Move CSA normalization models to ./data/ at the root of the SCT repo (

#3821) Co-authored-by: Julian McGinnis <julian.mcginnis@park-depot.de>
spinalcordtoolbox · Jun 29, 2022 · df9a633 · df9a633
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commit df9a633
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Showing 4 changed files with 1 addition and 2 deletions.
diff --git a/...normalization_models/brain-volume_sex.csv → ...normalization_models/brain-volume_sex.csv b/...normalization_models/brain-volume_sex.csv → ...normalization_models/brain-volume_sex.csv
diff --git a/...dels/brain-volume_sex_thalamus-volume.csv → ...dels/brain-volume_sex_thalamus-volume.csv b/...dels/brain-volume_sex_thalamus-volume.csv → ...dels/brain-volume_sex_thalamus-volume.csv
diff --git a/install_sct b/install_sct
@@ -672,7 +672,6 @@ if [[ -n "$NO_DATA_INSTALL" ]]; then
 else
   # Download data
   print info "Installing data..."
-  run rm -rf "$SCT_DIR/$DATA_DIR"
   run mkdir -p "$SCT_DIR/$DATA_DIR"
   for data in PAM50 gm_model optic_models pmj_models deepseg_sc_models deepseg_gm_models deepseg_lesion_models c2c3_disc_models; do
     run sct_download_data -d "$data"

diff --git a/spinalcordtoolbox/scripts/sct_process_segmentation.py b/spinalcordtoolbox/scripts/sct_process_segmentation.py
@@ -444,7 +444,7 @@ def main(argv=None):
     # Normalize CSA values (MEAN(area))
     if arguments.normalize is not None:
         data_subject = pd.DataFrame([arguments.normalize])
-        path_model = os.path.join(__sct_dir__, 'spinalcordtoolbox', 'data', 'csa_normalization_models',
+        path_model = os.path.join(__sct_dir__, 'data', 'csa_normalization_models',
                                   '_'.join(sorted(data_subject.columns)) + '.csv')
         if not os.path.isfile(path_model):
             raise parser.error('Invalid choice of predictors in -normalize. Please specify sex and brain-volume or sex, brain-volume and thalamus-volume.')