From Peter Karasev:

Initial symptom:
(1) extension kslice fails to load at startup but can be imported
subsequently in python shell of nightly build
(2) rebuilding slicer and running gives 'teem.dll missing!' crash

Problem: there was another version of python 2.7.3 built with vs2012
in the path and the following was in my settings:
PATH=%PATH%;C:\hped\builds\tfstools\vs2012\win32_64\python\2.7.3\win32_64\debug\python
PYTHONPATH=%PYTHONPATH%;C:\hped\builds\tfstools\vs2012\win32_64\python\2.7.3\win32_64\debug\python

Slicer ignores most of this but it picks up python27_d.lib throughout
superbuild for "python debug library" since it does not get created in
slicer's python-build. I would think that deleting the offending
directory from environment variables and re-running cmake at the
superbuild level would be enough, but, no dice.
Fully purging the debug python required manually editing
CMakeCache.txt for CTK, VTK, Slicer, and so on, re-running cmake for
each project, open solution file and launching build for each item in
the superbuild that uses python.

Maybe this rarely happens or is intended behavior, but I'd imagine it
is a possibility for anyone on windows that has a program adding
itself to the path that provides a library not used in slicer yet
searched for by the find_package() commands...

// ------------------------
From Jc:

Hi Peter,

This problem would occur only for developer build, in the case the user download a build package, I don't think he would have any issue.

For developers, I see two approaches:

1) the problem could probably be solved:

• ensuring all project calling "find_package(PythonLibs)" are patched to optionally passe the option "NO_SYSTEM_ENVIRONMENT_PATH"
• patching the module "FindPythonLibs.cmake" bundled in CMake so that it can use the option "NO_SYSTEM_ENVIRONMENT_PATH" to also pass it down to the different "find_library" calls.

2) Alternatively, project like CTK, VTK or Slicer could simply not call "find_package(PythonLibs)" and expect the variable PYTHON_EXECUTABLE, PYTHON_LIBRARIES, ... to be properly set. The "find_package" call would be done only if Slicer is build with Slicer_USE_SYSTEM_PYTHON.

I think option (2) is the way to go. The is capture by issue 0001739

Let me know what you think.

Can this be bumped to a high priority feature in 4.4?

All set - Changed into Feature with high priority.

Hi Jc,

this might not be the most elegant fix but it works for me. Would you except a patch like the following one as a basis for a real fix? I would use this option for the nightly dashboard submissions, it would allow me to turn on more tests because the machine doesn't have to recompile ITK etc...

diff --git a/SuperBuild/External_ITKv4.cmake b/SuperBuild/External_ITKv4.cmake
index 396aa02..b86fd1a 100644
--- a/SuperBuild/External_ITKv4.cmake
+++ b/SuperBuild/External_ITKv4.cmake
@@ -6,6 +6,20 @@ if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED)
endif()
set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1)

+if (Slicer_USE_SYSTEM_ITKv4)
+

• find_package(ITK REQUIRED)

• create dummy external project

• ExternalProject_Add(ITKv4
• SOURCE_DIR ${CMAKE_BINARY_DIR}
• CONFIGURE_COMMAND ""
• BUILD_COMMAND ""
• INSTALL_COMMAND ""
• )

• +else()

• Sanity checks

  if(DEFINED ITK_DIR AND NOT EXISTS ${ITK_DIR})
  message(FATAL_ERROR "ITK_DIR variable is defined but corresponds to non-existing directory")
  @@ -118,3 +132,5 @@ else()

  let's add an 'empty' one

  SlicerMacroEmptyExternalProject(${proj} "${ITKv4_DEPENDENCIES}")
  endif()

• +endif()
  diff --git a/SuperBuild/External_python.cmake b/SuperBuild/External_python.cmake
  index 0c8537f..4a69580 100644
  --- a/SuperBuild/External_python.cmake
  +++ b/SuperBuild/External_python.cmake
  @@ -6,6 +6,25 @@ if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED)
  endif()
  set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1)

