Merge pull request #784 from effigies/fix/better-nifti-check

FIX: Use a more reliable test of NIfTIness

niworkflows/data/nipreps.json

@@ -155,6 +155,7 @@
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2starmap|FLAIR|FLASH|PDmap|PD|PDT2|dseg|inplaneT[12]|angio|T2starw|MTw|TSE>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_hemi-{hemi<L|R>}[_space-{space}][_cohort-{cohort}][_den-{density}]_{suffix<wm|smoothwm|pial|midthickness|inflated|vinflated|sphere|flat|sulc|curv|thickness>}{extension<.surf.gii|.shape.gii>}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_den-{density}]_{suffix<sulc|curv|thickness>}{extension<.dscalar.nii|.json>}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_desc-{desc}_{suffix<mask>|mask}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_cohort-{cohort}][_res-{resolution}]_label-{label}[_desc-{desc}]_{suffix<probseg>|probseg}{extension<.nii|.nii.gz|.json>|.nii.gz}",
     "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_dir-{direction}][_run-{run}][_echo-{echo}][_part-{part}][_space-{space}][_cohort-{cohort}][_res-{resolution}][_desc-{desc}]_{suffix<bold|cbv|sbref|boldref|dseg>}{extension<.nii|.nii.gz|.json>|.nii.gz}",

niworkflows/interfaces/bids.py

@@ -22,6 +22,7 @@
 #
 """Interfaces for handling BIDS-like neuroimaging structures."""
 from collections import defaultdict
+from contextlib import suppress
 from json import dumps, loads
 from pathlib import Path
 import shutil
@@ -657,9 +658,10 @@ def _run_interface(self, runtime):
             # still None when it's time to write, just copy.
             new_data, new_header = None, None
 
-            is_nifti = out_file.name.endswith(
-                (".nii", ".nii.gz")
-            ) and not out_file.name.endswith((".dtseries.nii", ".dtseries.nii.gz"))
+            is_nifti = False
+            with suppress(nb.filebasedimages.ImageFileError):
+                is_nifti = isinstance(nb.load(orig_file), nb.Nifti1Image)
+
             data_dtype = self.inputs.data_dtype or self._default_dtypes[self.inputs.suffix]
             if is_nifti and any((self.inputs.check_hdr, data_dtype)):
                 nii = nb.load(orig_file)

niworkflows/interfaces/tests/test_bids.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Tests on BIDS compliance."""
+import sys
 import os
 from pathlib import Path
 import json
@@ -181,7 +182,7 @@
             {"space": "fsLR", "density": "91k"},
             "sub-100185/func/sub-100185_task-machinegame_run-01_"
             "space-fsLR_den-91k_bold.dtseries.nii",
-            "53d9b486d08fec5a952f68fcbcddb38a72818d4c",
+            "f7b8755c6ad0d8dcdb60676331b52a23ce288b61",
         ),
         (
             BOLD_PATH,
@@ -269,7 +270,15 @@ def test_DerivativesDataSink_build_path(
     ds_inputs = []
     for input_file in input_files:
         fname = tmp_path / input_file
-        if fname.name.rstrip(".gz").endswith(".nii"):
+        if fname.name.endswith(".dtseries.nii"):
+            axes = (nb.cifti2.SeriesAxis(start=0, step=2, size=20),
+                    nb.cifti2.BrainModelAxis.from_mask(np.ones((5, 5, 5))))
+            hdr = nb.cifti2.cifti2_axes.to_header(axes)
+            cifti = nb.Cifti2Image(np.zeros(hdr.matrix.get_data_shape(), dtype=np.float32),
+                                   header=hdr)
+            cifti.nifti_header.set_intent("ConnDenseSeries")
+            cifti.to_filename(fname)
+        elif fname.name.rstrip(".gz").endswith(".nii"):
             hdr = nb.Nifti1Header()
             hdr.set_qform(np.eye(4), code=2)
             hdr.set_sform(np.eye(4), code=2)
@@ -278,7 +287,7 @@ def test_DerivativesDataSink_build_path(
             hdr.set_xyzt_units(*units)
             nb.Nifti1Image(np.zeros(size), np.eye(4), hdr).to_filename(fname)
         else:
-            (tmp_path / input_file).write_text("")
+            fname.write_text("")
 
         ds_inputs.append(str(fname))
 
@@ -334,11 +343,16 @@ def test_DerivativesDataSink_build_path(
         # Regression - some images were given nan scale factors
         if out.endswith(".nii") or out.endswith(".nii.gz"):
             img = nb.load(out)
-            with nb.openers.ImageOpener(out) as fobj:
-                hdr = img.header.from_fileobj(fobj)
-            assert not np.isnan(hdr["scl_slope"])
-            assert not np.isnan(hdr["scl_inter"])
+            if isinstance(img, nb.Nifti1Image):
+                with nb.openers.ImageOpener(out) as fobj:
+                    hdr = img.header.from_fileobj(fobj)
+                assert not np.isnan(hdr["scl_slope"])
+                assert not np.isnan(hdr["scl_inter"])
     for out, chksum in zip(output, checksum):
+        if chksum == "f7b8755c6ad0d8dcdb60676331b52a23ce288b61" and sys.version_info < (3, 8):
+            # Python 3.8 began preserving insertion order of attributes in XML
+            # Therefore we get a different checksum before/after
+            chksum = "a37ffb1188dd9a7b708de5b8daef46dac56ef8d4"
         assert sha1(Path(out).read_bytes()).hexdigest() == chksum