BUG: Fix incorrect usage of self.maskArray

In full-python calculation of the GLDM matrix, calculation would fail when label != 1. Update GLDM to also work with different mask values.

Fix an additional bug in testUtils, where the Label value stored in the baseline was not passed to the checkMask function when loading a test case.

radiomics/gldm.py

@@ -78,7 +78,7 @@ def _calculateMatrix(self):
 
     # Set voxels outside delineation to padding value
     padVal = numpy.nan
-    self.matrix[(self.maskArray != self.label)] = padVal
+    self.matrix[~self.maskArray] = padVal
 
     angles = imageoperations.generateAngles(self.boundingBoxSize, **self.kwargs)
     angles = numpy.concatenate((angles, angles * -1))
@@ -109,7 +109,7 @@ def _calculateMatrix(self):
         depMat[~nanMask] += (numpy.abs(angMat[~nanMask]) <= self.gldm_a)
 
     grayLevels = self.coefficients['grayLevels']
-    dependenceSizes = numpy.unique(depMat[self.labelledVoxelCoordinates])
+    dependenceSizes = numpy.unique(depMat[self.maskArray])
     P_gldm = numpy.zeros((len(grayLevels), len(dependenceSizes)))
 
     with self.progressReporter(grayLevels, desc='calculate GLDM') as bar:

tests/testUtils.py

@@ -133,7 +133,7 @@ class or test case is changed, function returns True.
                                                                 interpolator,
                                                                 self._kwargs.get('label', 1),
                                                                 self._kwargs.get('padDistance', 5))
-      bb, correctedMask = imageoperations.checkMask(self._image, self._mask)
+      bb, correctedMask = imageoperations.checkMask(self._image, self._mask, **self._kwargs)
       if correctedMask is not None:
         self._mask = correctedMask
       self._image, self._mask = imageoperations.cropToTumorMask(self._image, self._mask, bb)