+if (Slicer_USE_SYSTEM_PYTHON)
+

• find_package(PythonLibs REQUIRED)
• find_package(PythonInterp REQUIRED)
• set(slicer_PYTHON_INCLUDE ${PYTHON_INCLUDE_DIRS})
• set(slicer_PYTHON_LIBRARY ${PYTHON_LIBRARIES})
• set(slicer_PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE})

• create dummy external project

• ExternalProject_Add(python
• SOURCE_DIR ${CMAKE_BINARY_DIR}
• CONFIGURE_COMMAND ""
• BUILD_COMMAND ""
• INSTALL_COMMAND ""
• )

• +else()

• Set dependency list

  set(python_DEPENDENCIES zlib CTKAPPLAUNCHER)
  if(Slicer_USE_PYTHONQT_WITH_TCL)
  @@ -173,6 +192,11 @@ else()
  SlicerMacroEmptyExternalProject(${proj} "${python_DEPENDENCIES}")
  endif()

+endif()
+
+message(STATUS "MSVC_VERSION:${MSVC_VERSION}")
+message(STATUS "python_URL:${python_URL}")
+message(STATUS "CMAKE_GENERATOR:${CMAKE_GENERATOR}")

message(STATUS "slicer_PYTHON_INCLUDE:${slicer_PYTHON_INCLUDE}")
You have new mail in /var/mail/domibel
domibel@sonne:~/Slicer$ git diff
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 5efb1d1..1c8c8a3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -208,6 +208,15 @@ mark_as_advanced(Slicer_FORCED_WC_REVISION)
#-----------------------------------------------------------------------------

External projects related options

#-----------------------------------------------------------------------------
+option(Slicer_USE_SYSTEM_PYTHON "Use python system libraries" OFF)
+mark_as_advanced(Slicer_USE_SYSTEM_PYTHON)
+
+option(Slicer_USE_SYSTEM_ITKv4 "Use itkv4 system libraries" OFF)
+mark_as_advanced(Slicer_USE_SYSTEM_ITKv4)
+
+option(Slicer_USE_SYSTEM_DCMTK "Use DCMTK system libraries" OFF)
+mark_as_advanced(Slicer_USE_SYSTEM_DCMTK)
+
CMAKE_DEPENDENT_OPTION(
Slicer_USE_PYTHONQT_WITH_OPENSSL "Enable PythonQt SSL support" OFF
"Slicer_USE_PYTHONQT" OFF)

 ITKZLIB

diff --git a/SuperBuild/External_DCMTK.cmake b/SuperBuild/External_DCMTK.cmake
index a53834d..1c1d04d 100644
--- a/SuperBuild/External_DCMTK.cmake
+++ b/SuperBuild/External_DCMTK.cmake
@@ -6,6 +6,21 @@ if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED)
endif()
set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1)

+if (Slicer_USE_SYSTEM_DCMTK)
+

• find_package(DCMTK REQUIRED)

• create dummy external project

• ExternalProject_Add(DCMTK
• SOURCE_DIR ${CMAKE_BINARY_DIR}
• CONFIGURE_COMMAND ""
• BUILD_COMMAND ""
• INSTALL_COMMAND ""
• )

• +else()

• Set dependency list

  set(DCMTK_DEPENDENCIES "zlib")

@@ -77,3 +92,5 @@ else()

let's add an 'empty' one

SlicerMacroEmptyExternalProject(${proj} "${DCMTK_DEPENDENCIES}")
endif()
+
+endif()
\ No newline at end of file
diff --git a/SuperBuild/External_ITKv4.cmake b/SuperBuild/External_ITKv4.cmake
index 396aa02..b86fd1a 100644
--- a/SuperBuild/External_ITKv4.cmake
+++ b/SuperBuild/External_ITKv4.cmake
@@ -6,6 +6,20 @@ if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED)
endif()
set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1)

+if (Slicer_USE_SYSTEM_ITKv4)
+

• find_package(ITK REQUIRED)

