Slicer3WrapITKPython - Revision history

Inorton at 23:16, 2 July 2011

2011-07-02T23:16:55Z

Inorton at 21:37, 15 October 2010

2010-10-15T21:37:10Z

Inorton at 21:36, 15 October 2010

2010-10-15T21:36:02Z

Inorton at 20:58, 15 October 2010

2010-10-15T20:58:52Z

Inorton at 20:52, 15 October 2010

2010-10-15T20:52:43Z

Inorton at 19:54, 15 October 2010

2010-10-15T19:54:23Z

Inorton: Created page with 'The recommended ITK wrapping To build Slicer3 with Python ITK wrapping, made the following changes: Edit /Slicer3/SuperBuild/External_Insight.cmake In the section CMAKE_ARGS, a…'

2010-10-15T19:54:01Z

Created page with 'The recommended ITK wrapping To build Slicer3 with Python ITK wrapping, made the following changes: Edit /Slicer3/SuperBuild/External_Insight.cmake In the section CMAKE_ARGS, a…'

New page

The recommended ITK wrapping To build Slicer3 with Python ITK wrapping, made the following changes:

Edit /Slicer3/SuperBuild/External_Insight.cmake
In the section CMAKE_ARGS, add the following arguments:

-DINSTALL_WRAP_ITK_COMPATIBILITY:BOOL=ON
-DUSE_WRAP_ITK:BOOL=ON
-DWRAP_ITK_PYTHON:BOOL=ON

Then save and make as usual. BE WARNED that WrapITK will take a long time to compile (>2 hrs on a quad

@@ Line 1: / Line 1: @@
-The recommended ITK wrapping is WrapITK. To build Slicer3 with Python ITK wrapping, make the following change:
+The recommended ITK wrapping is WrapITK. To build Slicer4 with Python ITK wrapping, make the following change:
-Edit this file:    '''''[path]''/Slicer3/SuperBuild/External_Insight.cmake'''
+Edit this file:    '''''[path]''/Slicer4/SuperBuild/External_Insight.cmake'''
 *In the section CMAKE_ARGS, add the following arguments:
@@ Line 8: / Line 8: @@
        -DUSE_WRAP_ITK:BOOL=ON
        -DWRAP_ITK_PYTHON:BOOL=ON
 </pre>
-Then save and make Slicer as usual. BE WARNED that WrapITK will take a long time to compile because of all the templating (>2 hrs on new&fast computer)
+Then save and make Slicer as usual. BE WARNED that WrapITK will take a long time to compile because of all the templating. Turning off Java and Tcl helps.
 If this works, the wrapping should build against the auto-detected system Python. There are options which could be added above so that ITK build uses the Slicer python, but since ITK (Insight) builds first that may cause some problems. Maybe CMake will automatically detect the dependency but I haven't tried it yet... So, the easy way is just let WrapITK do it's thing first, then add ITK manually to the Slicer python:
 *Edit Slicer3-SuperBuild/Insight-build/Wrapping/WrapITK/Python/WrapITK.pth
-*The first line should be ok, but must also add the ITK bin directory. My WrapITK.pth looks like this:
+*Leave the first line, but add the ITK bin directory. My WrapITK.pth looks like this:
 <pre>
-/cmn/dev/Slicer3-SuperBuild/Insight-build/Wrapping/WrapITK/Python
+/cmn/git/Slicer4-sb/Insight-build/Wrapping/WrapITK/Python
-/cmn/dev/Slicer3-SuperBuild/Insight-build/bin
+/cmn/dev/Slicer4-sb/Insight-build/bin
 </pre>
-*Now copy/link WrapITK.pth into the '''Slicer''' python site-packages directory. For example:
+*Now copy/link WrapITK.pth into the '''Slicer''' python site-packages directory, within the Slicer lib directory. For example:
 <pre>
-ln -s /cmn/dev/Slicer3-SuperBuild/Insight-build/Wrapping/WrapITK.Python/WrapITK.pth /cmn/dev/Slicer3-SuperBuild/python-build/lib/python2.6/site-packages/
+ln -s /cmn/dev/Slicer4-sb/Insight-build/Wrapping/WrapITK.Python/WrapITK.pth /cmn/git/Slicer4-sb/Slicer-build/lib/site-packages/
 </pre>
 '''Note that the full path to WrapITK.pth must be given for a correct link!'''
@@ Line 31: / Line 33: @@
 NB:
 * the first time "from itk import *" is called, Slicer/python will appear to hang for some time (+/- minutes). I assume this is because some templated calls are being unwound or files precompiled to pyc. There may also be some import errors, but they appear to only pertain to a small subset of ITK. Subsequent imports should be instantaneous.
 * the example in the screenshot is from here: http://www.insight-journal.org/browse/publication/85

@@ Line 20: / Line 20: @@
 /cmn/dev/Slicer3-SuperBuild/Insight-build/bin
 </pre>
-*Now copy/link WrapITK.pth into the python site-packages directory. For example:
+*Now copy/link WrapITK.pth into the '''Slicer''' python site-packages directory. For example:
 <pre>
 ln -s /cmn/dev/Slicer3-SuperBuild/Insight-build/Wrapping/WrapITK.Python/WrapITK.pth /cmn/dev/Slicer3-SuperBuild/python-build/lib/python2.6/site-packages/

← Older revision		Revision as of 21:36, 15 October 2010
Line 30:		Line 30:
	[[image:Slicer3PythonITK.png]]		[[image:Slicer3PythonITK.png]]

−	NB: the first time "from itk import *" is called, Slicer/python will appear to hang for some time (+/- minutes). I assume this is because some templated calls are being unwound or files precompiled to pyc. There may also be some import errors, but they appear to only pertain to a small subset of ITK. Subsequent imports should be instantaneous.	+	NB:
		+	* the first time "from itk import *" is called, Slicer/python will appear to hang for some time (+/- minutes). I assume this is because some templated calls are being unwound or files precompiled to pyc. There may also be some import errors, but they appear to only pertain to a small subset of ITK. Subsequent imports should be instantaneous.
		+	* the example in the screenshot is from here: http://www.insight-journal.org/browse/publication/85

@@ Line 1: / Line 1: @@
 The recommended ITK wrapping is WrapITK. To build Slicer3 with Python ITK wrapping, make the following change:
-Edit [path]/Slicer3/SuperBuild/External_Insight.cmake
+Edit this file:    '''''[path]''/Slicer3/SuperBuild/External_Insight.cmake'''
 *In the section CMAKE_ARGS, add the following arguments:
@@ Line 24: / Line 24: @@
 ln -s /cmn/dev/Slicer3-SuperBuild/Insight-build/Wrapping/WrapITK.Python/WrapITK.pth /cmn/dev/Slicer3-SuperBuild/python-build/lib/python2.6/site-packages/
 </pre>
-Note that you must give the full path to WrapITK.pth
+'''Note that the full path to WrapITK.pth must be given for a correct link!'''
 Now start Slicer and gain Insight!

← Older revision		Revision as of 19:54, 15 October 2010
Line 8:		Line 8:
	-DWRAP_ITK_PYTHON:BOOL=ON		-DWRAP_ITK_PYTHON:BOOL=ON

−	Then save and make as usual. BE WARNED that WrapITK will take a long time to compile (>2 hrs on a ~~quad~~	+	Then save and make as usual. BE WARNED that WrapITK will take a long time to compile (>2 hrs on a dual xeon w/ 8gb ram)