD_TYPE=Debug ../../Slicer4

You will get 2 files
Slicer3-build/.project
Slicer3-build/.cproject

Import the created project file into Eclipse

1. Import project using Menu File->Import
2. Select General->Existing projects into workspace:
3. Browse where your build tree is and select the root build tree directory. Keep "Copy projects into workspace" unchecked.
4. Click "Finish"
You get a fully functional eclipse project

* Add a -j<cores> to your make command (Properties->C/C++MakeProject)
* Under "Window->Preferences->General->Editors->Text Editors" please check "Insert spaces for tabs"

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment (Eclipse 3.5)=

<gallery>
Image:Slicer-editing-in-eclipse.png‎|A Slicer editing session in Eclipse 3.5 (Gallileo).
</gallery>

==Installing Eclipse:==
These instructions have been tested with Eclipse editions including "Ganymede" (3.4), "Galileo" (3.5), and "Helios" (3.6), but this should work with any Eclipse Version 3.3 or higher. The easiest way to get started is to select an eclipse distribution which already includes CDT, the C++ development tools, integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse by executing ./eclipse from the base directory of your eclipse installation.

==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/Users/dot/Projects/slicers/trunk-012210" contains the Slicer3* directories. So we could go into /Users/dot/Projects/slicers/trunk-012210/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/Users/dot/Projects/slicers/trunk-012210/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

[[Image:Eclipse-create-project.png|Create Project]]

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C Users/dot/Projects/slicers/trunk-012210/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

[[Image:Eclipse-build-ops.png|Eclipse Build Options Dialog]]

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

== Continuing with Debugging under Eclipse==
At this point, you should be able to build Slicer using Eclipse and run Slicer from inside Eclipse. If you want to debug Slicer interactively under Eclipse, there is a bit more configuration to perform. Please continue with the debugging instructions found below.

=Debugging with Eclipse Instructions=
There are a few key things about interactive debugging under Eclipse that once are done right, then it just works:

# build Slicer totally first the normal way, either with cmake or getbuildtest.tcl.
# Create the project in Eclipse by referring to the makefile and entering an external make command line

Assuming that Slicer is building under Eclipse, we'll take off from this point on:

==Understanding Slicer's startup process==
The executable ./Slicer3-build/Slicer3 is not the real program, instead it is just a "launcher". This executable sets up a bunch of paths and environment variables, then launches the real executable. The "real" Slicer3 program is stored in: ./Slicer3-build/bin/Slicer3-real. So when we are asking Eclipse to run Slicer under the debugger, we really want Eclipse to startup and attach to an instance of "Slicer3-real".

'''Step 1:''' There is a script in ./Slicer3-build/bin/Slicer3SetupPaths.sh or ./Slicer3-build/bin/Slicer3SetupPaths.csh which sets up the same paths as the launcher. If we run this script in a shell window (on Mac or Linux), then run eclipse from the same shell, we will have the environment defined. This is how to try it the first few times, but there is a cleaner way we will try after we know debugging is working. So if you are on either a Mac or Linux, open a shell and source this setup script, please.

Then in the same shell, start eclipse. It will be something like this:

#% source ./Slicer3-build/bin/Slicer3SetupPaths.sh
#% ~/Desktop/eclipse/eclipse &

'''Step 2:''' Then in the Eclipse window, open the Project/Properties by right-clicking on the Project Explorer entry for your Slicer build. Then select the "Run/Debug Settings" entry. We want to set the executable to point to "Slicer3-real" instead of "Slicer3". This plus running the script in the shell Eclipse was started from *may* be enough to get the debugger started on Slicer.

If you are using a Mac, shared library loading can be slow and gdb can timeout during Slicer's loading process. I have not had this problem on Linux and can't comment on Windows since I have not tried it in under Windows. It was helpful on Mac under Leopard and Snow Leopard to increase the default timeout allowed by Eclipse if your Mac needs a bit more time to get everything initialized when first beginning a debugging session.

== Note to Snow Leopard users ==
In the Summer of 2010, we found moving to Snow Leopard caused debugging to stop working. The newest (nightly build) of Eclipse was needed to get breakpoints to actually force the program to stop again. Debugging worked without tweaking Eclipse for systems running Tiger and Leopard. However, the 64-bit only mode of Snow Leopard meant a 64-bit Eclipse is needed for debugging. It is expected that these issues will be resolved in the release version of Eclipse 3.6 (Helios). Do remember that debugging only works using a 64-bit version of Eclipse on Snow Leopard (because the build is now a 64-bit build.)

=Old description from 2008=
==PreRequirements for compiling Slicer3:==
# [http://www.cmake.org/ CMake (2.4.1 or later)]
# [http://www.tcl.tk/ Tcl/Tk (8.4 or later)]
# [http://sourceforge.net/projects/incrtcl/ incrTcl (3.2.1)]
# [http://www.vtk.org/ VTK 5.0]
# [http://www.itk.org/ ITK 2.8]
# [http://www.kwwidgets.org/ KWWidgets CVS head]
==Installing Eclipse:==
I installed Eclipse 3.3 M4, but this should also be applicable with Eclipse Versions under this. Download Eclipse from www.eclipse.org and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
To get Eclipse handling these big source packages in a good manner it is good to tweak a little the properties of the eclipse startup. First it is very advisable to use Eclipse with JRE 1.5. Download it from [http://java.sun.com/javase/downloads/index.jsp] and put it in your project folder (or elsewhere). In addition I increased the size of the memory Java can use with the lower bound switch -Xms and the upper bound -Xmx.

So my Eclispe command looks like this: ./eclipse -Xms64m – Xmx512m -vm /<path to your jre base-directory>/bin/java

Because sun only offers a java JRE for AMDX64 and not for Xeon CPU's it is also possible to use the JRE from BEA [http://commerce.bea.com/products/weblogicjrockit/accept_terms50.jsp?DL=www_JRockit_5_d2d&WT.ac=DL_www_JRockit_5_d2d jorckit].
This should be faster but also a little less stable (I didn't feel that something was unstable!)

==Modules for Eclipse you need:==
Before integrate the source-code into Eclipse we need two separate modules.
# CDT – C++ Environment: [http://www.eclipse.org/cdt/downloads.php http://www.eclipse.org/cdt/downloads.php]
# SubClipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

I use right now [http://download.eclipse.org/tools/cdt/builds/4.0.0/index.html CDT 4.0 - nightly build] which is much more feature rich then 3.1.
On the other Hand this is still under development and though not stable in any situation.

* To install these Modules, start Eclipse and go to Help->Software Updates->Find And Install
[[Image:Eclipse-Step1.png]]
* Click on “Search for new features to install” and then on “Next”:
[[Image:Eclipse-Step2.png]]
* Now click the “New Remote Site...” Button and insert the appropriate informations in the input fields.
* For CDT this should look like this:
[[Image:Eclipse-Step3.png]]
* For SubClipse:
[[Image:Eclipse-Step4.png]]
After adding these to module Site just click on the “Next” Button and Install both items.

You will be prompt to restart Eclipse. After the restart you're ready to get the sources into Eclipse.
==Creating Project and getting the Source-Code for it:==
Now that you have setup eclipse we can focus an getting the code and compile it. One of the disadvantages of eclipse is the inability to use Cmake and CmakeLists.txt files directly. So some manual configuration is still necessary. But hopefully the Eclipse on Linux Project will close this gap in the future. Go to the na-mic.org Slicer3-Development website and create for each listed application a new project in Eclipse. For CVS based projects create a new CVS-Checkout-Project and for SVN the SVN counterpart. Then to checkout the source select the branch or the head sources and create a “Standard C++ Makefile Project”. (right now it is recommend to use for tcl and tk the 8.4 branch, because till now VTK, KWWidgets and ITK are not modified to match tcl/tk 8.5) Configure all projects in the sequence as stated above. All projects besides Cmake, VTK, ITK, KWWidgets and Slicer3 itself are autoconf/ configure based application. For tcl/tk it is necessary to change the default source path to unix.
* Right-Click on the project folder
* click on properties (or just press Alt+Enter)
[[Image:Eclipse-Step5.png]]
* then at C/C++ Make Project
[[Image:Eclipse-Step6.png]]
* click on “Workspace...”
* select the unix folder from tcl or tk
[[Image:Eclipse-Step7.png]]
==Compile the projects:==
After successfully configuring all projects eclipse should start automatically building the application. If this is not the case, right click on project and select “Build Project” and see how the project is compiling.
==Download==
[[Media:Howto - Eclipse And Slicer3.pdf| How to Setup Eclipse – Slicer3 Development Environment]]

Slicer3::New Eclipse Instructions

2010-08-24T12:30:34Z

Clisle: /* Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

<gallery>
Image:Slicer-editing-in-eclipse.png‎|A Slicer editing session in Eclipse 3.5 (Gallileo).
</gallery>

==Installing Eclipse:==
These instructions have been tested with Eclipse editions including "Ganymede" (3.4), "Galileo" (3.5), and "Helios" (3.6), but this should work with any Eclipse Version 3.3 or higher. The easiest way to get started is to select an eclipse distribution which already includes CDT, the C++ development tools, integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse by executing ./eclipse from the base directory of your eclipse installation.

==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/Users/dot/Projects/slicers/trunk-012210" contains the Slicer3* directories. So we could go into /Users/dot/Projects/slicers/trunk-012210/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/Users/dot/Projects/slicers/trunk-012210/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

[[Image:Eclipse-create-project.png|Create Project]]

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C Users/dot/Projects/slicers/trunk-012210/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

[[Image:Eclipse-build-ops.png|Eclipse Build Options Dialog]]

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

== Continuing with Debugging under Eclipse==
At this point, you should be able to build Slicer using Eclipse and run Slicer from inside Eclipse. If you want to debug Slicer interactively under Eclipse, there is a bit more configuration to perform. Please continue with the debugging instructions found at [http://wiki.slicer.org/slicerWiki/index.php/Slicer3::Debugging_with_Eclipse_Instructions http://wiki.slicer.org/slicerWiki/index.php/Slicer3::Debugging_with_Eclipse_Instructions].

Slicer3::Debugging with Eclipse Instructions

2010-08-24T12:26:03Z

Clisle: Created page with 'There are a few key things about interactive debugging under Eclipse that once are done right, then it just works: # build Slicer totally first the normal way, either with cmak…'

There are a few key things about interactive debugging under Eclipse that once are done right, then it just works:

# build Slicer totally first the normal way, either with cmake or getbuildtest.tcl.
# Create the project in Eclipse by referring to the makefile and entering an external make command line

Instructions for the build steps can be found at [http://www.slicer.org/slicerWiki/index.php/Slicer3::New_Eclipse_Instructions http://www.slicer.org/slicerWiki/index.php/Slicer3::New_Eclipse_Instructions]

Assuming that Slicer is building under Eclipse, we'll take off from this point on:

==Understanding Slicer's startup process==
The executable xxxx/Slicer3-build/Slicer3 is not the real program, instead it is just a "launcher". This executable sets up a bunch of paths and environment variables, then launches the real executable. The "real" Slicer3 program is stored in: xxxx/Slicer3-build/bin/Slicer3-real. So when we are asking Eclipse to run Slicer under the debugger, we really want Eclipse to startup and attach to an instance of "Slicer3-real".

'''Step 1:''' There is a script in xxx/Slicer3-build/bin/Slicer3SetupPaths.sh or Slicer3SetupPaths.csh which sets up the same paths as the launcher. If we run this script in a shell window (on Mac or Linux), then run eclipse from the same shell, we will have the environment defined. This is how to try it the first few times, but there is a cleaner way we will try after we know debugging is working. So if you are on either a Mac or Linux, open a shell and source this setup script, please.

Then in the same shell, start eclipse. It will be something like this:

#% source /usr/local/slicers/trunk/Slicer3-build/bin/Slicer3SetupPaths.sh
#% ~/Desktop/eclipse/eclipse &

'''Step 2:''' Then in the Eclipse window, open the Project/Properties by right-clicking on the Project Explorer entry for your Slicer build. Then select the "Run/Debug Settings" entry. We want to set the executable to point to "Slicer3-real" instead of "Slicer3". This plus running the script in the shell Eclipse was started from *may* be enough to get the debugger started on Slicer.

If you are using a Mac, shared library loading can be slow and gdb can timeout during Slicer's loading process. I have not had this problem on Linux and can't comment on Windows since I have not tried it in under Windows. It was helpful on Mac under Leopard and Snow Leopard to increase the default timeout allowed by Eclipse if your Mac needs a bit more time to get everything initialized when first beginning a debugging session.

== Note to Snow Leopard users ==
In the Summer of 2010, we found moving to Snow Leopard caused debugging to stop working. The newest (nightly build) of Eclipse was needed to get breakpoints to actually force the program to stop again. Debugging worked without tweaking Eclipse for systems running Tiger and Leopard. However, the 64-bit only mode of Snow Leopard meant a 64-bit Eclipse is needed for debugging. It is expected that these issues will be resolved in the release version of Eclipse 3.6 (Helios). Do remember that debugging only works using a 64-bit version of Eclipse on Snow Leopard (because the build is now a 64-bit build.)

Slicer3:Developers

2010-08-24T11:58:02Z

Clisle: /* Developer Documentation */

__NOTOC__
= Slicer 3 Developer Page =
[[Image:3DSlicerLogo-H-Color-212x121.png|right]]
*This page contains links to Slicer3 developer resources and events.
*For information about other versions of Slicer see [[Developers|here]]
*Click here for <big>'''[[Slicer3:Events|Slicer3 Events]]'''</big>

== Slicer 3 Architecture Overview ==
For more details on the slicer architecture see: [[media:Slicer 3-beta-2007-04-16.ppt | Architecture Slides]] (updated April, 2007).

<gallery caption="Highlights of the new architecture" widths="300px" heights="200px" perrow="3">
Image:Slicer3-Architecture.jpg
Image:Slicer3-Architecture-MRML.jpg
Image:ExecutionModelPlugins.png
</gallery>

= Quick Links for Developers =
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers.

== Slicer 3 Quick links to the Source code ==
The Slicer3 svn repository:

svn co http://svn.slicer.org/Slicer3/trunk Slicer3

{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''General Slicer3 Quick Links'''
|style="background:#ddf" width="40%"|'''Debugging Slicer3 Quick Links'''
|-
||[[Slicer3:Build_Instructions|Slicer3 build instructions]]
||[http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 Dashboard (After May 2, 2008)]
|-
||Use [http://viewvc.slicer.org ViewVC to browse the repository]
||[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard (Before May 2, 2008)]
|-
||[http://www.na-mic.org/Wiki/index.php/Engineering:SandBox Instructions for NA-MIC svn]
||[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]
|-
||[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Doxygen documentation for Slicer3].
||
|-
||The [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.
||
|-
||Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].
|
|}

==Developers' Mailing List ==
Discussion of Slicer3 takes place on the slicer-devel at massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: slicer-devel-request at massmail.spl.harvard.edu with the keyword '''''subscribe''''' as the subject. Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].
 
