From dff774e2d89b07a0b40b44219391e906616ef5f1 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 6 Jul 2020 09:32:33 -0400
Subject: [PATCH 1/9] RF: Allow kwargs within ``to_filename`` and
``instance_to_filename`` methods
---
nibabel/filebasedimages.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/nibabel/filebasedimages.py b/nibabel/filebasedimages.py
index 006b70d615..f610e87543 100644
--- a/nibabel/filebasedimages.py
+++ b/nibabel/filebasedimages.py
@@ -315,7 +315,7 @@ def filespec_to_file_map(klass, filespec):
def filespec_to_files(klass, filespec):
return klass.filespec_to_file_map(filespec)
- def to_filename(self, filename):
+ def to_filename(self, filename, **kwargs):
""" Write image to files implied by filename string
Parameters
@@ -381,7 +381,7 @@ def make_file_map(klass, mapping=None):
load = from_filename
@classmethod
- def instance_to_filename(klass, img, filename):
+ def instance_to_filename(klass, img, filename, **kwargs):
""" Save `img` in our own format, to name implied by `filename`
This is a class method
@@ -394,7 +394,7 @@ def instance_to_filename(klass, img, filename):
Filename, implying name to which to save image.
"""
img = klass.from_image(img)
- img.to_filename(filename)
+ img.to_filename(filename, **kwargs)
@classmethod
def from_image(klass, img):
From f78d7f1b54b2be05bf543152f7fe406b978c3bf8 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 6 Jul 2020 09:33:46 -0400
Subject: [PATCH 2/9] ENH: Add option to allow inferring of intent code based
on output file suffixes
---
nibabel/cifti2/cifti2.py | 50 ++++++++++++++++++++++---
nibabel/cifti2/tests/test_new_cifti2.py | 34 ++++++-----------
2 files changed, 56 insertions(+), 28 deletions(-)
diff --git a/nibabel/cifti2/cifti2.py b/nibabel/cifti2/cifti2.py
index 0b2b7f2a9a..2cc6931de7 100644
--- a/nibabel/cifti2/cifti2.py
+++ b/nibabel/cifti2/cifti2.py
@@ -89,6 +89,23 @@ class Cifti2HeaderError(Exception):
'CIFTI_STRUCTURE_THALAMUS_LEFT',
'CIFTI_STRUCTURE_THALAMUS_RIGHT')
+# "Standard CIFTI Mapping Combinations" within CIFTI-2 spec
+# https://www.nitrc.org/forum/attachment.php?attachid=341&group_id=454&forum_id=1955
+CIFTI_EXTENSIONS_TO_INTENTS = {
+ '.dconn': 'NIFTI_INTENT_CONNECTIVITY_DENSE',
+ '.dtseries': 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES',
+ '.pconn': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED',
+ '.ptseries': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES',
+ '.dscalar': 'NIFTI_INTENT_CONNECTIVITY_DENSE_SCALARS',
+ '.dlabel': 'NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS',
+ '.pscalar': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR',
+ '.pdconn': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE',
+ '.dpconn': 'NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED',
+ '.pconnseries': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SERIES',
+ '.pconnscalar': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SCALAR',
+ '.dfan': 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES',
+}
+
def _value_if_klass(val, klass):
if val is None or isinstance(val, klass):
@@ -1466,11 +1483,7 @@ def to_file_map(self, file_map=None):
raise ValueError(
f"Dataobj shape {self._dataobj.shape} does not match shape "
f"expected from CIFTI-2 header {self.header.matrix.get_data_shape()}")
- # if intent code is not set, default to unknown CIFTI
- if header.get_intent()[0] == 'none':
- header.set_intent('NIFTI_INTENT_CONNECTIVITY_UNKNOWN')
- data = reshape_dataobj(self.dataobj,
- (1, 1, 1, 1) + self.dataobj.shape)
+ data = reshape_dataobj(self.dataobj, (1, 1, 1, 1) + self.dataobj.shape)
# If qform not set, reset pixdim values so Nifti2 does not complain
if header['qform_code'] == 0:
header['pixdim'][:4] = 1
@@ -1509,6 +1522,33 @@ def get_data_dtype(self):
def set_data_dtype(self, dtype):
self._nifti_header.set_data_dtype(dtype)
+ def to_filename(self, filename, infer_intent=False):
+ """
+ Ensures NIfTI header intent code is set prior to saving.
+
+ Parameters
+ ----------
+ infer_intent : boolean, optional
+ If ``True``, attempt to infer and set intent code based on filename suffix.