• create dummy external project

• ExternalProject_Add(ITKv4
• SOURCE_DIR ${CMAKE_BINARY_DIR}
• CONFIGURE_COMMAND ""
• BUILD_COMMAND ""
• INSTALL_COMMAND ""
• )

• +else()

• Sanity checks

  if(DEFINED ITK_DIR AND NOT EXISTS ${ITK_DIR})
  message(FATAL_ERROR "ITK_DIR variable is defined but corresponds to non-existing directory")
  @@ -118,3 +132,5 @@ else()

  let's add an 'empty' one

  SlicerMacroEmptyExternalProject(${proj} "${ITKv4_DEPENDENCIES}")
  endif()

• +endif()
  diff --git a/SuperBuild/External_python.cmake b/SuperBuild/External_python.cmake
  index 0c8537f..4a69580 100644
  --- a/SuperBuild/External_python.cmake
  +++ b/SuperBuild/External_python.cmake
  @@ -6,6 +6,25 @@ if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED)
  endif()
  set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1)

+if (Slicer_USE_SYSTEM_PYTHON)
+

• find_package(PythonLibs REQUIRED)
• find_package(PythonInterp REQUIRED)
• set(slicer_PYTHON_INCLUDE ${PYTHON_INCLUDE_DIRS})
• set(slicer_PYTHON_LIBRARY ${PYTHON_LIBRARIES})
• set(slicer_PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE})

• create dummy external project

• ExternalProject_Add(python
• SOURCE_DIR ${CMAKE_BINARY_DIR}
• CONFIGURE_COMMAND ""
• BUILD_COMMAND ""
• INSTALL_COMMAND ""
• )

• +else()

• Set dependency list

  set(python_DEPENDENCIES zlib CTKAPPLAUNCHER)
  if(Slicer_USE_PYTHONQT_WITH_TCL)
  @@ -173,6 +192,11 @@ else()
  SlicerMacroEmptyExternalProject(${proj} "${python_DEPENDENCIES}")
  endif()

+endif()
+
+message(STATUS "MSVC_VERSION:${MSVC_VERSION}")
+message(STATUS "python_URL:${python_URL}")
+message(STATUS "CMAKE_GENERATOR:${CMAKE_GENERATOR}")

Hi Dominique,

Thanks for providing a initial patch.

I started to improve the current build system to support Slicer_USESYSTEM* option more exhaustively.

Here is the topic: https://github.com/jcfr/Slicer/commits/1739-support-use-system-option

This is still work in progress. It currently support options like:

-DSlicer_USE_SYSTEM_zlib:BOOL=ON
-DSlicer_USE_SYSTEM_python:BOOL=ON
-DSlicer_USE_SYSTEM_NUMPY:BOOL=ON
-DSlicer_USE_SYSTEM_tcl:BOOL=ON
-DSlicer_USE_SYSTEM_LibArchive:BOOL=ON

The interesting part is that by simply configuring with:

-DSlicer_USE_SYSTEM_python:BOOL=ON

Since python depends on the projects "zlib", "NUMPY", "tcl". These ones will be expected to be available on the system.

Let me know what you think.

Based on your feedback, I propose we continue the effort. I think the current approach will make packaging easier.

Jc

This looks very nice. One annoying library is 'slicerlibcurl', which is a unpatched copy of curl, so this can be added to the system package list as well.
(libcurl-dev on Debian)

Hi,

Agreed. Will try to work something out regarding "slicerlibcurl".

I noticed few things:

(1) The FindDCMTK.cmake of ITKv4 is broken, it can't find system DCMTK even after passing DCMTK_DIR:PATH=/usr ... I will see how to fix this in upstream ITK. By for example contributing this version: https://github.com/jcfr/CTK/compare/382-fix-find-dcmtk-issue

(2) installing libdcmtk2-dev on Ubuntu 13.10, I have to also manually pass -DHAVE_CONFIG_H when building ITK, CTK, Slicer. Is this fix in debian testing ? As a quick workaround, I locally added a "add_definitions(-DHAVE_CONFIG_H) to FindDCMTK.cmake. The good news is that more recent DCMTK won't have that issue I think.

