Merge branch 'maint/3.2.x'

Author: effigies

.mailmap

@@ -26,7 +26,8 @@ Christopher J. Markiewicz <[email protected]> Christopher J. Markiewicz <e
 Cindee Madison <[email protected]> CindeeM <[email protected]>
 Cindee Madison <[email protected]> cindeem <[email protected]>
 Demian Wassermann <[email protected]> Demian Wassermann <[email protected]>
-Dimitri Papadopoulos Orfanos <[email protected]> Dimitri Papadopoulos <[email protected]>
+Dimitri Papadopoulos Orfanos <[email protected]> <[email protected]>
+Dimitri Papadopoulos Orfanos <[email protected]> <[email protected]>
 Eric Larson <[email protected]> Eric89GXL <[email protected]>
 Eric Larson <[email protected]> larsoner <[email protected]>
 Fernando Pérez-García <[email protected]> Fernando <[email protected]>

.zenodo.json

@@ -141,10 +141,10 @@
       "orcid": "0000-0001-9791-4404"
     },
     {
-      "name": "Lepp\u00e4kangas, Jaakko"
+      "name": "S\u00f3lon, Anibal"
     },
     {
-      "name": "S\u00f3lon, Anibal"
+      "name": "Lepp\u00e4kangas, Jaakko"
     },
     {
       "name": "van den Bosch, Jasper J.F."
@@ -228,6 +228,11 @@
     {
       "name": "St-Jean, Samuel"
     },
+    {
+      "affiliation": "CEA",
+      "name": "Papadopoulos Orfanos, Dimitri",
+      "orcid": "0000-0002-1242-8990"
+    },
     {
       "name": "Panfilov, Egor",
       "orcid": "0000-0002-2500-6375"
@@ -286,6 +291,9 @@
     {
       "name": "Baratz, Zvi"
     },
+    {
+      "name": "Van, Andrew"
+    },
     {
       "affiliation": "Hospital for Sick Children",
       "name": "Darwin, Benjamin C"
@@ -298,11 +306,6 @@
     {
       "name": "Gauthier, Carl"
     },
-    {
-      "affiliation": "CEA",
-      "name": "Papadopoulos Orfanos, Dimitri",
-      "orcid": "0000-0002-1242-8990"
-    },
     {
       "name": "Solovey, Igor"
     },
@@ -326,6 +329,11 @@
       "affiliation": "National Technical University of Athens, Greece",
       "name": "Raktivan, Konstantinos"
     },
+    {
+      "affiliation": "Charite Universitatsmedizin Berlin, Germany",
+      "name": "Waller, Lea",
+      "orcid": "0000-0002-3239-6957"
+    },
     {
       "name": "Cal\u00e1bkov\u00e1, Mark\u00e9ta"
     },
@@ -346,6 +354,9 @@
     {
       "name": "Roos, Thomas"
     },
+    {
+      "name": "Hrn\u010diar, Tom\u00e1\u0161"
+    },
     {
       "affiliation": "National Institute of Mental Health and Neuro-Sciences, India",
       "name": "Reddam, Venkateswara Reddy",

Changelog

@@ -25,6 +25,36 @@ Eric Larson (EL), Demian Wassermann, Stephan Gerhard and Ross Markello (RM).
 
 References like "pr/298" refer to github pull request numbers.
 
+3.2.2 (Monday 7 February 2022)
+=================================
+
+Bug fix release in the 3.2.x series.
+
+Bug fixes
+---------
+* Reshape CIFTI-2 affines to 4x4 when encoded as row-major sequence (pr/1059)
+  (Andrew Van, reviewed by CM)
+* Suggest nibabel.save() on calls to deprecated giftiio.write() (pr/1055)
+  (Anibal Solon, reviewed by CM)
+* Various bugs and style issues detected by LGTM (pr/1043, pr/1048)
+  (Dimitri Papadopoulos, reviewed by CM)
+* Resolve unclosed file warning in GiftiImage (pr/1038) (Lea Waller, reviewed by CM)
+* Fix typos preventing deprecation warnings from being raised (pr/991)
+  (Jonathan Daniel, reviewed by MB)
+* Work around numpy SystemError to maintain expected error types (pr/1051) (CM)
+* Use more constrained mock when testing optpkg (pr/983) (CM, reviewed by YOH)
+
+Maintenance
+-----------
+* Add setuptools requirement to match usage (pr/1009)
+  (Tomáš Hrnčiar, reviewed by CM)
+* Fix grammar of headings in CoC (pr/996) (MB, reviewed by CM, Ariel Rokem)
+* Set minimum pydicom to 1.0.0 (pr/1050) (CM)
+* Submit coverage to codecov via pinned PyPI package (pr/1008) (CM)
+* Upgrade versioneer to 0.19 (pr/967) (CM)
+* Migrate to GitHub actions (pr/972) (CM, reviewed by Serge Koudoro)
+
+
 3.2.1 (Saturday 28 November 2020)
 =================================
 

doc/source/conf.py

@@ -92,7 +92,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = f"2006-2021, {metadata['maintainer']} <{metadata['author_email']}>"
+copyright = f"2006-2022, {metadata['maintainer']} <{metadata['author_email']}>"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/index.rst

