Merge branch 'master' into enh/cifti2_axes

MichielCottaar · MichielCottaar · commit 70588f2d6574 · 2019-03-22T12:18:26.000Z
diff --git a/COPYING b/COPYING
@@ -18,12 +18,13 @@ documentation is covered by the MIT license.
 
   The MIT License
 
-  Copyright (c) 2009-2014 Matthew Brett <matthew.brett@gmail.com>
+  Copyright (c) 2009-2019 Matthew Brett <matthew.brett@gmail.com>
   Copyright (c) 2010-2013 Stephan Gerhard <git@unidesign.ch>
   Copyright (c) 2006-2014 Michael Hanke <michael.hanke@gmail.com>
   Copyright (c) 2011 Christian Haselgrove <christian.haselgrove@umassmed.edu>
   Copyright (c) 2010-2011 Jarrod Millman <jarrod.millman@gmail.com>
-  Copyright (c) 2011-2014 Yaroslav Halchenko <debian@onerussian.com>
+  Copyright (c) 2011-2019 Yaroslav Halchenko <debian@onerussian.com>
+  Copyright (c) 2015-2019 Chris Markiewicz <effigies@gmail.com>
 
   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
diff --git a/Changelog b/Changelog
@@ -18,9 +18,10 @@ The full VCS changelog is available here:
 Nibabel releases
 ****************
 
-Most work on NiBabel so far has been by Matthew Brett (MB), Michael Hanke (MH)
-Ben Cipollini (BC), Marc-Alexandre Côté (MC), Chris Markiewicz (CM), Stephan
-Gerhard (SG), Eric Larson (EL), Yaroslav Halchenko (YOH) and Chris Cheng (CC).
+Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz
+(CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul
+McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG),
+Eric Larson (EL), Demien Wasserman, and Stephan Gerhard.
 
 References like "pr/298" refer to github pull request numbers.
 
@@ -116,16 +117,16 @@ Enhancements
 * Simplfiy MGHImage and add footer fields (pr/569) (CM, reviewed by MB)
 * Force sform/qform codes to be ints, rather than numpy types (pr/575) (Paul
   McCarthy, reviewed by MB, CM)
-* Auto-fill color table in FreeSurfer annotation file (pr/592) (Paul McCarthy,
+* Auto-fill color table in FreeSurfer annotation file (pr/592) (PM,
   reviewed by CM, MB)
 * Set default intent code for CIFTI2 images (pr/604) (Mathias Goncalves,
-  reviewed by CM, Satra Ghosh, MB, Tim Coalson)
+  reviewed by CM, SG, MB, Tim Coalson)
 * Raise informative error on empty files (pr/611) (Pradeep Raamana, reviewed
   by CM, MB)
 * Accept degenerate filenames such as ``.nii`` (pr/621) (Dimitri
   Papadopoulos-Orfanos, reviewed by Yaroslav Halchenko)
 * Take advantage of ``IndexedGzipFile`` ``drop_handles`` flag to release
-  filehandles by default (pr/614) (Paul McCarthy, reviewed by CM, MB)
+  filehandles by default (pr/614) (PM, reviewed by CM, MB)
 
 Bug fixes
 ---------
@@ -135,7 +136,7 @@ Bug fixes
   CM, MB)
 * Accept lower-case orientation codes in TRK files (pr/600) (Kesshi Jordan,
   MB, reviewed by MB, MC, CM)
-* Annotation file reading (pr/592) (Paul McCarthy, reviewed by CM, MB)
+* Annotation file reading (pr/592) (PM, reviewed by CM, MB)
 * Fix buffer size calculation in ArraySequence (pr/597) (Serge Koudoro,
   reviewed by MC, MB, Eleftherios Garyfallidis, CM)
 * Resolve ``UnboundLocalError`` in Python 3 (pr/607) (Jakub Kaczmarzyk,
@@ -175,14 +176,14 @@ Bug fixes
 
 * Set L/R labels in orthoview correctly (pr/564) (CM)
 * Defer use of ufunc / memmap test - allows "freezing" (pr/572) (MB, reviewed
-  by Satra Ghosh)
+  by SG)
 * Fix doctest failures with pre-release numpy (pr/582) (MB, reviewed by CM)
 
 Maintenance
 -----------
 
-* Update documentation around NIfTI qform/sform codes (pr/576) (Paul McCarthy,
-  reviewed by MB, CM) + (pr/580) (Bennet Fauber, reviewed by Paul McCarthy)
+* Update documentation around NIfTI qform/sform codes (pr/576) (PM,
+  reviewed by MB, CM) + (pr/580) (Bennet Fauber, reviewed by PM)
 * Skip precision test on macOS, newer numpy (pr/583) (MB, reviewed by CM)
 * Simplify AppVeyor script, removing conda (pr/584) (MB, reviewed by CM)
 
