Merge pull request #3609 from mauriliogenovese/origin/fix/dcm2niix_crop

[FIX] Add cropped files to dcm2niix output

Author: effigies

.zenodo.json

@@ -910,6 +910,11 @@
       "name": "Anijärv, Toomas Erik",
       "orcid": "0000-0002-3650-4230"
     },
+    {
+      "affiliation": "Azienda Ospedaliero-Universitaria di Modena",
+      "name": "Genovese, Maurilio",
+      "orcid": "0000-0002-8154-8224"
+    },
     {
       "affiliation": "Department of Psychology, Stanford University",
       "name": "Gorgolewski, Krzysztof J.",

nipype/interfaces/dcm2nii.py

@@ -470,7 +470,7 @@ def _parse_files(self, filenames):
 
         for filename in filenames:
             # search for relevant files, and sort accordingly
-            for fl in search_files(filename, outtypes):
+            for fl in search_files(filename, outtypes, self.inputs.crop):
                 if (
                     fl.endswith(".nii")
                     or fl.endswith(".gz")
@@ -508,7 +508,15 @@ def _list_outputs(self):
 
 
 # https://stackoverflow.com/a/4829130
-def search_files(prefix, outtypes):
-    return it.chain.from_iterable(
+def search_files(prefix, outtypes, search_crop):
+    found = it.chain.from_iterable(
         iglob(glob.escape(prefix + outtype)) for outtype in outtypes
     )
+    if search_crop:
+        found = it.chain(
+            it.chain.from_iterable(
+                iglob(glob.escape(prefix) + "_Crop_*" + outtype) for outtype in outtypes
+            ),
+            found,
+        )
+    return found

nipype/interfaces/tests/test_dcm2nii.py

@@ -5,17 +5,28 @@
 
 
 @pytest.mark.parametrize(
-    "fname, extension",
+    "fname, extension, search_crop",
     [
-        ("output_1", ".txt"),
-        ("output_w_[]_meta_1", ".json"),
-        ("output_w_**^$?_meta_2", ".txt"),
+        ("output_1", ".txt", False),
+        ("output_w_[]_meta_1", ".json", False),
+        ("output_w_**^$?_meta_2", ".txt", False),
+        ("output_cropped", ".txt", True),
     ],
 )
-def test_search_files(tmp_path, fname, extension):
+def test_search_files(tmp_path, fname, extension, search_crop):
     tmp_fname = fname + extension
     test_file = tmp_path / tmp_fname
     test_file.touch()
-    actual_files_list = dcm2nii.search_files(str(tmp_path / fname), [extension])
+    if search_crop:
+        tmp_cropped_fname = fname + "_Crop_1" + extension
+        test_cropped_file = tmp_path / tmp_cropped_fname
+        test_cropped_file.touch()
+
+    actual_files_list = dcm2nii.search_files(
+        str(tmp_path / fname), [extension], search_crop
+    )
     for f in actual_files_list:
-        assert str(test_file) == f
+        if search_crop:
+            assert f in (str(test_cropped_file), str(test_file))
+        else:
+            assert str(test_file) == f