def _calculateCMatrix(self):
self.logger.debug('Calculating GLSZM matrix in C')
# Do not pass kwargs directly, as distances may be specified, which must be forced to [1] for this class
angles = imageoperations.generateAngles(
self.boundingBoxSize,
force2D=self.kwargs.get('force2D', False),
force2Ddimension=self.kwargs.get('force2Ddimension', 0))
Ng = self.coefficients['Ng']
Ns = self.coefficients['Np']
P_glszm = cMatrices.calculate_glszm(self.matrix, self.maskArray,
angles, Ng, Ns)
# Delete rows that specify gray levels not present in the ROI
NgVector = range(1, Ng + 1) # All possible gray values
GrayLevels = self.coefficients[
'grayLevels'] # Gray values present in ROI
emptyGrayLevels = numpy.array(
list(set(NgVector) -
set(GrayLevels))) # Gray values NOT present in ROI
P_glszm = numpy.delete(P_glszm, emptyGrayLevels - 1, 0)
return P_glszm
def _calculateMatrix(self, voxelCoordinates=None):
"""
Number of times a region with a
gray level and voxel count occurs in an image. P_glszm[level, voxel_count] = # occurrences
For 3D-images this concerns a 26-connected region, for 2D an 8-connected region
"""
self.logger.debug('Calculating GLSZM matrix in C')
Ng = self.coefficients['Ng']
Ns = numpy.sum(self.maskArray)
matrix_args = [
self.imageArray, self.maskArray, Ng, Ns,
self.settings.get('force2D', False),
self.settings.get('force2Ddimension', 0)
]
if self.voxelBased:
matrix_args += [
self.settings.get('kernelRadius', 1), voxelCoordinates
]
P_glszm = cMatrices.calculate_glszm(
*matrix_args) # shape (Nvox, Ng, Ns)
# Delete rows that specify gray levels not present in the ROI
NgVector = range(1, Ng + 1) # All possible gray values
GrayLevels = self.coefficients[
'grayLevels'] # Gray values present in ROI
emptyGrayLevels = numpy.array(
list(set(NgVector) - set(GrayLevels)),
dtype=int) # Gray values NOT present in ROI
P_glszm = numpy.delete(P_glszm, emptyGrayLevels - 1, 1)
return P_glszm
def _calculateMatrix(self):
"""
Number of times a region with a
gray level and voxel count occurs in an image. P_glszm[level, voxel_count] = # occurrences
For 3D-images this concerns a 26-connected region, for 2D an 8-connected region
"""
self.logger.debug('Calculating GLSZM matrix in C')
Ng = self.coefficients['Ng']
Ns = self.coefficients['Np']
P_glszm, angles = cMatrices.calculate_glszm(
self.matrix, self.maskArray, Ng, Ns,
self.settings.get('force2D', False),
self.settings.get('force2Ddimension', 0))
# Delete rows that specify gray levels not present in the ROI
NgVector = range(1, Ng + 1) # All possible gray values
GrayLevels = self.coefficients[
'grayLevels'] # Gray values present in ROI
emptyGrayLevels = numpy.array(
list(set(NgVector) -
set(GrayLevels))) # Gray values NOT present in ROI
P_glszm = numpy.delete(P_glszm, emptyGrayLevels - 1, 0)
return P_glszm
def _calculateCMatrix(self):
self.logger.debug('Calculating GLSZM matrix in C')
size = numpy.max(self.matrixCoordinates, 1) - numpy.min(
self.matrixCoordinates, 1) + 1
angles = imageoperations.generateAngles(size, **self.kwargs)
Ng = self.coefficients['Ng']
Ns = self.coefficients['Np']
return cMatrices.calculate_glszm(self.matrix, self.maskArray, angles,
Ng, Ns)
def _calculateCMatrix(self):
self.logger.debug('Calculating GLSZM matrix in C')
size = numpy.max(self.matrixCoordinates, 1) - numpy.min(
self.matrixCoordinates, 1) + 1
# Do not pass kwargs directly, as distances may be specified, which must be forced to [1] for this class
angles = imageoperations.generateAngles(
size,
force2Dextraction=self.kwargs.get('force2D', False),
force2Ddimension=self.kwargs.get('force2Ddimension', 0))
Ng = self.coefficients['Ng']
Ns = self.coefficients['Np']
return cMatrices.calculate_glszm(self.matrix, self.maskArray, angles,
Ng, Ns)
def _calculateCMatrix(self):
self.logger.debug('Calculating GLSZM matrix in C')
Ng = self.coefficients['Ng']
Ns = self.coefficients['Np']
P_glszm, angles = cMatrices.calculate_glszm(
self.matrix, self.maskArray, Ng, Ns,
self.kwargs.get('force2D', False),
self.kwargs.get('force2Ddimension', 0))
# Delete rows that specify gray levels not present in the ROI
NgVector = range(1, Ng + 1) # All possible gray values
GrayLevels = self.coefficients[
'grayLevels'] # Gray values present in ROI
emptyGrayLevels = numpy.array(
list(set(NgVector) -
set(GrayLevels))) # Gray values NOT present in ROI
P_glszm = numpy.delete(P_glszm, emptyGrayLevels - 1, 0)
return P_glszm
