Put json back in

Author: VincentBeaud

scripts/scil_fibertube_score_tractogram.py

@@ -105,6 +105,7 @@ def _build_arg_parser():
                    help='If set, all random values will be generated \n'
                    'using the specified seed. [%(default)s]')
 
+    add_json_args(p)
     add_verbose_arg(p)
     add_overwrite_arg(p)
 
@@ -202,7 +203,8 @@ def main():
         'mae_med': np.median(mean_errors),
     }
     with open(args.out_metrics, 'w') as outfile:
-        json.dump(metrics, outfile)
+        json.dump(metrics, outfile,
+                  indent=args.indent, sort_keys=args.sort_keys)
 
     if args.save_error_tractogram:
         sft = StatefulTractogram.from_sft(error_tractogram, truth_sft)

scripts/scil_fibertube_tracking.py

@@ -156,6 +156,7 @@ def _build_arg_parser():
         'be saved at the specified location (must be .txt). If not given, \n'
         'the config will be printed in the console.')
 
+    add_json_args(out_g)
     add_overwrite_arg(out_g)
     add_processes_arg(p)
     add_verbose_arg(p)
@@ -274,10 +275,12 @@ def main():
     }
     if args.out_config:
         with open(args.out_config, 'w') as outfile:
-            json.dump(config, outfile)
+            json.dump(config, outfile,
+                      indent=args.indent, sort_keys=args.sort_keys)
     else:
         print('Config:\n',
-              json.dumps(config))
+              json.dumps(config, indent=args.indent,
+                         sort_keys=args.sort_keys))
 
 
 if __name__ == "__main__":

scripts/scil_tractogram_filter_collisions.py

@@ -137,6 +137,7 @@ def _build_arg_parser():
                    help='If set, all random values will be generated \n'
                    'using the specified seed. [%(default)s]')
 
+    add_json_args(p)
     add_overwrite_arg(p)
     add_verbose_arg(p)
 
@@ -244,7 +245,8 @@ def main():
             }
 
             with open(args.out_metrics, 'w') as outfile:
-                json.dump(metrics, outfile)
+                json.dump(metrics, outfile,
+                          indent=args.indent, sort_keys=args.sort_keys)
 
         if args.out_max_voxel_rotation is not None:
             max_voxel_rotated_transform = np.r_[np.c_[