ENH: Update provenance info, use error raising

Update the general info class, which will now be updated at multiple points in the extraction pipeline. This enables reflecting the various changes introduced by the pre-processing.

Instead of returning "None" when checks fail, raise a ValueError. This removes the need for checking for "None" and ensures that the extraction is cancelled, with a warning message shown to the user.

radiomics/featureextractor.py

@@ -45,6 +45,8 @@ def __init__(self, *args, **kwargs):
 
     self.featureClasses = getFeatureClasses()
 
+    self.generalInfo = None
+
     self.settings = {}
     self._enabledImagetypes = {}
     self._enabledFeatures = {}
@@ -359,6 +361,13 @@ def execute(self, imageFilepath, maskFilepath, label=None, voxelBased=False):
     if label is not None:
       self.settings['label'] = label
 
+    if self.settings['additionalInfo']:
+      self.generalInfo = generalinfo.GeneralInfo()
+      self.generalInfo.addGeneralSettings(self.settings)
+      self.generalInfo.addEnabledImageTypes(self._enabledImagetypes)
+    else:
+      self.generalInfo = None
+
     self.settings['voxelBased'] = voxelBased
     if voxelBased:
       self.logger.info('Starting voxel based extraction')
@@ -377,27 +386,36 @@ def execute(self, imageFilepath, maskFilepath, label=None, voxelBased=False):
     featureVector = collections.OrderedDict()
     image, mask = self.loadImage(imageFilepath, maskFilepath)
 
-    if image is None or mask is None:
-      # No features can be extracted, return the empty featureVector
-      return featureVector
-
     # 2. Check whether loaded mask contains a valid ROI for feature extraction and get bounding box
+    # Raises a ValueError if the ROI is invalid
     boundingBox, correctedMask = imageoperations.checkMask(image, mask, **self.settings)
 
     # Update the mask if it had to be resampled
     if correctedMask is not None:
+      if self.generalInfo is not None:
+        self.generalInfo.addMaskElements(image, correctedMask, self.settings['label'], 'corrected')
       mask = correctedMask
 
-    if boundingBox is None:
-      # Mask checks failed, do not extract features and return the empty featureVector
-      return featureVector
-
     self.logger.debug('Image and Mask loaded and valid, starting extraction')
 
+    # 5. Resegment the mask if enabled (parameter regsegmentMask is not None)
+    resegmentedMask = None
+    resegmentRange = self.settings.get('resegmentRange', None)
+    if resegmentRange is not None:
+      resegmentMode = self.settings.get('resegmentMode', 'absolute')
+      resegmentedMask = imageoperations.resegmentMask(image, mask, resegmentRange, resegmentMode,
+                                                      self.settings['label'])
+
+      # Recheck to see if the mask is still valid, raises a ValueError if not
+      boundingBox, correctedMask = imageoperations.checkMask(image, resegmentedMask, **self.settings)
+
+      if self.generalInfo is not None:
+        self.generalInfo.addMaskElements(image, resegmentedMask, self.settings['label'], 'resegmented')
+
     if not voxelBased:
       # 3. Add the additional information if enabled
-      if self.settings['additionalInfo']:
-        featureVector.update(self.getProvenance(imageFilepath, maskFilepath, mask))
+      if self.generalInfo is not None:
+        featureVector.update(self.generalInfo.getGeneralInfo())
 
       # 4. If shape descriptors should be calculated, handle it separately here
       if 'shape' in self._enabledFeatures.keys():
@@ -416,24 +434,8 @@ def execute(self, imageFilepath, maskFilepath, label=None, voxelBased=False):
           newFeatureName = 'original_shape_%s' % featureName
           featureVector[newFeatureName] = featureValue
 
