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Fix bug when creating symmetrical GLCM #261

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merged 2 commits into from Jun 1, 2017
Merged

Fix bug when creating symmetrical GLCM #261

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d8032f3
BUG: Fix symmetrical GLCM
JoostJM May 30, 2017
9aa8c01
DOCS: Document symmetrical GLCM bugfix
JoostJM May 31, 2017
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8 changes: 8 additions & 0 deletions CHANGES.rst
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Expand Up @@ -6,6 +6,14 @@ Release Notes
Next Release
------------

Bug fixes
#########

- In GLCM, the matrix is made symmetrical by adding the transposed matrix. However, ``numpy.transpose`` returns a view
and not a copy of the array, causing erroneous results when adding it to the original array. use
``numpy.ndarray.copy`` to prevent this bug. **N.B. This affects the feature values calculated by GLCM when symmetrical
matrix is enabled (as is the default setting).**

-----------------
PyRadiomics 1.2.0
-----------------
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4 changes: 3 additions & 1 deletion radiomics/glcm.py
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Expand Up @@ -186,7 +186,9 @@ def _applyMatrixOptions(self, P_glcm, angles):
# Optionally make GLCMs symmetrical for each angle
if self.symmetricalGLCM:
self.logger.debug('Create symmetrical matrix')
P_glcm += numpy.transpose(P_glcm, (1, 0, 2))
# Transpose and copy GLCM and add it to P_glcm. Numpy.transpose returns a view if possible, use .copy() to ensure
# a copy of the array is used and not just a view (otherwise erroneous additions can occur)
P_glcm += numpy.transpose(P_glcm, (1, 0, 2)).copy()

# Optionally apply a weighting factor
if self.weightingNorm is not None:
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