+ """
+ header = self._nifti_header
+ if infer_intent:
+ # try to infer intent code based on filename suffix
+ intent = _infer_intent_from_filename(filename)
+ if intent is not None:
+ header.set_intent(intent)
+ # if intent code is not set, default to unknown
+ if header.get_intent()[0] == 'none':
+ header.set_intent('NIFTI_INTENT_CONNECTIVITY_UNKNOWN')
+ super().to_filename(filename)
+
+
+def _infer_intent_from_filename(filename):
+ """Parses output filename for common suffixes and fetches corresponding intent code"""
+ from pathlib import Path
+ ext = Path(filename).suffixes[0]
+ return CIFTI_EXTENSIONS_TO_INTENTS.get(ext)
+
load = Cifti2Image.from_filename
save = Cifti2Image.instance_to_filename
diff --git a/nibabel/cifti2/tests/test_new_cifti2.py b/nibabel/cifti2/tests/test_new_cifti2.py
index 65ef95c316..5ee6f4a7c3 100644
--- a/nibabel/cifti2/tests/test_new_cifti2.py
+++ b/nibabel/cifti2/tests/test_new_cifti2.py
@@ -237,10 +237,9 @@ def test_dtseries():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(13, 10)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES')
with InTemporaryDirectory():
- ci.save(img, 'test.dtseries.nii')
+ ci.save(img, 'test.dtseries.nii', infer_intent=True)
img2 = nib.load('test.dtseries.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnDenseSeries'
assert isinstance(img2, ci.Cifti2Image)
@@ -281,10 +280,9 @@ def test_dlabel():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(2, 10)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS')
with InTemporaryDirectory():
- ci.save(img, 'test.dlabel.nii')
+ ci.save(img, 'test.dlabel.nii', infer_intent=True)
img2 = nib.load('test.dlabel.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnDenseLabel'
assert isinstance(img2, ci.Cifti2Image)
@@ -301,10 +299,9 @@ def test_dconn():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(10, 10)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE')
with InTemporaryDirectory():
- ci.save(img, 'test.dconn.nii')
+ ci.save(img, 'test.dconn.nii', infer_intent=True)
img2 = nib.load('test.dconn.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnDense'
assert isinstance(img2, ci.Cifti2Image)
@@ -323,10 +320,9 @@ def test_ptseries():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(13, 4)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES')
with InTemporaryDirectory():
- ci.save(img, 'test.ptseries.nii')
+ ci.save(img, 'test.ptseries.nii', infer_intent=True)
img2 = nib.load('test.ptseries.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnParcelSries'
assert isinstance(img2, ci.Cifti2Image)
@@ -345,10 +341,9 @@ def test_pscalar():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(2, 4)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR')
with InTemporaryDirectory():
- ci.save(img, 'test.pscalar.nii')
+ ci.save(img, 'test.pscalar.nii', infer_intent=True)
img2 = nib.load('test.pscalar.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnParcelScalr'
assert isinstance(img2, ci.Cifti2Image)
@@ -367,10 +362,9 @@ def test_pdconn():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(10, 4)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE')
with InTemporaryDirectory():
- ci.save(img, 'test.pdconn.nii')
+ ci.save(img, 'test.pdconn.nii', infer_intent=True)
img2 = ci.load('test.pdconn.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnParcelDense'
assert isinstance(img2, ci.Cifti2Image)
@@ -389,10 +383,9 @@ def test_dpconn():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(4, 10)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED')
with InTemporaryDirectory():
- ci.save(img, 'test.dpconn.nii')
+ ci.save(img, 'test.dpconn.nii', infer_intent=True)
img2 = ci.load('test.dpconn.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnDenseParcel'
assert isinstance(img2, ci.Cifti2Image)
@@ -430,10 +423,9 @@ def test_pconn():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(4, 4)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED')
with InTemporaryDirectory():
- ci.save(img, 'test.pconn.nii')
+ ci.save(img, 'test.pconn.nii', infer_intent=True)
img2 = ci.load('test.pconn.nii')
assert img.nifti_header.get_intent()[0] == 'ConnParcels'
assert isinstance(img2, ci.Cifti2Image)
@@ -453,11 +445,9 @@ def test_pconnseries():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(4, 4, 13)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_'
- 'PARCELLATED_SERIES')
with InTemporaryDirectory():
- ci.save(img, 'test.pconnseries.nii')
+ ci.save(img, 'test.pconnseries.nii', infer_intent=True)
img2 = ci.load('test.pconnseries.nii')
assert img.nifti_header.get_intent()[0] == 'ConnPPSr'
assert isinstance(img2, ci.Cifti2Image)
@@ -478,11 +468,9 @@ def test_pconnscalar():
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(4, 4, 2)
img = ci.Cifti2Image(data, hdr)
- img.nifti_header.set_intent('NIFTI_INTENT_CONNECTIVITY_PARCELLATED_'
- 'PARCELLATED_SCALAR')
with InTemporaryDirectory():
- ci.save(img, 'test.pconnscalar.nii')
+ ci.save(img, 'test.pconnscalar.nii', infer_intent=True)
img2 = ci.load('test.pconnscalar.nii')
assert img.nifti_header.get_intent()[0] == 'ConnPPSc'
assert isinstance(img2, ci.Cifti2Image)
@@ -517,7 +505,7 @@ def test_wrong_shape():
ci.Cifti2Image(data, hdr)
with suppress_warnings():
img = ci.Cifti2Image(data, hdr)
-
+
with pytest.raises(ValueError):
img.to_file_map()
From 2b6b328173d52b8909c005bfba64ea60330ce4c1 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 2 Oct 2020 16:25:58 -0400
Subject: [PATCH 3/9] ENH: Add validation when saving CIFTI2 images
- Enabled by default, validation will parse the output filename for a valid CIFTI2 extension.
