Documentation/Labs/SlicerCondaIntegration

Slicer currently builds a custom python distribution from source, but not all useful packages are available. But Anaconda provides a set of binaries that might provide a more comprehensive ecosystem.

Before attempting to use the whole Anaconda package, the first approach has been to use Miniconda, which is a reduced version of Anaconda.

Note: the platform used is MacOSX 10.9.5 with XCode 6

Compile Slicer against miniconda

 ccmake -DCMAKE_BUILD_TYPE:STRING=Debug -DQT_QMAKE_EXECUTABLE:FILEPATH=/usr/bin/qmake -DPYTHON_EXECUTABLE:FILEPATH=/Users/Jorge/miniconda/bin/python 
 -DPYTHON_INCLUDE_DIR:PATH=/Users/Jorge/miniconda/include/python2.7 -DPYTHON_LIBRARY:FILEPATH=/Users/Jorge/miniconda/lib/libpython2.7.dylib 
 -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9 -DCMAKE_OSX_SYSROOT:FILEPATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer
 /SDKs/MacOSX10.9.sdk  -G  "Eclipse CDT4 - Unix Makefiles" ../Slicer

Doing this, it seems that the Slicer superbuild works ok, and some packages are installed in /Users/Jorge/miniconda/lib/python2.7/site-packages. Ex: gitdb, numpy, SimpleITK-0.9.0.dev656-py2.7-macosx-10.5-x86_64.egg

SimpleITK is not properly installed, when I run miniconda interpreter and try to import it, I get an error:

 import SimpleITK
 Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/Users/Jorge/miniconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.5-x86_64.egg/SimpleITK/__init__.py", line 1, in <module>
   from .SimpleITK import *
 File "/Users/Jorge/miniconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 28, in <module>
   _SimpleITK = swig_import_helper()
 File "/Users/Jorge/miniconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.5-x86_64.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper
   _mod = imp.load_module('_SimpleITK', fp, pathname, description)
 ImportError: dlopen(/Users/Jorge/miniconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libSimpleITKBasicFilters12-0.9.1.dylib
 Referenced from: /Users/Jorge/miniconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.5-x86_64.egg/SimpleITK/_SimpleITK.so
 Reason: image not found

Other libraries like gitdb or numpy seem to work properly.

Compile Slicer using System Python

In order to compare the behaviors, I also compiled another version of Slicer using my System Python:

 ccmake -DCMAKE_BUILD_TYPE:STRING=Debug -DQT_QMAKE_EXECUTABLE:FILEPATH=/usr/bin/qmake  -DCMAKE_OSX_DEPLOYMENT_TARGET:STRING=10.9  
 -DCMAKE_OSX_SYSROOT:FILEPATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk  
 -G  "Eclipse CDT4 - Unix Makefiles" -DSlicer_USE_SYSTEM_python:BOOL=TRUE ../Slicer

Checking my System Python folder, everything seems to be properly installed.

Common issues in Miniconda and System python

There is a difference between executing Slicer-Superbuild/Slicer-build/bin/Slicer.app and Slicer-Superbuild/Slicer-build/Slicer when I open a Slicer Python console. In the former case, Slicer cannot find some libraries. When I open the console I get:

 Python 2.7.5 (default, Mar  9 2014, 22:15:05) 
 [GCC 4.2.1 Compatible Apple LLVM 5.0 (clang-500.0.68)] on darwin
 >>> Traceback (most recent call last):
 File "<string>", line 1, in <module>
 File "/Users/Jorge/Projects/BWH/Slicer-Superbuild-SystemPython/Slicer-build/lib/Slicer-4.4/qt-scripted-modules/SimpleFilters.py", line 3, in <module>
   import SimpleITK as sitk
 File "/Library/Python/2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.9-intel.egg/SimpleITK/__init__.py", line 1, in <module>
   from .SimpleITK import *
 File "/Library/Python/2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.9-intel.egg/SimpleITK/SimpleITK.py", line 28, in <module>
   _SimpleITK = swig_import_helper()
 File "/Library/Python/2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.9-intel.egg/SimpleITK/SimpleITK.py", line 24, in swig_import_helper
   _mod = imp.load_module('_SimpleITK', fp, pathname, description)
 ImportError: dlopen(/Library/Python/2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.9-intel.egg/SimpleITK/_SimpleITK.so, 2): Library not loaded: libSimpleITKBasicFilters12-0.9.1.dylib
 Referenced from: /Library/Python/2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.9-intel.egg/SimpleITK/_SimpleITK.so
 Reason: image not found

If I run Slicer-Superbuild/Slicer-build/Slicer, everything seems to work fine.

However, in both cases Slicer is loading my System python!

Next step: isolating the Python console problem

Following the advice of Steve Pieper, I tried to replicate the problem just in the CTK Python console, without running Slicer. To do that, I enabled the setting CTK_APP_ctkSimplePythonShell, inside Slicer-Superbuild/CTK-build/CTK-build. I had exactly the same behavior that I had within Slicer.

I tried to set exactly the same settings in my "Slicer Python" version and in my "Miniconda" version, replacing just the settings PYTHON_EXECUTABLE, PYTHON_INCLUDE_DIR and PYTHON_LIBRARY. Still some behavior...

