NF - added add_json_args to the arguments, format the output json

scripts/scil_volume_stats_in_ROI.py

@@ -97,19 +97,19 @@ def main():
         # Discussion about the way the normalization is done.
         # https://github.com/scilus/scilpy/pull/202#discussion_r411355609
         # Summary:
-        # 1) We don't want to normalize with data = (data-min) / (max-min) because
-        # it zeroes out the minimal values of the array. This is not a large error
-        # source, but not preferable.
-        # 2) data = data / max(data) or data = data / sum(data): in practice, when
-        # we use them in numpy using their weights argument, leads to the same
-        # result.
+        # 1) We don't want to normalize with data = (data-min) / (max-min)
+        # because it zeroes out the minimal values of the array. This is 
+        # not a large error source, but not preferable.
+        # 2) data = data / max(data) or data = data / sum(data): in practice, 
+        # when we use them in numpy using their weights argument, leads to the
+        # same result.
         if args.normalize_weights:
             roi_data /= np.max(roi_data)
         elif args.bin:
             roi_data[np.where(roi_data > 0.0)] = 1.0
         elif np.min(roi_data) < 0.0 or np.max(roi_data) > 1.0:
-            parser.error('ROI {} data should only contain values between 0 and 1. '
-                         'Try --normalize_weights.'
+            parser.error('ROI {} data should only contain values between 0 '
+                         'and 1. Try --normalize_weights.'
                          .format(roi_filename))
 
         # Load and process all metrics files.

scripts/scil_volume_stats_in_labels.py

@@ -20,7 +20,7 @@
 import numpy as np
 
 from scilpy.image.labels import get_data_as_labels, get_stats_in_label
-from scilpy.io.utils import (add_overwrite_arg, add_verbose_arg,
+from scilpy.io.utils import (add_json_args, add_overwrite_arg, add_verbose_arg,
                              assert_inputs_exist, assert_headers_compatible)
 from scilpy.utils.filenames import split_name_with_nii
 
@@ -43,7 +43,7 @@ def _build_arg_parser():
                     metavar='file',
                     help='Metrics nifti filename. List of the names of the '
                          'metrics file, \nin nifti format.')
-
+    add_json_args(p)
     add_verbose_arg(p)
     add_overwrite_arg(p)
 
@@ -69,7 +69,8 @@ def main():
                                   for f in tmp_file_list]
     else:
         assert_inputs_exist(parser, [args.in_labels] + args.metrics_file_list)
-    assert_headers_compatible(parser, [args.in_labels] + args.metrics_file_list)
+    assert_headers_compatible(parser,
+                              [args.in_labels] + args.metrics_file_list)
 
     # Loading
     label_data = get_data_as_labels(nib.load(args.in_labels))
@@ -90,7 +91,7 @@ def main():
 
     if len(args.metrics_file_list) == 1:
         json_stats = json_stats[metric_name]
-    print(json.dumps(json_stats))
+    print(json.dumps(json_stats, indent=args.indent, sort_keys=args.sort_keys))
 
 
 if __name__ == "__main__":