 

== Developer Documentation ==

The following links provide more detail on internal aspects of the code. If you need more information, please follow up with email to the listed developers or the developer mailing list.

{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Introduction to Slicer3'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:Build_Instructions | Getting the software and troubleshooting]]
||
|-
||[[media:Slicer 3-beta-2007-01-10.ppt | Overall Architecture]] and [[Slicer3:Style|Slicer 3 Coding Style]]
||
|-
||[[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]
||
|-
|style="background:#ddf"|'''Three module types (Command line, Loadable, Scriptable)'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Media:Integrating with Slicer3.ppt | Integrating with the 3D Slicer]] || Jim and Steve
|-
||[[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]] and [[media:Slicer3Plugins.ppt|Tutorial]]
||Jim
|-
|style="background:#ddf"|'''MRML''' Medical Reality Modeling Language (MRML) is a language implemented as a type of XML document, with new tags defined to handle medical image data types such as volumes, models or coordinate transforms. [http://www.na-mic.org/Wiki/images/e/e3/Slicer3_MRML.ppt MRML Slides]
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]]
||Alex
|-
||[[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]]
||Alex
|-
||[[Slicer3:Data_Model#Undo/Redo_Mechanism | How undo/redo works, and how to enable it in your code]]
||Alex
|-
|style="background:#ddf"|'''GUI'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:EventBindings | Adding keyboard shortcuts]]
||Wendy
|-
||[[Slicer3:Human_Interface_and_Style_Guide_for_Developers | GUI style guidelines (undergoing change for move to Qt)]]
||Wendy
|-
||[[Slicer3:Usability#User-centered_design_practice_for_3DSlicer | User-centered design practice]]
||Wendy
|-
||[[Slicer3:Slicer3Brand | 3DSlicer's logo and visual communication guidelines]]
||Wendy
|-
||[[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]]
||Jim
|-
||[[Slicer3:GUI_Experiments | Some experiments/advanced techniques for developing slicer3 interfaces]]
||Steve
|-
|style="background:#ddf"|'''Engineering'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||Tips for avoiding memory leaks: Current Practice
||Steve
|-
||Tips for avoiding memory leaks: [[Slicer3:Memory Management | Suggested change to SmartPointers]]
||Jim
|-
||Generating tests
||Bill
|-
||[[Slicer3:Testing | Setting up Testing]]
||
|-
||[[Slicer3:Builds | Build Information]]
||
|-
||[[Slicer3:Launcher| The Launcher]]
||
|-
|style="background:#ddf"|'''Documenting your module''' Infrastructure has been added to link to wiki pages from the "Help & Acknowledgment" panel in your module's GUI. We ask developers to fill out a brief document describing your module and its use. [[Documentation-3.5#Requirements_for_Modules|See here for more information.]]
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:DocumentationWink|Documenting a module with wink]]
||
|-
|style="background:#ddf"|'''Integrate Slicer3 into a development environment'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3::Eclipse | Original Eclipse]]
||Michael Keilhack
|-
||[[Slicer3::New Eclipse Instructions | Revised Eclipse Instructions]]
||Curtis Lisle
|-
||[[Slicer3::Debugging with Eclipse Instructions | Debugging Slicer with Eclipse Instructions]]
||Curtis Lisle
|-
||[[Slicer3::MSVS200X | Microsoft Visual Studio 200x]]
||
|}
 

== Quick Links to Slicer3 Projects ==

Pending feature requests are [http://www.na-mic.org/Bug/search.php?project_id=1&severity_id=10&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 stored in the slicer bug tracker with severity setting of 'feature']. Please also refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.

Many Slicer related projects are worked on during the '''[http://wiki.na-mic.org/Wiki/index.php/Engineering:Programming_Events NA-MIC Project Events]''', please check there for recent updates.

 
{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Slicer3 Projects'''
|bgcolor="#ddf" valign="top"|'''Key People''' Bold names are responsible for an aspect of the project.
|-
||[[Slicer3:LUTs_and_Ontologies|Lookup tables and Ontologies]]
||'''Michael Halle'''
|-
||[[Slicer3:Data_Model|Data Model / libMRML]]
||'''Alex Yarmarkovich''', Steve Pieper
|-
||[[Slicer3:Execution_Model_Documentation|Execution Model / Command Line Modules]]
||'''Jim Miller''', Bill Lorensen
|-
||[[Slicer3:UIDesign|User Interface Design]]
||'''Wendy Plesniak''', Qt: Julien Finet, Jean-Christophe Fillion-Robin. KWWidgets: Sebastien Barre, Yumin Yuan
|-
||[[Slicer3:DTMRI|DTMRI]]
||'''Alex Yarmarkovich''' with help from Diffusion Images: '''Raul San Jose Estepar''', Tractography: '''Lauren O'Donnell''' [http://lmi.bwh.harvard.edu LMI]
|-
||[[Slicer3:Editor|Editor]]
||'''Steve Pieper'''
|-
||[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit Image Guided Therapy]
||'''Haiying Liu'''
|-
||[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]
||'''Steve Pieper'''
|-
||[[Slicer3:Batchmake_Integration|Batchmake/GRID Integration]]
||'''Julien Jomier''', Stephen Aylward
|-
||[[Slicer3:Registration|Registration Modules]]
||'''Domink Meier'''
|-
||[[Slicer3:Python|Python Integration]]
||'''Dan Blezek''', Steve Pieper
|-
||[[Slicer3:GPURayCaster | Volume Rendering using the VTK GPU acclerated Ray Caster]]
||'''Lisa Avila / Sebastien Barre'''
|-
||[[Slicer3:Loadable Modules |Loadable Modules]]
||'''Alex Yarmarkovich''', Steve Pieper, Terry Lorber
|-
||[[Slicer3:Extensions |Extensions]]
||'''Steve Pieper''', Terry Lorber
|-
|style="background:#ddf" width="60%"|'''Project Snapshots'''
|bgcolor="#ddf" valign="top"|This is list of projects which are not active at this time, or the linked pages show a snapshot of the project at a certain time.
|-
||[[Slicer3:Architecture/Features|Architecture/Features]]
||'''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata
|-
||[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]
||'''Jim Miller''', Bill Lorensen
|-
||[[Slicer3:Interface_Design|Interface Design and Usability ]]
||'''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan
|-
||[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]
||'''Nicole Aucoin'''
|-
||[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]
||'''Haiying Liu'''
|-
||[[EMSegmenter-Overview|EMSegment Interface]]
||'''Kilian Pohl'''
|-
||[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]
||'''Katie Hayes'''
|-
||[[Slicer3:Grid_Interface|Grid Interface]]
||'''Jeff Grethe''', Marco Ruiz
|-
||[[Slicer3:Volume Rendering |Volume Rendering]]
||'''Yanling Liu'''
|-
||[[Slicer3:XNAT |XNAT Interface]]
||'''Steve''', Wendy, Dan Marcus, Tim Olsen
|-
||[[Slicer3:Web Presence |Web Presence]]
||'''Nicole Aucoin''', Zack Galbreath
|-
||[[Slicer3:TimeSeries and Multi-Volume Data | TimeSeries and Multi-Volume Data]]
||Junichi Tokuda, Steve Pieper, Daniel Blezek, Dominik Meier, Wendy Plesniak
|-
||[[Slicer3:Remote Data Handling | Remote Data Handling]]
||'''Steve Pieper, Nicole Aucoin, Wendy Plesniak'''
|-
||[[Slicer3:Module:QueryAtlas |Query Atlas]]
||'''Wendy Plesniak'''
|-
||[[Slicer3:RadiologicalReview | Radiological review]]
||'''Jim Miller'''
|-
||[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]
||'''Nicole Aucoin''', Katie Hayes, Wendy Plesniak, Mathieu Malaterre
|-
||[http://wiki.slicer.org/slicerWiki/index.php/Modules:Volumes:Diffusion_Editor-Documentation-3.6 Diffusion Editor]
||'''Kerstin'''
|-
||[[Slicer3:MistSlicer | MistSlicer]]
||'''Yuichiro Hayashi''', Kensaku Mori, Nobuhiko Hata
|-
||[[Slicer3:LDDMM |LDDMM Interface]]
||'''Steve''', Anthony Kolasny
|-
||[[Slicer3:Volume Rendering With Cuda|Volume Rendering With CUDA (NOT Active)]]
||'''Ben'''
|-
||[[Slicer3:Pipeline_Integration|Loni Pipeline Integration]]
||'''Jags'''
|-
||[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]
||'''Katie Hayes'''
|-
||[[Slicer3:ThreadingToolKit|Threading ToolKit]]
||'''Dan Blezek, James Miller, Stephen Aylward'''
|-
||[[Slicer3:BrainlabModule|Brainlab Integration]]
||'''Haiying Liu, Noby Hata, Ron Kikinis'''
|}

== Design Information ==
*May 23, 2006: [http://www.na-mic.org/Wiki/index.php/Algorithms:Core1Visit_May06 Algorithm Core workshop.]
*April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.
*Discussion page about using [[Qt in Slicer3|Slicer3:Qt]].
*Implementation priorities from the slicer3 port are shown in this '''[[Slicer3:Status_Summary|Status Summary]]'''.

== Resources ==

Several books are available on the core topics related to slicer programming:

* [http://kitware.com/products/books.html Kitware's books on VTK, ITK, CMake]
* [http://www.akpeters.com/product.asp?ProdCode=2175 the ITK theory book]
* [http://bioimagesuite.org/vtkbook5/index.html Xenios's book on Medical Imaging and VTK - many useful examples in tcl]

Slicer3::New Eclipse Instructions

2010-08-24T11:43:51Z

Clisle: /* Installing Eclipse: */

Slicer3:3.6 Final Issues

2010-07-17T17:32:58Z

Clisle: /* meshing module update from trunk performed - CRL */

==Issues to include in 3.6.1 patch release==

* Fixes for EMSegment command line working with BRAINS (Kilian)
* VTK GPU Ray Cast flashing (Julien)
* Picking NCI GPU Raycasting on machine that doesn't support it causes lockup (Yanling)
* make sure all BRAINS and Registration fixes are in the 3.6 branch (Hans and Jim with help from Dominik)
* Import scene does not update 3D viewer (Nicole, Wendy) http://na-mic.org/Mantis/view.php?id=840
* tractography seeding issue (Alexy) http://www.na-mic.org/Bug/view.php?id=885
* brackets in filenames (Steve - fixed in trunk, migrate to branch if tests well) http://www.na-mic.org/Bug/view.php?id=851
* changes to avoid error messages when using single-slice volumes (Steve) - in trunk, need to move to branch

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

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

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

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

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

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

Modules:IA FEMesh-Documentation-3.6

2010-06-15T15:29:53Z

Clisle: /* Tutorials */

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

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

__NOTOC__
===IA_FEMesh===
IA-FEMesh

{|
|[[Image:IAFEmeshSlicer3Wizard.png|thumb|280px|User Interface]]
|[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]
|[[Image:IAFEMESHWithSpine.png|thumb|280px|User Interface with spine surface loaded]]
|}

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

Type: Interactive

Category: Wizard

===Authors, Collaborators & Contact===
* Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]
* Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]
* Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]
* Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]
* Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]
* Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]
* Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)

{|
|[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]
|[[Image:LogoIsomics.gif|thumb|100px|Isomics]]
|[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]
|}

===Module Description===
This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.

== Usage ==

===Use Cases, Examples===

The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:

* '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed.
* '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.
* '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation.
* '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired.
* '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file.
* '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.

===Tutorials===

Links to tutorials explaining how to use this module:

'''2009'''

* [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial 2009 Meshing Tutorial]
** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip 2009 Tutorial Data Set]
* [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]

'''2010'''

*[http://wiki.na-mic.org/Wiki/index.php/Slicer3:IAFEMesh_TutorialContestSummer2010 2010 Tutorial page containing slides, datasets, and screencasts]

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

The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.

{|
|
* '''Image:'''
** '''Load'''
** '''Delete'''
* '''Surface:'''
** '''Load'''
** '''Delete'''
** '''Save'''
* '''Block(s):'''
** '''Create'''
** '''Load'''
** '''Build/Edit'''
** '''Delete'''
** '''Save'''
* '''Mesh:'''
** '''Assign/Edit Mesh Seeds'''
** '''Create'''
** '''Load'''
** '''Renumber Nodes/Elements'''
** '''Export ABAQUS File'''
** '''Delete'''
** '''Save'''
* '''Quality:'''
** '''Evaluate/Display Mesh Quality'''
** '''Mesh Improvement'''
** '''Export Abaqus File'''
** '''Save'''
* '''Materials:'''
** '''User-Defined'''
** '''Image Based'''
** '''Display Material Properties'''
** '''Export ABAQUS File'''
** '''Save'''
* '''Load/BC:'''
** '''Step - Load/BC Assignments'''
** '''Export ABAQUS File'''
** '''Save'''
|[[Image:MeshingTabs.png|thumb|200px|IA-FEMesh Tabbed Wizard Interface]]
| [[Image:IAFEMeshBlockEdit.png|thumb|200px|Block Editing Interface. From left to right: Edit, Split, Add, Delete, Combine, Mirror, Merge]]
| [[Image:IAFEMeshQualityTab.png|thumb|200px|Mesh Quality Interface. Options include: Volume, Jacobian, Edge Collapse, Skew, Angle Out of Bounds]]
|}

== Development ==

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

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

===Dependencies===

* [http://www.itk.org ITK]
* [http://www.vtk.org VTK]
* [http://www.kwwidgets.org KWWidgets]

===Tests===

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

* MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]
* MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]
* MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]
* MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]
* MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]
* MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]
* MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]
* MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]
* MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]
* MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]
* MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]
* MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]
* MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]
* MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]
* MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]
* MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]
* MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]

===Known bugs===

MRML scene snapshots and restores are not yet supported. Please save your work using the file save dialogs in the user interface.

===Usability issues===

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

===Source code & documentation===

[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:
*Adapter - Converts between ITK and VTK data structures
*BuildingBlock - Classes to implement the KWWidgets user interface
*Common - Custom data structures used for the meshing algorithms
*Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.
*IA_FEMesh - Loadable module for meshing
*IO - Loading and saving of data
*Mesh - Meshing routines implemented using ITK
*Testing - Testing infrastructure
*Widgets - Custom 3D VTK widgets to support user interaction during mesh generation

Doxygen documentation:
*'''Common'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]

*'''Filter'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]

*'''IO'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]

'''Adapter'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]

*'''Widgets'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]

== More Information ==

===Acknowledgment===
This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.

===References===
#Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.
#Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.
#Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.
#Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.
#Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.
#Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.
#DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.
#Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.
#Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.
#Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.
#Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.
#Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.
#Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.

