Documentation/Labs/SlicerCondaIntegration
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Revision as of 16:28, 24 February 2015 by Jonieva (talk | contribs) (→Compile Slicer using System Python)
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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
Contents
Compile Slicer against miniconda
Mac
- Download the source code hosted in https://github.com/jonieva/Slicer/tree/Conda
- Build (assuming MacOSX 10.9):
cmake \ -DSlicer_USE_CONDA_python:BOOL=ON \ -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 \ -DSlicer_BUILD_CLI:BOOL=OFF \ -DSlicer_USE_PYTHONQT_WITH_TCL:BOOL=OFF \ ../Slicer
The only changes in the source code are in Superbuild/External_python.cmake and in Superbuild/External_NUMPY.cmake files (in the current version Slicer will use Anaconda Numpy). For the sake of testing, the next Python Conda modules are installed by default: numpy, scikit-learn.
Issues
- libsqlite3.dylib library in miniconda has a conflict with CTK:
Compiling python scripts: CTKScriptingPythonCore
Compiling python scripts: ctkSimplePythonShell
Linking CXX shared module ../../bin/CTKCorePythonQt.so
dyld: Symbol not found: _sqlite3_intarray_bind
Referenced from: /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
Expected in: /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/python-miniconda/lib/libsqlite3.dylib
in /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
dyld: Symbol not found: _sqlite3_intarray_bind
Referenced from: /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
Expected in: /Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/python-miniconda/lib/libsqlite3.dylib
in /System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
Workaround: delete or rename the file (there is a hack included in the External_python.cmake file to this end).
- When running Slicer.app (not the binary file in Slicer-Superbuild-Conda/Slicer-build) the program is not using Miniconda, but the System Python, so it doesn't find the right libraries:
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-Conda/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
So, in order that the system works, Slicer must be started from a terminal running the file Slicer-Superbuild-Conda/Slicer-build/Slicer
Linux
- Download the source code in https://github.com/jonieva/Slicer/tree/Conda
- Build Slicer normally, except for the setting Slicer_USE_CONDA_python. Example:
cmake \ '''-DSlicer_USE_CONDA_python:BOOL=ON''' \ -DCMAKE_BUILD_TYPE:STRING=Debug \ -DQT_QMAKE_EXECUTABLE:FILEPATH=/usr/bin/qmake \ -DSlicer_BUILD_CLI:BOOL=OFF \ -DSlicer_USE_PYTHONQT_WITH_TCL:BOOL=OFF \ ../Slicer
Different approach
The following worked for me (Steve Pieper, 2015-02-04) using ubuntu 13.10 and miniconda 3.8.4-py27_0
cmake \
-DCMAKE_BUILD_TYPE:STRING=Debug \
-DQT_QMAKE_EXECUTABLE:FILEPATH=/usr/bin/qmake \
-DPYTHON_EXECUTABLE:FILEPATH=${HOME}/miniconda/bin/python \
-DPYTHON_INCLUDE_DIR:PATH=${HOME}/miniconda/include/python2.7 \
-DPYTHON_LIBRARY:FILEPATH=${HOME}/miniconda/lib/libpython2.7.so \
-DSlicer_BUILD_CLI:BOOL=OFF \
-DSlicer_USE_PYTHONQT_WITH_TCL:BOOL=OFF \
../Slicer
make -j20
export PYTHONHOME=${USER}/miniconda
./Slicer-build/Slicer
But after it ran there was slicer's build of numpy inside miniconda, so I needed to do this:
bin/conda uninstall numpy bin/conda install numpy
I tried using this:
-DSlicer_USE_SYSTEM_NUMPY:BOOL=ON
but got this error:
... -- SuperBuild - CTKAPPLAUNCHER[OK] (SYSTEM) CMake Error at SuperBuild/External_CTKAPPLAUNCHER.cmake:21 (message): Enabling Slicer_USE_SYSTEM_CTKAPPLAUNCHER is not supported ! Call Stack (most recent call first): CMake/ExternalProjectDependency.cmake:561 (include) SuperBuild/External_python.cmake:21 (ExternalProject_Include_Dependencies) CMake/ExternalProjectDependency.cmake:561 (include) SuperBuild/External_VTKv6.cmake:11 (ExternalProject_Include_Dependencies) CMake/ExternalProjectDependency.cmake:561 (include) SuperBuild/External_teem.cmake:11 (ExternalProject_Include_Dependencies) CMake/ExternalProjectDependency.cmake:561 (include) CMake/ExternalProjectDependency.cmake:607 (ExternalProject_Include_Dependencies) SuperBuild.cmake:320 (ExternalProject_Include_Dependencies) CMakeLists.txt:599 (include)
-- Configuring incomplet
- Building a Slicer-Python with Miniconda
It should work without problems if you download the branch "Conda" in https://github.com/jonieva/Slicer/tree/Conda and running this command:
cmake -DCMAKE_BUILD_TYPE:STRING=Debug -DQT_QMAKE_EXECUTABLE:FILEPATH=/usr/bin/qmake -DSlicer_BUILD_CLI:BOOL=OFF -DSlicer_USE_PYTHONQT_WITH_TCL:BOOL=OFF -DSlicer_USE_CONDA_python:BOOL=ON ../Slicer
Windows
Although the code in https://github.com/jonieva/Slicer/tree/Conda should work with Windows too (using the setting Slicer_USE_CONDA_python=ON), it has not been tested at the moment.
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. Even when 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), I still got the same behavior. Following JC advice (thanks!), I used instal_name_tool to add manually the rpath to libpython2.7.dylib:
install_name_tool -id /Users/Jorge/miniconda/lib/libpython2.7.dylib /Users/Jorge/miniconda/lib/libpython2.7.dylib
Voila! Now we can rebuild and the ctkSimplePythonShell will use the correct Python! However, we will have to set up some environment variables in order than all the libraries are found. I tried some of the most important and checked that they were properly loaded in the Python console, but we will need the same ones that we are adding when building the current "SlicerPython":
export PYTHONHOME="/Users/Jorge/miniconda/" export PYTHONPATH="/Users/Jorge/miniconda/:/Users/Jorge/miniconda/lib/:/Users/Jorge/miniconda/lib/python2.7/site-packages/: /Users/Jorge/miniconda/lib/python2.7/lib-dynload/ :/Users/Jorge/miniconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.5-x86_64.egg/SimpleITK/ :/Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/" export DYLD_LIBRARY_PATH="/Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/SimpleITK-build/lib/ :/Users/Jorge/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/"
I also checked that the Python console works inside Slicer, as long as I launch the Slicer binary from a terminal that has all these environment variables initialized.
