[FEAT EXTRACTION] - IndexError: Error filling GLSZM.

[daivagyapareek]

I am using 32 GB MBP and I am getting following error for one image, not sure what causing it.

---

IndexError Traceback (most recent call last)
in
5 print(len(comp_time),patient,(comp_time[-1]-comp_time[0])/60)
6 # try:
----> 7 result = extractor.execute(train_nrrd+patient+'/segmented.nrrd',train_nrrd+patient+'/filter.nrrd')
8 key_val = [(key,np.float64(val)) for key,val in result.items() if key in featureList]
9 key_val.append(('patientID',str(patient)))

~/opt/anaconda3/lib/python3.8/site-packages/radiomics/featureextractor.py in execute(self, imageFilepath, maskFilepath, label, label_channel, voxelBased)
328 logger.info('Calculating features for %s image', imageTypeName)
329 inputImage, inputMask = imageoperations.cropToTumorMask(inputImage, mask, boundingBox, padDistance=kernelRadius)
--> 330 featureVector.update(self.computeFeatures(inputImage, inputMask, imageTypeName, **inputKwargs))
331
332 logger.debug('Features extracted')

~/opt/anaconda3/lib/python3.8/site-packages/radiomics/featureextractor.py in computeFeatures(self, image, mask, imageTypeName, **kwargs)
515 featureClass.enableFeatureByName(feature)
516
--> 517 for (featureName, featureValue) in six.iteritems(featureClass.execute()):
518 newFeatureName = '%s_%s_%s' % (imageTypeName, featureClassName, featureName)
519 featureVector[newFeatureName] = featureValue

~/opt/anaconda3/lib/python3.8/site-packages/radiomics/base.py in execute(self)
183 self._calculateVoxels()
184 else:
--> 185 self._calculateSegment()
186
187 return self.featureValues

~/opt/anaconda3/lib/python3.8/site-packages/radiomics/base.py in _calculateSegment(self)
222 def _calculateSegment(self):
223 # Get the feature values using the current segment.
--> 224 for success, featureName, featureValue in self._calculateFeatures():
225 # Always store the result. In case of an error, featureValue will be NaN
226 self.featureValues[featureName] = numpy.squeeze(featureValue)

~/opt/anaconda3/lib/python3.8/site-packages/radiomics/base.py in _calculateFeatures(self, voxelCoordinates)
229 # Initialize the calculation
230 # This function serves to calculate the texture matrices where applicable
--> 231 self._initCalculation(voxelCoordinates)
232
233 self.logger.debug('Calculating features')

~/opt/anaconda3/lib/python3.8/site-packages/radiomics/glszm.py in _initCalculation(self, voxelCoordinates)
63
64 def _initCalculation(self, voxelCoordinates=None):
---> 65 self.P_glszm = self._calculateMatrix(voxelCoordinates)
66
67 self._calculateCoefficients()

~/opt/anaconda3/lib/python3.8/site-packages/radiomics/glszm.py in _calculateMatrix(self, voxelCoordinates)
91 matrix_args += [self.settings.get('kernelRadius', 1), voxelCoordinates]
92
---> 93 P_glszm = cMatrices.calculate_glszm(*matrix_args) # shape (Nvox, Ng, Ns)
94
95 # Delete rows that specify gray levels not present in the ROI

IndexError: Error filling GLSZM.

[JoostJM]

Which version of PyRadiomics did you install?

[JoostJM]

Possibly related to #615, #617, #600, and fixed by #635 (part of the 3.0.1 release)

[JoostJM]

Stale issue. Closing issue