File:IAFEMeshData-TutorialContestSummer2010.zip

2010-06-15T13:05:18Z

Clisle: Tutorial Data to match the content of the IA-FEMesh tutorial submitted for judging for Summer 2010

Tutorial Data to match the content of the IA-FEMesh tutorial submitted for judging for Summer 2010

Modules:StereoViewing-3.6

2010-06-03T19:50:38Z

Clisle: /* Stereo Modes Explained */

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

[[Image:StereoViewing3.6.png|left|The Stereo Viewing Icon]]

=Purpose=

Slicer has the capability to display data in the 3D Viewer stereoscopically in a number of fashions including Red/Blue, Anaglyphic and Interlaced. When you start slicer from the command line, make sure to use the --stereo flag.

=Stereo Modes Explained=

The first two algorithms require only 3D glasses, not any special computer hardware configurations. The last two algorithms require special stereo-ready display systems:

'''Red/Blue''' - For use with red/blue glasses commonly available in magazines or on the internet (see http://www.3dglassesdirect.com) The scene is drawn twice (once in each color from the location of each eye). Using the glasses separates the views and recreates perspective. There is some "bleedthrough" of the images to the opposite eye, but users can generally see depth using this algorithm. The drawback to this algorithm is the natural color of objects is lost due to the red & blue only rendering.

'''Analglyph''' - This algorithm uses the same glasses as the red/blue algorithm but preserves much of the natural color of rendered objects. In general, this preserves the colors in the rendered scene, but adds depth. Some "bleedthrough" still occurs between the eyes, but there are less visual artifacts compared with the red/blue algorithm.

'''Interlaced''' - In this algorithm the pixel lines from each eye are intermixed as the picture is rendered from top to bottom. With an ordinary monitor the lines will seem "jaggy" because we are observing the left and right eye's version of the scene superimposed. However, a stereo image results when interlaced signals are fed to a specially-configured stereo monitor or stereo display panel. The Hyundai S465D is one example of a panel with a vertical interlaced rendering mode.

'''CrystalEyes''' - This stereo mode is named after the famous, legacy glasses now sold by RealD (please see the products at the following website: http://www.reald.com/Content/Crystal-Eyes-5.aspx ). This mode is also sometimes called "active stereo" or "frame sequential stereo". In this mode, successive video frames alternate between the left and right eyes as time progresses. A pair of special goggles or a special display route the signals to one eye or the other in quick succession. As long as the framerate is fast enough so the user doesn't see excessive flicker, this is a convincing rendering approach. However, this algorithm makes the most demands on the computing and display systems of all stereo options. Only some GPUs can produce active stereo, as support for OpenGL quad-buffered stereo mode is required. CrystalEyes rendering with 3D Slicer has been tested successfully on NVIDIA FX 1500, FX 4600, and FX 5600 GPUs, though these are not the only GPUs which are capable of frame sequential stereo.The display device (panel, projector, CRT, etc.) attached to the workstation must also be able to handle frame sequential stereo modes as well. Not all display devices support this rendering mode.

Invoking Slicer3 from the command line and using the --stereo option is only required for CrystalEyes mode. This option instructs 3D Slicer to configure a window using OpenGL Quad-buffered stereo. If you have troubles with this mode, be sure you are using current drivers for the GPU .

Modules:StereoViewing-3.6

2010-06-03T19:32:22Z

Clisle: /* Stereo Modes Explained */

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

[[Image:StereoViewing3.6.png|left|The Stereo Viewing Icon]]

=Purpose=

Slicer has the capability to display data in the 3D Viewer stereoscopically in a number of fashions including Red/Blue, Anaglyphic and Interlaced. When you start slicer from the command line, make sure to use the --stereo flag.

=Stereo Modes Explained=

The first two algorithms require only 3D glasses, not any special computer hardware configurations. The last two algorithms require special stereo-ready display systems:

'''Red/Blue''' - For use with red/blue glasses commonly available in magazines or on the internet (see http://www.3dglassesdirect.com) The scene is drawn twice (once in each color from the location of each eye). Using the glasses separates the views and recreates perspective. There is some "bleedthrough" of the images to the opposite eye, but users can generally see depth using this algorithm. The drawback to this algorithm is the natural color of objects is lost due to the red & blue only rendering.

'''Analglyph''' - This algorithm uses the same glasses as the red/blue algorithm but preserves much of the natural color of rendered objects. In general, this preserves the colors in the rendered scene, but adds depth. Some "bleedthrough" still occurs between the eyes, but there are less visual artifacts compared with the red/blue algorithm.

'''Interlaced''' - In this algorithm the pixel lines from each eye are intermixed as the picture is rendered from top to bottom. With an ordinary monitor the lines will seem "jaggy" because we are observing the left and right eye's version of the scene superimposed. However, a stereo image results when interlaced signals are fed to a specially-configured stereo monitor or stereo display panel. The Hyundai S465D is one example of a panel with a vertical interlaced rendering mode.

'''CrystalEyes''' - This stereo mode is named after the famous, legacy glasses now sold by RealD (please see the products at the following website: http://www.reald.com/Content/Crystal-Eyes-5.aspx ). This mode is also sometimes called "active stereo" or "frame sequential stereo". In this mode, successive video frames alternate between the left and right eyes as time progresses. A pair of special goggles or a special display route the signals to one eye or the other in quick succession. As long as the framerate is fast enough so the user doesn't see excessive flicker, this is a convincing rendering approach. However, this algorithm makes the most demands on the computing and display systems of all stereo options. Only some GPUs can produce active stereo, as support for OpenGL quad-buffered stereo mode is required. CrystalEyes rendering with 3D Slicer has been tested successfully on NVIDIA FX 1500, FX 4600, and FX 5600 GPUs, though these are not the only GPUs which also capable of frame sequential stereo.The display device (panel, projector, CRT, etc.) attached to the workstation must also be able to handle frame sequential stereo modes as well. Not all display devices support this rendering mode.

Invoking Slicer3 from the command line and using the --stereo option is only required for CrystalEyes mode. This option instructs 3D Slicer to configure a window using OpenGL Quad-buffered stereo. If you have troubles with this mode, be sure you are using current drivers for the GPU .

Modules:StereoViewing-3.6

2010-06-03T17:02:54Z

Clisle: /* Stereo Modes Explained */

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

[[Image:StereoViewing3.6.png|left|The Stereo Viewing Icon]]

=Purpose=

Slicer has the capability to display data in the 3D Viewer stereoscopically in a number of fashions including Red/Blue, Anaglyphic and Interlaced. When you start slicer from the command line, make sure to use the --stereo flag.

=Stereo Modes Explained=

The first two algorithms require only 3D glasses, not any special computer hardware configurations. The last two algorithms require special stereo-ready display systems:

'''Red/Blue''' - For use with red/blue glasses commonly available in magazines or on the internet (see http://www.3dglassesdirect.com) The scene is drawn twice (once in each color from the location of each eye). Using the glasses separates the views and recreates perspective. There is some "bleedthrough" of the images to the opposite eye, but users can generally see depth using this algortihm. The drawback to this algorithm is the natural color of objects is lost due to the red & blue rendering.

'''Analglyph''' - This algorithm uses the same glasses as the red/blue algorithm but preserves the natural color of objects.

'''Interlaced''' - In this algorithm the pixel lines from each eye are intermixed as the picture is rendered from top to bottom. With an ordinary monitor the lines will seem "jaggy" because we are observing the left and right eye's version of the scene superimposed. However, a stereo image results when interlaced signals are fed to a specially-configured stereo monitor or stereo display panel. The Hyundai S465D is one example of a panel with a vertical interlaced rendering mode.

'''CrystalEyes''' - This stereo mode is named after the famous, legacy glasses now sold by RealD (please see the products at the following website: http://www.reald.com/Content/Crystal-Eyes-5.aspx ). This mode is also sometimes called "active stereo" or "frame sequential stereo". In this mode, successive video frames alternate between the left and right eyes as time progresses. A pair of special goggles or a special display route the signals to one eye or the other in quick succession. As long as the framerate is fast enough so the user doesn't see excessive flicker, this is a convincing rendering approach. However, this algorithm makes the most demands on the computing and display systems of all stereo options. Only some GPUs can produce active stereo, as support for OpenGL quad-buffered stereo mode is required. CrystalEyes rendering with 3D Slicer has been tested successfully on NVIDIA FX 1500, FX 4600, and FX 5600 GPUs, though these are not the only GPUs which also capable of frame sequential stereo.The display device (panel, projector, CRT, etc.) attached to the workstation must also be able to handle frame sequential stereo modes as well. Not all display devices support this rendering mode.

Invoking Slicer3 from the command line and using the --stereo option is only required for CrystalEyes mode. This option instructs 3D Slicer to configure a window using OpenGL Quad-buffered stereo. If you have troubles with this mode, be sure you are using current drivers for the GPU .

Modules:StereoViewing-3.6

2010-06-03T16:58:25Z

Clisle: /* Stereo Modes Explained */

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

[[Image:StereoViewing3.6.png|left|The Stereo Viewing Icon]]

=Purpose=

Slicer has the capability to display data in the 3D Viewer stereoscopically in a number of fashions including Red/Blue, Anaglyphic and Interlaced. When you start slicer from the command line, make sure to use the --stereo flag.

=Stereo Modes Explained=

The first two algorithms require only 3D glasses, not any special computer hardware configurations. The last two algorithms require special stereo-ready display systems:

'''Red/Blue''' - For use with red/blue glasses commonly available in magazines or on the internet (see http://www.3dglassesdirect.com) The scene is drawn twice (once in each color from the location of each eye). Using the glasses separates the views and recreates perspective. There is some "bleedthrough" of the images to the opposite eye, but users can generally see depth using this algortihm. The drawback to this algorithm is the natural color of objects is lost due to the red & blue rendering.

'''Analglyph''' - This algorithm uses the same glasses as the red/blue algorithm but preserves the natural color of objects.

'''Interlaced''' - In this algorithm the pixel lines from each eye are intermixed as the picture is rendered from top to bottom. With an ordinary monitor the lines will seem "jaggy" because we are observing the left and right eye's version of the scene superimposed. However, a stereo image results when interlaced signals are fed to a specially-configured stereo monitor or stereo display panel. The Hyundai S465D is one example of a panel with a vertical interlaced rendering mode.

'''CrystalEyes''' - This stereo mode is named after the famous, legacy glasses now sold by RealD (please see the products at the following website: http://www.reald.com/Content/Crystal-Eyes-5.aspx ). This mode is also sometimes called "active stereo" or "frame sequential stereo". In this mode, successive video frames alternate between the left and right eyes as time progresses. A pair of special goggles or a special display route the signals to one eye or the other in quick succession. As long as the framerate is fast enough so the user doesn't see excessive flicker, this is a convincing rendering approach. However, this algorithm makes the most demands on the computing and display systems of all stereo options. Only some GPUs can produce active stereo, as support for OpenGL quad-buffered stereo mode is required. CrystalEyes rendering with 3D Slicer has been tested successfully on NVIDIA FX 1500, FX 4600, and FX 5600 GPUs, though these are not the only GPUs which also capable of frame sequential stereo.

Invoking Slicer3 from the command line and using the --stereo option is only required for CrystalEyes mode.

Modules:StereoViewing-3.6

2010-06-03T16:57:46Z

Clisle: /* Stereo Modes Explained */

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

[[Image:StereoViewing3.6.png|left|The Stereo Viewing Icon]]

=Purpose=

Slicer has the capability to display data in the 3D Viewer stereoscopically in a number of fashions including Red/Blue, Anaglyphic and Interlaced. When you start slicer from the command line, make sure to use the --stereo flag.

=Stereo Modes Explained=

The first two algorithms require only 3D glasses, not any special computer hardware configurations. The last two algorithms require special stereo-ready display systems:

'''Red/Blue''' - For use with red/blue glasses commonly available in magazines or on the internet (see http://www.3dglassesdirect.com) The scene is drawn twice (once in each color from the location of each eye). Using the glasses separates the views and recreates perspective. There is some "bleedthrough" of the images to the opposite eye, but users can generally see depth using this algortihm. The drawback to this algorithm is the natural color of objects is lost due to the red & blue rendering.

'''Analglyph''' - This algorithm uses the same glasses as the red/blue algorithm but preserves the natural color of objects.

'''Interlaced''' - In this algorithm the pixel lines from each eye are intermixed as the picture is rendered from top to bottom. With an ordinary monitor the lines will seem "jaggy" because we are observing the left and right eye's version of the scene superimposed. However, a stereo image results when interlaced signals are fed to a specially-configured stereo monitor or stereo display panel. The Hyundai S465D is one example of a panel with a vertical interlaced rendering mode.

'''CrystalEyes''' - This stereo mode is named after the famous, legacy glasses now sold by RealD (please see the products at the following website: http://www.reald.com/Content/Crystal-Eyes-5.aspx ). This mode is also sometimes called "active stereo" or "frame sequential stereo". In this mode, successive video frames alternate between the left and right eyes as time progresses. A pair of special goggles or a special display route the signals to one eye or the other in quick succession. As long as the framerate is fast enough so the user doesn't see excessive flicker, this is a convincing rendering approach. However, this algorithm makes the most demands on the computing and display systems of all stereo options. Only some GPUs can produce active stereo, as support for OpenGL quad-buffered stereo mode is required.

CrystalEyes rendering with 3D Slicer has been tested successfully on NVIDIA FX 1500, FX 4600, and FX 5600 GPUs, though these are not the only GPUs which also capable of frame sequential stereo.

Invoking Slicer3 from the command line and using the --stereo option is only required for CrystalEyes mode.

Modules:StereoViewing-3.6

2010-06-03T16:55:31Z

Clisle: /* Stereo Modes Explained */

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

[[Image:StereoViewing3.6.png|left|The Stereo Viewing Icon]]

=Purpose=

Slicer has the capability to display data in the 3D Viewer stereoscopically in a number of fashions including Red/Blue, Anaglyphic and Interlaced. When you start slicer from the command line, make sure to use the --stereo flag.

=Stereo Modes Explained=

The first two algorithms require only 3D glasses, not any special computer hardware configurations. The last two algorithms require special stereo-ready display systems:

'''Red/Blue''' - For use with red/blue glasses commonly available in magazines or on the internet (see http://www.3dglassesdirect.com) The scene is drawn twice (once in each color from the location of each eye). Using the glasses separates the views and recreates perspective. There is some "bleedthrough" of the images to the opposite eye, but users can generally see depth using this algortihm. The drawback to this algorithm is the natural color of objects is lost due to the red & blue rendering.

'''Analglyph''' - This algorithm uses the same glasses as the red/blue algorithm but preserves the natural color of objects.

'''Interlaced''' - In this algorithm the pixel lines from each eye are intermixed as the picture is rendered from top to bottom. With an ordinary monitor the lines will seem "jaggy" because we are observing the left and right eye's version of the scene superimposed. However, a stereo image results when interlaced signals are fed to a specially-configured stereo monitor or stereo display panel. The Hyundai S465D is one example of a panel with a vertical interlaced rendering mode.

