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FIX: Use a more reliable test of NIfTIness #784

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merged 4 commits into from
Mar 2, 2023
Merged

FIX: Use a more reliable test of NIfTIness #784

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86a4971
FIX: Use a more reliably test of NIfTIness
effigies Mar 1, 2023
47806db
ENH: While we're here, add dscalar niftis
effigies Mar 1, 2023
51d45c1
TEST: Generate CIFTI files for testing
effigies Mar 1, 2023
4e11ead
TEST: Py37 compatibility hack
effigies Mar 1, 2023
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1 change: 1 addition & 0 deletions niworkflows/data/nipreps.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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}",
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8 changes: 5 additions & 3 deletions niworkflows/interfaces/bids.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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)
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28 changes: 21 additions & 7 deletions niworkflows/interfaces/tests/test_bids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
# https://www.nipreps.org/community/licensing/
#
"""Tests on BIDS compliance."""
import sys
import os
from pathlib import Path
import json
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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)
Expand All @@ -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))

Expand Down Expand Up @@ -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


Expand Down