Documentation/4.1/Developers/Python scripting

1. do this before building slicer4 - or do "cd Slicer4-superbuild/; rm -rf python* ; make"

sudo apt-get install libreadline6-dev

cd Slicer4-superbuild

1. this should be done in superbuild script

(cd ./VTK-build/Wrapping/Python;  ../../../Slicer-build/Slicer4 --launch ../../../python-build/bin/python setup.py install)

git clone git://github.com/ipython/ipython.git git checkout 0.10.2

(cd ./ipython;  ../Slicer-build/Slicer4 --launch ../python-build/bin/python setup.py install)

svn co https://matplotlib.svn.sourceforge.net/svnroot/matplotlib/branches/v1_0_maint matplotlib-source

(cd ./matplotlib-source;  ../Slicer-build/Slicer4 --launch ../python-build/bin/python setup.py install)

rm -rf matplotlib-source

./Slicer-build --launch xterm &

1. in xterm:

./python-build/bin/ipython

import vtk import slicer mrml = slicer.vtkMRMLScene() vl = slicer.vtkSlicerVolumesLogic() vl.SetAndObserveMRMLScene(mrml) n = vl.AddArchetypeVolume('../Slicer4/Testing/Data/Input/MRHeadResampled.nhdr', 'CTC') i = n.GetImageData() print (i.GetScalarRange())

import vtk.util.numpy_support a = vtk.util.numpy_support.vtk_to_numpy(i.GetPointData().GetScalars()) print(a.min(),a.max())

import matplotlib import matplotlib.pyplot n, bins, patches = matplotlib.pyplot.hist(a, 50, facecolor='g', alpha=0.75) matplotlib.pyplot.show()