'''CrystalEyes''' - This stereo mode is named after the famous, legacy glasses now sold by RealD (please see the products at the following website: http://www.reald.com/Content/Crystal-Eyes-5.aspx ). This mode is also sometimes called "active stereo" or "frame sequential stereo". In this mode, successive video frames alternate between the left and right eyes as time progresses. A pair of special goggles or a special display route the signals to one eye or the other in quick succession. As long as the framerate is fast enough so the user doesn't see excessive flicker, this is a convincing rendering approach. However, this algorithm makes the most demands on the computing and display systems of all stereo options. Only some GPUs can produce active stereo, as support for OpenGL quad-buffered stereo mode is required.

CrystalEyes rendering with 3D Slicer has been tested successfully on NVIDIA FX 1500, FX 4600, and FX 5600 GPUs, though these are not the only GPUs which also capable of frame sequential stereo.

Modules:StereoViewing-3.6

2010-06-03T16:38:12Z

Clisle: adding stereo algorithm descriptions

Modules:IA FEMesh-Documentation-3.6

2010-04-13T18:53:18Z

Clisle: /* Known bugs */

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

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

__NOTOC__
===IA_FEMesh===
IA-FEMesh

{|
|[[Image:IAFEmeshSlicer3Wizard.png|thumb|280px|User Interface]]
|[[Image:IAMeshResult1.png|thumb|280px|Phalanx Bone Mesh]]
|[[Image:IAFEMESHWithSpine.png|thumb|280px|User Interface with spine surface loaded]]
|}

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

Type: Interactive

Category: Wizard

===Authors, Collaborators & Contact===
* Nicole Grosland: The University of Iowa - Departments of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering] and [http://www.uihealthcare.com/depts/med/orthopaedicsurgery/ Orthopaedic Surgery], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]
* Vincent Magnotta: The University of Iowa - Departments of [http://www.healthcare.uiowa.edu/Radiology/ Radiology], [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], and [http://www.uihealthcare.com/depts/med/psychiatry/ Psychiatry], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]
* Kiran Shivanna: The University of Iowa - [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]
* Austin Ramme: The University of Iowa - Department of [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/ Center for Computer Aided Design (CCAD)], [http://www.ccad.uiowa.edu/mimx/ Musculoskeletal Imaging, Modeling, and EXperimentation (MIMX)]
* Steve Pieper: [http://sites.google.com/a/isomics.com/www/ Isomics]
* Curt Lisle: [http://www.curtislisle.com/Kvis/Welcome.html KnowledgeViz]
* Contact: Nicole Grosland (grosland@engineering.uiowa.edu) or Vincent Magnotta (vincent-magnotta@uiowa.edu)

{|
|[[Image:LogoMimx.gif|thumb|100px|Iowa - MIMX]]
|[[Image:LogoIsomics.gif|thumb|100px|Isomics]]
|[[Image:logoKvis.jpg|thumb|100px|KnowledgeViz]]
|}

===Module Description===
This module allows the creation and editing of volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.

== Usage ==

===Use Cases, Examples===

The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:

* '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed.
* '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.
* '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation.
* '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired.
* '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file.
* '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.

===Tutorials===

Links to tutorials explaining how to use this module:

* [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Tutorial]
** [http://www.na-mic.org/Wiki/images/5/5a/MeshTutorialExampleData.zip Tutorial Data Set]
* [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf Users Guide]

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

The IA-FEMesh interface uses a wizard workflow. The wizard is implemented using a tabbed notebook with each tab corresponding to the type of data that the user will work with in that step of the meshing process. While there is a logical order where the user will work from left to right in the tabs, a strict linear ordering is not required and the user can freely go back and forth between the tabs. Described below are the tabs and the main features that each provides.

{|
|
* '''Image:'''
** '''Load'''
** '''Delete'''
* '''Surface:'''
** '''Load'''
** '''Delete'''
** '''Save'''
* '''Block(s):'''
** '''Create'''
** '''Load'''
** '''Build/Edit'''
** '''Delete'''
** '''Save'''
* '''Mesh:'''
** '''Assign/Edit Mesh Seeds'''
** '''Create'''
** '''Load'''
** '''Renumber Nodes/Elements'''
** '''Export ABAQUS File'''
** '''Delete'''
** '''Save'''
* '''Quality:'''
** '''Evaluate/Display Mesh Quality'''
** '''Mesh Improvement'''
** '''Export Abaqus File'''
** '''Save'''
* '''Materials:'''
** '''User-Defined'''
** '''Image Based'''
** '''Display Material Properties'''
** '''Export ABAQUS File'''
** '''Save'''
* '''Load/BC:'''
** '''Step - Load/BC Assignments'''
** '''Export ABAQUS File'''
** '''Save'''
|[[Image:MeshingTabs.png|thumb|200px|IA-FEMesh Tabbed Wizard Interface]]
| [[Image:IAFEMeshBlockEdit.png|thumb|200px|Block Editing Interface. From left to right: Edit, Split, Add, Delete, Combine, Mirror, Merge]]
| [[Image:IAFEMeshQualityTab.png|thumb|200px|Mesh Quality Interface. Options include: Volume, Jacobian, Edge Collapse, Skew, Angle Out of Bounds]]
|}

== Development ==

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

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

===Dependencies===

* [http://www.itk.org ITK]
* [http://www.vtk.org VTK]
* [http://www.kwwidgets.org KWWidgets]

===Tests===

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

* MimxitkImageToVtkUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/itkImageToVtkUnstructuredGridTest.cxx itkImageToVtkUnstructuredGridTest.cxx]
* MimxAddUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainAddUnstructuredHexahedronGridCellTest.cxx MainAddUnstructuredHexahedronGridCellTest.cxx]
* MimxDeleteUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainDeleteUnstructuredHexahedronGridCellTest.cxx MainDeleteUnstructuredHexahedronGridCellTest.cxx]
* MimxSplitUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainSplitUnstructuredHexahedronGridCellTest.cxx MainSplitUnstructuredHexahedronGridCellTest.cxx]
* MimxMirrorUnstructuredHexahedronGridCellTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMirrorUnstructuredHexahedronGridCellTest.cxx MainMirrorUnstructuredHexahedronGridCellTest.cxx]
* MimxBoundingBoxFromUnstructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromUnstructuredGridTest.cxx MainBoundingBoxFromUnstructuredGridTest.cxx]
* MimxEquivalancePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainEquivalancePointsTest.cxx MainEquivalancePointsTest.cxx]
* MimxExtractSurfaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractSurfaceTest.cxx MainExtractSurfaceTest.cxx]
* MimxBoundingBoxFromBoundsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxFromBoundsTest.cxx MainBoundingBoxFromBoundsTest.cxx]
* MimxExtractStructuredGridEdgeTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridEdgeTest.cxx MainExtractStructuredGridEdgeTest.cxx]
* MimxExtractStructuredGridFaceTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainExtractStructuredGridFaceTest.cxx MainExtractStructuredGridFaceTest.cxx]
* MimxGeometryFilterTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainGeometryFilterTest.cxx MainGeometryFilterTest.cxx]
* MimxBoundingBoxToStructuredGridsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainBoundingBoxToStructuredGridsTest.cxx MainBoundingBoxToStructuredGridsTest.cxx]
* MimxMorphStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMorphStructuredGridTest.cxx MainMorphStructuredGridTest.cxx]
* MimxUnstructuredToStructuredGridTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainUnstructuredToStructuredGridTest.cxx MainUnstructuredToStructuredGridTest.cxx]
* MimxMergePointsTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainMergePointsTest.cxx MainMergePointsTest.cxx]
* MimxRecalculateInteriorNodesTest [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/Testing/MainRecalculateInteriorNodesTest.cxx MainRecalculateInteriorNodesTest.cxx]

===Known bugs===

MRML scene snapshots and restores are not yet supported. Please save your work using the file save dialogs in the user interface.

===Usability issues===

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

===Source code & documentation===

[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/Meshing/ IA-FEMesh] Source code. It consists of several subdirectories:
*Adapter - Converts between ITK and VTK data structures
*BuildingBlock - Classes to implement the KWWidgets user interface
*Common - Custom data structures used for the meshing algorithms
*Filter - Filters to convert between custom data structures. Implements the underlying code for mesh generation.
*IA_FEMesh - Loadable module for meshing
*IO - Loading and saving of data
*Mesh - Meshing routines implemented using ITK
*Testing - Testing infrastructure
*Widgets - Custom 3D VTK widgets to support user interaction during mesh generation

Doxygen documentation:
*'''Common'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractIterator.html vtkAbstractIterator]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkAbstractList.html vtkAbstractList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkContainer.html vtkContainer]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFESurfaceList.html vtkFESurfaceList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementBuildingBlockList.html vtkFiniteElementBuildingBlockList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFiniteElementMeshList.html vtkFiniteElementMeshList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedList.html vtkLinkedList]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListIterator.html vtkLinkedListIterator]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapper.html vtkLinkedListWrapper]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLinkedListWrapperTree.html vtkLinkedListWrapperTree]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalAxesActor.html vtkLocalAxesActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkLocalLinkedListWrapper.html vtkLocalLinkedListWrapper]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityClass.html vtkMeshQualityClass]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxActorBase.html vtkMimxActorBase]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyNodeElementNumbers.html vtkMimxApplyNodeElementNumbers]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundaryConditionActor.html vtkMimxBoundaryConditionActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSource.html vtkMimxBoundingBoxSource]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxColorCodeMeshSeedActor.html vtkMimxColorCodeMeshSeedActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCurve.html vtkMimxCurve]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEntryValueChangedCallback.html vtkMimxEntryValueChangedCallback]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxErrorCallback.html vtkMimxErrorCallback]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxImageActor.html vtkMimxImageActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxInteractorStyleUser.html vtkMimxInteractorStyleUser]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergeNodesPointAndCellData.html vtkMimxMergeNodesPointAndCellData]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshActor.html vtkMimxMeshActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarStructuredGridSource.html vtkMimxPlanarStructuredGridSource]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidStructuredGridSource.html vtkMimxSolidStructuredGridSource]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSTLSource.html vtkMimxSTLSource]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSurfacePolyDataActor.html vtkMimxSurfacePolyDataActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTestErrorCallback.html vtkMimxTestErrorCallback]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUGrid.html vtkMimxUGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridActor.html vtkMimxUnstructuredGridActor]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFESurfaceNode.html vtkMRMLFESurfaceNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockDisplayNode.html vtkMRMLFiniteElementBuildingBlockDisplayNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementBuildingBlockNode.html vtkMRMLFiniteElementBuildingBlockNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshDisplayNode.html vtkMRMLFiniteElementMeshDisplayNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLFiniteElementMeshNode.html vtkMRMLFiniteElementMeshNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLNullDisplayNode.html vtkMRMLNullDisplayNode]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPVAxesActor.html vtkPVAxesActor]

*'''Filter'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkFaceHedgeHog.html vtkFaceHedgeHog]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMeshQualityExtended.html vtkMeshQualityExtended]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAddUnstructuredHexahedronGridCell.html vtkMimxAddUnstructuredHexahedronGridCell]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxApplyImageBasedMaterialProperties.html vtkMimxApplyImageBasedMaterialProperties]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAttachBoundingBoxMesh.html vtkMimxAttachBoundingBoxMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromBounds.html vtkMimxBoundingBoxFromBounds]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxFromUnstructuredGrid.html vtkMimxBoundingBoxFromUnstructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxSurfaceMesh.html vtkMimxBoundingBoxSurfaceMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxToStructuredGrids.html vtkMimxBoundingBoxToStructuredGrids]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxClipImageFromBox.html vtkMimxClipImageFromBox]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxComputeNormalsFromPolydataFilter.html vtkMimxComputeNormalsFromPolydataFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxConstrainedSmoothPolyDataFilter.html vtkMimxConstrainedSmoothPolyDataFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCylindricalMesh.html vtkMimxCylindricalMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxDeleteUnstructuredHexahedronGridCell.html vtkMimxDeleteUnstructuredHexahedronGridCell]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToPlanarStructuredGrid.html vtkMimxEdgeToPlanarStructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEdgeToStructuredGrid.html vtkMimxEdgeToStructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEditUnstructuredHexahedronGrid.html vtkMimxEditUnstructuredHexahedronGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxEquivalancePoints.html vtkMimxEquivalancePoints]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractElementNumbersOfaFaceFilter.html vtkMimxExtractElementNumbersOfaFaceFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridEdge.html vtkMimxExtractStructuredGridEdge]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractStructuredGridFace.html vtkMimxExtractStructuredGridFace]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractSurface.html vtkMimxExtractSurface]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtrudePolyData.html vtkMimxExtrudePolyData]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFilterWin32Header.html vtkMimxFilterWin32Header]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxFourPointsToStructuredPlanarMesh.html vtkMimxFourPointsToStructuredPlanarMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGenerateHexahedronMesh.html vtkMimxGenerateHexahedronMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxGeometryFilter.html vtkMimxGeometryFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMapOriginalCellAndPointIds.html vtkMimxMapOriginalCellAndPointIds]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMergePoints.html vtkMimxMergePoints]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMeshSeed.html vtkMimxMeshSeed]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMirrorUnstructuredHexahedronGridCell.html vtkMimxMirrorUnstructuredHexahedronGridCell]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxMorphStructuredGrid.html vtkMimxMorphStructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPatchSurfaceMesh.html vtkMimxPatchSurfaceMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarEllipticalInterpolation.html vtkMimxPlanarEllipticalInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTransfiniteInterpolation.html vtkMimxPlanarTransfiniteInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlanarTrilinearInterpolation.html vtkMimxPlanarTrilinearInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataSingleSourceShortestPath.html vtkMimxPolyDataSingleSourceShortestPath]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRebinMaterialProperty.html vtkMimxRebinMaterialProperty]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodes.html vtkMimxRecalculateInteriorNodes]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxRecalculateInteriorNodesTPS.html vtkMimxRecalculateInteriorNodesTPS]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectSurface.html vtkMimxSelectSurface]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridEdge.html vtkMimxSetStructuredGridEdge]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSetStructuredGridFace.html vtkMimxSetStructuredGridFace]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSmoothUnstructuredGridFilter.html vtkMimxSmoothUnstructuredGridFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidEllipticalInterpolation.html vtkMimxSolidEllipticalInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTransfiniteInterpolation.html vtkMimxSolidTransfiniteInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSolidTrilinearInterpolation.html vtkMimxSolidTrilinearInterpolation]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSplitUnstructuredHexahedronGridCell.html vtkMimxSplitUnstructuredHexahedronGridCell]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxStructuredPlanarToStructuredSolidGrid.html vtkMimxStructuredPlanarToStructuredSolidGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideBoundingBox.html vtkMimxSubdivideBoundingBox]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSubdivideCurve.html vtkMimxSubdivideCurve]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromBoundingBox.html vtkMimxUnstructuredGridFromBoundingBox]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridFromFourPoints.html vtkMimxUnstructuredGridFromFourPoints]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredToStructuredGrid.html vtkMimxUnstructuredToStructuredGrid]

*'''IO'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1itkMimxAbaqusMeshFileWriter.html itkMimxAbaqusMeshFileWriter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ReadHistogramBinValuesFilter.html itkMimxReadHistogramBinValuesFilter]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxAbaqusFileWriter.html vtkMimxAbaqusFileWriter]

'''Adapter'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitk_1_1ItkMeshToFEMMesh.html ItkMeshToFEMMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkPolyData.html itkMeshTovtkPolyData]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classitkMeshTovtkUnstructuredGrid.html itkMeshTovtkUnstructuredGrid]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkPolyDataToitkMesh.html vtkPolyDataToitkMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkUnstructuredGridToitkMesh.html vtkUnstructuredGridToitkMesh]

*'''Widgets'''
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBoundingBoxWidget.html vtkMimxBoundingBoxWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxBWidgetPlusIPWidget.html vtkMimxBWidgetPlusIPWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateBuildingBlockFromPickWidget.html vtkMimxCreateBuildingBlockFromPickWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxCreateElementSetWidgetFEMesh.html vtkMimxCreateElementSetWidgetFEMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractCellWidget.html vtkMimxExtractCellWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractEdgeWidget.html vtkMimxExtractEdgeWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractFaceWidget.html vtkMimxExtractFaceWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxExtractMultipleFaceWidget.html vtkMimxExtractMultipleFaceWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxModPointWidget.html vtkMimxModPointWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPlaceLocalAxesWidget.html vtkMimxPlaceLocalAxesWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxPolyDataWidget.html vtkMimxPolyDataWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidgetFEMesh.html vtkMimxSelectCellsWidgetFEMesh]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectCellsWidget.html vtkMimxSelectCellsWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxSelectPointsWidget.html vtkMimxSelectPointsWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxTraceContourWidget.html vtkMimxTraceContourWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridExtractWidget.html vtkMimxUnstructuredGridExtractWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxUnstructuredGridWidget.html vtkMimxUnstructuredGridWidget]
**[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMimxViewMergePointsWidget.html vtkMimxViewMergePointsWidget]

== More Information ==

===Acknowledgment===
This work is supported in part by NIH/NIBIB awards R01EB005973 and R21EB001501.