In this process, I found out two things that are different in the "Slicer Python" and "Miniconda":

If I run otool in my ctkSimplePythonShell, there is a difference in libpython2.7.dylib

~/Projects/BWH/Slicer-Superbuild-Debug/CTK-build/CTK-build/bin$ otool -L ctkSimplePythonShell

 ctkSimplePythonShell:
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/CTK-build/CTK-build/bin/libCTKScriptingPythonWidgets.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/CTK-build/CTK-build/bin/libCTKVisualizationVTKCore.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/CTK-build/CTK-build/bin/libCTKWidgets.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/CTK-build/QtTesting-build/libQtTesting.dylib (compatibility version 0.0.0, current version 0.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/CTK-build/CTK-build/bin/libCTKScriptingPythonCore.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkInteraction-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkFiltersHybrid-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkOpenGL-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkImagingHybrid-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkIO-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /System/Library/Frameworks/AGL.framework/Versions/A/AGL (compatibility version 1.0.0, current version 1.0.0)
 /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 20.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkTestingRendering-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkRendering-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkFilters-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkalglib-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkverdict-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkftgl-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkfreetype-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 48.0.0)
 /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0)
 /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkImaging-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/CTK-build/CMakeExternals/Install/lib/libPythonQt.dylib (compatibility version 0.0.0, current version 0.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkWrappingPython27Core-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtkCommon-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/python-install/lib/libpython2.7.dylib (compatibility version 0.0.0, current version 0.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/VTKv6-build/lib/libvtksys-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Debug/CTK-build/CTK-build/bin/libCTKCore.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 QtOpenGL.framework/Versions/4/QtOpenGL (compatibility version 4.8.0, current version 4.8.6)
 QtXmlPatterns.framework/Versions/4/QtXmlPatterns (compatibility version 4.8.0, current version 4.8.6)
 QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.6)
 QtXml.framework/Versions/4/QtXml (compatibility version 4.8.0, current version 4.8.6)
 QtSql.framework/Versions/4/QtSql (compatibility version 4.8.0, current version 4.8.6)
 QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.6)
 QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.6)
 /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
 /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)

~/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/CTK-build/CTK-build/bin$ otool -L ctkSimplePythonShell

ctkSimplePythonShell:
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/CTK-build/CTK-build/bin/libCTKScriptingPythonWidgets.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/CTK-build/CTK-build/bin/libCTKVisualizationVTKCore.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/CTK-build/CTK-build/bin/libCTKWidgets.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/CTK-build/QtTesting-build/libQtTesting.dylib (compatibility version 0.0.0, current version 0.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/CTK-build/CTK-build/bin/libCTKScriptingPythonCore.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkInteraction-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkFiltersHybrid-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkOpenGL-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkImagingHybrid-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkIO-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /System/Library/Frameworks/AGL.framework/Versions/A/AGL (compatibility version 1.0.0, current version 1.0.0)
 /System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa (compatibility version 1.0.0, current version 20.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkTestingRendering-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkRendering-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkFilters-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkalglib-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkverdict-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkftgl-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkfreetype-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices (compatibility version 1.0.0, current version 48.0.0)
 /System/Library/Frameworks/CoreServices.framework/Versions/A/CoreServices (compatibility version 1.0.0, current version 59.0.0)
 /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkImaging-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/CTK-build/CMakeExternals/Install/lib/libPythonQt.dylib (compatibility version 0.0.0, current version 0.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkWrappingPython27Core-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtkCommon-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 libpython2.7.dylib (compatibility version 2.7.0, current version 2.7.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/libvtksys-6.2.1.dylib (compatibility version 1.0.0, current version 1.0.0)
 /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/CTK-build/CTK-build/bin/libCTKCore.0.1.dylib (compatibility version 0.1.0, current version 0.1.0)
 QtOpenGL.framework/Versions/4/QtOpenGL (compatibility version 4.8.0, current version 4.8.6)
 QtXmlPatterns.framework/Versions/4/QtXmlPatterns (compatibility version 4.8.0, current version 4.8.6)
 QtGui.framework/Versions/4/QtGui (compatibility version 4.8.0, current version 4.8.6)
 QtXml.framework/Versions/4/QtXml (compatibility version 4.8.0, current version 4.8.6)
 QtSql.framework/Versions/4/QtSql (compatibility version 4.8.0, current version 4.8.6)
 QtNetwork.framework/Versions/4/QtNetwork (compatibility version 4.8.0, current version 4.8.6)
 QtCore.framework/Versions/4/QtCore (compatibility version 4.8.0, current version 4.8.6)
 /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
 /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)

So, it looks like there is a problem with the rpath of the library. However, I tried to copy the python executable and the library itself to the same bin folder where the ctkSimplePython is (Slicer-Superbuild-Conda-Eclipse/CTK-build/CTK-build/bin) and still I get the same behaviour, so although it may be necessary to work on it, it doesn't seem to be the main cause of the problem.

Future steps

I observed there is a big difference in the structure of the folders in the Slicer Python and Miniconda that could be affecting. There is a Libs folder inside the /Slicer-Superbuild-Debug/CTK-build/CTK-build that contain many classes that seem required to run a console that uses a Python version different than the system. I hope that someone can guide me a little bit in this...