Tracking changes to allow updating old models and re-using them

bash_utilities/scil_score_ismrm_Renauld2023.sh

@@ -5,13 +5,18 @@ then
     echo "-----"
     echo "Usage: "
     echo ">> scil_score_ismrm_Renauld2023.sh tractogram out_dir scoring_data"
+    echo "If you are using an old version of scilpy (<2.2.0), the '.py' extensions"
+    echo "were required when calling python scripts"
+    echo "Then, usage becomes:"
+    echo ">> scil_score_ismrm_Renauld2023.sh tractogram out_dir scoring_data .py "
     echo "-----"
     exit
 fi
 
 tractogram=$1
 out_dir=$2
 scoring_data=$3
+ext=$4
 
 config_file_segmentation=$scoring_data/config_file_segmentation.json
 config_file_tractometry=$scoring_data/config_file_tractometry.json
@@ -31,30 +36,30 @@ fi
 
 
 echo '------------- SEGMENTATION ------------'
-scil_tractogram_segment_with_ROI_and_score $tractogram $config_file_segmentation $out_dir --no_empty \
+scil_tractogram_segment_with_ROI_and_score$ext $tractogram $config_file_segmentation $out_dir --no_empty \
     --gt_dir $scoring_data --reference $ref --json_prefix tmp_ --no_bbox_check;
 
 echo '------------- Merging CC sub-bundles ------------'
 CC_files=$(ls $out_dir/segmented_VB/CC* 2> /dev/null)
 if [ "$CC_files" != '' ]
 then
-    scil_tractogram_math lazy_concatenate $CC_files $out_dir/segmented_VB/CC_VS.trk;
+    scil_tractogram_math$ext lazy_concatenate $CC_files $out_dir/segmented_VB/CC_VS.trk;
 fi
 echo '------------- Merging ICP left sub-bundles ------------'
 ICP_left_files=$(ls $out_dir/segmented_VB/ICP_left* 2> /dev/null)
 if [ "$ICP_left_files" != '' ]
 then
-    scil_tractogram_math lazy_concatenate $ICP_left_files $out_dir/segmented_VB/ICP_left_VS.trk;
+    scil_tractogram_math$ext lazy_concatenate $ICP_left_files $out_dir/segmented_VB/ICP_left_VS.trk;
 fi
 echo '------------- Merging ICP right sub-bundles ------------'
 ICP_right_files=$(ls $out_dir/segmented_VB/ICP_right* 2> /dev/null)
 if [ "$ICP_right_files" != '' ]
 then
-    scil_tractogram_math lazy_concatenate $ICP_right_files  $out_dir/segmented_VB/ICP_right_VS.trk;
+    scil_tractogram_math$ext lazy_concatenate $ICP_right_files  $out_dir/segmented_VB/ICP_right_VS.trk;
 fi
 
 echo '------------- FINAL SCORING ------------'
-scil_bundle_score_many_bundles_one_tractogram $config_file_tractometry $out_dir \
+scil_bundle_score_many_bundles_one_tractogram$ext $config_file_tractometry $out_dir \
       --gt_dir $scoring_data --reference $ref --no_bbox_check -v 
 
 cat $out_dir/results.json

pyproject.toml

@@ -56,7 +56,6 @@ ae_train_model = "dwi_ml.cli.ae_train_model:main"
 dwiml_compute_connectivity_matrix_from_blocs = "dwi_ml.cli.dwiml_compute_connectivity_matrix_from_blocs:main"
 dwiml_compute_connectivity_matrix_from_labels = "dwi_ml.cli.dwiml_compute_connectivity_matrix_from_labels:main"
 dwiml_compute_connectivity_score = "dwi_ml.cli.dwiml_compute_connectivity_score:main"
-dwiml_compute_loss_copy_previous = "dwi_ml.cli.dwiml_compute_loss_copy_previous:main"
 dwiml_create_hdf5_dataset = "dwi_ml.cli.dwiml_create_hdf5_dataset:main"
 dwiml_divide_volume_into_blocs = "dwi_ml.cli.dwiml_divide_volume_into_blocs:main"
 dwiml_hdf5_extract_data = "dwi_ml.cli.dwiml_hdf5_extract_data:main"
@@ -76,5 +75,6 @@ l2t_visualize_weights_evolution = "dwi_ml.cli.l2t_visualize_weights_evolution:ma
 tt_resume_training_from_checkpoint = "dwi_ml.cli.tt_resume_training_from_checkpoint:main"
 tt_track_from_model = "dwi_ml.cli.tt_track_from_model:main"
 tt_train_model = "dwi_ml.cli.tt_train_model:main"
+tt_update_deprecated_exp = "dwi_ml.cli.tt_update_deprecated_exp:main"
 tt_visualize_loss = "dwi_ml.cli.tt_visualize_loss:main"
 tt_visualize_weights = "dwi_ml.cli.tt_visualize_weights:main"

src/dwi_ml/cli/dwiml_send_value_to_comet_from_log.py

@@ -32,10 +32,11 @@ def _build_arg_parser():
                    help="Comet.ml's metric name(s). Must contain the same "
                         "number of inputs as --logs.\n"
                         "If not set, we will suggest you the probable name(s) "
-                        "but we will not run the script.")
-    p.add_argument('--use_suggested_name', action='store_true',
-                   help="If set and --metric_name is not set, will run with "
-                        "the suggested name(s).")
+                        "but we will not run the script, unless you add "
+                        "--use_suggested_names")
+    p.add_argument('--use_suggested_names', action='store_true',
+                   help="If set and --metric_names is not set, guess the "
+                        "metric names.")
     p.add_argument('--use_best', action='store_true',
                    help="If set, uses only the best value in segment [0, t] "
                         "as value at time t. (Best = lowest).")
@@ -67,7 +68,7 @@ def main():
         if args.use_best:
             print("Not sure what to suggest you for --metric_name with "
                   "option --use_best. Probably 'best_loss'!?")
-            args.use_suggested_name = False
+            args.use_suggested_names = False
         else:
             for log in log_paths:
                 # Based on current implementation of things:
@@ -91,7 +92,7 @@ def main():
                 args.metric_names.append(metric_name)
 
         # Possibly stop now
-        if not args.use_suggested_name:
+        if not args.use_suggested_names:
             return
 
     # Verify