===References===
#Tadepalli SC, Shivanna KH, Magnotta VA, Kallemeyn NA, Grosland NM, [http://www.hindawi.com/journals/asp/2010/190293.html Toward the development of virtual surgical tools to aid orthopaedic FE analyses] EURASIP Journal on Advances in Signal Processing, 2009, vol. 2010.
#Devries NA, Shivanna KH, Tadepalli SC, Magnotta VA, Grosland NM. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723692/pdf/iowa0029-0048.pdf Ia-FEMesh: anatomic fe models--a check of mesh accuracy and validity]. Iowa Orthop J. 29:48-54, 2009.
#Kallemeyn NA, Tadepalli SC, Shivanna KH, Grosland NM. [http://www.cmpbjournal.com/article/S0169-2607%2809%2900095-9/abstract An interactive multiblock approach to meshing the spine]. Comput Methods Programs Biomed. 95(3):227-35, 2009.
#Grosland NM, Shivanna KH, Magnotta VA, Kallemeyn NA, DeVries NA, Tadepalli SC, Lisle C. [http://www.cmpbjournal.com/article/S0169-2607(08)00264-2/abstract IA-FEMesh: an open-source, interactive, multiblock approach to anatomic finite element model development]. Comput Methods Programs Biomed. 94(1):96-107, 2009.
#Ramme AJ, Devries N, Kallemyn NA, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/h972u63630311g78/ Semi-automated Phalanx Bone Segmentation Using the Expectation Maximization Algorithm]. J Digit Imaging. 2008.
#Grosland NM, Bafna R, Magnotta VA. [http://www.informaworld.com/smpp/content~db=all?content=10.1080/10255840802136143 Automated hexahedral meshing of anatomic structures using deformable registration]. Comput Methods Biomech Biomed Engin. 12(1):35-43, 2009.
#DeVries NA, Gassman EE, Kallemeyn NA, Shivanna KH, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/u36v5957k17536wt/ Validation of phalanx bone three-dimensional surface segmentation from computed tomography images using laser scanning]. Skeletal Radiol. 37(1):35-42, 2008.
#Gassman EE, Powell SM, Kallemeyn NA, Devries NA, Shivanna KH, Magnotta VA, Ramme AJ, Adams BD, Grosland NM. [http://www.springerlink.com/content/b15376vwx00v5088/ Automated bony region identification using artificial neural networks: reliability and validation measurements]. Skeletal Radiol. 37(4):313-9, 2008.
#Magnotta V, Li W, Grosland N. [http://hdl.handle.net/10380/1490 Comparison of Displacement-Based and Force-Based Mapped Meshing]. Workshop on Computational Biomechanics for Medicine at MICCAI 2008. Insight Journal, http://hdl.handle.net/10380/1490 , 2008.
#Shivanna K, Kallemeyn N, Tadepalli S, DeVries N, Magnotta V, Grosland N. [http://www.x-cd.com/sbc08/pdfs/192782.pdf Ia-FeMesh: An Interactive All Hexahedral Mesh Generator For Discrete Anatomic Closed Surfaces]. Proceedings of the 2008 Summer Bioengineering Conference, 2008.
#Grosland NM, Lisle C, Shivanna KH, Pieper S, Magnotta VA. [http://www.asbweb.org/conferences/2007/40.pdf A Check Of Mesh Quality], American Society Of Biomechanics, August 22-27, 2007.
#Pébay PP, Thompson D, Shepherd J, Knupp P, Lisle C, Magnotta VA, Grosland NM. [http://www.springerlink.com/content/r40715v33h024nl8/ New Applications of the Verdict Library for Standardized Mesh Verification Pre, Post, and End-to-End Processing], Proceedings of the 16th International Meshing Roundtable, 2007.
#Shivanna KH, Adams BD, Magnotta VA, Grosland NM. [http://cbm2006.mech.uwa.edu.au/CBM_2006.pdf Towards Automating Patient-Specific Finite Element Model Development]. Proceedings Computational Biomechanics For Medicine, 2006.

Slicer3::New Eclipse Instructions

2010-02-18T21:54:23Z

Clisle: /* Creating an Eclipse Project for Slicer3: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

<gallery>
Image:Slicer-editing-in-eclipse.png‎|A Slicer editing session in Eclipse 3.5 (Gallileo).
</gallery>

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/Users/dot/Projects/slicers/trunk-012210" contains the Slicer3* directories. So we could go into /Users/dot/Projects/slicers/trunk-012210/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/Users/dot/Projects/slicers/trunk-012210/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

[[Image:Eclipse-create-project.png|Create Project]]

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C Users/dot/Projects/slicers/trunk-012210/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

[[Image:Eclipse-build-ops.png|Eclipse Build Options Dialog]]

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

Slicer3::New Eclipse Instructions

2010-02-18T21:52:32Z

Clisle: /* Creating an Eclipse Project for Slicer3: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

<gallery>
Image:Slicer-editing-in-eclipse.png‎|A Slicer editing session in Eclipse 3.5 (Gallileo).
</gallery>

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/Users/dot/Projects/slicers/trunk-012210" contains the Slicer3* directories. So we could go into /Users/dot/Projects/slicers/trunk-012210/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/Users/dot/Projects/slicers/trunk-012210/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

[[Image:Eclipse-create-project.png|Create Project]]

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C Users/dot/Projects/slicers/trunk-012210/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

[[Image:Eclipse-build-ops.png|Eclipse Build Options Dialog]]

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /Users/dot/Projects/slicers/trunk-012210/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

File:Eclipse-build-ops.png

2010-02-18T21:48:24Z

Clisle:

Slicer3::New Eclipse Instructions

2010-02-18T21:45:13Z

Clisle: /* Creating an Eclipse Project for Slicer3: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

<gallery>
Image:Slicer-editing-in-eclipse.png‎|A Slicer editing session in Eclipse 3.5 (Gallileo).
</gallery>

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

[[Image:Eclipse-create-project.png|Create Project]]

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C /usr/local/slicers/trunk/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

[[Image:Eclipse-build-options.png|Eclipse Build Options Dialog]]

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/usr/local/slicers/trunk/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /usr/local/slicers/trunk/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

File:Eclipse-build-options.png

2010-02-18T21:44:06Z

Clisle:

Slicer3::New Eclipse Instructions

2010-02-18T21:40:41Z

Clisle: /* Creating an Eclipse Project for Slicer3: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

<gallery>
Image:Slicer-editing-in-eclipse.png‎|A Slicer editing session in Eclipse 3.5 (Gallileo).
</gallery>

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

[[Image:Eclipse-create-project.png|Create Project]]

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C /usr/local/slicers/trunk/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/usr/local/slicers/trunk/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /usr/local/slicers/trunk/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

Slicer3::New Eclipse Instructions

2010-02-18T21:39:37Z

Clisle: /* Creating an Eclipse Project for Slicer3: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

<gallery>
Image:Slicer-editing-in-eclipse.png‎|A Slicer editing session in Eclipse 3.5 (Gallileo).
</gallery>

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

[[Image::Eclipse-create-project.png|Create Project]]

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C /usr/local/slicers/trunk/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/usr/local/slicers/trunk/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /usr/local/slicers/trunk/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

File:Eclipse-create-project.png

2010-02-18T21:38:30Z

Clisle:

Slicer3::New Eclipse Instructions

2010-02-18T21:31:23Z

Clisle:

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

<gallery>
Image:Slicer-editing-in-eclipse.png‎|A Slicer editing session in Eclipse 3.5 (Gallileo).
</gallery>

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C /usr/local/slicers/trunk/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/usr/local/slicers/trunk/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /usr/local/slicers/trunk/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

File:Slicer-editing-in-eclipse.png

2010-02-18T21:27:56Z

Clisle: a screenshot of an editing session using the Eclipse IDE to edit, compile, and debug Slicer3.

a screenshot of an editing session using the Eclipse IDE to edit, compile, and debug Slicer3.

Slicer3::New Eclipse Instructions

2010-02-18T21:21:33Z

Clisle: /* Download */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C /usr/local/slicers/trunk/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (''/usr/local/slicers/trunk/Slicer3-build/bin/Slicer3Setup.sh'' in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /usr/local/slicers/trunk/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

Slicer3::New Eclipse Instructions

2010-02-18T21:09:57Z

Clisle: /* Compile the projects: */

Slicer3::New Eclipse Instructions

2010-02-18T21:09:39Z

Clisle: /* Creating an Eclipse Project for Slicer3: */

Slicer3::New Eclipse Instructions

2010-02-18T21:08:14Z

Clisle: /* Creating an Eclipse Project for Slicer3: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:'''make -j 4 -C /usr/local/slicers/trunk/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (/usr/local/slicers/trunk/Slicer3-build/bin/Slicer3Setup.sh in our example). A shortcut can be created, using a shell alias, similar to the following example. I define this in my list of aliases auto created during login:

:'''alias trunk='source /usr/local/slicers/trunk/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

==Compile the projects:==
After successfully configuring all projects eclipse should start automatically building the application. If this is not the case, right click on project and select “Build Project” and see how the project is compiling.
=Download=
[[Media:Howto - Eclipse And Slicer3.pdf| How to Setup Eclipse – Slicer3 Development Environment]]

Slicer3::New Eclipse Instructions

2010-02-18T20:54:25Z

Clisle: /* Creating an Eclipse Project for Slicer3: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

:first '''make -j 4 -C /usr/local/slicers/trunk/Slicer3-build'''

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom. At this point, Eclipse will be able to compile Slicer3 but not able to run Slicer3 from the execute project icon, yet.

'''Step 8:''' Quit Eclipse and setup a shell which has the Slicer3 environment defined in the shell ''before'' running Eclipse inside the shell. In Linux or Mac, this can be done using a Bash shell script found in the Slicer3 build directory (/usr/local/slicers/trunk/Slicer3-build/bin/Slicer3Setup.sh in our example). A shortcut can be created, using a shell alias, similar to the following example:

:first '''alias trunk='source /usr/local/slicers/trunk/Slicer3-build/bin/Slicer3SetupPaths.sh; ~/Desktop/eclipse/eclipse ' '''

We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

==Compile the projects:==
After successfully configuring all projects eclipse should start automatically building the application. If this is not the case, right click on project and select “Build Project” and see how the project is compiling.
=Download=
[[Media:Howto - Eclipse And Slicer3.pdf| How to Setup Eclipse – Slicer3 Development Environment]]

Slicer3::New Eclipse Instructions

2010-02-18T20:44:33Z

Clisle: /* Creating Project and getting the Source-Code for it: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating an Eclipse Project for Slicer3:==

'''Step 1:''' Build Slicer3 outside of Eclipse using getbuildtest.tcl or your alternate build system of choice.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

make -j 4 -C /usr/local/slicers/trunk/Slicer3-build

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom.

We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

Anyone interested in using Eclipse, try these steps to get started. In a later email, or on the wiki, I'll talk about how to configure for debugging through the Eclipse interface.

==Compile the projects:==
After successfully configuring all projects eclipse should start automatically building the application. If this is not the case, right click on project and select “Build Project” and see how the project is compiling.
=Download=
[[Media:Howto - Eclipse And Slicer3.pdf| How to Setup Eclipse – Slicer3 Development Environment]]

Slicer3::New Eclipse Instructions

2010-02-18T20:35:56Z

Clisle: /* Creating Project and getting the Source-Code for it: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating Project and getting the Source-Code for it:==

'''Step 1:''' Build Slicer using getbuildtest.tcl or your favorite build system.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

'''Step2:''' Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

'''Step 3:''' Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

'''Step 4:''' You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

'''Step 5:''' Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

'''Step 6:''' Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

make -j 4 -C /usr/local/slicers/trunk/Slicer3-build

'''Step 7:''' In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom.

We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

Anyone interested in using Eclipse, try these steps to get started. In a later email, or on the wiki, I'll talk about how to configure for debugging through the Eclipse interface.

==Compile the projects:==
After successfully configuring all projects eclipse should start automatically building the application. If this is not the case, right click on project and select “Build Project” and see how the project is compiling.
=Download=
[[Media:Howto - Eclipse And Slicer3.pdf| How to Setup Eclipse – Slicer3 Development Environment]]

Slicer3::New Eclipse Instructions

2010-02-18T20:33:58Z

Clisle: /* Creating Project and getting the Source-Code for it: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating Project and getting the Source-Code for it:==

# Build Slicer using getbuildtest.tcl or your favorite build system.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

# Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".
# Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.
#: You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.
# Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .
#: Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

make -j 4 -C /usr/local/slicers/trunk/Slicer3-build

# In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom.

We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

Anyone interested in using Eclipse, try these steps to get started. In a later email, or on the wiki, I'll talk about how to configure for debugging through the Eclipse interface.

