Update Slicer and adopt SlicerCustomAppTemplate v2

[jcfr]

No description provided.

[jcfr]

@laurapascal @bpaniagua This is ready for review and integration.

[vicory]

@jcfr Any more changes coming or is this ready for review?

[jcfr]

I suggest to move forward and integrate.

[jcfr]

Also after integrating this PR, #38 and #39 could be closed.

[vicory]

There are currently conflicts with ShapePopulationViewer and Qt5/VTK 9, I'm working on a fix.

[jcfr]

Indeed, if i recall ShapePopulationViewer should be updated to support Qt5/VTK9

…

On Thu, Apr 19, 2018, 1:10 PM vicory ***@***.***> wrote: There are currently conflicts with ShapePopulationViewer and Qt5/VTK 9, I'm working on a fix. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#40 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AANXo8mljAeKNamAbGjO1_Umac4odJCsks5tqNMMgaJpZM4SXjNB> .

[vicory]

ShapePopulationViewer problems should be fixed, but I've discovered a new issue: the qMRML widgets are not showing up under qt.QUiLoader().availableWidgets(), causing scripted modules to not work properly.

[jcfr]

the qMRML widgets are not showing up under qt.QUiLoader().availableWidgets()

Is this specific to a platform ? Or reproducible on Linux, macOS and Windows ?

[vicory]

I've only tested on Linux thus far.

[phcerdan]

I am going to test this, it should be a priority. If we do not have to maintain backwards compatibility... better to get up-to-date with slicer master and go for qt5.

[bpaniagua]

Thank you, Pablo. After you test it let us know how it goes.

[phcerdan]

One issue found, not sure if this is the expected behavior. If I want to pass settings to Slicer, I have to use SlicerSALT as a prefix, not Slicer.

Slicer_USE_SYSTEM_python:BOOL=ON is ignored, and Slicer will fetch and build python.
However SlicerSALT_USE_SYSTEM_python:BOOL=ON works.

This is because ${CMAKE_PROJECT_NAME} is SlicerSALT in Slicer/Superbuild.cmake and in all the scripts External_xxx.cmake

[bpaniagua]

Seems about right to me. @jcfr @vicory what do you think?

[jcfr]

@phcerdan Makes sense.

From a usability stand point, it looks like we should always have the option starting with Slicer_.

Would that help reduce confusion ?

[jcfr]

Would that help reduce confusion ?

Replying to my own question. Answer is yes and the change will be added to Slicer shortly.

[jcfr]

Slicer_USE_SYSTEM_python:BOOL=ON is ignored, and Slicer will fetch and build python

Following Slicer r27286, option associated with Slicer core will all start with Slicer_

[phcerdan]

Awesome @jcfr, I agree that it will reduce confusion, thanks!

[phcerdan]

Getting there! After using the latest SlicerCustomAppTemplate, and doing a merge of the generated template and this PR... it compiles!

But, at running time, with python disabled, I get that the "internal" module: Home is not registered. With python enabled vtkCommonKitPython is not found. See the commit messages of my branch on top of this PR: https://github.com/phcerdan/SlicerSALT/commits/jcfr_update. Hopefully you can test it from there too. As a node, I am using Slicer_USE_SYSTEM_python:BOOL=ON @jcfr

Errors:

./Slicer-build/SlicerSALT
Traceback (most recent call last):
  File "<string>", line 7, in <module>
  File "/home/user/Software/Shape/SALT/buildRelWithDebInfo/Slicer-build/bin/Python/slicer/slicerqt.py", line 6, in <module>
    import vtk
  File "/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/VTKv9-build/lib/python2.7/site-packages/vtk.py", line 12, in <module>
    all_m = importlib.import_module('vtkmodules.all')
  File "/usr/lib64/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
  File "/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/VTKv9-build/lib/python2.7/site-packages/vtkmodules/all.py", line 7, in <module>
    from .vtkCommonKit import *
  File "/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/VTKv9-build/lib/python2.7/site-packages/vtkmodules/vtkCommonKit.py", line 9, in <module>
    from vtkCommonKitPython import *
ImportError: No module named vtkCommonKitPython
Traceback (most recent call last):
  File "<string>", line 1, in <module>
NameError: name 'getSlicerRCFileName' is not defined
error: [/home/user/Software/Shape/SALT/buildRelWithDebInfo/Slicer-build/bin/./SlicerSALTApp-real] exit abnormally - Report the problem.

Disabling python:

./Slicer-build/SlicerSALT --disable-python

The module "Home" has not been registered.
The following modules have been registered: ("Annotations", "Cameras", "Colors", "CropVolume", "Data", "DoubleArrays", "EventBroker", "Markups", "MeshToLabelMap", "ModelMaker", "Models", "Plots", "Reformat", "ResampleDTIVolume", "ResampleScalarVectorDWIVolume", "Segmentations", "SubjectHierarchy", "Tables", "Terminologies", "Transforms", "Units", "VolumeRendering", "Volumes")
error: [/home/user/Software/Shape/SALT/buildRelWithDebInfo/Slicer-build/bin/./SlicerSALTApp-real] exit abnormally - Report the problem.