- If found, the intent code of the image will be set. Also, the CIFTI2Header will be check for compliant index maps for the intent code
---
nibabel/cifti2/cifti2.py | 107 +++++++++++++++++-------
nibabel/cifti2/tests/test_new_cifti2.py | 62 +++++++++++---
2 files changed, 131 insertions(+), 38 deletions(-)
diff --git a/nibabel/cifti2/cifti2.py b/nibabel/cifti2/cifti2.py
index 2cc6931de7..a6ec086718 100644
--- a/nibabel/cifti2/cifti2.py
+++ b/nibabel/cifti2/cifti2.py
@@ -25,6 +25,7 @@
from ..nifti1 import Nifti1Extensions
from ..nifti2 import Nifti2Image, Nifti2Header
from ..arrayproxy import reshape_dataobj
+from ..volumeutils import Recoder
from warnings import warn
@@ -91,20 +92,50 @@ class Cifti2HeaderError(Exception):
# "Standard CIFTI Mapping Combinations" within CIFTI-2 spec
# https://www.nitrc.org/forum/attachment.php?attachid=341&group_id=454&forum_id=1955
-CIFTI_EXTENSIONS_TO_INTENTS = {
- '.dconn': 'NIFTI_INTENT_CONNECTIVITY_DENSE',
- '.dtseries': 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES',
- '.pconn': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED',
- '.ptseries': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES',
- '.dscalar': 'NIFTI_INTENT_CONNECTIVITY_DENSE_SCALARS',
- '.dlabel': 'NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS',
- '.pscalar': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR',
- '.pdconn': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE',
- '.dpconn': 'NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED',
- '.pconnseries': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SERIES',
- '.pconnscalar': 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SCALAR',
- '.dfan': 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES',
-}
+CIFTI_CODES = Recoder((
+ ('dconn', 'NIFTI_INTENT_CONNECTIVITY_DENSE', (
+ 'CIFTI_INDEX_TYPE_BRAIN_MODELS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
+ )),
+ ('dtseries', 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES', (
+ 'CIFTI_INDEX_TYPE_SERIES', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
+ )),
+ ('pconn', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED', (
+ 'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_PARCELS',
+ )),
+ ('ptseries', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES', (
+ 'CIFTI_INDEX_TYPE_SERIES', 'CIFTI_INDEX_TYPE_PARCELS',
+ )),
+ ('dscalar', 'NIFTI_INTENT_CONNECTIVITY_DENSE_SCALARS', (
+ 'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
+ )),
+ ('dlabel', 'NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS', (
+ 'CIFTI_INDEX_TYPE_LABELS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
+ )),
+ ('pscalar', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR', (
+ 'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_PARCELS',
+ )),
+ ('pdconn', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE', (
+ 'CIFTI_INDEX_TYPE_BRAIN_MODELS', 'CIFTI_INDEX_TYPE_PARCELS',
+ )),
+ ('dpconn', 'NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED', (
+ 'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
+ )),
+ ('pconnseries', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SERIES', (
+ 'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_SERIES',
+ )),
+ ('pconnscalar', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SCALAR', (
+ 'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_SCALARS',
+ )),
+ ('dfan', 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES', (
+ 'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
+ )),
+ ('dfibersamp', 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN', (
+ 'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
+ )),
+ ('dfansamp', 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN', (
+ 'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
+ )),
+), fields=('extension', 'niistring', 'map_types'))
def _value_if_klass(val, klass):
@@ -1522,32 +1553,52 @@ def get_data_dtype(self):
def set_data_dtype(self, dtype):
self._nifti_header.set_data_dtype(dtype)
- def to_filename(self, filename, infer_intent=False):
+ def to_filename(self, filename, validate=True):
"""
Ensures NIfTI header intent code is set prior to saving.
Parameters
----------
- infer_intent : boolean, optional
- If ``True``, attempt to infer and set intent code based on filename suffix.
+ validate : boolean, optional
+ If ``True``, infer and validate CIFTI type based on filename suffix.
+ This includes the setting of the NIfTI intent code and checking the ``CIFTI2Matrix``
+ for the expected IndicesMaps attributes.
+ If validation fails, an error will be raised instead.
"""
- header = self._nifti_header
- if infer_intent:
- # try to infer intent code based on filename suffix
- intent = _infer_intent_from_filename(filename)
- if intent is not None:
- header.set_intent(intent)
+ nheader = self._nifti_header
+ # try to infer intent code based on filename suffix
+ if validate:
+ ext = _extract_cifti_extension(filename)
+ try:
+ CIFTI_CODES.extension[ext]
+ except KeyError as err:
+ raise KeyError(
+ f"Validation failed: No information for extension {ext} available"
+ ) from err
+ intent = CIFTI_CODES.niistring[ext]
+ nheader.set_intent(intent)
+ # validate matrix indices
+ for idx, mtype in enumerate(CIFTI_CODES.map_types[ext]):
+ try:
+ assert self.header.matrix.get_index_map(idx).indices_map_to_data_type == mtype
+ except Exception:
+ raise Cifti2HeaderError(
+ f"Validation failed: Cifti2Matrix index map {idx} does "
+ f"not match expected type {mtype}"
+ )
# if intent code is not set, default to unknown
- if header.get_intent()[0] == 'none':
- header.set_intent('NIFTI_INTENT_CONNECTIVITY_UNKNOWN')
+ if nheader.get_intent()[0] == 'none':
+ nheader.set_intent('NIFTI_INTENT_CONNECTIVITY_UNKNOWN')
super().to_filename(filename)
-def _infer_intent_from_filename(filename):
+def _extract_cifti_extension(filename):
"""Parses output filename for common suffixes and fetches corresponding intent code"""
from pathlib import Path
- ext = Path(filename).suffixes[0]
- return CIFTI_EXTENSIONS_TO_INTENTS.get(ext)
+ _suf = Path(filename).suffixes
+ # select second to last if possible (.<suffix>.nii)
+ ext = _suf[-2] if len(_suf) >= 2 else _suf[0]
+ return ext.lstrip('.')