==Compile the projects:==
After successfully configuring all projects eclipse should start automatically building the application. If this is not the case, right click on project and select “Build Project” and see how the project is compiling.
=Download=
[[Media:Howto - Eclipse And Slicer3.pdf| How to Setup Eclipse – Slicer3 Development Environment]]

Slicer3::New Eclipse Instructions

2010-02-18T20:33:15Z

Clisle: /* Creating Project and getting the Source-Code for it: */

=Revised Howto Setup Eclipse to build/edit the Slicer3 Development Environment:=

==Installing Eclipse:==
I currently use Eclipse "Ganymede" (3.4) and "Galileo" (3.5) versions, but this also works with Eclipse Version 3.3 and higher. The easiest way to get started is to select an eclipse distribution which already includes CDT (the C++ tools) integrated. This is available from [http://www.eclipse.org/downloads http://www.eclipse.org/downloads]. Download Eclipse and unpack the downloaded archive to the destination you want. You start Eclipse with ./eclipse from the base directory of your eclipse installation.
==Configure Eclipse:==
As computers become more powerful, it is less necessary to adjust the runtime parameters of Eclipse, but some tweaking hints are listed on the original Eclipse page [[Slicer3::Eclipse | here]].

==Modules for Eclipse you need:==
As mentioned above, it is easiest to start with an integrated Eclipse containing CDT already. However these prebuilt configurations were available only in 32-bit versions the time of this writing. So some users who need full 64-bit versions may need to configure Eclipse by hand. If this is the case, the CDT tools can be integrated by hand into Eclipse. If you want to use Eclipse to connect to Slicer's SVN repository and compare versions, update source, etc. (highly recommended), then you'll need to add the Subclipse package to Eclipse. Please see the original Eclipse Wiki page [[Slicer3::Eclipse | here]] for instructions adding these packages into Eclipse. The URLs for these two Eclipse plug-ins are:

# CDT – C++ Environment: [http://www.eclipse.org/cdt http://www.eclipse.org/cdt]
# Subclipse: [http://subclipse.tigris.org/install.html http://subclipse.tigris.org/install.html]

==Creating Project and getting the Source-Code for it:==

# Build Slicer using getbuildtest.tcl or your favorite build system.

For this discussion, lets assume "/usr/local/slicers/trunk" contains the Slicer3* directories. So we could go into /usr/local/slicers/trunk/Slicer3-build and type "make".

# Create a new C++ project in Eclipse. Yes, it is a Makefile project. Uncheck "Use default location". Select the Browse function and navigator to the Slicer3 source directory for the Eclipse project location. In our example case, we would select "/usr/local/slicers/trunk/Slicer3". In my version of Eclipse (Galileo), it now has more options for the Project. I selected "Makefile Project" and specified "Empty Project".

# Click "Finish" to create the project. We will edit the project info later to get it really working. The C++ indexer may take a few minutes the first time it is consuming the whole Slicer tree during this step. After this, it is pretty fast.

#: You should see the project in the Explorer tab on the left now. Select then right click the project we just created. Mine was called "Slicer-trunk" and edit the project properties (the entry at the very bottom of the pop-up menu). The project properties dialog should pop up.

# Select the "C/C++ Build" branch of the tree diagram on the left of the dialog. In "Builder Settings", uncheck "Use default build command" .

#: Enter the make command we want to use. Notice that we specified four jobs (to build faster) and specified the location to use as the current directory for the build:

make -j 4 -C /usr/local/slicers/trunk/Slicer3-build

# In the same pop-up window, enter the build directory again in the "Build location" dialog (same pathname as you just entered above in step 6). Now you can click OK to accept these entries. Eclipse should start building the project right away. You can see the C++ compilations go by in the "Console" tab at the bottom.

We are using Eclipse to fire off the makefile built by cmake. This means we can still go outside Eclipse and type "make" by hand anytime. Eclipse just knows how to fire off the make when necessary.

Anyone interested in using Eclipse, try these steps to get started. In a later email, or on the wiki, I'll talk about how to configure for debugging through the Eclipse interface.

==Compile the projects:==
After successfully configuring all projects eclipse should start automatically building the application. If this is not the case, right click on project and select “Build Project” and see how the project is compiling.
=Download=
[[Media:Howto - Eclipse And Slicer3.pdf| How to Setup Eclipse – Slicer3 Development Environment]]

Slicer3::New Eclipse Instructions

2010-02-18T20:31:49Z

Clisle: /* Modules for Eclipse you need: */

Slicer3::New Eclipse Instructions

2010-02-18T20:31:19Z

Clisle: /* Configure Eclipse: */

Slicer3::New Eclipse Instructions

2010-02-18T20:30:42Z

Clisle: /* Configure Eclipse: */

Slicer3::New Eclipse Instructions

2010-02-18T18:11:25Z

Clisle: /* Configure Eclipse: */

Slicer3::New Eclipse Instructions

2010-02-18T18:09:44Z

Clisle: /* Configure Eclipse: */

Slicer3::New Eclipse Instructions

2010-02-18T18:09:07Z

Clisle: /* Configure Eclipse: */

Slicer3::New Eclipse Instructions

2010-02-18T18:07:58Z

Clisle: /* Configure Eclipse: */

Slicer3::New Eclipse Instructions

2010-02-18T18:06:43Z

Clisle:

Slicer3:Developers

2010-02-18T17:58:51Z

Clisle: /* Developer Documentation */

__NOTOC__
= Slicer 3 Developer Page =
[[Image:3DSlicerLogo-H-Color-212x121.png|right]]
This page contains links to Slicer3 developer resources and events.

Click here for <big><big>'''[[Slicer3:Events|Slicer3 Events]]'''</big></big>

== Slicer 3 Architecture Overview ==
For more details on the slicer architecture see: [[media:Slicer 3-beta-2007-04-16.ppt | Architecture Slides]] (updated April, 2007).

<gallery caption="Highlights of the new architecture" widths="300px" heights="200px" perrow="3">
Image:Slicer3-Architecture.jpg
Image:Slicer3-Architecture-MRML.jpg
Image:ExecutionModelPlugins.png
</gallery>

= Quick Links for Developers =
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers.

== Slicer 3 Quick links to the Source code ==
The Slicer3 svn repository:

svn co http://svn.slicer.org/Slicer3/trunk Slicer3

{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''General Slicer3 Quick Links'''
|style="background:#ddf" width="40%"|'''Debugging Slicer3 Quick Links'''
|-
||[[Slicer3:Build_Instructions|Slicer3 build instructions]]
||[http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 Dashboard (After May 2, 2008)]
|-
||Use [http://viewvc.slicer.org ViewVC to browse the repository]
||[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard (Before May 2, 2008)]
|-
||[http://www.na-mic.org/Wiki/index.php/Engineering:SandBox Instructions for NA-MIC svn]
||[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]
|-
||[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Doxygen documentation for Slicer3].
||
|-
||The [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.
||
|-
||Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].
|
|}

==Developers' Mailing List ==
Discussion of Slicer3 takes place on the slicer-devel at massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: slicer-devel-request at massmail.spl.harvard.edu with the keyword '''''subscribe''''' as the subject. Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].
 
 

== Developer Documentation ==

The following links provide more detail on internal aspects of the code. If you need more information, please follow up with email to the listed developers or the developer mailing list.

{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Introduction to Slicer3'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:Build_Instructions | Getting the software and troubleshooting]]
||
|-
||[[media:Slicer 3-beta-2007-01-10.ppt | Overall Architecture]] and [[Slicer3:Style|Slicer 3 Coding Style]]
||
|-
||[[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]
||
|-
|style="background:#ddf"|'''Three module types (Command line, Loadable, Scriptable)'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Media:Integrating with Slicer3.ppt | Integrating with the 3D Slicer]] || Jim and Steve
|-
||[[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]] and [[media:Slicer3Plugins.ppt|Tutorial]]
||Jim
|-
|style="background:#ddf"|'''MRML''' Medical Reality Modeling Language (MRML) is a language implemented as a type of XML document, with new tags defined to handle medical image data types such as volumes, models or coordinate transforms. [http://www.na-mic.org/Wiki/images/e/e3/Slicer3_MRML.ppt MRML Slides]
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]]
||Alex
|-
||[[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]]
||Alex
|-
||[[Slicer3:Data_Model#Undo/Redo_Mechanism | How undo/redo works, and how to enable it in your code]]
||Alex
|-
|style="background:#ddf"|'''GUI'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:EventBindings | Adding keyboard shortcuts]]
||Wendy
|-
||[[Slicer3:Human_Interface_and_Style_Guide_for_Developers | GUI style guidelines (undergoing change for move to Qt)]]
||Wendy
|-
||[[Slicer3:Usability#User-centered_design_practice_for_3DSlicer | User-centered design practice]]
||Wendy
|-
||[[Slicer3:Slicer3Brand | 3DSlicer's logo and visual communication guidelines]]
||Wendy
|-
||[[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]]
||Jim
|-
||[[Slicer3:GUI_Experiments | Some experiments/advanced techniques for developing slicer3 interfaces]]
||Steve
|-
|style="background:#ddf"|'''Engineering'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||Tips for avoiding memory leaks: Current Practice
||Steve
|-
||Tips for avoiding memory leaks: [[Slicer3:Memory Management | Suggested change to SmartPointers]]
||Jim
|-
||Generating tests
||Bill
|-
||[[Slicer3:Testing | Setting up Testing]]
||
|-
||[[Slicer3:Builds | Build Information]]
||
|-
||[[Slicer3:Launcher| The Launcher]]
||
|-
|style="background:#ddf"|'''Documenting your module''' Infrastructure has been added to link to wiki pages from the "Help & Acknowledgment" panel in your module's GUI. We ask developers to fill out a brief document describing your module and its use. [[Documentation-3.5#Requirements_for_Modules|See here for more information.]]
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:DocumentationWink|Documenting a module with wink]]
||
|-
|style="background:#ddf"|'''Integrate Slicer3 into a development environment'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3::Eclipse | Original Eclipse]]
||Michael Keilhack
|-
||[[Slicer3::New Eclipse Instructions | Revised Eclipse Instructions]]
||Curtis Lisle
|-
||[[Slicer3::MSVS200X | Microsoft Visual Studio 200x]]
||
|}
 

== Quick Links to Slicer3 Projects ==

Pending feature requests are [http://www.na-mic.org/Bug/search.php?project_id=1&severity_id=10&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 stored in the slicer bug tracker with severity setting of 'feature']. Please also refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.

Many Slicer related projects are worked on during the '''[http://wiki.na-mic.org/Wiki/index.php/Engineering:Programming_Events NA-MIC Project Events]''', please check there for recent updates.

 
{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Slicer3 Projects'''
|bgcolor="#ddf" valign="top"|'''Key People''' Bold names are responsible for an aspect of the project.
|-
||[[Slicer3:Data_Model|Data Model / libMRML]]
||'''Alex Yarmarkovich''', Steve Pieper
|-
||[[Slicer3:Execution_Model_Documentation|Execution Model / Command Line Modules]]
||'''Jim Miller''', Bill Lorensen
|-
||[[Slicer3:UIDesign|User Interface Design]]
||'''Wendy Plesniak''', Qt: Julien Finet, Jean-Christophe Fillion-Robin. KWWidgets: Sebastien Barre, Yumin Yuan
|-
||[[Slicer3:DTMRI|DTMRI]]
||'''Alex Yarmarkovich''' with help from Diffusion Images: '''Raul San Jose Estepar''', Tractography: '''Lauren O'Donnell''' [http://lmi.bwh.harvard.edu LMI]
|-
||[[Slicer3:Editor|Editor]]
||'''Steve Pieper'''
|-
||[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit Image Guided Therapy]
||'''Haiying Liu'''
|-
||[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]
||'''Steve Pieper'''
|-
||[[Slicer3:Batchmake_Integration|Batchmake/GRID Integration]]
||'''Julien Jomier''', Stephen Aylward
|-
||[[Slicer3:Registration|Registration Modules]]
||'''Domink Meier'''
|-
||[[Slicer3:Python|Python Integration]]
||'''Dan Blezek''', Steve Pieper
|-
||[[Slicer3:GPURayCaster | Volume Rendering using the VTK GPU acclerated Ray Caster]]
||'''Lisa Avila / Sebastien Barre'''
|-
||[[Slicer3:Loadable Modules |Loadable Modules]]
||'''Alex Yarmarkovich''', Steve Pieper, Terry Lorber
|-
||[[Slicer3:Extensions |Extensions]]
||'''Steve Pieper''', Terry Lorber
|-
|style="background:#ddf" width="60%"|'''Project Snapshots'''
|bgcolor="#ddf" valign="top"|This is list of projects which are not active at this time, or the linked pages show a snapshot of the project at a certain time.
|-
||[[Slicer3:Architecture/Features|Architecture/Features]]
||'''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata
|-
||[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]
||'''Jim Miller''', Bill Lorensen
|-
||[[Slicer3:Interface_Design|Interface Design and Usability ]]
||'''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan
|-
||[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]
||'''Nicole Aucoin'''
|-
||[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]
||'''Haiying Liu'''
|-
||[[Slicer3:EM|EMSegment Interface]]
||'''Kilian Pohl'''
|-
||[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]
||'''Katie Hayes'''
|-
||[[Slicer3:Grid_Interface|Grid Interface]]
||'''Jeff Grethe''', Marco Ruiz
|-
||[[Slicer3:Volume Rendering |Volume Rendering]]
||'''Yanling Liu'''
|-
||[[Slicer3:XNAT |XNAT Interface]]
||'''Steve''', Wendy, Dan Marcus, Tim Olsen
|-
||[[Slicer3:Web Presence |Web Presence]]
||'''Nicole Aucoin''', Zack Galbreath
|-
||[[Slicer3:TimeSeries and Multi-Volume Data | TimeSeries and Multi-Volume Data]]
||Junichi Tokuda, Steve Pieper, Daniel Blezek, Dominik Meier, Wendy Plesniak
|-
||[[Slicer3:Remote Data Handling | Remote Data Handling]]
||'''Steve Pieper, Nicole Aucoin, Wendy Plesniak'''
|-
||[[Slicer3:Module:QueryAtlas |Query Atlas]]
||'''Wendy Plesniak'''
|-
||[[Slicer3:RadiologicalReview | Radiological review]]
||'''Jim Miller'''
|-
||[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]
||'''Nicole Aucoin''', Katie Hayes, Wendy Plesniak, Mathieu Malaterre
|-
||[http://www.slicer.org/slicerWiki/index.php/Modules:Volumes:Diffusion_Editor-Documentation Diffusion Editor]
||'''Kerstin'''
|-
||[[Slicer3:MistSlicer | MistSlicer]]
||'''Yuichiro Hayashi''', Kensaku Mori, Nobuhiko Hata
|-
||[[Slicer3:LDDMM |LDDMM Interface]]
||'''Steve''', Anthony Kolasny
|-
||[[Slicer3:Volume Rendering With Cuda|Volume Rendering With CUDA (NOT Active)]]
||'''Ben'''
|-
||[[Slicer3:Pipeline_Integration|Loni Pipeline Integration]]
||'''Jags'''
|-
||[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]
||'''Katie Hayes'''
|-
||[[Slicer3:ThreadingToolKit|Threading ToolKit]]
||'''Dan Blezek, James Miller, Stephen Aylward'''
|}

== Design Information ==
*May 23, 2006: [http://www.na-mic.org/Wiki/index.php/Algorithms:Core1Visit_May06 Algorithm Core workshop.]
*April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.
*Discussion page about using [[Qt in Slicer3|Slicer3:Qt]].
*Implementation priorities from the slicer3 port are shown in this '''[[Slicer3:Status_Summary|Status Summary]]'''.