@@ -114,6 +114,9 @@ contributed code and discussion (in rough order of appearance):
 * Markéta Calábková
 * Carl Gauthier
 * Julian Klug
+* Lea Waller
+* Tomáš Hrnčiar
+* Andrew Van
 
 License reprise
 ===============

nibabel/dft.py

@@ -24,8 +24,9 @@
 from io import BytesIO
 
 from .nifti1 import Nifti1Header
+from nibabel.optpkg import optional_package
 
-from .pydicom_compat import pydicom, read_file
+pydicom = optional_package("pydicom")[0]
 
 logger = logging.getLogger('nibabel.dft')
 
@@ -241,7 +242,7 @@ def __getattribute__(self, name):
         return val
 
     def dicom(self):
-        return read_file(self.files[0])
+        return pydicom.read_file(self.files[0])
 
 
 class _db_nochange:
@@ -386,7 +387,7 @@ def _update_dir(c, dir, files, studies, series, storage_instances):
 
 def _update_file(c, path, fname, studies, series, storage_instances):
     try:
-        do = read_file(f'{path}/{fname}')
+        do = pydicom.read_file(f'{path}/{fname}')
     except pydicom.filereader.InvalidDicomError:
         logger.debug('        not a DICOM file')
         return None

nibabel/nicom/dicomwrappers.py

@@ -17,13 +17,15 @@
 
 import numpy as np
 
+from nibabel.optpkg import optional_package
 from . import csareader as csar
 from .dwiparams import B2q, nearest_pos_semi_def, q2bg
 from ..openers import ImageOpener
 from ..onetime import auto_attr as one_time
-from ..pydicom_compat import tag_for_keyword, Sequence
 from ..deprecated import deprecate_with_version
 
+pydicom = optional_package("pydicom")[0]
+
 
 class WrapperError(Exception):
     pass
@@ -52,10 +54,8 @@ def wrapper_from_file(file_like, *args, **kwargs):
     dcm_w : ``dicomwrappers.Wrapper`` or subclass
        DICOM wrapper corresponding to DICOM data type
     """
-    from ..pydicom_compat import read_file
-
     with ImageOpener(file_like) as fobj:
-        dcm_data = read_file(fobj, *args, **kwargs)
+        dcm_data = pydicom.read_file(fobj, *args, **kwargs)
     return wrapper_from_data(dcm_data)
 
 
@@ -520,7 +520,7 @@ def image_shape(self):
         if hasattr(first_frame, 'get') and first_frame.get([0x18, 0x9117]):
             # DWI image may include derived isotropic, ADC or trace volume
             try:
-                self.frames = Sequence(
+                self.frames = pydicom.Sequence(
                     frame for frame in self.frames if
                     frame.MRDiffusionSequence[0].DiffusionDirectionality
                     != 'ISOTROPIC'
@@ -550,15 +550,15 @@ def image_shape(self):
         # Determine if one of the dimension indices refers to the stack id
         dim_seq = [dim.DimensionIndexPointer
                    for dim in self.get('DimensionIndexSequence')]
-        stackid_tag = tag_for_keyword('StackID')
+        stackid_tag = pydicom.datadict.tag_for_keyword('StackID')
         # remove the stack id axis if present
         if stackid_tag in dim_seq:
             stackid_dim_idx = dim_seq.index(stackid_tag)
             frame_indices = np.delete(frame_indices, stackid_dim_idx, axis=1)
             dim_seq.pop(stackid_dim_idx)
         if has_derived:
             # derived volume is included
-            derived_tag = tag_for_keyword("DiffusionBValue")
+            derived_tag = pydicom.datadict.tag_for_keyword("DiffusionBValue")
             if derived_tag not in dim_seq:
                 raise WrapperError("Missing information, cannot remove indices "
                                    "with confidence.")

nibabel/nicom/tests/__init__.py

@@ -1,4 +1,6 @@
-from ...pydicom_compat import have_dicom
 import unittest
+from nibabel.optpkg import optional_package
 
-dicom_test = unittest.skipUnless(have_dicom, "Could not import dicom or pydicom")
+pydicom, have_dicom, _ = optional_package("pydicom")
+
+dicom_test = unittest.skipUnless(have_dicom, "Could not import pydicom")

nibabel/nicom/tests/test_csareader.py

@@ -7,12 +7,11 @@
 
 import numpy as np
 
-from ...pydicom_compat import pydicom
 from .. import csareader as csa
 from .. import dwiparams as dwp
 
 import pytest
-from . import dicom_test
+from . import pydicom, dicom_test
 from .test_dicomwrappers import IO_DATA_PATH, DATA
 