(3) Mickael Onken from Offis (DCMTK folks) is working on integrating my last patches into DCMTK allowing to get rid of FindDCMTK.cmake.

(4) Is there a way for me to install ITKv4 and CTK package from debian-testing on my Ubuntu 13.10 ? By using an alternative source ?

Regarding curl, you might need those patches. (Taken from my old Slicer3 package)

-find_package(SLICERLIBCURL REQUIRED)
-include(${SLICERLIBCURL_USE_FILE})
+find_package(CURL REQUIRED)
+include_directories(${CURL_INCLUDE_DIRS})

• ${SLICERLIBCURL_LIBRARIES} ITKIO MRMLIDIO)
• ${CURL_LIBRARIES} ITKIO MRMLIDIO)

-#include <slicerlibcurl/slicerlibcurl.h>
+#include <curl/curl.h>

(2)
Debian testing doesn't contain the newest version yet, but it will soon.

(4)
The source would be the same, but you have to generate the right binaries which might be incompatible with 1310.

dget http://http.debian.net/debian/pool/main/c/ctk/ctk_0.1.0+git20131105~b8307961b6-2.dsc
cd ctk-0.1.0+git20131105~b8307961b6
debuild

#same with itk4:
dget http://http.debian.net/debian/pool/main/i/insighttoolkit4/insighttoolkit4_4.4.2-4.dsc
cd insight....
debuild

but 1310 might have already a working ITK version , just type aptitude install libinsighttoolkit4-dev

In my updated topic [1] there is now a new option Slicer_USE_SYSTEM_curl. It also now build the regular curl source that are now CMake'ified.

What is next:

• Update CTK build system to also support the "CTK_USESYSTEM*" variable
• Add support for Slicer_USE_SYSTEM(ITK,VTK,CTK) (Currently through a fatal error message if used)

When this topic will be integrated. You shouldn't have to do any thing crazy to have Slicer built and be ready for debian packaging :)

[1] https://github.com/jcfr/Slicer/tree/1739-support-use-system-option

Fixed in r22724
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&amp;revision=22724

// ---------------------------------
COMP: Support Slicer_USESYSTEM* option. Fixes 0001739

This commit implements four main changes:

(1) it updates Slicer build system to support configuring Slicer passing
Slicer_USESYSTEM* CMake variables

(2) it updates to a newer version of CTK able to understand CTK_USESYSTEM*
options. List of CTK contribution associated with this update are
reported below.

(3) it changes curl library from "slicerlibcurl/cmcurl/curl" v7.12.1
to the more recent official CMake'ified curl v7.33.0. This has the
benefit of making it easier to build against the corresponding
system library.

(4) It implements workaround allowing some CLIs to built on Debian-like
distribution that is providing DCMTK 3.6.0.
See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=637687
EMSegment project has also been updated to implement a similar
workaround.

The macro "SlicerMacroCheckExternalProjectDependency" allowing to
recursively traverse the external project dependency tree has been
updated.

The traversal is now done in two passes. The first pass traverses the
complete tree to set the value of Slicer_USESYSTEM*.

The second pass invokes the "ExternalProject_Add" function and displays
informative messages. In addition to the usual "[OK]" and "[INCLUDED]"
suffixes, an additional text "(SYSTEM)" is displayed. It means the
corresponding libraries (and headers) installed on the system will be
used.

On Ubuntu 13.10, support for the following options have been
tested simultaneously:
-DSlicer_USE_PYTHONQT_WITH_OPENSSL:BOOL=ON
-DSlicer_USE_SYSTEM_python:BOOL=ON
-DSlicer_USE_SYSTEM_DCMTK:BOOL=ON
-DSlicer_USE_SYSTEM_LibArchive:BOOL=ON
-DSlicer_USE_SYSTEM_curl:BOOL=ON
-DSlicer_USE_SYSTEM_teem:BOOL=ON
-DSlicer_USE_SYSTEM_OpenIGTLink:BOOL=ON
-DSlicer_USE_SYSTEM_OpenSSL:BOOL=ON # Implicitly set because python depends

on OpenSSL.

