ENH: Add option for UNIX path sep for voxel-based output

This allows the user to force the path separators in the output to be "/", even when running on Windows-based systems.

radiomics/scripts/__init__.py

@@ -97,6 +97,9 @@ def getParser(cls):
                                   '"absolute" (Default): Absolute file paths.\n'
                                   '"relative": File paths relative to current working directory.\n'
                                   '"basename": Only stores filename.')
+    outputGroup.add_argument('--unix-path', '-up', action='store_true',
+                             help='If specified, ensures that all paths in the output\n'
+                                  'use unix-style path separators ("/").')
 
     loggingGroup = parser.add_argument_group(title='Logging',
                                              description='Controls the (amount of) logging output to the '
@@ -241,7 +244,8 @@ def _processCases(self, case_generator):
         task = pool.map_async(partial(self.parallel_func,
                                       extractor=extractor,
                                       out_dir=self.args.out_dir,
-                                      logging_config=self.logging_config),
+                                      logging_config=self.logging_config,
+                                      unix_path=self.args.unix_path),
                               case_generator,
                               chunksize=min(10, self.case_count))
         # Wait for the results to be done. task.get() without timeout performs a blocking call, which prevents
@@ -260,7 +264,10 @@ def _processCases(self, case_generator):
                        self.case_count)
       results = []
       for case in case_generator:
-        results.append(self.serial_func(*case, extractor=extractor, out_dir=self.args.out_dir))
+        results.append(self.serial_func(*case,
+                                        extractor=extractor,
+                                        out_dir=self.args.out_dir,
+                                        unix_path=self.args.unix_path))
     else:
       # No cases defined in the batch
       self.logger.error('No cases to process...')
@@ -305,6 +312,10 @@ def _processOutput(self, results):
       case['Image'] = pathFormatter(case['Image'])
       case['Mask'] = pathFormatter(case['Mask'])
 
+      if self.args.unix_path and os.path.sep != '/':
+        case['Image'] = case['Image'].replace(os.path.sep, '/')
+        case['Mask'] = case['Mask'].replace(os.path.sep, '/')
+
       # Write out results per case if format is 'csv' or 'txt', handle 'json' outside of this loop (issue #483)
       if self.args.format == 'csv':
         writer = csv.DictWriter(self.args.out, headers, lineterminator='\n', extrasaction='ignore')

radiomics/scripts/segment.py

@@ -14,9 +14,11 @@
 _parallel_extraction_configured = False
 
 
-def extractSegment(case_idx, case, extractor, out_dir):
+def extractSegment(case_idx, case, extractor, **kwargs):
   global caseLogger
 
+  out_dir = kwargs.get('out_dir', None)
+
   if out_dir is None:
     return _extractFeatures(case_idx, case, extractor)
 
@@ -82,15 +84,15 @@ def _extractFeatures(case_idx, case, extractor):
   return feature_vector
 
 
-def extractSegment_parallel(args, extractor, out_dir=None, logging_config=None):
+def extractSegment_parallel(args, logging_config=None, **kwargs):
   try:
     # set thread name to patient name
     threading.current_thread().name = 'case %s' % args[0]  # args[0] = case_idx
 
     if logging_config is not None:
       _configureParallelExtraction(logging_config)
 
-    return extractSegment(*args, extractor=extractor, out_dir=out_dir)
+    return extractSegment(*args, **kwargs)
   except (KeyboardInterrupt, SystemExit):
     # Catch the error here, as this represents the interrupt of the child process.
     # The main process is also interrupted, and cancellation is further handled there

radiomics/scripts/voxel.py

@@ -13,9 +13,12 @@
 _parallel_extraction_configured = False
 
 
-def extractVoxel(case_idx, case, extractor, out_dir):
+def extractVoxel(case_idx, case, extractor, **kwargs):
   global caseLogger
 
+  out_dir = kwargs.get('out_dir', None)
+  unix_path = kwargs.get('unix_path', False)
+
   # Instantiate the output
   feature_vector = OrderedDict(case)
 
@@ -45,6 +48,8 @@ def extractVoxel(case_idx, case, extractor, out_dir):
       if isinstance(result[k], sitk.Image):
         target = os.path.join(out_dir, 'Case-%i_%s.nrrd' % (case_idx, k))
         sitk.WriteImage(result[k], target, True)
+        if unix_path and os.path.sep != '/':
+          target = target.replace(os.path.sep, '/')
         feature_vector[k] = target
       else:
         feature_vector[k] = result[k]
@@ -64,15 +69,15 @@ def extractVoxel(case_idx, case, extractor, out_dir):
   return feature_vector
 
 
-def extractVoxel_parallel(args, extractor, out_dir=None, logging_config=None):
+def extractVoxel_parallel(args, logging_config=None, **kwargs):
   try:
     # set thread name to patient name
     threading.current_thread().name = 'case %s' % args[0]  # args[0] = case_idx
 
     if logging_config is not None:
       _configureParallelExtraction(logging_config)
 
-    return extractVoxel(*args, extractor=extractor, out_dir=out_dir)
+    return extractVoxel(*args, **kwargs)
   except (KeyboardInterrupt, SystemExit):
     # Catch the error here, as this represents the interrupt of the child process.
     # The main process is also interrupted, and cancellation is further handled there