load = Cifti2Image.from_filename
diff --git a/nibabel/cifti2/tests/test_new_cifti2.py b/nibabel/cifti2/tests/test_new_cifti2.py
index 5ee6f4a7c3..948e1aca41 100644
--- a/nibabel/cifti2/tests/test_new_cifti2.py
+++ b/nibabel/cifti2/tests/test_new_cifti2.py
@@ -239,7 +239,7 @@ def test_dtseries():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.dtseries.nii', infer_intent=True)
+ ci.save(img, 'test.dtseries.nii')
img2 = nib.load('test.dtseries.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnDenseSeries'
assert isinstance(img2, ci.Cifti2Image)
@@ -282,7 +282,7 @@ def test_dlabel():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.dlabel.nii', infer_intent=True)
+ ci.save(img, 'test.dlabel.nii')
img2 = nib.load('test.dlabel.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnDenseLabel'
assert isinstance(img2, ci.Cifti2Image)
@@ -301,7 +301,7 @@ def test_dconn():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.dconn.nii', infer_intent=True)
+ ci.save(img, 'test.dconn.nii')
img2 = nib.load('test.dconn.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnDense'
assert isinstance(img2, ci.Cifti2Image)
@@ -322,7 +322,7 @@ def test_ptseries():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.ptseries.nii', infer_intent=True)
+ ci.save(img, 'test.ptseries.nii')
img2 = nib.load('test.ptseries.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnParcelSries'
assert isinstance(img2, ci.Cifti2Image)
@@ -343,7 +343,7 @@ def test_pscalar():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.pscalar.nii', infer_intent=True)
+ ci.save(img, 'test.pscalar.nii')
img2 = nib.load('test.pscalar.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnParcelScalr'
assert isinstance(img2, ci.Cifti2Image)
@@ -364,7 +364,7 @@ def test_pdconn():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.pdconn.nii', infer_intent=True)
+ ci.save(img, 'test.pdconn.nii')
img2 = ci.load('test.pdconn.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnParcelDense'
assert isinstance(img2, ci.Cifti2Image)
@@ -385,7 +385,7 @@ def test_dpconn():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.dpconn.nii', infer_intent=True)
+ ci.save(img, 'test.dpconn.nii')
img2 = ci.load('test.dpconn.nii')
assert img2.nifti_header.get_intent()[0] == 'ConnDenseParcel'
assert isinstance(img2, ci.Cifti2Image)
@@ -425,7 +425,7 @@ def test_pconn():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.pconn.nii', infer_intent=True)
+ ci.save(img, 'test.pconn.nii')
img2 = ci.load('test.pconn.nii')
assert img.nifti_header.get_intent()[0] == 'ConnParcels'
assert isinstance(img2, ci.Cifti2Image)
@@ -447,7 +447,7 @@ def test_pconnseries():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.pconnseries.nii', infer_intent=True)
+ ci.save(img, 'test.pconnseries.nii')
img2 = ci.load('test.pconnseries.nii')
assert img.nifti_header.get_intent()[0] == 'ConnPPSr'
assert isinstance(img2, ci.Cifti2Image)
@@ -470,7 +470,7 @@ def test_pconnscalar():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.pconnscalar.nii', infer_intent=True)
+ ci.save(img, 'test.pconnscalar.nii')
img2 = ci.load('test.pconnscalar.nii')
assert img.nifti_header.get_intent()[0] == 'ConnPPSc'
assert isinstance(img2, ci.Cifti2Image)
@@ -509,3 +509,45 @@ def test_wrong_shape():
with pytest.raises(ValueError):
img.to_file_map()
+
+def test_cifti_validation():
+ # flip label / brain_model index maps
+ geometry_map = create_geometry_map((0, ))
+ label_map = create_label_map((1, ))
+ matrix = ci.Cifti2Matrix()
+ matrix.append(label_map)
+ matrix.append(geometry_map)
+ hdr = ci.Cifti2Header(matrix)
+ data = np.random.randn(10, 2)
+ img = ci.Cifti2Image(data, hdr)
+
+ # attempt to save and validate with an invalid extension
+ with pytest.raises(KeyError):
+ ci.save(img, 'test.dlabelz.nii')
+ # even with a proper extension, flipped index maps will fail
+ with pytest.raises(ci.Cifti2HeaderError):
+ ci.save(img, 'test.dlabel.nii')
+
+ label_map = create_label_map((0, ))
+ geometry_map = create_geometry_map((1, ))
+ matrix = ci.Cifti2Matrix()
+ matrix.append(label_map)
+ matrix.append(geometry_map)
+ hdr = ci.Cifti2Header(matrix)
+ data = np.random.randn(2, 10)
+ img = ci.Cifti2Image(data, hdr)
+
+ with InTemporaryDirectory():
+ # still fail with invalid extension and validation
+ with pytest.raises(KeyError):
+ ci.save(img, 'test.dlabelz.nii')
+ # but removing validation should work (though intent code will be unknown)
+ ci.save(img, 'test.dlabelz.nii', validate=False)
+
+ img2 = nib.load('test.dlabelz.nii')
+ assert img2.nifti_header.get_intent()[0] == 'ConnUnknown'
+ assert isinstance(img2, ci.Cifti2Image)
+ assert_array_equal(img2.get_fdata(), data)
+ check_label_map(img2.header.matrix.get_index_map(0))
