[med-svn] [Git][med-team/nibabel][upstream] New upstream version 5.3.3
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Thu Dec 11 19:17:49 GMT 2025
Étienne Mollier pushed to branch upstream at Debian Med / nibabel
Commits:
e83d30af by Étienne Mollier at 2025-12-11T20:13:54+01:00
New upstream version 5.3.3
- - - - -
7 changed files:
- .git_archival.txt
- Changelog
- nibabel/nicom/dicomwrappers.py
- nibabel/nicom/tests/test_dicomwrappers.py
- nibabel/pkg_info.py
- nibabel/tests/test_api_validators.py
- tox.ini
Changes:
=====================================
.git_archival.txt
=====================================
@@ -1,4 +1,4 @@
-node: 7b5060e4bb105ed0c08c203db3dc5cf536d9c2aa
-node-date: 2024-10-23T09:33:51-04:00
-describe-name: 5.3.2
-ref-names: tag: 5.3.2
+node: 41756d3190851822c73880bbdeed53f0658e5809
+node-date: 2025-12-05T13:12:23-05:00
+describe-name: 5.3.3
+ref-names: tag: 5.3.3
=====================================
Changelog
=====================================
@@ -25,6 +25,17 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
References like "pr/298" refer to github pull request numbers.
+5.3.3 (Friday 5 December 2025)
+==============================
+
+Bug-fix release in the 5.3.x series.
+
+Bug fixes
+---------
+* Fix frame order for single-frame DICOM files (pr/1387) (Brendan Moloney, reviewed by CM)
+* Replace :class:`dict` literal with :class:`set` in test. (pr/1382) (CM)
+
+
5.3.2 (Wednesday 23 October 2024)
=================================
=====================================
nibabel/nicom/dicomwrappers.py
=====================================
@@ -532,8 +532,8 @@ class Wrapper:
class FrameFilter:
"""Base class for defining how to filter out (ignore) frames from a multiframe file
- It is guaranteed that the `applies` method will on a dataset before the `keep` method
- is called on any of the frames inside.
+ It is guaranteed that the `applies` method will called on a dataset before the `keep`
+ method is called on any of the frames inside.
"""
def applies(self, dcm_wrp) -> bool:
@@ -549,7 +549,7 @@ class FilterMultiStack(FrameFilter):
"""Filter out all but one `StackID`"""
def __init__(self, keep_id=None):
- self._keep_id = keep_id
+ self._keep_id = str(keep_id) if keep_id is not None else None
def applies(self, dcm_wrp) -> bool:
first_fcs = dcm_wrp.frames[0].get('FrameContentSequence', (None,))[0]
@@ -562,10 +562,16 @@ class FilterMultiStack(FrameFilter):
self._selected = self._keep_id
if len(stack_ids) > 1:
if self._keep_id is None:
+ try:
+ sids = [int(x) for x in stack_ids]
+ except:
+ self._selected = dcm_wrp.frames[0].FrameContentSequence[0].StackID
+ else:
+ self._selected = str(min(sids))
warnings.warn(
- 'A multi-stack file was passed without an explicit filter, just using lowest StackID'
+ 'A multi-stack file was passed without an explicit filter, '
+ f'using StackID = {self._selected}'
)
- self._selected = min(stack_ids)
return True
return False
@@ -707,6 +713,7 @@ class MultiframeWrapper(Wrapper):
@cached_property
def frame_order(self):
+ """The ordering of frames to make nD array"""
if self._frame_indices is None:
_ = self.image_shape
return np.lexsort(self._frame_indices.T)
@@ -742,14 +749,20 @@ class MultiframeWrapper(Wrapper):
rows, cols = self.get('Rows'), self.get('Columns')
if None in (rows, cols):
raise WrapperError('Rows and/or Columns are empty.')