-DSlicer_BUILD_OpenIGTLinkIF:BOOL=OFF # Only openigtlink version1 are available

and code does NOT supports only v2.

To successfully build Slicer against system libraries, the corresponding
packages have been installed:
sudo apt-get install libssl-dev \
libdcmtk-dev \
libarchive-dev \
libpython2.7-dev \
python-numpy \
libcurl4-openssl-dev \
libteem-dev \
tk-dev \
tcl-dev \
itcl3-dev \
libopenigtlink1-dev

While not tested, support for the following option has also been
implemented:
-DSlicer_USE_SYSTEM_ITKv4:BOOL=ON
-DSlicer_USE_SYSTEM_VTK:BOOL=ON

CTK updates:

$ git shortlog 91cdf9e0f...02ecc27d0

Jean-Christophe Fillion-Robin (39):
Ensure CTK_INSTALL_QTPLUGIN_DIR is properly set
Ensure "CMAKE_INSTALL_PREFIX" is properly passed to inner project.
By default, do not install application headers
Install CTK's .cmake files
Merge branch '65-packaging-support' into 403-relocatable-ctkconfig-usectk
Set plugin install rules for target and include files
Remove commented code and unused vars from CTKConfig / CTKGenerateCTKConfig
Explicitly set default value for CTK_INSTALL_QTPLUGIN_DIR
Remove explicit setting of CMake policies.
Improve FindDCMTK.cmake documentation
Add DCMTK 3.6.0 support to ctkDICOMUtil.cpp
Ensure DCMTK libraries can be found on system without setting DCMTK_DIR
FindDCMTK - Workaround bug in packaging of DCMTK 3.6.0 on Debian.
Add support for install-able and relocatable package.
Merge branch '382-fix-find-dcmtk-issue'
Merge branch '403-relocatable-ctkconfig-usectk'
Merge branch '405-support-dcmtk-360'
Fix -Wunused-but-set-variable in transfer function tests
Merge branch '209-fix-vtk-transfer-function-test-warnings'
Fix linking of VTKCoreCppTest by adding a check for linker capabilities
Merge branch 'fix-vtk-core-test-link-error'
COMP: FindDCMTK - Exclude -D from DCMTK_DEFINITIONS for easier re-use
Merge branch '382-fix-find-dcmtk-issue'
Associate DCMTK_DEFINITIONS to CTKDICOMCore
Merge branch '413-associated-dcmtk-definitions-to-ctkdicomcore'
Merge pull request 0000410 from NifTK/409-widgets-on-ctkPopupWidget-do-not-get-keyboard-focus
Add DCMTK 3.6.0 support to CTK application.
Merge branch '405-support-dcmtk-360'
Fix configuration of CTKConfig based on DCMTK_HAVE_CONFIG_H_OPTIONAL value
Merge branch '413-associated-dcmtk-definitions-to-ctkdicomcore'
Add convenience function "ctk_list_to_string"
Automatically reformat list passed to "CTK" inner build.
COMP: Add support for CTK_USESYSTEM options
Merge branch '418-support-use-system-option'
FindDCMTK - Do not explicitly set DCMTK_DEFINITIONS
FindDCMTK - Clean white spaces
Merge branch '382-fix-find-dcmtk-issue' into 413-associated-dcmtk-definitions-to-ctkdicomcore
Associate CTKDICOMCore with DCMTK_DEFINITIONS in build and install tree
Merge branch '413-associated-dcmtk-definitions-to-ctkdicomcore'

Miklos Espak (1):
Active window flag transferred on RequestSoftwareInputPanel event

Steve Pieper (2):
Put all tags for a given instance into a list for a single batch insert
Merge pull request 0000415 from pieper/414-batch-insert-tags
// ---------------------------------

Closing resolved issues that have not been updated in more than 3 months

Fix committed to 2145-support-for-installing-extension-from-file branch.