Merge remote-tracking branch 'upstream/maint/3.1.x'

Author: effigies

nibabel/cifti2/cifti2.py

@@ -1473,16 +1473,28 @@ def to_file_map(self, file_map=None):
     def update_headers(self):
         """ Harmonize NIfTI headers with image data
 
+        Ensures that the NIfTI-2 header records the data shape in the last three
+        ``dim`` fields. Per the spec:
+
+            Because the first four dimensions in NIfTI are reserved for space and time, the CIFTI
+            dimensions are stored in the NIfTI header in dim[5] and up, where dim[5] is the length
+            of the first CIFTI dimension (number of values in a row), dim[6] is the length of the
+            second CIFTI dimension, and dim[7] is the length of the third CIFTI dimension, if
+            applicable. The fields dim[1] through dim[4] will be 1; dim[0] will be 6 or 7,
+            depending on whether a third matrix dimension exists.
+
         >>> import numpy as np
         >>> data = np.zeros((2,3,4))
         >>> img = Cifti2Image(data)
         >>> img.shape == (2, 3, 4)
         True
         >>> img.update_headers()
-        >>> img.nifti_header.get_data_shape() == (2, 3, 4)
+        >>> img.nifti_header.get_data_shape() == (1, 1, 1, 1, 2, 3, 4)
+        True
+        >>> img.shape == (2, 3, 4)
         True
         """
-        self._nifti_header.set_data_shape(self._dataobj.shape)
+        self._nifti_header.set_data_shape((1, 1, 1, 1) + self._dataobj.shape)
 
     def get_data_dtype(self):
         return self._nifti_header.get_data_dtype()

nibabel/parrec.py

@@ -772,7 +772,8 @@ def as_analyze_map(self):
                  f"{self.general_info['protocol_name']}"
                  )[:80]  # max len
         is_fmri = (self.general_info['max_dynamics'] > 1)
-        t = 'msec' if is_fmri else 'unknown'
+        # PAR/REC uses msec, but in _calc_zooms we convert to sec
+        t = 'sec' if is_fmri else 'unknown'
         xyzt_units = unit_codes['mm'] + unit_codes[t]
         return dict(descr=descr, xyzt_units=xyzt_units)  # , pixdim=pixdim)
 

nibabel/tests/test_parrec.py

@@ -9,7 +9,7 @@
 from numpy import array as npa
 
 from .. import load as top_load
-from ..nifti1 import Nifti1Image, Nifti1Extension
+from ..nifti1 import Nifti1Image, Nifti1Extension, Nifti1Header
 from .. import parrec
 from ..parrec import (parse_PAR_header, PARRECHeader, PARRECError, vol_numbers,
                       vol_is_full, PARRECImage, PARRECArrayProxy, exts2pars)
@@ -549,6 +549,18 @@ def test_epi_params():
         assert_almost_equal(epi_hdr.get_zooms()[-1], 2.0)
 
 
+def test_xyzt_unit_conversion():
+    # Check conversion to NIfTI-like has sensible units
+    for par_root in ('T2_-interleaved', 'T2_', 'phantom_EPI_asc_CLEAR_2_1'):
+        epi_par = pjoin(DATA_PATH, par_root + '.PAR')
+        with open(epi_par, 'rt') as fobj:
+            epi_hdr = PARRECHeader.from_fileobj(fobj)
+        nifti_hdr = Nifti1Header.from_header(epi_hdr)
+        assert len(nifti_hdr.get_data_shape()) == 4
+        assert_almost_equal(nifti_hdr.get_zooms()[-1], 2.0)
+        assert nifti_hdr.get_xyzt_units() == ('mm', 'sec')
+
+
 def test_truncations():
     # Test tests for truncation
     par = pjoin(DATA_PATH, 'T2_.PAR')