+ check_geometry_map(img2.header.matrix.get_index_map(1))
+ del img2
From ad6adfa5b30e317939990962f188aaf72aca8161 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Fri, 2 Oct 2020 18:57:59 -0400
Subject: [PATCH 4/9] RF: Avoid validation when testing CIFTI saving
---
nibabel/cifti2/tests/test_cifti2.py | 15 +++++++++++++++
nibabel/cifti2/tests/test_cifti2io_axes.py | 2 +-
nibabel/cifti2/tests/test_new_cifti2.py | 2 +-
nibabel/tests/test_image_api.py | 20 ++++++++++----------
4 files changed, 27 insertions(+), 12 deletions(-)
diff --git a/nibabel/cifti2/tests/test_cifti2.py b/nibabel/cifti2/tests/test_cifti2.py
index ea571065de..f64e11c5df 100644
--- a/nibabel/cifti2/tests/test_cifti2.py
+++ b/nibabel/cifti2/tests/test_cifti2.py
@@ -427,3 +427,18 @@ def make_imaker(self, arr, header=None, ni_header=None):
)
header.matrix.append(mim)
return lambda: self.image_maker(arr.copy(), header, ni_header)
+
+ def validate_filenames(self, imaker, params, validate=False):
+ super().validate_filenames(imaker, params, validate=validate)
+
+ def validate_mmap_parameter(self, imaker, params, validate=False):
+ super().validate_mmap_parameter(imaker, params, validate=validate)
+
+ def validate_to_bytes(self, imaker, params, validate=False):
+ super().validate_to_bytes(imaker, params, validate=validate)
+
+ def validate_from_bytes(self, imaker, params, validate=False):
+ super().validate_from_bytes(imaker, params, validate=validate)
+
+ def validate_to_from_bytes(self, imaker, params, validate=False):
+ super().validate_to_from_bytes(imaker, params, validate=validate)
diff --git a/nibabel/cifti2/tests/test_cifti2io_axes.py b/nibabel/cifti2/tests/test_cifti2io_axes.py
index c237e3c61a..1abd129ae5 100644
--- a/nibabel/cifti2/tests/test_cifti2io_axes.py
+++ b/nibabel/cifti2/tests/test_cifti2io_axes.py
@@ -91,7 +91,7 @@ def check_rewrite(arr, axes, extension='.nii'):
custom extension to use
"""
(fd, name) = tempfile.mkstemp(extension)
- cifti2.Cifti2Image(arr, header=axes).to_filename(name)
+ cifti2.Cifti2Image(arr, header=axes).to_filename(name, validate=False)
img = nib.load(name)
arr2 = img.get_fdata()
assert np.allclose(arr, arr2)
diff --git a/nibabel/cifti2/tests/test_new_cifti2.py b/nibabel/cifti2/tests/test_new_cifti2.py
index 948e1aca41..2bc6da3b47 100644
--- a/nibabel/cifti2/tests/test_new_cifti2.py
+++ b/nibabel/cifti2/tests/test_new_cifti2.py
@@ -406,7 +406,7 @@ def test_plabel():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- ci.save(img, 'test.plabel.nii')
+ ci.save(img, 'test.plabel.nii', validate=False)
img2 = ci.load('test.plabel.nii')
assert img.nifti_header.get_intent()[0] == 'ConnUnknown'
assert isinstance(img2, ci.Cifti2Image)
diff --git a/nibabel/tests/test_image_api.py b/nibabel/tests/test_image_api.py
index 392a493e53..9a9ae040c4 100644
--- a/nibabel/tests/test_image_api.py
+++ b/nibabel/tests/test_image_api.py
@@ -123,7 +123,7 @@ def validate_header_deprecated(self, imaker, params):
hdr = img.get_header()
assert hdr is img.header
- def validate_filenames(self, imaker, params):
+ def validate_filenames(self, imaker, params, **kwargs):
# Validate the filename, file_map interface
if not self.can_save:
@@ -160,7 +160,7 @@ def validate_filenames(self, imaker, params):
warnings.filterwarnings('error',
category=DeprecationWarning,
module=r"nibabel.*")
- img.to_filename(path)
+ img.to_filename(path, **kwargs)
rt_img = img.__class__.from_filename(path)
assert_array_equal(img.shape, rt_img.shape)
assert_almost_equal(img.get_fdata(), rt_img.get_fdata())
@@ -456,7 +456,7 @@ def validate_shape_deprecated(self, imaker, params):
with pytest.raises(ExpiredDeprecationError):
img.get_shape()
- def validate_mmap_parameter(self, imaker, params):
+ def validate_mmap_parameter(self, imaker, params, **kwargs):
img = imaker()
fname = img.get_filename()
with InTemporaryDirectory():
@@ -468,7 +468,7 @@ def validate_mmap_parameter(self, imaker, params):
if not img.rw or not img.valid_exts:
return
fname = 'image' + img.valid_exts[0]
- img.to_filename(fname)
+ img.to_filename(fname, **kwargs)
rt_img = img.__class__.from_filename(fname, mmap=True)
assert_almost_equal(img.get_fdata(), rt_img.get_fdata())
rt_img = img.__class__.from_filename(fname, mmap=False)
@@ -533,22 +533,22 @@ def validate_affine_deprecated(self, imaker, params):
class SerializeMixin(object):
- def validate_to_bytes(self, imaker, params):
+ def validate_to_bytes(self, imaker, params, **kwargs):
img = imaker()
serialized = img.to_bytes()
with InTemporaryDirectory():
fname = 'img' + self.standard_extension
- img.to_filename(fname)
+ img.to_filename(fname, **kwargs)
with open(fname, 'rb') as fobj:
file_contents = fobj.read()
assert serialized == file_contents
- def validate_from_bytes(self, imaker, params):
