Documentation/Labs/SlicerCondaIntegration

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Home < 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

Mac

    • First approach: install Miniconda manually and then build Slicer against it

Assuming that we already installed Miniconda in the default folder ({HOME}/miniconda), we could build Slicer against it: 

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.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  \
	-DSlicer_BUILD_CLI:BOOL=OFF \
	-DSlicer_USE_PYTHONQT_WITH_TCL:BOOL=OFF \
	../Slicer

At the moment there are also some additional actions to take, like setting some environment variables: 

 export PYTHONHOME="${HOME}/miniconda/"

It is also possible that you have to set another ones like: 

 export PYTHONPATH="{HOME}/miniconda/:{HOME}/miniconda/lib/:{HOME}/miniconda/lib/python2.7/site-packages/:{HOME}/miniconda/lib/python2.7/lib-dynload/
 :{HOME}/miniconda/lib/python2.7/site-packages/SimpleITK-0.9.0.dev656-py2.7-macosx-10.5-x86_64.egg/SimpleITK/:{HOME}/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/"
 
 export DYLD_LIBRARY_PATH="{HOME}/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/SimpleITK-build/lib/:{HOME}/Projects/BWH/Slicer-Superbuild-Conda-Eclipse/VTKv6-build/lib/"

Besides, it is necessary to fix rpath in the library: 

 install_name_tool -id {HOME}/miniconda/lib/libpython2.7.dylib {HOME}/miniconda/lib/libpython2.7.dylib
 Note: the paths have to be absolute, so you want to replace {HOME} for your home folder.
    • Second approach: to build a "SlicerPython" using Miniconda

I created a fork from Slicer to implement this approach, packaging Miniconda and installing it in a similar way that SlicerPython is used now. You can download the code in https://github.com/jonieva/Slicer

To build with this code: 

 cmake -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 -DSlicer_USE_CONDA_python:BOOL=ON ../Slicer

The only changes are in Superbuild/External_python.cmake file. There is a commented block that you can use to implement the first approach.

However, at the moment I get a build error: 

 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

NOTE: This problem can be "solved" if we replace the libsqlite3.dylib by a link to the /usr/lib/libsqlite3.dylib library, or even just removing the library from Miniconda. There is a hack included in the External_python.cmake file to this end.

Also, when I run Slicer.app the program crashes: 

Process:         Slicer [1333]
  Path:            /Users/USER/*/Slicer.app/Contents/MacOS/./Slicer
  Identifier:      ???
  Version:         4.4.0 (4.4.0-2015-02-10)
  Code Type:       X86-64 (Native)
  Parent Process:  Slicer [1332]
  Responsible:     Terminal [205]
  User ID:         501

  Date/Time:       2015-02-10 17:51:57.975 -0500
  OS Version:      Mac OS X 10.9.5 (13F34)
  Report Version:  11
  Anonymous UUID:  F95E6C4D-DD65-A370-437D-3C54CFE11E49

  Sleep/Wake UUID: C450E55A-B4B9-4F0B-A350-F80A3FD33CB7

  Crashed Thread:  0  Dispatch queue: com.apple.main-thread

  Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
  Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000098

  VM Regions Near 0x98:
  --> 
      __TEXT                 000000010858f000-00000001085bf000 [  192K] r-x/rwx SM=COW  /Users/USER/*/Slicer.app/Contents/MacOS/Slicer

  Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
  0   libpython2.7.dylib            	0x000000011eecbd18 subtype_dealloc + 216
  1   libPythonQt.dylib             	0x000000010cec58d0 PythonQtObjectPtr::~PythonQtObjectPtr() + 96 (PythonQtObjectPtr.cpp:52)
  2   libPythonQt.dylib             	0x000000010cec58f5 PythonQtObjectPtr::~PythonQtObjectPtr() + 21 (PythonQtObjectPtr.cpp:53)
  3   libPythonQt.dylib             	0x000000010cde6e5c PythonQtMemberInfo::~PythonQtMemberInfo() + 28 (PythonQtClassInfo.h:45)
  4   libPythonQt.dylib             	0x000000010cdde605 PythonQtMemberInfo::~PythonQtMemberInfo() + 21 (PythonQtClassInfo.h:45)
  5   libPythonQt.dylib             	0x000000010cde051c QHashNode<QByteArray, PythonQtMemberInfo>::~QHashNode() + 28 (qhash.h:216)
  6   libPythonQt.dylib             	0x000000010cde04f5 QHashNode<QByteArray, PythonQtMemberInfo>::~QHashNode() + 21 (qhash.h:216)
  7   libPythonQt.dylib             	0x000000010cde03dd QHash<QByteArray, PythonQtMemberInfo>::deleteNode2(QHashData::Node*) + 29 (qhash.h:523)
  8   QtCore                        	0x000000011947b73a QHashData::free_helper(void (*)(QHashData::Node*)) + 138
  9   libPythonQt.dylib             	0x000000010cde0473 QHash<QByteArray, PythonQtMemberInfo>::freeData(QHashData*) + 35 (qhash.h:571)
  10  libPythonQt.dylib             	0x000000010cde5d7c QHash<QByteArray, PythonQtMemberInfo>::~QHash() + 60 (qhash.h:283)
  11  libPythonQt.dylib             	0x000000010cdde355 QHash<QByteArray, PythonQtMemberInfo>::~QHash() + 21 (qhash.h:283)
  12  libPythonQt.dylib             	0x000000010cdd84c4 PythonQtClassInfo::~PythonQtClassInfo() + 500 (PythonQtClassInfo.cpp:78)
  13  libPythonQt.dylib             	0x000000010cdd87a5 PythonQtClassInfo::~PythonQtClassInfo() + 21 (PythonQtClassInfo.cpp:78)
  14  libPythonQt.dylib             	0x000000010cdfb2f6 PythonQtPrivate::~PythonQtPrivate() + 230 (PythonQt.cpp:231)
  15  libPythonQt.dylib             	0x000000010cdfb695 PythonQtPrivate::~PythonQtPrivate() + 21 (PythonQt.cpp:239)
  16  libPythonQt.dylib             	0x000000010cdfb6b8 PythonQtPrivate::~PythonQtPrivate() + 24 (PythonQt.cpp:224)
  17  libPythonQt.dylib             	0x000000010cdfb148 PythonQt::~PythonQt() + 72 (PythonQt.cpp:220)
  18  libPythonQt.dylib             	0x000000010cdfb1b5 PythonQt::~PythonQt() + 21 (PythonQt.cpp:222)
  19  libPythonQt.dylib             	0x000000010cdfb1d8 PythonQt::~PythonQt() + 24 (PythonQt.cpp:219)
  20  libPythonQt.dylib             	0x000000010cdfa46d PythonQt::cleanup() + 61 (PythonQt.cpp:155)
  21  libCTKScriptingPythonCore.0.1.dylib	0x000000010c4ce7fe ctkAbstractPythonManager::~ctkAbstractPythonManager() + 110 (ctkAbstractPythonManager.cpp:90)
  22  libqSlicerBaseQTCore.dylib    	0x000000010b8f9409 qSlicerCorePythonManager::~qSlicerCorePythonManager() + 153 (qSlicerCorePythonManager.cxx:59)
  23  libqSlicerBaseQTGUI.dylib     	0x0000000108a16115 qSlicerPythonManager::~qSlicerPythonManager() + 21 (qSlicerPythonManager.cxx:37)
  24  libqSlicerBaseQTGUI.dylib     	0x0000000108a16135 qSlicerPythonManager::~qSlicerPythonManager() + 21 (qSlicerPythonManager.cxx:37)
