rename some scripts

scripts/legacy/scil_detect_dwi_volume_outliers.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_dwi_detect_volume_outliers import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_dwi_detect_volume_outliers.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_detect_dwi_volume_outliers.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/scil_detect_dwi_volume_outliers.py → scripts/scil_dwi_detect_volume_outliers.py

@@ -85,7 +85,6 @@ def main():
             dot_product = np.clip(np.tensordot(shell, vec, axes=1), -1, 1)
             angle = np.arccos(dot_product) * 180 / math.pi
             angle[np.isnan(angle)] = 0
-
             idx = np.argpartition(angle, 4).tolist()
             idx.remove(i)
 

scripts/tests/test_dwi_detect_volume_outliers.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import os
+import tempfile
+
+from scilpy.io.fetcher import fetch_data, get_home, get_testing_files_dict
+
+# If they already exist, this only takes 5 seconds (check md5sum)
+fetch_data(get_testing_files_dict(), keys=['processing.zip'])
+tmp_dir = tempfile.TemporaryDirectory()
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_dwi_detect_volume_outliers.py', '--help')
+    assert ret.success
+
+
+def test_execution(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(get_home(), 'processing',
+                          'dwi_crop.nii.gz')
+    in_bval = os.path.join(get_home(), 'processing',
+                           'dwi.bval')
+    in_bvec = os.path.join(get_home(), 'processing',
+                           'dwi.bvec')
+    ret = script_runner.run('scil_dwi_detect_volume_outliers.py', in_dwi,
+                            in_bval, in_bvec)
+    assert ret.success