TubeTK/Events/2011.07.05: Difference between revisions
Ilknur.kabul (talk | contribs) No edit summary |
Jamie.snape (talk | contribs) No edit summary |
||
| (9 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
Danielle & Ilknur: | Danielle & Ilknur: | ||
== Adding TubeTK CLIs to Slicer == | |||
Instructions for adding TubeTK CLIs to Slicer can be found in: | Instructions for adding TubeTK CLIs to Slicer can be found in: | ||
http://www.cmake.org/Wiki/TubeTK/Slicer | http://www.cmake.org/Wiki/TubeTK/Slicer | ||
Basically, these steps should be followed for tubetk: | Basically, these steps should be followed for tubetk: | ||
# From tubetk, point code to Slicer CLI Repository for build and superbuild | # From tubetk, point code to Slicer CLI Repository for build and superbuild. (findpackage(Slicer)) | ||
# From Slicer, add paths for CLI or python (this can be done from the Slicer GUI) | # From Slicer, add paths for CLI or python (this can be done from the Slicer GUI) | ||
# # From JC's info today - CMakeLists to look at for Qt scripted modules (python): ~/Slicer4Trunk/Slicer4/Extensions/Testing/ExtensionTemplate/CMakeLists.txt | ## From JC's info today - CMakeLists to look at for Qt scripted modules (python): ~/Slicer4Trunk/Slicer4/Extensions/Testing/ExtensionTemplate/CMakeLists.txt | ||
Note: | |||
* You should be able to pass fiberbundles as CLI parameters, using the XML tag: | |||
<geometry [type="fiberbundle"]> | <geometry [type="fiberbundle"]> | ||
For example, see the "Labelmap Seeding" module - it has an output parameter "Output fiber bundle" | For example, see the "Labelmap Seeding" module - it has an output parameter "Output fiber bundle" | ||
* Instructions to copy CLI's to Slicer directory: | |||
cp <YourTubeTKBuildDirectory>/TubeTK-Build/lib/TubeTK/Plugins/*tube <YourSlicerDirectory>/lib/Slicer3/Plugins | |||
We should specify <YourTubeTKBuildDirectory>/TubeTK-Build/lib/TubeTK/Plugins as the external module directory in Slicer's settings | |||
BUT this will cause a crash in Slicer because it tries to read the non-plugin executables as well: | |||
We should | |||
BUT | |||
this will cause a crash in Slicer because it tries to read the non-plugin executables as well: | |||
> 4218 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - | > 4218 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - | ||
| Line 41: | Line 38: | ||
Additional small TODOs: | Additional small TODOs: | ||
- hide external ITK/VTK/CTK directories as advanced CMake parameters, or hide them completely so that they can only be specified on the command line | - hide external ITK/VTK/CTK directories as advanced CMake parameters, or hide them completely so that they can only be specified on the command line | ||
== Creating Mantis for TubeTK == | |||
# Creation of TubeTK project in Kitware's bug tracker: | |||
## This is done. It is in http://public.kitware.com/Bug/my_view_page.php | |||
# Setup the python-based hooks for linking with the bug tracker so that git commits to tubetk must be tied to mantis issues. | |||
#Setup the main git repo to be at public.kitware.com/tubetk.git. This will be used instead of the tubetk git repo on gitorous http://gitorious.org/tubetk/ | |||
[[Category:TubeTK Events and Meetings|2011.07.05]] | |||
Latest revision as of 18:53, 26 July 2013
Danielle & Ilknur:
Adding TubeTK CLIs to Slicer
Instructions for adding TubeTK CLIs to Slicer can be found in: http://www.cmake.org/Wiki/TubeTK/Slicer Basically, these steps should be followed for tubetk:
- From tubetk, point code to Slicer CLI Repository for build and superbuild. (findpackage(Slicer))
- From Slicer, add paths for CLI or python (this can be done from the Slicer GUI)
- From JC's info today - CMakeLists to look at for Qt scripted modules (python): ~/Slicer4Trunk/Slicer4/Extensions/Testing/ExtensionTemplate/CMakeLists.txt
Note:
- You should be able to pass fiberbundles as CLI parameters, using the XML tag:
<geometry [type="fiberbundle"]>
For example, see the "Labelmap Seeding" module - it has an output parameter "Output fiber bundle"
- Instructions to copy CLI's to Slicer directory:
cp <YourTubeTKBuildDirectory>/TubeTK-Build/lib/TubeTK/Plugins/*tube <YourSlicerDirectory>/lib/Slicer3/Plugins
We should specify <YourTubeTKBuildDirectory>/TubeTK-Build/lib/TubeTK/Plugins as the external module directory in Slicer's settings BUT this will cause a crash in Slicer because it tries to read the non-plugin executables as well:
> 4218 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - > registerIO qSlicerVolumesIO > 4478 [] TRACE org.slicer.base.qtcore.qSlicerCoreIOManager - > registerIO qSlicerFiberBundleIO > ASSERT: "!_moduleTitle.isEmpty()" in file > /home/andrey/Slicer/Slicer4/Base/QTCore/qSlicerModuleManager.cxx, line > 141 > Aborted > > Launch /usr/local/andrey/Slicer4-Qt-debug/Slicer-build/bin/SlicerQT-real > returned with error: child process exited abnormally >
In particular, this is because of TextCompareCommand and ImageCompareCommand, which should be changed to build somewhere else.
Additional small TODOs: - hide external ITK/VTK/CTK directories as advanced CMake parameters, or hide them completely so that they can only be specified on the command line
Creating Mantis for TubeTK
- Creation of TubeTK project in Kitware's bug tracker:
- This is done. It is in http://public.kitware.com/Bug/my_view_page.php
- Setup the python-based hooks for linking with the bug tracker so that git commits to tubetk must be tied to mantis issues.
- Setup the main git repo to be at public.kitware.com/tubetk.git. This will be used instead of the tubetk git repo on gitorous http://gitorious.org/tubetk/