- # Check number of frames, initialize array of frame indices
+ # Check number of frames and handle single frame files
n_frames = len(self.frames)
+ if n_frames == 1:
+ self._frame_indices = np.array([[0]], dtype=np.int64)
+ return (rows, cols)
+ # Initialize array of frame indices
try:
frame_indices = np.array(
[frame.FrameContentSequence[0].DimensionIndexValues for frame in self.frames]
)
except AttributeError:
raise WrapperError("Can't find frame 'DimensionIndexValues'")
+ if len(frame_indices.shape) == 1:
+ frame_indices = frame_indices.reshape(frame_indices.shape + (1,))
# Determine the shape and which indices to use
shape = [rows, cols]
curr_parts = n_frames
=====================================
nibabel/nicom/tests/test_dicomwrappers.py
=====================================
@@ -427,13 +427,6 @@ def fake_shape_dependents(
generate ipp values so slice location is negatively correlated with slice index
"""
- class PrintBase:
- def __repr__(self):
- attr_strs = [
- f'{attr}={getattr(self, attr)}' for attr in dir(self) if attr[0].isupper()
- ]
- return f"{self.__class__.__name__}({', '.join(attr_strs)})"
-
class DimIdxSeqElem(pydicom.Dataset):
def __init__(self, dip=(0, 0), fgp=None):
super().__init__()
@@ -444,8 +437,8 @@ def fake_shape_dependents(
class FrmContSeqElem(pydicom.Dataset):
def __init__(self, div, sid):
super().__init__()
- self.DimensionIndexValues = div
- self.StackID = sid
+ self.DimensionIndexValues = list(div)
+ self.StackID = str(sid)
class PlnPosSeqElem(pydicom.Dataset):
def __init__(self, ipp):
@@ -545,17 +538,28 @@ class TestMultiFrameWrapper(TestCase):
with pytest.raises(didw.WrapperError):
dw.image_shape
fake_mf.Rows = 32
- # No frame data raises WrapperError
+ # Single frame doesn't need dimension index values
+ assert dw.image_shape == (32, 64)
+ assert len(dw.frame_order) == 1
+ assert dw.frame_order[0] == 0
+ # Multiple frames do require dimension index values
+ fake_mf.PerFrameFunctionalGroupsSequence = [pydicom.Dataset(), pydicom.Dataset()]
with pytest.raises(didw.WrapperError):
- dw.image_shape
+ MFW(fake_mf).image_shape
# check 2D shape with StackID index is 0
div_seq = ((1, 1),)
fake_mf.update(fake_shape_dependents(div_seq, sid_dim=0))
- assert MFW(fake_mf).image_shape == (32, 64)
+ dw = MFW(fake_mf)
+ assert dw.image_shape == (32, 64)
+ assert len(dw.frame_order) == 1
+ assert dw.frame_order[0] == 0
# Check 2D shape with extraneous extra indices
div_seq = ((1, 1, 2),)
fake_mf.update(fake_shape_dependents(div_seq, sid_dim=0))
- assert MFW(fake_mf).image_shape == (32, 64)
+ dw = MFW(fake_mf)
+ assert dw.image_shape == (32, 64)
+ assert len(dw.frame_order) == 1
+ assert dw.frame_order[0] == 0
# Check 2D plus time
div_seq = ((1, 1, 1), (1, 1, 2), (1, 1, 3))
fake_mf.update(fake_shape_dependents(div_seq, sid_dim=0))
@@ -569,7 +573,7 @@ class TestMultiFrameWrapper(TestCase):
fake_mf.update(fake_shape_dependents(div_seq, sid_dim=0))
with pytest.warns(
UserWarning,
- match='A multi-stack file was passed without an explicit filter, just using lowest StackID',
+ match='A multi-stack file was passed without an explicit filter,',
):
assert MFW(fake_mf).image_shape == (32, 64, 3)
# No warning if we expclitly select that StackID to keep
@@ -581,7 +585,7 @@ class TestMultiFrameWrapper(TestCase):
fake_mf.update(fake_shape_dependents(div_seq, sid_seq=sid_seq))
with pytest.warns(
UserWarning,
