adjustment of args and tqdm updates.

src/frd/frd_score.py

@@ -64,6 +64,7 @@ def parse_args() -> argparse.Namespace:
     )
 
     parser.add_argument(
+        "-m",
         "--paths_masks",
         type=str,
         nargs=2,
@@ -72,60 +73,68 @@ def parse_args() -> argparse.Namespace:
     )
 
     parser.add_argument(
+        "-f",
+        "--feature_groups",
+        nargs='+',
+        type=str,
+        default=[
+            "firstorder",
+            "glcm",
+            "glrlm",
+            "gldm",
+            "glszm",
+            "ngtdm",
+            "shape",
+            "shape2D",
+        ],
+        help="The pyradiomics feature groups to be used for the frd calculation. Can be 'firstorder', "
+        "'glcm', 'glrlm', 'gldm', 'glszm', 'ngtdm', 'shape', 'shape2D' ",
+    )
+
+    parser.add_argument(
+        "-is_m",
         "--is_mask_used",
         action="store_true",
         help="Generate radiomics based on either available mask or for the whole image.",
     )
 
     parser.add_argument(
+        "-r",
         "--resize_size",
         type=int,
         default=None,
         help="In case the input images (and masks) are to be resized to a specific pixel dimension. "
     )
 
     parser.add_argument(
+        "-s",
         "--save_stats",
         action="store_true",
         help="Generate an npz archive from a directory of samples. The first path is used as input and "
         "the second as output.",
     )
 
     parser.add_argument(
+        "-nr",
         "--normalization_range",
-        type=list,
-        default=[0, 7.45670747756958],
+        nargs=2,
+        type=float,
+        default=[0., 7.45670747756958],
         help="The allowed value range of features. Based on these values the frd features will be "
         "normalized. The range should be [min, max]. Default is [0, 7.45670747756958]. "
         "If normalization_type is 'zscore', we recommend ignoring normalization range by setting "
         "it to [0, 1].",
     )
 
     parser.add_argument(
+        "-nt",
         "--normalization_type",
         type=str,
         default="minmax",
         help="The strategy with which the frd features will be normalized. Can be 'minmax' "
         "or 'zscore'.",
     )
 
-    parser.add_argument(
-        "--feature_groups",
-        type=list,
-        default=[
-            "firstorder",
-            "glcm",
-            "glrlm",
-            "gldm",
-            "glszm",
-            "ngtdm",
-            "shape",
-            "shape2D",
-        ],
-        help="The pyradiomics feature groups to be used for the frd calculation. Can be 'firstorder', "
-        "'glcm', 'glrlm', 'gldm', 'glszm', 'ngtdm', 'shape', 'shape2D' ",
-    )
-
     parser.add_argument(
         "--features",
         type=str,
@@ -135,12 +144,14 @@ def parse_args() -> argparse.Namespace:
     )
 
     parser.add_argument(
+        "-v",
         "--verbose",
         action="store_true",
         help="You may enable more detailed logging (logging.info) console logs by providing the 'verbose' argument.",
     )
 
     parser.add_argument(
+        "-sf",
         "--save_features",
         action="store_true",
         help="Indicates whether radiomics feature values (normalized and non-normalized) should be stored in a csv file. "
@@ -313,7 +324,7 @@ def get_activations(
                 logging.debug(
                     f"Total number of features extracted for image {i}: {len(pred_arr[i])}"
                 )
-        pbar.update(1)
+            pbar.update(1)
 
     if radiomics_results:
         sample_dict = radiomics_results[0]