Merge pull request #835 from arnaudbore/update_philips_reorder

Rename reorder_dwi

scripts/legacy/scil_reorder_dwi_philips.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_dwi_reorder_philips import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_dwi_reorder_philips.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_reorder_dwi_philips.py", DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/scil_reorder_dwi_philips.py → scripts/scil_dwi_reorder_philips.py

@@ -2,11 +2,15 @@
 # -*- coding: utf-8 -*-
 
 """
-Re-order gradient according to original table
+Re-order gradient according to original table (Philips)
+This script is not needed for version 5.6 and higher
 """
 
 import argparse
+import json
 import logging
+from packaging import version
+import sys
 
 from dipy.io.gradients import read_bvals_bvecs
 import nibabel as nib
@@ -19,6 +23,8 @@
                              assert_outputs_exist)
 from scilpy.utils.filenames import split_name_with_nii
 
+SOFTWARE_VERSION_MIN = '5.6'
+
 
 def _build_arg_parser():
     p = argparse.ArgumentParser(description=__doc__,
@@ -35,6 +41,10 @@ def _build_arg_parser():
     p.add_argument('out_basename',
                    help='Basename output file.')
 
+    p.add_argument('--json',
+                   help='If you json file, it will check if you need'
+                        ' to reorder your Philips dwi.')
+
     add_overwrite_arg(p)
     add_verbose_arg(p)
 
@@ -55,9 +65,24 @@ def main():
                         args.out_basename + '.bval',
                         args.out_basename + '.bvec']
 
-    assert_inputs_exist(parser, required_args)
+    assert_inputs_exist(parser, required_args, args.json)
     assert_outputs_exist(parser, args, output_filenames)
 
+    if args.json and not args.overwrite:
+        with open(args.json) as curr_json:
+            dwi_json = json.load(curr_json)
+        if 'SoftwareVersions' in dwi_json.keys():
+            curr_version = dwi_json['SoftwareVersions']
+            curr_version = curr_version.replace('\\',
+                                                ' ').replace('_',
+                                                             ' ').split()[0]
+            if version.parse(SOFTWARE_VERSION_MIN) <= version.parse(curr_version):
+                sys.exit('ERROR: There is no need for reording since your '
+                         'dwi comes from a Philips machine with '
+                         'version {}. '.format(curr_version) +
+                         'No file will be created. \n'
+                         'Use -f to force overwriting.')
+
     philips_table = np.loadtxt(args.in_table, skiprows=1)
     bvals, bvecs = read_bvals_bvecs(args.in_bval, args.in_bvec)
     dwi = nib.load(args.in_dwi)

scripts/tests/test_dwi_reorder_philips.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run('scil_dwi_reorder_philips.py', '--help')
+    assert ret.success