[jcfr]

Thanks for the late update ...

Next week, could you report here the content of SlicerSALTLauncherSettings.ini ? (it is available in the Slicer-build directory)

In a regular build directory, the VTK module is found here: ./VTKv9-build/lib/python2.7/site-packages/vtkmodules/vtkCommonKitPython.so

In you case, I am assuming you built from a virtual environment ? can you locate that libraries ?

I suspect that the launcher settings doesn't account for the path /home/phc/Software/Slicer/buildSystemQtPython-RelWithDebInfo/VTKv9-build/lib/python2.7/site-packages/vtkmodules/ ...

[phcerdan]

I suspect that the launcher settings doesn't account for the path /home/phc/Software/Slicer/buildSystemQtPython-RelWithDebInfo/VTKv9-build/lib/python2.7/site-packages/vtkmodules/

Spot on, it shouldn't, it makes no sense for my SALT installation (in folder Software/Shape/SALT/buildRelWithDebInfo) to know anything about my independent Slicer installation (in folder Software/Slicer/buildRelWithDebInfo). I wonder how this happens (ccache ?). Anyway, solved if I remove the lines referencing the other Slicer in SlicerSALTLauncherSettings.ini. It works!

For completion, your requested files,

SlicerSALTLauncherSettings.ini

[General]
launcherNoSplashScreen=false
launcherSplashImagePath=/home/user/Software/Shape/SALT/src/Applications/SlicerSALTApp/Resources/Images/SplashScreen.png
launcherSplashScreenHideDelayMs=3000
additionalLauncherHelpShortArgument=-h
additionalLauncherHelpLongArgument=--help
additionalLauncherNoSplashArguments=--no-splash,--help,--version,--home,--program-path,--no-main-window,--settings-path,--temporary-path





[Application]
path=<APPLAUNCHER_DIR>/bin/./SlicerSALTApp-real
arguments=
name=SlicerSALT
revision=04917a6
organizationDomain=kitware.com
organizationName=Kitware, Inc.

[ExtraApplicationToLaunch]

designer/shortArgument=
designer/help=Start Qt designer using Slicer plugins
designer/path=/usr/bin/designer
designer/arguments=

gnome-terminal/shortArgument=
gnome-terminal/help=Start gnome-terminal
gnome-terminal/path=/usr/bin/gnome-terminal
gnome-terminal/arguments=

ddd/shortArgument=
ddd/help=Start ddd
ddd/path=/usr/bin/ddd
ddd/arguments=

gdb/shortArgument=
gdb/help=Start gdb
gdb/path=/usr/bin/gdb
gdb/arguments=


[Environment]
additionalPathVariables=QT_PLUGIN_PATH,PYTHONPATH

[LibraryPaths]
1\path=<APPLAUNCHER_SETTINGS_DIR>/bin/.
2\path=../lib/SlicerSALT-4.9/qt-loadable-modules
3\path=<APPLAUNCHER_SETTINGS_DIR>/lib/SlicerSALT-4.9/cli-modules/.
4\path=<APPLAUNCHER_SETTINGS_DIR>/lib/SlicerSALT-4.9/qt-loadable-modules/.
5\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/VTKv9-build/lib/.
6\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/teem-build/bin/.
7\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/DCMTK-build/lib/.
8\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/ITKv4-build/lib/.
9\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/CTK-build/CTK-build/bin/.
10\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/CTK-build/PythonQt-build/.
11\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/LibArchive-install/lib
12\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/SlicerExecutionModel-build/ModuleDescriptionParser/bin/.
size=12

[Paths]
1\path=<APPLAUNCHER_SETTINGS_DIR>/bin/.
2\path=<APPLAUNCHER_SETTINGS_DIR>/lib/SlicerSALT-4.9/cli-modules/.
3\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/teem-build/bin/.
size=3

[EnvironmentVariables]
SLICER_HOME=/home/user/Software/Shape/SALT/buildRelWithDebInfo/Slicer-build
ITK_AUTOLOAD_PATH=<APPLAUNCHER_SETTINGS_DIR>/lib/SlicerSALT-4.9/ITKFactories/.
SSL_CERT_FILE=<APPLAUNCHER_SETTINGS_DIR>/share/SlicerSALT-4.9/Slicer.crt



[QT_PLUGIN_PATH]
1\path=<APPLAUNCHER_SETTINGS_DIR>/bin
2\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/CTK-build/CTK-build/bin
3\path=/usr/plugins
size=3