== Resources ==

Several books are available on the core topics related to slicer programming:

* [http://kitware.com/products/books.html Kitware's books on VTK, ITK, CMake]
* [http://www.akpeters.com/product.asp?ProdCode=2175 the ITK theory book]
* [http://bioimagesuite.org/vtkbook5/index.html Xenios's book on Medical Imaging and VTK - many useful examples in tcl]

Slicer3::New Eclipse Instructions

2010-02-18T17:55:21Z

Clisle: Creating revised Eclipse instructions

Slicer3:Developers

2010-02-18T17:42:30Z

Clisle: Adding new Eclipse page

__NOTOC__
= Slicer 3 Developer Page =
[[Image:3DSlicerLogo-H-Color-212x121.png|right]]
This page contains links to Slicer3 developer resources and events.

Click here for <big><big>'''[[Slicer3:Events|Slicer3 Events]]'''</big></big>

== Slicer 3 Architecture Overview ==
For more details on the slicer architecture see: [[media:Slicer 3-beta-2007-04-16.ppt | Architecture Slides]] (updated April, 2007).

<gallery caption="Highlights of the new architecture" widths="300px" heights="200px" perrow="3">
Image:Slicer3-Architecture.jpg
Image:Slicer3-Architecture-MRML.jpg
Image:ExecutionModelPlugins.png
</gallery>

= Quick Links for Developers =
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers.

== Slicer 3 Quick links to the Source code ==
The Slicer3 svn repository:

svn co http://svn.slicer.org/Slicer3/trunk Slicer3

{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''General Slicer3 Quick Links'''
|style="background:#ddf" width="40%"|'''Debugging Slicer3 Quick Links'''
|-
||[[Slicer3:Build_Instructions|Slicer3 build instructions]]
||[http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 Dashboard (After May 2, 2008)]
|-
||Use [http://viewvc.slicer.org ViewVC to browse the repository]
||[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard (Before May 2, 2008)]
|-
||[http://www.na-mic.org/Wiki/index.php/Engineering:SandBox Instructions for NA-MIC svn]
||[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]
|-
||[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Doxygen documentation for Slicer3].
||
|-
||The [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.
||
|-
||Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].
|
|}

==Developers' Mailing List ==
Discussion of Slicer3 takes place on the slicer-devel at massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: slicer-devel-request at massmail.spl.harvard.edu with the keyword '''''subscribe''''' as the subject. Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].
 
 

== Developer Documentation ==

The following links provide more detail on internal aspects of the code. If you need more information, please follow up with email to the listed developers or the developer mailing list.

{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Introduction to Slicer3'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:Build_Instructions | Getting the software and troubleshooting]]
||
|-
||[[media:Slicer 3-beta-2007-01-10.ppt | Overall Architecture]] and [[Slicer3:Style|Slicer 3 Coding Style]]
||
|-
||[[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]
||
|-
|style="background:#ddf"|'''Three module types (Command line, Loadable, Scriptable)'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Media:Integrating with Slicer3.ppt | Integrating with the 3D Slicer]] || Jim and Steve
|-
||[[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]] and [[media:Slicer3Plugins.ppt|Tutorial]]
||Jim
|-
|style="background:#ddf"|'''MRML''' Medical Reality Modeling Language (MRML) is a language implemented as a type of XML document, with new tags defined to handle medical image data types such as volumes, models or coordinate transforms. [http://www.na-mic.org/Wiki/images/e/e3/Slicer3_MRML.ppt MRML Slides]
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]]
||Alex
|-
||[[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]]
||Alex
|-
||[[Slicer3:Data_Model#Undo/Redo_Mechanism | How undo/redo works, and how to enable it in your code]]
||Alex
|-
|style="background:#ddf"|'''GUI'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:EventBindings | Adding keyboard shortcuts]]
||Wendy
|-
||[[Slicer3:Human_Interface_and_Style_Guide_for_Developers | GUI style guidelines (undergoing change for move to Qt)]]
||Wendy
|-
||[[Slicer3:Usability#User-centered_design_practice_for_3DSlicer | User-centered design practice]]
||Wendy
|-
||[[Slicer3:Slicer3Brand | 3DSlicer's logo and visual communication guidelines]]
||Wendy
|-
||[[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]]
||Jim
|-
||[[Slicer3:GUI_Experiments | Some experiments/advanced techniques for developing slicer3 interfaces]]
||Steve
|-
|style="background:#ddf"|'''Engineering'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||Tips for avoiding memory leaks: Current Practice
||Steve
|-
||Tips for avoiding memory leaks: [[Slicer3:Memory Management | Suggested change to SmartPointers]]
||Jim
|-
||Generating tests
||Bill
|-
||[[Slicer3:Testing | Setting up Testing]]
||
|-
||[[Slicer3:Builds | Build Information]]
||
|-
||[[Slicer3:Launcher| The Launcher]]
||
|-
|style="background:#ddf"|'''Documenting your module''' Infrastructure has been added to link to wiki pages from the "Help & Acknowledgment" panel in your module's GUI. We ask developers to fill out a brief document describing your module and its use. [[Documentation-3.5#Requirements_for_Modules|See here for more information.]]
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:DocumentationWink|Documenting a module with wink]]
||
|-
|style="background:#ddf"|'''Integrate Slicer3 into a development environment'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3::Eclipse | Original Eclipse]]
||Michael Keilhack
|-
||[[Slicer3::New Eclipse Instructions | Eclipse2]]
||Curtis Lisle
|-
||[[Slicer3::MSVS200X | Microsoft Visual Studio 200x]]
||
|}
 

== Quick Links to Slicer3 Projects ==

Pending feature requests are [http://www.na-mic.org/Bug/search.php?project_id=1&severity_id=10&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 stored in the slicer bug tracker with severity setting of 'feature']. Please also refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.

Many Slicer related projects are worked on during the '''[http://wiki.na-mic.org/Wiki/index.php/Engineering:Programming_Events NA-MIC Project Events]''', please check there for recent updates.

 
{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Slicer3 Projects'''
|bgcolor="#ddf" valign="top"|'''Key People''' Bold names are responsible for an aspect of the project.
|-
||[[Slicer3:Data_Model|Data Model / libMRML]]
||'''Alex Yarmarkovich''', Steve Pieper
|-
||[[Slicer3:Execution_Model_Documentation|Execution Model / Command Line Modules]]
||'''Jim Miller''', Bill Lorensen
|-
||[[Slicer3:UIDesign|User Interface Design]]
||'''Wendy Plesniak''', Qt: Julien Finet, Jean-Christophe Fillion-Robin. KWWidgets: Sebastien Barre, Yumin Yuan
|-
||[[Slicer3:DTMRI|DTMRI]]
||'''Alex Yarmarkovich''' with help from Diffusion Images: '''Raul San Jose Estepar''', Tractography: '''Lauren O'Donnell''' [http://lmi.bwh.harvard.edu LMI]
|-
||[[Slicer3:Editor|Editor]]
||'''Steve Pieper'''
|-
||[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit Image Guided Therapy]
||'''Haiying Liu'''
|-
||[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]
||'''Steve Pieper'''
|-
||[[Slicer3:Batchmake_Integration|Batchmake/GRID Integration]]
||'''Julien Jomier''', Stephen Aylward
|-
||[[Slicer3:Registration|Registration Modules]]
||'''Domink Meier'''
|-
||[[Slicer3:Python|Python Integration]]
||'''Dan Blezek''', Steve Pieper
|-
||[[Slicer3:GPURayCaster | Volume Rendering using the VTK GPU acclerated Ray Caster]]
||'''Lisa Avila / Sebastien Barre'''
|-
||[[Slicer3:Loadable Modules |Loadable Modules]]
||'''Alex Yarmarkovich''', Steve Pieper, Terry Lorber
|-
||[[Slicer3:Extensions |Extensions]]
||'''Steve Pieper''', Terry Lorber
|-
|style="background:#ddf" width="60%"|'''Project Snapshots'''
|bgcolor="#ddf" valign="top"|This is list of projects which are not active at this time, or the linked pages show a snapshot of the project at a certain time.
|-
||[[Slicer3:Architecture/Features|Architecture/Features]]
||'''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata
|-
||[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]
||'''Jim Miller''', Bill Lorensen
|-
||[[Slicer3:Interface_Design|Interface Design and Usability ]]
||'''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan
|-
||[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]
||'''Nicole Aucoin'''
|-
||[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]
||'''Haiying Liu'''
|-
||[[Slicer3:EM|EMSegment Interface]]
||'''Kilian Pohl'''
|-
||[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]
||'''Katie Hayes'''
|-
||[[Slicer3:Grid_Interface|Grid Interface]]
||'''Jeff Grethe''', Marco Ruiz
|-
||[[Slicer3:Volume Rendering |Volume Rendering]]
||'''Yanling Liu'''
|-
||[[Slicer3:XNAT |XNAT Interface]]
||'''Steve''', Wendy, Dan Marcus, Tim Olsen
|-
||[[Slicer3:Web Presence |Web Presence]]
||'''Nicole Aucoin''', Zack Galbreath
|-
||[[Slicer3:TimeSeries and Multi-Volume Data | TimeSeries and Multi-Volume Data]]
||Junichi Tokuda, Steve Pieper, Daniel Blezek, Dominik Meier, Wendy Plesniak
|-
||[[Slicer3:Remote Data Handling | Remote Data Handling]]
||'''Steve Pieper, Nicole Aucoin, Wendy Plesniak'''
|-
||[[Slicer3:Module:QueryAtlas |Query Atlas]]
||'''Wendy Plesniak'''
|-
||[[Slicer3:RadiologicalReview | Radiological review]]
||'''Jim Miller'''
|-
||[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]
||'''Nicole Aucoin''', Katie Hayes, Wendy Plesniak, Mathieu Malaterre
|-
||[http://www.slicer.org/slicerWiki/index.php/Modules:Volumes:Diffusion_Editor-Documentation Diffusion Editor]
||'''Kerstin'''
|-
||[[Slicer3:MistSlicer | MistSlicer]]
||'''Yuichiro Hayashi''', Kensaku Mori, Nobuhiko Hata
|-
||[[Slicer3:LDDMM |LDDMM Interface]]
||'''Steve''', Anthony Kolasny
|-
||[[Slicer3:Volume Rendering With Cuda|Volume Rendering With CUDA (NOT Active)]]
||'''Ben'''
|-
||[[Slicer3:Pipeline_Integration|Loni Pipeline Integration]]
||'''Jags'''
|-
||[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]
||'''Katie Hayes'''
|-
||[[Slicer3:ThreadingToolKit|Threading ToolKit]]
||'''Dan Blezek, James Miller, Stephen Aylward'''
|}

== Design Information ==
*May 23, 2006: [http://www.na-mic.org/Wiki/index.php/Algorithms:Core1Visit_May06 Algorithm Core workshop.]
*April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.
*Discussion page about using [[Qt in Slicer3|Slicer3:Qt]].
*Implementation priorities from the slicer3 port are shown in this '''[[Slicer3:Status_Summary|Status Summary]]'''.

== Resources ==

Several books are available on the core topics related to slicer programming:

* [http://kitware.com/products/books.html Kitware's books on VTK, ITK, CMake]
* [http://www.akpeters.com/product.asp?ProdCode=2175 the ITK theory book]
* [http://bioimagesuite.org/vtkbook5/index.html Xenios's book on Medical Imaging and VTK - many useful examples in tcl]

Slicer3:Developers

2010-02-18T17:40:23Z

Clisle:

__NOTOC__
= Slicer 3 Developer Page =
[[Image:3DSlicerLogo-H-Color-212x121.png|right]]
This page contains links to Slicer3 developer resources and events.

Click here for <big><big>'''[[Slicer3:Events|Slicer3 Events]]'''</big></big>

== Slicer 3 Architecture Overview ==
For more details on the slicer architecture see: [[media:Slicer 3-beta-2007-04-16.ppt | Architecture Slides]] (updated April, 2007).

<gallery caption="Highlights of the new architecture" widths="300px" heights="200px" perrow="3">
Image:Slicer3-Architecture.jpg
Image:Slicer3-Architecture-MRML.jpg
Image:ExecutionModelPlugins.png
</gallery>

= Quick Links for Developers =
This section centrally locates many existing (and developing) wiki pages useful to Slicer3 developers.

== Slicer 3 Quick links to the Source code ==
The Slicer3 svn repository:

svn co http://svn.slicer.org/Slicer3/trunk Slicer3

{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''General Slicer3 Quick Links'''
|style="background:#ddf" width="40%"|'''Debugging Slicer3 Quick Links'''
|-
||[[Slicer3:Build_Instructions|Slicer3 build instructions]]
||[http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 Dashboard (After May 2, 2008)]
|-
||Use [http://viewvc.slicer.org ViewVC to browse the repository]
||[http://www.na-mic.org/Slicer3/Dashboard Slicer3 Dashboard (Before May 2, 2008)]
|-
||[http://www.na-mic.org/Wiki/index.php/Engineering:SandBox Instructions for NA-MIC svn]
||[http://na-mic.org/Mantis/main_page.php Slicer Bug Tracker]
|-
||[http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/ Doxygen documentation for Slicer3].
||
|-
||The [[Slicer3:VisualBlog|Slicer3 VisualBlog]] shows screenshots of slicer developments.
||
|-
||Developers should follow the [[Slicer3:Style|Slicer 3 Coding Style]].
|
|}

==Developers' Mailing List ==
Discussion of Slicer3 takes place on the slicer-devel at massmail.spl.harvard.edu list. To join developer's mailing list, send a request to: slicer-devel-request at massmail.spl.harvard.edu with the keyword '''''subscribe''''' as the subject. Or access the [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel slicer-devel archives and web administration interface].
 
 

== Developer Documentation ==

The following links provide more detail on internal aspects of the code. If you need more information, please follow up with email to the listed developers or the developer mailing list.

