ENH: Implement force-cast while loading mask

PyRadiomics requires the mask to be of an integer data type. Force type to UInt32 upon load from file (string input), or apply a Cast (SimpleITK.Image input).

Remove now unnecessary cast in `imageoperations.cropToTumorMask`

radiomics/featureextractor.py

@@ -508,6 +508,9 @@ def loadImage(self, ImageFilePath, MaskFilePath):
       # It is therefore possible that image and mask do not align, or even have different sizes.
       self.generalInfo.addMaskElements(None, mask, label)
 
+    # Force the mask to unsigned 32 bits integer
+    mask = sitk.Cast(mask, sitk.sitkUInt32)
+
     # This point is only reached if image and mask loaded correctly
     if normalize:
       image = imageoperations.normalizeImage(image, **self.settings)

radiomics/imageoperations.py

@@ -337,8 +337,6 @@ def cropToTumorMask(imageNode, maskNode, boundingBox, **kwargs):
   global logger
   padDistance = kwargs.get('padDistance', 0)
 
-  oldMaskID = maskNode.GetPixelID()
-  maskNode = sitk.Cast(maskNode, sitk.sitkInt32)
   size = numpy.array(maskNode.GetSize())
 
   ijkMinBounds = boundingBox[0::2] - padDistance
@@ -361,8 +359,6 @@ def cropToTumorMask(imageNode, maskNode, boundingBox, **kwargs):
   croppedImageNode = cif.Execute(imageNode)
   croppedMaskNode = cif.Execute(maskNode)
 
-  croppedMaskNode = sitk.Cast(croppedMaskNode, oldMaskID)
-
   return croppedImageNode, croppedMaskNode
 
 

tests/testUtils.py

@@ -173,6 +173,8 @@ class or test case is changed, function returns True.
       if 'MaskHash' in self._current_config:
         assert sitk.Hash(self._mask) == self._current_config['MaskHash']
 
+      self._mask = sitk.Cast(self._mask, sitk.sitkUInt32)
+
       settings = self._current_config.get('Settings', {})
 
       interpolator = settings.get('interpolator', sitk.sitkBSpline)