+ def validate_from_bytes(self, imaker, params, **kwargs):
img = imaker()
klass = getattr(self, 'klass', img.__class__)
with InTemporaryDirectory():
fname = 'img' + self.standard_extension
- img.to_filename(fname)
+ img.to_filename(fname, **kwargs)
all_images = list(getattr(self, 'example_images', [])) + [{'fname': fname}]
for img_params in all_images:
@@ -561,12 +561,12 @@ def validate_from_bytes(self, imaker, params):
del img_a
del img_b
- def validate_to_from_bytes(self, imaker, params):
+ def validate_to_from_bytes(self, imaker, params, **kwargs):
img = imaker()
klass = getattr(self, 'klass', img.__class__)
with InTemporaryDirectory():
fname = 'img' + self.standard_extension
- img.to_filename(fname)
+ img.to_filename(fname, **kwargs)
all_images = list(getattr(self, 'example_images', [])) + [{'fname': fname}]
for img_params in all_images:
From 2a20433db3f58c5fc30bc316c066fec661be0167 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 5 Oct 2020 11:05:49 -0400
Subject: [PATCH 5/9] RF: Extract nifti header update from ``to_filename``
---
nibabel/cifti2/cifti2.py | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/nibabel/cifti2/cifti2.py b/nibabel/cifti2/cifti2.py
index a6ec086718..98e4a83a89 100644
--- a/nibabel/cifti2/cifti2.py
+++ b/nibabel/cifti2/cifti2.py
@@ -1545,7 +1545,11 @@ def update_headers(self):
>>> img.shape == (2, 3, 4)
True
"""
- self._nifti_header.set_data_shape((1, 1, 1, 1) + self._dataobj.shape)
+ header = self._nifti_header
+ header.set_data_shape((1, 1, 1, 1) + self._dataobj.shape)
+ # if intent code is not set, default to unknown
+ if header.get_intent()[0] == 'none':
+ header.set_intent('NIFTI_INTENT_CONNECTIVITY_UNKNOWN')
def get_data_dtype(self):
return self._nifti_header.get_data_dtype()
@@ -1565,8 +1569,6 @@ def to_filename(self, filename, validate=True):
for the expected IndicesMaps attributes.
If validation fails, an error will be raised instead.
"""
- nheader = self._nifti_header
- # try to infer intent code based on filename suffix
if validate:
ext = _extract_cifti_extension(filename)
try:
@@ -1576,7 +1578,7 @@ def to_filename(self, filename, validate=True):
f"Validation failed: No information for extension {ext} available"
) from err
intent = CIFTI_CODES.niistring[ext]
- nheader.set_intent(intent)
+ self._nifti_header.set_intent(intent)
# validate matrix indices
for idx, mtype in enumerate(CIFTI_CODES.map_types[ext]):
try:
@@ -1586,9 +1588,6 @@ def to_filename(self, filename, validate=True):
f"Validation failed: Cifti2Matrix index map {idx} does "
f"not match expected type {mtype}"
)
- # if intent code is not set, default to unknown
- if nheader.get_intent()[0] == 'none':
- nheader.set_intent('NIFTI_INTENT_CONNECTIVITY_UNKNOWN')
super().to_filename(filename)
From 619295e9c6990f0ce6cbeb08f266a562b9da8d86 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 5 Oct 2020 11:37:23 -0400
Subject: [PATCH 6/9] FIX: remove validation for remaining tests
---
nibabel/cifti2/tests/test_cifti2io_header.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/nibabel/cifti2/tests/test_cifti2io_header.py b/nibabel/cifti2/tests/test_cifti2io_header.py
index df4fe10fcd..f1f1f6c811 100644
--- a/nibabel/cifti2/tests/test_cifti2io_header.py
+++ b/nibabel/cifti2/tests/test_cifti2io_header.py
@@ -83,7 +83,7 @@ def test_readwritedata():
with InTemporaryDirectory():
for name in datafiles:
img = ci.load(name)
- ci.save(img, 'test.nii')
+ ci.save(img, 'test.nii', validate=False)
img2 = ci.load('test.nii')
assert len(img.header.matrix) == len(img2.header.matrix)
# Order should be preserved in load/save
@@ -109,7 +109,7 @@ def test_nibabel_readwritedata():
with InTemporaryDirectory():
for name in datafiles:
img = nib.load(name)
- nib.save(img, 'test.nii')
+ nib.save(img, 'test.nii', validate=False)
img2 = nib.load('test.nii')
assert len(img.header.matrix) == len(img2.header.matrix)
# Order should be preserved in load/save
From 62be507ccd01f3568dd52ea3d0649440e1a75913 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 5 Oct 2020 12:53:25 -0400
Subject: [PATCH 7/9] ENH: Allow kwargs in generic save method
---
nibabel/loadsave.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/nibabel/loadsave.py b/nibabel/loadsave.py
index f3a2b5876b..eb112b158c 100644
--- a/nibabel/loadsave.py
+++ b/nibabel/loadsave.py
@@ -78,7 +78,7 @@ def guessed_image_type(filename):
raise ImageFileError(f'Cannot work out file type of "{filename}"')
-def save(img, filename):
+def save(img, filename, **kwargs):
""" Save an image to file adapting format to `filename`
Parameters
@@ -96,7 +96,7 @@ def save(img, filename):
# Save the type as expected
try:
- img.to_filename(filename)
+ img.to_filename(filename, **kwargs)
except ImageFileError:
pass
else:
@@ -144,7 +144,7 @@ def save(img, filename):