{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Introduction to Slicer3'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:Build_Instructions | Getting the software and troubleshooting]]
||
|-
||[[media:Slicer 3-beta-2007-01-10.ppt | Overall Architecture]] and [[Slicer3:Style|Slicer 3 Coding Style]]
||
|-
||[[Slicer3:Contributing_codes_to_Slicer3| Contributing codes to Slicer3]]
||
|-
|style="background:#ddf"|'''Three module types (Command line, Loadable, Scriptable)'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Media:Integrating with Slicer3.ppt | Integrating with the 3D Slicer]] || Jim and Steve
|-
||[[Slicer3:Execution_Model_Documentation | Command line modules and how to implement one]] and [[media:Slicer3Plugins.ppt|Tutorial]]
||Jim
|-
|style="background:#ddf"|'''MRML''' Medical Reality Modeling Language (MRML) is a language implemented as a type of XML document, with new tags defined to handle medical image data types such as volumes, models or coordinate transforms. [http://www.na-mic.org/Wiki/images/e/e3/Slicer3_MRML.ppt MRML Slides]
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:Data_Model#Creating_Custom_MRML_Node_Classes | Creating and using new MRML node types]]
||Alex
|-
||[[Slicer3:Data_Model#References_to_MRML_Nodes | Keeping references to MRML nodes ]]
||Alex
|-
||[[Slicer3:Data_Model#Undo/Redo_Mechanism | How undo/redo works, and how to enable it in your code]]
||Alex
|-
|style="background:#ddf"|'''GUI'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:EventBindings | Adding keyboard shortcuts]]
||Wendy
|-
||[[Slicer3:Human_Interface_and_Style_Guide_for_Developers | GUI style guidelines (undergoing change for move to Qt)]]
||Wendy
|-
||[[Slicer3:Usability#User-centered_design_practice_for_3DSlicer | User-centered design practice]]
||Wendy
|-
||[[Slicer3:Slicer3Brand | 3DSlicer's logo and visual communication guidelines]]
||Wendy
|-
||[[Slicer3:Execution_Model_Documentation#Adding_Module_Logos_to_Slicer3 | Incorporating your group's logo and attributions]]
||Jim
|-
||[[Slicer3:GUI_Experiments | Some experiments/advanced techniques for developing slicer3 interfaces]]
||Steve
|-
|style="background:#ddf"|'''Engineering'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||Tips for avoiding memory leaks: Current Practice
||Steve
|-
||Tips for avoiding memory leaks: [[Slicer3:Memory Management | Suggested change to SmartPointers]]
||Jim
|-
||Generating tests
||Bill
|-
||[[Slicer3:Testing | Setting up Testing]]
||
|-
||[[Slicer3:Builds | Build Information]]
||
|-
||[[Slicer3:Launcher| The Launcher]]
||
|-
|style="background:#ddf"|'''Documenting your module''' Infrastructure has been added to link to wiki pages from the "Help & Acknowledgment" panel in your module's GUI. We ask developers to fill out a brief document describing your module and its use. [[Documentation-3.5#Requirements_for_Modules|See here for more information.]]
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3:DocumentationWink|Documenting a module with wink]]
||
|-
|style="background:#ddf"|'''Integrate Slicer3 into a development environment'''
|bgcolor="#ddf" valign="top"|'''Key People'''
|-
||[[Slicer3::Original Eclipse Page | Eclipse]]
||Michael Keilhack
|-
||[[Slicer3::New Eclipse Instructions | Eclipse2]]
||Curtis Lisle
|-
||[[Slicer3::MSVS200X | Microsoft Visual Studio 200x]]
||
|}
 

== Quick Links to Slicer3 Projects ==

Pending feature requests are [http://www.na-mic.org/Bug/search.php?project_id=1&severity_id=10&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 stored in the slicer bug tracker with severity setting of 'feature']. Please also refer to the '''[[Slicer3:FeatureRequests|Feature Requests]]''' from users when planning your implementations.

Many Slicer related projects are worked on during the '''[http://wiki.na-mic.org/Wiki/index.php/Engineering:Programming_Events NA-MIC Project Events]''', please check there for recent updates.

 
{|width="800px" border="1"
|-
|style="background:#ddf" width="60%"|'''Slicer3 Projects'''
|bgcolor="#ddf" valign="top"|'''Key People''' Bold names are responsible for an aspect of the project.
|-
||[[Slicer3:Data_Model|Data Model / libMRML]]
||'''Alex Yarmarkovich''', Steve Pieper
|-
||[[Slicer3:Execution_Model_Documentation|Execution Model / Command Line Modules]]
||'''Jim Miller''', Bill Lorensen
|-
||[[Slicer3:UIDesign|User Interface Design]]
||'''Wendy Plesniak''', Qt: Julien Finet, Jean-Christophe Fillion-Robin. KWWidgets: Sebastien Barre, Yumin Yuan
|-
||[[Slicer3:DTMRI|DTMRI]]
||'''Alex Yarmarkovich''' with help from Diffusion Images: '''Raul San Jose Estepar''', Tractography: '''Lauren O'Donnell''' [http://lmi.bwh.harvard.edu LMI]
|-
||[[Slicer3:Editor|Editor]]
||'''Steve Pieper'''
|-
||[http://www.na-mic.org/Wiki/index.php/IGT:ToolKit Image Guided Therapy]
||'''Haiying Liu'''
|-
||[[Slicer3:Slicer_Daemon|SlicerDaemon Interface (for unu, matlab)]]
||'''Steve Pieper'''
|-
||[[Slicer3:Batchmake_Integration|Batchmake/GRID Integration]]
||'''Julien Jomier''', Stephen Aylward
|-
||[[Slicer3:Registration|Registration Modules]]
||'''Domink Meier'''
|-
||[[Slicer3:Python|Python Integration]]
||'''Dan Blezek''', Steve Pieper
|-
||[[Slicer3:GPURayCaster | Volume Rendering using the VTK GPU acclerated Ray Caster]]
||'''Lisa Avila / Sebastien Barre'''
|-
||[[Slicer3:Loadable Modules |Loadable Modules]]
||'''Alex Yarmarkovich''', Steve Pieper, Terry Lorber
|-
||[[Slicer3:Extensions |Extensions]]
||'''Steve Pieper''', Terry Lorber
|-
|style="background:#ddf" width="60%"|'''Project Snapshots'''
|bgcolor="#ddf" valign="top"|This is list of projects which are not active at this time, or the linked pages show a snapshot of the project at a certain time.
|-
||[[Slicer3:Architecture/Features|Architecture/Features]]
||'''Steve Pieper''', Group: Bill Lorensen, Ron Kikinis, Mike Halle, Noby Hata
|-
||[[Slicer3:Execution_Model|Execution Model / Command Line Modules]]
||'''Jim Miller''', Bill Lorensen
|-
||[[Slicer3:Interface_Design|Interface Design and Usability ]]
||'''Wendy Plesniak''', KWWidgets: Sebastien Barre, Yumin Yuan
|-
||[[Slicer3:ColorsFiducialsFreesurferModelmaker|Colors, Fiducials, FreeSurfer, ModelMaker]]
||'''Nicole Aucoin'''
|-
||[[Slicer3:_Image_Guided_Therapy_%28IGT%29|IGT, Trackers]]
||'''Haiying Liu'''
|-
||[[Slicer3:EM|EMSegment Interface]]
||'''Kilian Pohl'''
|-
||[[Slicer3:Build/Test/Deploy|Build/Test/Deploy System]]
||'''Katie Hayes'''
|-
||[[Slicer3:Grid_Interface|Grid Interface]]
||'''Jeff Grethe''', Marco Ruiz
|-
||[[Slicer3:Volume Rendering |Volume Rendering]]
||'''Yanling Liu'''
|-
||[[Slicer3:XNAT |XNAT Interface]]
||'''Steve''', Wendy, Dan Marcus, Tim Olsen
|-
||[[Slicer3:Web Presence |Web Presence]]
||'''Nicole Aucoin''', Zack Galbreath
|-
||[[Slicer3:TimeSeries and Multi-Volume Data | TimeSeries and Multi-Volume Data]]
||Junichi Tokuda, Steve Pieper, Daniel Blezek, Dominik Meier, Wendy Plesniak
|-
||[[Slicer3:Remote Data Handling | Remote Data Handling]]
||'''Steve Pieper, Nicole Aucoin, Wendy Plesniak'''
|-
||[[Slicer3:Module:QueryAtlas |Query Atlas]]
||'''Wendy Plesniak'''
|-
||[[Slicer3:RadiologicalReview | Radiological review]]
||'''Jim Miller'''
|-
||[[Slicer3:Transition_of_Slicer2.x_Modules|Transition of Selected Slicer2.x Modules to Slicer3]]
||'''Nicole Aucoin''', Katie Hayes, Wendy Plesniak, Mathieu Malaterre
|-
||[http://www.slicer.org/slicerWiki/index.php/Modules:Volumes:Diffusion_Editor-Documentation Diffusion Editor]
||'''Kerstin'''
|-
||[[Slicer3:MistSlicer | MistSlicer]]
||'''Yuichiro Hayashi''', Kensaku Mori, Nobuhiko Hata
|-
||[[Slicer3:LDDMM |LDDMM Interface]]
||'''Steve''', Anthony Kolasny
|-
||[[Slicer3:Volume Rendering With Cuda|Volume Rendering With CUDA (NOT Active)]]
||'''Ben'''
|-
||[[Slicer3:Pipeline_Integration|Loni Pipeline Integration]]
||'''Jags'''
|-
||[[Slicer3:Performance_Analysis|Slicer3:Performance Analysis]]
||'''Katie Hayes'''
|-
||[[Slicer3:ThreadingToolKit|Threading ToolKit]]
||'''Dan Blezek, James Miller, Stephen Aylward'''
|}

== Design Information ==
*May 23, 2006: [http://www.na-mic.org/Wiki/index.php/Algorithms:Core1Visit_May06 Algorithm Core workshop.]
*April 3, 2006: [[Media:Slicer_3-alpha-2006-04-03.ppt| Slicer 3 alpha]] technical powerpoint presentation.
*Discussion page about using [[Qt in Slicer3|Slicer3:Qt]].
*Implementation priorities from the slicer3 port are shown in this '''[[Slicer3:Status_Summary|Status Summary]]'''.

== Resources ==

Several books are available on the core topics related to slicer programming:

* [http://kitware.com/products/books.html Kitware's books on VTK, ITK, CMake]
* [http://www.akpeters.com/product.asp?ProdCode=2175 the ITK theory book]
* [http://bioimagesuite.org/vtkbook5/index.html Xenios's book on Medical Imaging and VTK - many useful examples in tcl]

Modules:IA FEMesh-Documentation-3.4

2009-02-24T20:46:41Z

Clisle: /* Module Description */

[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
__NOTOC__
===Module Name===
IA_FEMesh (Finite Element Meshing Module from the University of Iowa)

{|
|[[Image:Femesh-in-trunk-120808.png|thumb|340px|IA-FEMesh Module in Slicer3 ]]
|}

== General Information ==
A loadable module to automate the creation of surface and volumetric meshes for finite element analysis.

===Module Type & Category===

Type: Interactive

Category: Meshing

===Authors, Collaborators & Contact===
* Nicole Grosland, University of Iowa, grosland@engineering.uiowa.edu
* Vince Magnotta, University of Iowa, vincent-magnotta@uiowa.edu
* Kiran Shivanna, University of Iowa, kshivann@engineering.uiowa.edu
* Austin Ramme, University of Iowa
* Steve Pieper, Isomics, pieper@bwh.harvard.edu
* Curtis Lisle, KnowledgeVis, clisle@knowledgevis.com

===Module Description===
This module allows the creation and editing of surface and volumetric meshes. Polygonal surfaces in VTK or STL format are imported to begin the process. Then a unique and intuitive bounding surface (called Building Blocks) are created interactively by the user and used to guide automated meshing algorithms. The module includes visualization and analysis reports of the quality of mesh elements. Meshes can be written out in Abaqus or VTK format for later processing.

== Usage ==

===Examples, Use Cases & Tutorials===

* IA_FEMesh is particularly well suited for quickly developing quality hexahedral meshes for artificial joint research and prothesis design. Its intuitive interface allows the user to mesh and review moderate sized objects, such as bone surfaces, efficiently. However, the use cases are not restricted to this application area.
* [http://www.na-mic.org/Wiki/index.php/Iowa_Meshing_Tutorial Meshing Module Tutorial]
* [https://mri.radiology.uiowa.edu/downloads/IA-FEMesh_Manual_version1.pdf IA_FEMesh Users Manual]

===Quick Tour of Features and Use===
The user interface for IA_FEMesh is organized as a set of tabs, with each tab corresponding to a group of related activities. Often the user will move back and forth between the tabs during the meshing process. The tabs organize related operations yet allow free movement, depending on the users needs. The tabs and associated operations are listed below:

* '''Surface:''' This tab allows input and saving of surface files used to define the object which will be meshed.
* '''Building Block:''' After a 3D object surface is input, the user interactively creates, modifies, and views a control surface used to guide meshing algorithms. Under this tab, operations for editing, copying, deleting, and splitting building blocks provide the tools for rapid building block creation. The operations can be applied to all or a selected subset of building blocks.
* '''Mesh Creation:'''This tab contains the algorithms for projecting points along the building block walls down onto the selected surface mesh. A solid mesh is created using transfinite or elliptical interploation.
* '''Mesh Quality:''' After a mesh is created, tools inside this tab allow for interactive viewing, exploration, and mesh improvement algorithms to be run if desired.
* '''Material Properties:''' Meshes are composed of multiple surface and/or volume elements. Individual elements or groups of elements are selected and given material properties with the tools inside this tab. Material properties stay with the mesh and are output when the mesh is saved as an external file.
* '''Boundary Conditions:''' Multi-step boundary conditions, including external forces, can be defined by the GUI tools defined under this tab. A user can create an Abaqus input file and visually preview if conditions have been specified correctly before beginning an external finite element simulation.

== Development ==

===Dependencies===
IA_FEMesh has no external dependcies. The module creates meshes in ABAQUS format. To perform finite element analysis, the user will have to provide a suitable simulation environment.

As far as the software building process, all required support libraries, that extend the Slicer3 base, are built from source code during the Slicer3 build process automatically.

===Known bugs===
This module isn't fully integrated with MRML yet. MRML scene snapshots and restores are not yet supported. Please save your work using the file save dialogs in the user interface.

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

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

===Source code & documentation===

IA_FEMesh was developed as a standalone program and has been integrated for use in Slicer3 as one of the products of a NA-MIC External Collaboration. A design goal for this effort is to allow software development to continue on both the standalone and integrated module versions while working off a common code base.

To browse the module source code, click [http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/Meshing/ here].

Custom GUI classes were created to group meshing operations -- inheriting from a common parent class developed for this module. Doxygen generated documentation of the abstract parent class and the operations as derived classes is available [http://www.na-mic.org/Slicer/Documentation/Slicer3/html/classvtkKWMimxGroupBase.html here].

== More Information ==

===Acknowledgment===

[http://wiki.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development PAR-05-063: NIH Grant R01EB005973 Automated FE Mesh Development]

===References===
Please see the publications section of the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_NCBC_Collaboration:Automated_FE_Mesh_Development grant description page] also listed directly above.