Add missing test + remove unused fcts

scripts_python/dwiml_compute_connectivity_matrix_from_blocs.py

@@ -82,14 +82,14 @@ def main():
     in_img = nib.load(args.in_volume)
 
     matrix, start_blocs, end_blocs = compute_triu_connectivity_from_blocs(
-        in_sft._streamlines_getter, in_img.shape, args.connectivity_nb_blocs)
+        in_sft.streamlines, in_img.shape, args.connectivity_nb_blocs)
 
     # Options to try to investigate the connectivity matrix:
     if args.save_biggest is not None:
         i, j = np.unravel_index(np.argmax(matrix, axis=None), matrix.shape)
         print("Saving biggest bundle: {} streamlines.".format(matrix[i, j]))
         biggest = find_streamlines_with_chosen_connectivity(
-            in_sft._streamlines_getter, i, j, start_blocs, end_blocs)
+            in_sft.streamlines, i, j, start_blocs, end_blocs)
         sft = in_sft.from_sft(biggest, in_sft)
         save_tractogram(sft, args.save_biggest)
 
@@ -98,25 +98,27 @@ def main():
         i, j = np.unravel_index(tmp_matrix.argmin(axis=None), matrix.shape)
         print("Saving smallest bundle: {} streamlines.".format(matrix[i, j]))
         biggest = find_streamlines_with_chosen_connectivity(
-            in_sft._streamlines_getter, i, j, start_blocs, end_blocs)
+            in_sft.streamlines, i, j, start_blocs, end_blocs)
         sft = in_sft.from_sft(biggest, in_sft)
         save_tractogram(sft, args.save_smallest)
 
-    if args.show_now:
-        plt.imshow(matrix)
-        plt.colorbar()
+    plt.imshow(matrix)
+    plt.colorbar()
 
-        plt.figure()
-        plt.imshow(matrix > 0)
-        plt.title('Binary')
+    plt.figure()
+    plt.imshow(matrix > 0)
+    plt.title('Binary')
 
     if args.binary:
         matrix = matrix > 0
 
     # Save results.
     np.save(args.out_file, matrix)
+
     plt.savefig(out_fig)
-    plt.show()
+
+    if args.show_now:
+        plt.show()
 
 
 if __name__ == '__main__':

scripts_python/tests/test_compute_connectivity_matrix_from_blocs.py

@@ -1,6 +1,33 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
+import os
+import tempfile
+
+from dwi_ml.unit_tests.utils.data_and_models_for_tests import fetch_testing_data
+
+data_dir = fetch_testing_data()
+tmp_dir = tempfile.TemporaryDirectory()
+
+
 def test_help_option(script_runner):
-    ret = script_runner.run('dwiml_compute_connectivity_matrix_from_blocs.py', '--help')
+    ret = script_runner.run('dwiml_compute_connectivity_matrix_from_blocs.py',
+                            '--help')
+    assert ret.success
+
+
+def test_run(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+
+    dwi_ml_folder = os.path.join(data_dir, 'dwi_ml_ready', 'subjX')
+    in_volume = os.path.join(dwi_ml_folder, 'anat', 't1.nii.gz')
+    streamlines = os.path.join(dwi_ml_folder, 'example_bundle', 'Fornix.trk')
+
+    out_file = 'test_matrix_connectivity.npy'
+    biggest = 'test_biggest.trk'
+
+    nb_blocs = '4'
+    ret = script_runner.run('dwiml_compute_connectivity_matrix_from_blocs.py',
+                            in_volume, streamlines, out_file, nb_blocs,
+                            '--binary', '--save_biggest', biggest)
     assert ret.success