Pieper at 18:44, 8 November 2010

2010-11-08T18:44:20Z

Pieper: New page: This is part of a [http://www.na-mic.org/Wiki/index.php/Summer2009:Using_ITK_in_python NA-MIC Summer Project Week 2009 Project].

 """ A simple example to show how to use weave with I...

2009-06-19T14:50:54Z

New page: This is part of a [http://www.na-mic.org/Wiki/index.php/Summer2009:Using_ITK_in_python NA-MIC Summer Project Week 2009 Project]. <pre> """ A simple example to show how to use weave with I...

New page

This is part of a [http://www.na-mic.org/Wiki/index.php/Summer2009:Using_ITK_in_python NA-MIC Summer Project Week 2009 Project].

<pre>
""" A simple example to show how to use weave with ITK. This lets one
pass numpy arrays to ITK for processing.

based on vtk_example.py from weave distribution.

Author: Steve Pieper
Copyright (c) 2009, Steve Pieper
License: BSD Style.
"""

d = '/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/'
packages = ['matplotlib', 'neuroimaging', 'numpy', '', 'scipy']
for p in packages:
sys.path.append(d+p)

import scipy.weave as weave
import numpy

import sys
import time
import os

# from ITKConfig.cmake - TODO: extract automatically, along with build flags etc (or invoke cmake via distutils?!)
inc_dirs = ['/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/Algorithms', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/BasicFilters', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/Common', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/Numerics', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/IO', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/Numerics/FEM', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/Numerics/Statistics', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/Numerics/NeuralNetworks', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/SpatialObject', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/MetaIO', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/NrrdIO', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build/Utilities/NrrdIO', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/DICOMParser', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build/Utilities/DICOMParser', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build/Utilities/expat', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/expat', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/nifti/niftilib', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/nifti/znzlib', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/itkExtHdrs', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build/Utilities', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/vxl/v3p/netlib', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/vxl/vcl', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/vxl/core', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build/Utilities/vxl/v3p/netlib', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build/Utilities/vxl/vcl', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build/Utilities/vxl/core', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build/Utilities/gdcm', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Utilities/gdcm/src', '/Users/pieper/slicer3/latest/Slicer3-lib/Insight/Code/Review']

# The ITK library directories.
lib_dirs = ['/Users/pieper/slicer3/latest/Slicer3-lib/Insight-build/bin']

def writer_test():
"""A simple example of how you can use ITK code in weave
to write a volume to a file.
"""

fileName = '/tmp/rand.nrrd'
array = numpy.arange(0,24,dtype='float64').reshape(2,3,4)

code=r"""
typedef itk::Image<double,3> ImageType; // TODO: construct from dtype and shape
ImageType::Pointer image = ImageType::New();
image->GetPixelContainer()->SetImportPointer( array, Narray[0]*Narray[1]*Narray[2], false );

ImageType::RegionType region;
ImageType::IndexType index;
ImageType::SizeType size;
index[0] = index[1] = index[2] = 0;
size[0] = Narray[0]; size[1] = Narray[1]; size[2] = Narray[2];
region.SetIndex(index);
region.SetSize(size);
image->SetLargestPossibleRegion(region);
image->SetBufferedRegion(region);

itk::ImageFileWriter< ImageType >::Pointer writer = WriterType::New();
writer->SetFileName( fileName );
writer->SetInput( image );
writer->Update();
"""

weave.inline(code, ['fileName', 'array'],
include_dirs = inc_dirs,
library_dirs = lib_dirs,
headers=['"itkImage.h"', '"itkImageFileWriter.h"'],
libraries=['itkCommon', 'itkIO'])

TODO = """
- apply a filter (volume in and out, where output size may be different from input)
- compile on windows
- interface with cmake?
- how to deploy built libs in cpacked binary
-- how to trigger weave compilation during build process for packaging
"""

if __name__ == "__main__":
writer_test()

</pre>

Slicer3:Python:pitky - Revision history

Pieper at 18:44, 8 November 2010

Pieper: New page: This is part of a [http://www.na-mic.org/Wiki/index.php/Summer2009:Using_ITK_in_python NA-MIC Summer Project Week 2009 Project].
""" A simple example to show how to use weave with I...