  25  libqSlicerBaseQTGUI.dylib     	0x0000000108a16158 qSlicerPythonManager::~qSlicerPythonManager() + 24 (qSlicerPythonManager.cxx:33)
  26  libqSlicerBaseQTCore.dylib    	0x000000010b8a3903 QtSharedPointer::ExternalRefCount<qSlicerCorePythonManager>::deref(QtSharedPointer::ExternalRefCountData*, qSlicerCorePythonManager*) + 115 (qsharedpointer_impl.h:342)
  27  libqSlicerBaseQTCore.dylib    	0x000000010b8a37d9 void QtSharedPointer::ExternalRefCount<qSlicerCorePythonManager>::internalCopy<qSlicerCorePythonManager>(QtSharedPointer::ExternalRefCount<qSlicerCorePythonManager> const&) + 121 (qsharedpointer_impl.h:413)
  28  libqSlicerBaseQTCore.dylib    	0x000000010b8a2357 QSharedPointer<qSlicerCorePythonManager>::operator=(QSharedPointer<qSlicerCorePythonManager> const&) + 39 (qsharedpointer_impl.h:484)
  29  libqSlicerBaseQTCore.dylib    	0x000000010b8a13ad QSharedPointer<qSlicerCorePythonManager>::clear() + 45 (qsharedpointer_impl.h:543)
  30  libqSlicerBaseQTCore.dylib    	0x000000010b8978b2 qSlicerCoreApplicationPrivate::~qSlicerCoreApplicationPrivate() + 82 (qSlicerCoreApplication.cxx:138)
  31  libqSlicerBaseQTGUI.dylib     	0x000000010897a595 qSlicerApplicationPrivate::~qSlicerApplicationPrivate() + 261 (qSlicerApplication.cxx:157)
  32  libqSlicerBaseQTGUI.dylib     	0x000000010897a615 qSlicerApplicationPrivate::~qSlicerApplicationPrivate() + 21 (qSlicerApplication.cxx:157)
  33  libqSlicerBaseQTGUI.dylib     	0x000000010897a638 qSlicerApplicationPrivate::~qSlicerApplicationPrivate() + 24 (qSlicerApplication.cxx:146)
  34  libqSlicerBaseQTCore.dylib    	0x000000010b8a457e QScopedPointerDeleter<qSlicerCoreApplicationPrivate>::cleanup(qSlicerCoreApplicationPrivate*) + 46 (qscopedpointer.h:63)
  35  libqSlicerBaseQTCore.dylib    	0x000000010b8a4537 QScopedPointer<qSlicerCoreApplicationPrivate, QScopedPointerDeleter<qSlicerCoreApplicationPrivate> >::~QScopedPointer() + 39 (qscopedpointer.h:101)
  36  libqSlicerBaseQTCore.dylib    	0x000000010b8a1c25 QScopedPointer<qSlicerCoreApplicationPrivate, QScopedPointerDeleter<qSlicerCoreApplicationPrivate> >::~QScopedPointer() + 21 (qscopedpointer.h:102)
  37  libqSlicerBaseQTCore.dylib    	0x000000010b89ccca qSlicerCoreApplication::~qSlicerCoreApplication() + 42 (qSlicerCoreApplication.cxx:670)
  38  libqSlicerBaseQTGUI.dylib     	0x000000010897cda5 qSlicerApplication::~qSlicerApplication() + 21 (qSlicerApplication.cxx:316)
  39  libqSlicerBaseQTGUI.dylib     	0x000000010897cdc5 qSlicerApplication::~qSlicerApplication() + 21 (qSlicerApplication.cxx:316)
  40                                	0x00000001085bb989 (anonymous namespace)::SlicerAppMain(int, char**) + 4825
  41                                	0x00000001085ba6a2 main + 34
  42  libdyld.dylib                 	0x00007fff8b4bc5fd start + 1

Linux

The following worked for me (Steve Pieper, 2015-02-04) using ubuntu 13.10 and miniconda 3.8.4-py27_0

Slicer-conda-linux-2015-02-04.png 
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

Windows

TBD

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. 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.

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