[PYTHONPATH]
1\path=<APPLAUNCHER_SETTINGS_DIR>/bin/.
2\path=<APPLAUNCHER_SETTINGS_DIR>/bin/Python
3\path=<APPLAUNCHER_SETTINGS_DIR>/lib/SlicerSALT-4.9/qt-loadable-modules/.
4\path=<APPLAUNCHER_SETTINGS_DIR>/lib/SlicerSALT-4.9/qt-loadable-modules/Python
5\path=<APPLAUNCHER_SETTINGS_DIR>/lib/SlicerSALT-4.9/qt-scripted-modules
6\path=/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/Slicer-build/bin
7\path=/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/Slicer-build/bin/Python
8\path=/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/Slicer-build/lib/Slicer-4.9/qt-loadable-modules
9\path=/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/Slicer-build/lib/Slicer-4.9/qt-loadable-modules/Python
10\path=/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/Slicer-build/lib/Slicer-4.9/qt-scripted-modules
11\path=/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/VTKv9-build/lib/python2.7/site-packages
12\path=/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/CTK-build/CTK-build/bin/Python
13\path=/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/CTK-build/CTK-build/bin
14\path=/home/user/.virtualenvs/slicer/lib/python27.zip
15\path=/home/user/.virtualenvs/slicer/lib/python2.7
16\path=/home/user/.virtualenvs/slicer/lib/python2.7/plat-linux2
17\path=/home/user/.virtualenvs/slicer/lib/python2.7/lib-tk
18\path=/home/user/.virtualenvs/slicer/lib/python2.7/lib-old
19\path=/home/user/.virtualenvs/slicer/lib/python2.7/lib-dynload
20\path=/usr/lib64/python2.7
21\path=/usr/lib/python2.7
22\path=/usr/lib/python2.7/plat-linux2
23\path=/usr/lib64/python2.7/lib-tk
24\path=/usr/lib/python2.7/lib-tk
25\path=/home/user/.virtualenvs/slicer/lib/python2.7/site-packages
26\path=/home/user/Software/ITK/build-master/Wrapping/Generators/Python
27\path=/home/user/Software/ITK/build-master/lib
28\path=/home/user/.virtualenvs/slicer/lib/python2.7/site-packages
29\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/VTKv9-build/lib/python2.7/site-packages
30\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/CTK-build/CTK-build/bin/Python
31\path=/home/user/Software/Shape/SALT/buildRelWithDebInfo/CTK-build/CTK-build/bin/.
size=31

I am using system python, but VTK still wraps python at build time, the vtkCommonKitPython.so is there:

/home/usr/Software/Shape/SALT/buildRelWithDebInfo/VTKv9-build/lib/libvtkCommonKitPython27D-9.0.so
/home/usr/Software/Shape/SALT/buildRelWithDebInfo/VTKv9-build/lib/libvtkCommonKitPython27D-9.0.so.1
/home/usr/Software/Shape/SALT/buildRelWithDebInfo/VTKv9-build/lib/python2.7/site-packages/vtkmodules/vtkCommonKitPython.so

[phcerdan]

Next steps:

• Enable Sequences
  Working after update to the tip of current master 4b32e8225 in SlicerRt/Sequences
  Found small issue reported in Python module SequenceSampleData depends on disabled SampleData #50
• Enable External Modules.
  Solved in commit 16ac69898

[jcfr]

@phcerdan Thanks for your help, this topic (and the one in your fork) have been updated

[phcerdan]

Thanks @jcfr, testing it, and hopefully, we can merge soon and start adding external projects.

[phcerdan]

It works but hitting #44

-- Build files have been written to: /home/user/Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/ShapeRegressionExtension-build
[13/16] Performing build step for 'ShapeRegressionExtension'
ninja: error: build.ninja:962: multiple rules generate lib/SlicerSALT-4.9/qt-scripted-modules/Resources/Icons/ShapeRegressionExtension.png [-w dupbuild=err]

FAILED: ShapeRegressionExtension-prefix/src/ShapeRegressionExtension-stamp/ShapeRegressionExtension-build
cd /home/user/Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build/ShapeRegressionExtension-build && /usr/bin/cmake --build .
ninja: build stopped: subcommand failed.
FAILED: ShapeRegressionExtension-prefix/src/ShapeRegressionExtension-stamp/ShapeRegressionExtension-build
cd /home/user/Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-build && /usr/bin/cmake --build . && /usr/bin/cmake -E touch /home/user/Software/Shape/SALT/buildRelWithDebInfo/ShapeRegressionExtension-prefix/src/ShapeRegressionExtension-stamp/ShapeRegressionExtension-build
ninja: build stopped: subcommand failed.

"Solved" using:
ninja -w dupbuild=warn ShapePopulationViewer

[jcfr]

So that we can move forward with the integration, would be great to get one positive review.

Packaging of all extensions work as expected.

There only few minor issues that should be addressed afterward:

• the logo on the left is huge. This is tracked by Use Qt::AA_UseHighDpiPixmaps KitwareMedical/SlicerCustomAppTemplate#6
• the loading of SequenceSampleData trigger an error. This is tracked by ENH: Add option to disable module SequencesSampleData SlicerRt/Sequences#50 and Python module SequenceSampleData depends on disabled SampleData #50

[phcerdan]

This really simplifies the infrastructure. Tested with the current enabled modules and extensions in linux and it works. We can solve the minor issues in other PRs

[jcfr]

Thanks @phcerdan ✌️ 🍾 🎉