Merge pull request #1080 from karanphil/add_test_single_shell_noddi

Add test single shell NODDI

scripts/scil_NODDI_maps.py

@@ -120,12 +120,13 @@ def main():
     shells_centroids, indices_shells = identify_shells(bvals, args.tolerance,
                                                        round_centroids=True)
 
-    nb_shells = len(shells_centroids)
+    non_b0_shells = shells_centroids[shells_centroids > args.tolerance]
+    nb_shells = len(non_b0_shells)
     if nb_shells <= 1:
         raise ValueError("Amico's NODDI works with data with more than one "
                          "shell, but you seem to have single-shell data (we "
-                         "found shells {}). Change tolerance if necessary."
-                         .format(np.sort(shells_centroids)))
+                         "found shell {}). Change tolerance if necessary."
+                         .format(non_b0_shells[0]))
 
     logging.info('Will compute NODDI with AMICO on {} shells at found at {}.'
                  .format(len(shells_centroids), np.sort(shells_centroids)))

scripts/tests/test_NODDI_maps.py

@@ -8,7 +8,8 @@
 from scilpy.io.fetcher import fetch_data, get_testing_files_dict
 
 # If they already exist, this only takes 5 seconds (check md5sum)
-fetch_data(get_testing_files_dict(), keys=['commit_amico.zip'])
+fetch_data(get_testing_files_dict(), keys=['commit_amico.zip',
+                                           'processing.zip'])
 tmp_dir = tempfile.TemporaryDirectory()
 
 
@@ -32,5 +33,22 @@ def test_execution_commit_amico(script_runner, monkeypatch):
                             '--out_dir', 'noddi', '--tol', '30',
                             '--para_diff', '0.0017', '--iso_diff', '0.003',
                             '--lambda1', '0.5', '--lambda2', '0.001',
-                            '--processes', '1')
+                            '--processes', '1', '-f')
     assert ret.success
+
+
+def test_single_shell_fail(script_runner, monkeypatch):
+    monkeypatch.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(SCILPY_HOME, 'processing',
+                          'dwi_crop_1000.nii.gz')
+    in_bval = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bval')
+    in_bvec = os.path.join(SCILPY_HOME, 'processing',
+                           '1000.bvec')
+    ret = script_runner.run('scil_NODDI_maps.py', in_dwi,
+                            in_bval, in_bvec,
+                            '--out_dir', 'noddi', '--tol', '30',
+                            '--para_diff', '0.0017', '--iso_diff', '0.003',
+                            '--lambda1', '0.5', '--lambda2', '0.001',
+                            '--processes', '1', '-f')
+    assert not ret.success