Merge branch 'rf/docfix' into 'master'

Rf/docfix

See merge request fsl/fslpy!279

CHANGELOG.rst

@@ -2,6 +2,20 @@ This document contains the ``fslpy`` release history in reverse chronological
 order.
 
 
+3.5.2 (Friday 29th January 2021)
+---------------------------------
+
+
+Fixed
+^^^^^
+
+
+* Adjusted the :func:`.dicom.scanDir` function so that it will set a
+  default value for ``SeriesDescription`` if it is not present in the
+  ``dcm2niix`` ``json`` output.
+* Fixed some issues with API documentation generation.
+
+
 3.5.1 (Thursday 21st January 2021)
 ----------------------------------
 

doc/mock_modules.txt

@@ -9,3 +9,4 @@ numpy.linalg
 scipy
 scipy.ndimage
 scipy.ndimage.interpolation
+six

fsl/data/cifti.py

@@ -343,7 +343,7 @@ class BrainStructure(object):
 
         :param primary: Name of the brain structure (e.g. cortex, thalamus)
         :param secondary: Further specification of which part of the brain structure is described (e.g. 'white' or
-        'pial' for the cortex)
+                          'pial' for the cortex)
         :param hemisphere: which hemisphere is the brain structure in ('left', 'right', or 'both')
         :param geometry: does the parent object describe the 'volume' or the 'surface'
         """
@@ -490,4 +490,3 @@ def load(filename, mask_values=(0, np.nan), writable=False) -> Union[DenseCifti,
     if writable:
         raise ValueError("Can not open NIFTI file in writable mode")
     return Cifti.from_image(vol_img, mask_values)
-

fsl/data/dicom.py

@@ -194,6 +194,10 @@ def scanDir(dcmdir):
             with open(fn, 'rt') as f:
                 meta             = json.load(f)
                 meta['DicomDir'] = dcmdir
+                # SeriesDescription is not
+                # guaranteed to be present
+                if 'SeriesDescription' not in meta:
+                    meta['SeriesDescription'] = meta['SeriesNumber']
                 series.append(meta)
 
     # sort by series number

fsl/wrappers/wrapperutils.py

@@ -168,6 +168,7 @@ def genxwrapper(func, runner):
 
     The following keyword arguments will be intercepted by the wrapper
     function, and will *not* be passed to ``func``:
+
       - ``stdout``:   Passed to ``runner``. Defaults to ``True``.
       - ``stderr``:   Passed to ``runner``. Defaults to ``True``.
       - ``exitcode``: Passed to ``runner``. Defaults to ``False``.

tests/test_dicom.py

@@ -189,7 +189,8 @@ def test_loadSeries():
                     assert 'PatientName'                      in img.metaKeys()
                     assert 'MCCARTHY_PAUL'                    in img.metaValues() or \
                            'MCCARTHY^PAUL'                    in img.metaValues() or \
-                           'MCCARTHY_PAUL_2'                  in img.metaValues()
+                           'MCCARTHY_PAUL_2'                  in img.metaValues() or \
+                           'MCCARTHY^PAUL^2'                  in img.metaValues()
                     assert ('PatientName', 'MCCARTHY_PAUL')   in img.metaItems() or \
                            ('PatientName', 'MCCARTHY^PAUL')   in img.metaItems() or \
                            ('PatientName', 'MCCARTHY_PAUL_2') in img.metaItems() or \