catching no given arguments

Author: peterneher

.gitlab-ci.yml

@@ -41,14 +41,14 @@ test_pytest:
   rules:
     - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
 
-#test_run_parcellate:
-#  extends: test_pytest
-#  before_script:
-#    - *default_before_script
-#    - pip install .
-#    - mkdir test/test_results/ -p
-#  script:
-#    - radtract_parcellate --streamlines tests/test_data/test_tract.trk --envelope tests/test_data/test_tract_envelope.nii.gz --start tests/test_data/test_tract_b.nii.gz --num_parcels 5 --output test/test_results/hyperplane_parcellation_command.nii.gz
+test_run_parcellate:
+ extends: test_pytest
+ before_script:
+   - *default_before_script
+   - pip install .
+   - mkdir tests/test_results/ -p
+ script:
+   - radtract_parcellate --streamlines tests/test_data/test_tract.trk --envelope tests/test_data/test_tract_envelope.nii.gz --start tests/test_data/test_tract_b.nii.gz --num_parcels 5 --output tests/test_results/hyperplane_parcellation_command.nii.gz
 
 #test_run_features:
 #  extends: test_run_parcellate

radtract/features.py

@@ -13,6 +13,7 @@
 from nibabel.affines import apply_affine
 import SimpleITK as sitk
 from cmdint.Utils import ProgressBar
+import sys
 
 
 def map_check(data: np.ndarray,
@@ -341,6 +342,10 @@ def load_features(feature_file_names: list, select=[], drop=[], expected_parcels
 
 def main():
 
+    if len(sys.argv) == 1:
+        print('type \'radtract_features -h\' for help')
+        return
+
     parser = argparse.ArgumentParser(description='RadTract Feature Calculation')
     parser.add_argument('--parcellation', type=str, help='Input parcellation file')
     parser.add_argument('--map', type=str, help='Parameter map file (e.g. fractional anisotropy)')

radtract/parcellation.py

@@ -3,7 +3,6 @@
 # SPDX-License-Identifier: Apache-2.0
 
 import nibabel as nib
-import numpy.linalg
 from nibabel.affines import apply_affine
 from skimage.morphology import binary_dilation, binary_closing
 from sklearn.svm import SVC
@@ -19,6 +18,7 @@
 import argparse
 import joblib
 import multiprocessing
+import sys
 
 
 def load_trk_streamlines(filename: str):
@@ -518,6 +518,11 @@ def parcellate_tract(streamlines: nib.streamlines.array_sequence.ArraySequence,
 
 
 def main():
+
+    if len(sys.argv) == 1:
+        print('type \'radtract_parcellate -h\' for help')
+        return
+
     parser = argparse.ArgumentParser(description='RadTract Tract Parcellation')
     parser.add_argument('--streamlines', type=str, help='Input streamline file')
     parser.add_argument('--envelope', type=str, help='Input streamline envelope file', default=None)

radtract/prediction.py

@@ -154,11 +154,3 @@ def run_cv_experiment(feature_files, targets, remove_map_substrings=[], n_jobs=-
     print('Done')
 
     return predictions, ground_truth, classifiers
-
-
-def main():
-    pass
-
-
-if __name__ == '__main__':
-    main()