- match='A multi-stack file was passed without an explicit filter, just using lowest StackID',
+ match='A multi-stack file was passed without an explicit filter,',
):
assert MFW(fake_mf).image_shape == (32, 64, 3)
# No warning if we expclitly select that StackID to keep
@@ -590,6 +594,17 @@ class TestMultiFrameWrapper(TestCase):
# Check for error when explicitly requested StackID is missing
with pytest.raises(didw.WrapperError):
MFW(fake_mf, frame_filters=(didw.FilterMultiStack(3),))
+ # StackID can be a string
+ div_seq = ((1,), (2,), (3,), (4,))
+ sid_seq = ('a', 'a', 'a', 'b')
+ fake_mf.update(fake_shape_dependents(div_seq, sid_seq=sid_seq))
+ with pytest.warns(
+ UserWarning,
+ match='A multi-stack file was passed without an explicit filter,',
+ ):
+ assert MFW(fake_mf).image_shape == (32, 64, 3)
+ assert MFW(fake_mf, frame_filters=(didw.FilterMultiStack('a'),)).image_shape == (32, 64, 3)
+ assert MFW(fake_mf, frame_filters=(didw.FilterMultiStack('b'),)).image_shape == (32, 64)
# Make some fake frame data for 4D when StackID index is 0
div_seq = ((1, 1, 1), (1, 2, 1), (1, 1, 2), (1, 2, 2), (1, 1, 3), (1, 2, 3))
fake_mf.update(fake_shape_dependents(div_seq, sid_dim=0))
@@ -599,7 +614,7 @@ class TestMultiFrameWrapper(TestCase):
fake_mf.update(fake_shape_dependents(div_seq, sid_dim=0))
with pytest.warns(
UserWarning,
- match='A multi-stack file was passed without an explicit filter, just using lowest StackID',
+ match='A multi-stack file was passed without an explicit filter,',
):
with pytest.raises(didw.WrapperError):
MFW(fake_mf).image_shape
@@ -638,7 +653,7 @@ class TestMultiFrameWrapper(TestCase):
fake_mf.update(fake_shape_dependents(div_seq, sid_seq=sid_seq))
with pytest.warns(
UserWarning,
- match='A multi-stack file was passed without an explicit filter, just using lowest StackID',
+ match='A multi-stack file was passed without an explicit filter,',
):
with pytest.raises(didw.WrapperError):
MFW(fake_mf).image_shape
@@ -651,7 +666,7 @@ class TestMultiFrameWrapper(TestCase):
fake_mf.update(fake_shape_dependents(div_seq, sid_dim=1))
with pytest.warns(
UserWarning,
- match='A multi-stack file was passed without an explicit filter, just using lowest StackID',
+ match='A multi-stack file was passed without an explicit filter,',
):
assert MFW(fake_mf).image_shape == (32, 64, 3)
# Make some fake frame data for 4D when StackID index is 1
=====================================
nibabel/pkg_info.py
=====================================
@@ -12,7 +12,7 @@ except ImportError:
__version__ = '0+unknown'
-COMMIT_HASH = '7b5060e4bb'
+COMMIT_HASH = '41756d3190'
def _cmp(a: Version, b: Version) -> int:
=====================================
nibabel/tests/test_api_validators.py
=====================================
@@ -99,7 +99,7 @@ class TestRunAllTests(ValidateAPI):
We check this in the module teardown function
"""
- run_tests = {}
+ run_tests = set()
def obj_params(self):
yield 1, 2
=====================================
tox.ini
=====================================
@@ -70,8 +70,6 @@ pass_env =
NO_COLOR
CLICOLOR
CLICOLOR_FORCE
-set_env =
- py313: PYTHON_GIL=0
extras = test
deps =
# General minimum dependencies: pin based on API usage
View it on GitLab: https://salsa.debian.org/med-team/nibabel/-/commit/e83d30af18daa1e094b7880b7789fbc7b2635013
--
View it on GitLab: https://salsa.debian.org/med-team/nibabel/-/commit/e83d30af18daa1e094b7880b7789fbc7b2635013
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