-    # 5. Resegment the mask if enabled (parameter regsegmentMask is not None)
-    resegmentRange = self.settings.get('resegmentRange', None)
-    if resegmentRange is not None:
-      resegmentMode = self.settings.get('resegmentMode', 'absolute')
-      resegmentedMask = imageoperations.resegmentMask(image, mask, resegmentRange, resegmentMode,
-                                                      self.settings['label'])
-
-      # Recheck to see if the mask is still valid
-      boundingBox, correctedMask = imageoperations.checkMask(image, resegmentedMask, **self.settings)
-      # Update the mask if it had to be resampled
-      if correctedMask is not None:
-        resegmentedMask = correctedMask
-
-      if boundingBox is None:
-        # Mask checks failed, do not extract features and return the empty featureVector
-        return featureVector
-
-      # Resegmentation successful
+    # Only use resegemented mask for feature classes other than shape
+    if resegmentedMask is not None:
       mask = resegmentedMask
 
     # 6. Calculate other enabled feature classes using enabled image types
@@ -476,16 +478,18 @@ def loadImage(self, ImageFilePath, MaskFilePath):
     elif isinstance(ImageFilePath, sitk.SimpleITK.Image):
       image = ImageFilePath
     else:
-      self.logger.warning('Error reading image Filepath or SimpleITK object')
-      return None, None  # this function is expected to always return a tuple of 2 elements
+      raise ValueError('Error reading image Filepath or SimpleITK object')
 
     if isinstance(MaskFilePath, six.string_types) and os.path.isfile(MaskFilePath):
       mask = sitk.ReadImage(MaskFilePath)
     elif isinstance(MaskFilePath, sitk.SimpleITK.Image):
       mask = MaskFilePath
     else:
-      self.logger.warning('Error reading mask Filepath or SimpleITK object')
-      return None, None  # this function is expected to always return a tuple of 2 elements
+      raise ValueError('Error reading mask Filepath or SimpleITK object')
+
+    if self.generalInfo is not None:
+      self.generalInfo.addImageElements(image)
+      self.generalInfo.addMaskElements(image, mask, self.settings.get('label', 1))
 
     # This point is only reached if image and mask loaded correctly
     if self.settings['normalize']:
@@ -497,36 +501,23 @@ def loadImage(self, ImageFilePath, MaskFilePath):
                                                   self.settings['interpolator'],
                                                   self.settings['label'],
                                                   self.settings['padDistance'])
+      if self.generalInfo is not None:
+        self.generalInfo.addImageElements(image, 'interpolated')
+        self.generalInfo.addMaskElements(image, mask, self.settings.get('label', 1), 'interpolated')
+
     elif self.settings['preCrop']:
       bb, correctedMask = imageoperations.checkMask(image, mask, **self.settings)
       if correctedMask is not None:
         # Update the mask if it had to be resampled
         mask = correctedMask
       if bb is None:
         # Mask checks failed
-        return None, None
+        raise ValueError('Mask checks failed during pre-crop')
+
       image, mask = imageoperations.cropToTumorMask(image, mask, bb, self.settings['padDistance'])
 
     return image, mask
 
-  def getProvenance(self, imageFilepath, maskFilepath, mask):
-    """
-    Generates provenance information for reproducibility. Takes the original image & mask filepath, as well as the
-    resampled mask which is passed to the feature classes. Returns a dictionary with keynames coded as
-    "general_info_<item>". For more information on generated items, see :ref:`generalinfo<radiomics-generalinfo-label>`
-    """
-    self.logger.info('Adding additional extraction information')
-
-    provenanceVector = collections.OrderedDict()
-    generalinfoClass = generalinfo.GeneralInfo(imageFilepath,
-                                               maskFilepath,
-                                               mask,
-                                               self.settings,
-                                               self._enabledImagetypes)
-    for k, v in six.iteritems(generalinfoClass.execute()):
-      provenanceVector['general_info_%s' % k] = v
-    return provenanceVector
-
   def computeFeatures(self, image, mask, imageTypeName, **kwargs):
     """
     Compute signature using image, mask, \*\*kwargs settings.