Difference between revisions of "Documentation/Labs/SlicerCondaIntegration"
From Slicer Wiki
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Slicer currently builds a custom python distribution from source, but not all useful packages are available. But [https://store.continuum.io/cshop/anaconda/ Anaconda] provides a set of binaries that might provide a more comprehensive ecosystem. | Slicer currently builds a custom python distribution from source, but not all useful packages are available. But [https://store.continuum.io/cshop/anaconda/ 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. | + | 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 | ||
==1: compile Slicer against miniconda== | ==1: 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 | + | 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 | 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 | ||
| Line 23: | Line 28: | ||
Reason: image not found | Reason: image not found | ||
| − | + | Other libraries like gitdb or numpy seem to work properly. | |
| + | |||
| + | == 2: 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... | ||
Revision as of 22:09, 30 January 2015
Home < Documentation < Labs < SlicerCondaIntegrationSlicer 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
1: 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.
2: 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...
