Merge pull request #307 from JoostJM/update-batch-script

Add additional checks to batch processing script

radiomics/featureextractor.py

@@ -415,15 +415,15 @@ def loadImage(self, ImageFilePath, MaskFilePath):
     padding as specified in padDistance) after assignment of image and mask.
     """
     self.logger.info('Loading image and mask')
-    if isinstance(ImageFilePath, six.string_types) and os.path.exists(ImageFilePath):
+    if isinstance(ImageFilePath, six.string_types) and os.path.isfile(ImageFilePath):
       image = sitk.ReadImage(ImageFilePath)
     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
 
-    if isinstance(MaskFilePath, six.string_types) and os.path.exists(MaskFilePath):
+    if isinstance(MaskFilePath, six.string_types) and os.path.isfile(MaskFilePath):
       mask = sitk.ReadImage(MaskFilePath)
     elif isinstance(MaskFilePath, sitk.SimpleITK.Image):
       mask = MaskFilePath

radiomics/scripts/commandlinebatch.py

@@ -68,12 +68,16 @@ def main():
     cr = csv.DictReader(args.inFile, lineterminator='\n')
     flists = [row for row in cr]
     args.inFile.close()
+
+    # Check if required Image and Mask columns are present
+    if 'Image' not in cr.fieldnames:
+      logger.error('Required column "Image" not present in input, unable to extract features...')
+      exit(-1)
+    if 'Mask' not in cr.fieldnames:
+      logger.error('Required column "Mask" not present in input, unable to extract features...')
+      exit(-1)
   except Exception:
     logging.error('CSV READ FAILED', exc_info=True)
-    args.inFile.close()
-    args.outFile.close()
-    if args.log_file is not None:
-      args.log_file.close()
     exit(-1)
 
   # Initialize extractor
@@ -85,22 +89,34 @@ def main():
       extractor = featureextractor.RadiomicsFeaturesExtractor()
   except Exception:
     logger.error('EXTRACTOR INITIALIZATION FAILED', exc_info=True)
-    args.outFile.close()
-    args.log_file.close()
     exit(-1)
 
   # Extract features
   logger.info('Extracting features with kwarg settings: %s', str(extractor.settings))
 
   headers = None
   for idx, entry in enumerate(flists, start=1):
+    # Check if the required columns have a value, if not, skip them.
+    if entry['Image'] is '':
+      logger.error('Missing value in column "Image", cannot process. Skipping patient (%d/%d)', idx, len(flists))
+      continue
+    if entry['Mask'] is '':
+      logger.error('Missing value in column "Mask", cannot process. Skipping patient (%d/%d)', idx, len(flists))
+      continue
 
     logger.info("(%d/%d) Processing Patient (Image: %s, Mask: %s)", idx, len(flists), entry['Image'], entry['Mask'])
 
     imageFilepath = entry['Image']
     maskFilepath = entry['Mask']
 
     if (imageFilepath is not None) and (maskFilepath is not None):
+      if not os.path.isabs(imageFilepath):
+        imageFilepath = os.path.abspath(os.path.join(os.path.dirname(args.inFile.name), imageFilepath))
+        logger.debug('Updated relative image filepath to be relative to input CSV: %s', imageFilepath)
+      if not os.path.isabs(maskFilepath):
+        maskFilepath = os.path.abspath(os.path.join(os.path.dirname(args.inFile.name), maskFilepath))
+        logger.debug('Updated relative mask filepath to be relative to input CSV: %s', maskFilepath)
+
       featureVector = collections.OrderedDict(entry)
       if args.shorten:
         featureVector['Image'] = os.path.basename(imageFilepath)