# Here, we either have a klass or a converted image.
if converted is None:
converted = klass.from_image(img)
- converted.to_filename(filename)
+ converted.to_filename(filename, **kwargs)
@deprecate_with_version('read_img_data deprecated. '
From 03ef43d65f497d2a16facc0262d3b823e677ab24 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 19 Oct 2020 13:33:45 -0400
Subject: [PATCH 8/9] FIX: Lower severity of failed validation checks
---
nibabel/cifti2/cifti2.py | 87 ++++++++++++++++++++--------------------
1 file changed, 43 insertions(+), 44 deletions(-)
diff --git a/nibabel/cifti2/cifti2.py b/nibabel/cifti2/cifti2.py
index 98e4a83a89..a0cd22fa58 100644
--- a/nibabel/cifti2/cifti2.py
+++ b/nibabel/cifti2/cifti2.py
@@ -93,46 +93,46 @@ class Cifti2HeaderError(Exception):
# "Standard CIFTI Mapping Combinations" within CIFTI-2 spec
# https://www.nitrc.org/forum/attachment.php?attachid=341&group_id=454&forum_id=1955
CIFTI_CODES = Recoder((
- ('dconn', 'NIFTI_INTENT_CONNECTIVITY_DENSE', (
+ ('.dconn.nii', 'NIFTI_INTENT_CONNECTIVITY_DENSE', (
'CIFTI_INDEX_TYPE_BRAIN_MODELS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
)),
- ('dtseries', 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES', (
+ ('.dtseries.nii', 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES', (
'CIFTI_INDEX_TYPE_SERIES', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
)),
- ('pconn', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED', (
+ ('.pconn.nii', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED', (
'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_PARCELS',
)),
- ('ptseries', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES', (
+ ('.ptseries.nii', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SERIES', (
'CIFTI_INDEX_TYPE_SERIES', 'CIFTI_INDEX_TYPE_PARCELS',
)),
- ('dscalar', 'NIFTI_INTENT_CONNECTIVITY_DENSE_SCALARS', (
+ ('.dscalar.nii', 'NIFTI_INTENT_CONNECTIVITY_DENSE_SCALARS', (
'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
)),
- ('dlabel', 'NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS', (
+ ('.dlabel.nii', 'NIFTI_INTENT_CONNECTIVITY_DENSE_LABELS', (
'CIFTI_INDEX_TYPE_LABELS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
)),
- ('pscalar', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR', (
+ ('.pscalar.nii', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_SCALAR', (
'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_PARCELS',
)),
- ('pdconn', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE', (
+ ('.pdconn.nii', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_DENSE', (
'CIFTI_INDEX_TYPE_BRAIN_MODELS', 'CIFTI_INDEX_TYPE_PARCELS',
)),
- ('dpconn', 'NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED', (
+ ('.dpconn.nii', 'NIFTI_INTENT_CONNECTIVITY_DENSE_PARCELLATED', (
'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
)),
- ('pconnseries', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SERIES', (
+ ('.pconnseries.nii', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SERIES', (
'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_SERIES',
)),
- ('pconnscalar', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SCALAR', (
+ ('.pconnscalar.nii', 'NIFTI_INTENT_CONNECTIVITY_PARCELLATED_PARCELLATED_SCALAR', (
'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_PARCELS', 'CIFTI_INDEX_TYPE_SCALARS',
)),
- ('dfan', 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES', (
+ ('.dfan.nii', 'NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES', (
'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
)),
- ('dfibersamp', 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN', (
+ ('.dfibersamp.nii', 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN', (
'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
)),
- ('dfansamp', 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN', (
+ ('.dfansamp.nii', 'NIFTI_INTENT_CONNECTIVITY_UNKNOWN', (
'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_SCALARS', 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
)),
), fields=('extension', 'niistring', 'map_types'))
@@ -1564,40 +1564,39 @@ def to_filename(self, filename, validate=True):
Parameters
----------
validate : boolean, optional
- If ``True``, infer and validate CIFTI type based on filename suffix.
- This includes the setting of the NIfTI intent code and checking the ``CIFTI2Matrix``
- for the expected IndicesMaps attributes.
- If validation fails, an error will be raised instead.
+ If ``True``, infer and validate CIFTI type based on MatrixIndicesMap values.
+ This includes the setting of the relevant intent code within the NIfTI header.
+ If validation fails, a UserWarning is issued and saving continues.