 CSA2_B0 = open(pjoin(IO_DATA_PATH, 'csa2_b0.bin'), 'rb').read()

nibabel/nicom/tests/test_dicomreaders.py

@@ -6,26 +6,23 @@
 
 import numpy as np
 
+from nibabel.optpkg import optional_package
 from .. import dicomreaders as didr
-from ...pydicom_compat import pydicom
-
-import pytest
-from . import dicom_test
-
 from .test_dicomwrappers import EXPECTED_AFFINE, EXPECTED_PARAMS, IO_DATA_PATH, DATA
 
+import pytest
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 
+pydicom, _, setup_module = optional_package("pydicom")
+
 
-@dicom_test
 def test_read_dwi():
     img = didr.mosaic_to_nii(DATA)
     arr = img.get_fdata()
     assert arr.shape == (128, 128, 48)
     assert_array_almost_equal(img.affine, EXPECTED_AFFINE)
 
 
-@dicom_test
 def test_read_dwis():
     data, aff, bs, gs = didr.read_mosaic_dwi_dir(IO_DATA_PATH,
                                                  'siemens_dwi_*.dcm.gz')
@@ -37,7 +34,6 @@ def test_read_dwis():
         didr.read_mosaic_dwi_dir('improbable')
 
 
-@dicom_test
 def test_passing_kwds():
     # Check that we correctly pass keywords to dicom
     dwi_glob = 'siemens_dwi_*.dcm.gz'
@@ -61,7 +57,7 @@ def test_passing_kwds():
         with pytest.raises(didr.DicomReadError):
             func(IO_DATA_PATH, csa_glob, dicom_kwargs=dict(force=True))
 
-@dicom_test
+
 def test_slices_to_series():
     dicom_files = (pjoin(IO_DATA_PATH, "%d.dcm" % i) for i in range(2))
     wrappers = [didr.wrapper_from_file(f) for f in dicom_files]

nibabel/nicom/tests/test_dicomwrappers.py

@@ -9,15 +9,13 @@
 
 import numpy as np
 
-from nibabel.pydicom_compat import have_dicom, pydicom, read_file, tag_for_keyword
-
+from . import pydicom, have_dicom, dicom_test
 from .. import dicomwrappers as didw
 from .. import dicomreaders as didr
 from ...volumeutils import endian_codes
 
 import pytest
 from unittest import TestCase
-from . import dicom_test
 
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 from ...tests.nibabel_data import get_nibabel_data, needs_nibabel_data
@@ -26,8 +24,8 @@
 DATA_FILE = pjoin(IO_DATA_PATH, 'siemens_dwi_1000.dcm.gz')
 DATA_FILE_PHILIPS = pjoin(IO_DATA_PATH, 'philips_mprage.dcm.gz')
 if have_dicom:
-    DATA = read_file(gzip.open(DATA_FILE))
-    DATA_PHILIPS = read_file(gzip.open(DATA_FILE_PHILIPS))
+    DATA = pydicom.read_file(gzip.open(DATA_FILE))
+    DATA_PHILIPS = pydicom.read_file(gzip.open(DATA_FILE_PHILIPS))
 else:
     DATA = None
     DATA_PHILIPS = None
@@ -434,8 +432,8 @@ def __init__(self, div, sid):
     dim_idx_seq = [DimIdxSeqElem()] * num_of_frames
     # add an entry for StackID into the DimensionIndexSequence
     if sid_dim is not None:
-        sid_tag = tag_for_keyword('StackID')
-        fcs_tag = tag_for_keyword('FrameContentSequence')
+        sid_tag = pydicom.datadict.tag_for_keyword('StackID')
+        fcs_tag = pydicom.datadict.tag_for_keyword('FrameContentSequence')
         dim_idx_seq[sid_dim] = DimIdxSeqElem(sid_tag, fcs_tag)
     # create the PerFrameFunctionalGroupsSequence
     frames = [PerFrmFuncGrpSeqElem(div, sid)

nibabel/nicom/tests/test_utils.py

@@ -2,14 +2,13 @@
 """
 import re
 
+from nibabel.optpkg import optional_package
+from .test_dicomwrappers import DATA, DATA_PHILIPS
 from ..utils import find_private_section
 
-from . import dicom_test
-from ...pydicom_compat import pydicom
-from .test_dicomwrappers import DATA, DATA_PHILIPS
+pydicom, _, setup_module = optional_package("pydicom")
 
 
-@dicom_test
 def test_find_private_section_real():
     # Find section containing named private creator information
     # On real data first

nibabel/nifti1.py

@@ -17,6 +17,7 @@
 import numpy.linalg as npl
 from numpy.compat.py3k import asstr
 
+from .optpkg import optional_package
 from .filebasedimages import SerializableImage
 from .volumeutils import Recoder, make_dt_codes, endian_codes
 from .spatialimages import HeaderDataError, ImageFileError
@@ -25,7 +26,8 @@
 from . import analyze  # module import
 from .spm99analyze import SpmAnalyzeHeader
 from .casting import have_binary128
-from .pydicom_compat import have_dicom, pydicom as pdcm
+
+pdcm, have_dicom, _ = optional_package("pydicom")
 
 # nifti1 flat header definition for Analyze-like first 348 bytes
 # first number in comments indicates offset in file header in bytes