"""
if validate:
- ext = _extract_cifti_extension(filename)
- try:
- CIFTI_CODES.extension[ext]
- except KeyError as err:
- raise KeyError(
- f"Validation failed: No information for extension {ext} available"
- ) from err
- intent = CIFTI_CODES.niistring[ext]
- self._nifti_header.set_intent(intent)
- # validate matrix indices
- for idx, mtype in enumerate(CIFTI_CODES.map_types[ext]):
- try:
- assert self.header.matrix.get_index_map(idx).indices_map_to_data_type == mtype
- except Exception:
- raise Cifti2HeaderError(
- f"Validation failed: Cifti2Matrix index map {idx} does "
- f"not match expected type {mtype}"
- )
- super().to_filename(filename)
+ # Determine CIFTI type via index maps
+ from .parse_cifti2 import intent_codes
+ matrix = self.header.matrix
+ map_types = tuple(
+ matrix.get_index_map(idx).indices_map_to_data_type for idx
+ in sorted(matrix.mapped_indices)
+ )
+ try:
+ expected_intent = CIFTI_CODES.niistring[map_types]
+ expected_ext = CIFTI_CODES.extension[map_types]
+ except KeyError: # unknown
+ expected_intent = "NIFTI_INTENT_CONNECTIVITY_UNKNOWN"
+ expected_ext = None
+ warn(
+ "No information found for matrix containing the following index maps:"
+ f"{map_types}, defaulting to unknown."
+ )
-def _extract_cifti_extension(filename):
- """Parses output filename for common suffixes and fetches corresponding intent code"""
- from pathlib import Path
- _suf = Path(filename).suffixes
- # select second to last if possible (.<suffix>.nii)
- ext = _suf[-2] if len(_suf) >= 2 else _suf[0]
- return ext.lstrip('.')
+ orig_intent = self._nifti_header.get_intent()[0]
+ if expected_intent != intent_codes.niistring[orig_intent]:
+ warn(
+ f"Expected NIfTI intent: {expected_intent} has been automatically set."
+ )
+ self._nifti_header.set_intent(expected_intent)
+ if expected_ext is not None and not filename.endswith(expected_ext):
+ warn(f"Filename does not end with expected extension: {expected_ext}")
+ super().to_filename(filename)
load = Cifti2Image.from_filename
From af7265ceee16cbdfa753355908eca8c0505bd988 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Mon, 19 Oct 2020 13:34:33 -0400
Subject: [PATCH 9/9] TST: Clean up test
---
nibabel/cifti2/tests/test_new_cifti2.py | 31 +++++++++++--------------
1 file changed, 13 insertions(+), 18 deletions(-)
diff --git a/nibabel/cifti2/tests/test_new_cifti2.py b/nibabel/cifti2/tests/test_new_cifti2.py
index 2bc6da3b47..026fc920f0 100644
--- a/nibabel/cifti2/tests/test_new_cifti2.py
+++ b/nibabel/cifti2/tests/test_new_cifti2.py
@@ -7,12 +7,11 @@
scratch.
"""
import numpy as np
-
import nibabel as nib
from nibabel import cifti2 as ci
from nibabel.tmpdirs import InTemporaryDirectory
-
import pytest
+
from ...testing import (
clear_and_catch_warnings, error_warnings, suppress_warnings, assert_array_equal)
@@ -515,17 +514,13 @@ def test_cifti_validation():
geometry_map = create_geometry_map((0, ))
label_map = create_label_map((1, ))
matrix = ci.Cifti2Matrix()
- matrix.append(label_map)
matrix.append(geometry_map)
+ matrix.append(label_map)
hdr = ci.Cifti2Header(matrix)
data = np.random.randn(10, 2)
img = ci.Cifti2Image(data, hdr)
-
- # attempt to save and validate with an invalid extension
- with pytest.raises(KeyError):
- ci.save(img, 'test.dlabelz.nii')
- # even with a proper extension, flipped index maps will fail
- with pytest.raises(ci.Cifti2HeaderError):
+ # flipped index maps will warn
+ with InTemporaryDirectory(), pytest.warns(UserWarning):
ci.save(img, 'test.dlabel.nii')
label_map = create_label_map((0, ))
@@ -538,16 +533,16 @@ def test_cifti_validation():
img = ci.Cifti2Image(data, hdr)
with InTemporaryDirectory():
- # still fail with invalid extension and validation
- with pytest.raises(KeyError):
- ci.save(img, 'test.dlabelz.nii')
- # but removing validation should work (though intent code will be unknown)
- ci.save(img, 'test.dlabelz.nii', validate=False)
-
- img2 = nib.load('test.dlabelz.nii')
- assert img2.nifti_header.get_intent()[0] == 'ConnUnknown'
+ ci.save(img, 'test.validate.nii', validate=False)
+ ci.save(img, 'test.dlabel.nii')
+
+ img2 = nib.load('test.dlabel.nii')
+ img3 = nib.load('test.validate.nii')
+ assert img2.nifti_header.get_intent()[0] == 'ConnDenseLabel'
+ assert img3.nifti_header.get_intent()[0] == 'ConnUnknown'
assert isinstance(img2, ci.Cifti2Image)
+ assert isinstance(img3, ci.Cifti2Image)
assert_array_equal(img2.get_fdata(), data)
check_label_map(img2.header.matrix.get_index_map(0))
check_geometry_map(img2.header.matrix.get_index_map(1))
- del img2
+ del img2, img3
\ No newline at end of file