@@ -192,12 +193,11 @@ Maintenance
 New features
 ------------
 
-* CIFTI support (pr/249) (Satra Ghosh, Michiel Cottaar, BC, CM, Demian
-  Wassermann, MB)
+* CIFTI support (pr/249) (SG, Michiel Cottaar, BC, CM, Demian Wasserman, MB)
 * Support for MRtrix TCK streamlines file format (pr/486) (MC, reviewed by
   MB, Arnaud Bore, J-Donald Tournier, Jean-Christophe Houde)
 * Added ``get_fdata()`` as default method to retrieve scaled floating point
-  data from ``DataobjImage``s (pr/551) (MB, reviewed by CM, Satra Ghosh)
+  data from ``DataobjImage``s (pr/551) (MB, reviewed by CM, SG)
 
 Enhancements
 ------------
@@ -211,19 +211,19 @@ Enhancements
 * Allow dtype specifiers as fileslice input (pr/485) (MB)
 * Support "headerless" ArrayProxy specification, enabling memory-efficient
   ArrayProxy reshaping (pr/521) (CM)
-* Allow unknown NIfTI intent codes, add FSL codes (pr/528) (Paul McCarthy)
+* Allow unknown NIfTI intent codes, add FSL codes (pr/528) (PM)
 * Improve error handling for ``img.__getitem__`` (pr/533) (Ariel Rokem)
 * Delegate reorientation to SpatialImage classes (pr/544) (Mark Hymers, CM,
   reviewed by MB)
 * Enable using ``indexed_gzip`` to reduce memory usage when reading from
-  gzipped NIfTI and MGH files (pr/552) (Paul McCarthy, reviewed by MB, CM)
+  gzipped NIfTI and MGH files (pr/552) (PM, reviewed by MB, CM)
 
 Bug fixes
 ---------
 
 * Miscellaneous MINC reader fixes (pr/493) (Robert D. Vincent, reviewed by CM,
   MB)
-* Fix corner case in ``wrapstruct.get`` (pr/516) (Paul McCarthy, reviewed by
+* Fix corner case in ``wrapstruct.get`` (pr/516) (PM, reviewed by
   CM, MB)
 
 Maintenance
@@ -524,7 +524,7 @@ Special thanks to Chris Burns, Jarrod Millman and Yaroslav Halchenko.
 
 * New feature release
 * Python 3.2 support
-* Substantially enhanced gifti reading support (SG)
+* Substantially enhanced gifti reading support (Stephan Gerhard)
 * Refactoring of trackvis read / write to allow reading and writing of voxel
   points and mm points in tracks.  Deprecate use of negative voxel sizes;
   set voxel_order field in trackvis header.  Thanks to Chris Filo
diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -27,9 +27,9 @@ discussions, release procedure and more.
 Authors and Contributors
 ========================
 
-The main authors of NiBabel are `Matthew Brett`_, `Michael Hanke`_, `Ben
-Cipollini`_, `Marc-Alexandre Côté`_, Chris Markiewicz, `Stephan Gerhard`_ and
-`Eric Larson`_.  The authors are grateful to the following people who have
+Most work on NiBabel so far has been by `Matthew Brett`_, Chris Markiewicz,
+`Michael Hanke`_, `Marc-Alexandre Côté`_, `Ben Cipollini`_, Paul McCarthy and
+Chris Cheng.  The authors are grateful to the following people who have
 contributed code and discussion (in rough order of appearance):
 
 * `Yaroslav O. Halchenko`_
diff --git a/nibabel/info.py b/nibabel/info.py
@@ -192,7 +192,7 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 
 # Main setup parameters
 NAME = 'nibabel'
-MAINTAINER = "Matthew Brett, Michael Hanke, Eric Larson, Chris Markiewicz"
+MAINTAINER = "Chris Markiewicz"
 MAINTAINER_EMAIL = "neuroimaging@python.org"
 DESCRIPTION = description
 LONG_DESCRIPTION = long_description
diff --git a/nibabel/nicom/dicomreaders.py b/nibabel/nicom/dicomreaders.py
@@ -146,7 +146,7 @@ def slices_to_series(wrappers):
     out_vol_lists = []
     for vol_list in volume_lists:
         if len(vol_list) > 1:
-            vol_list.sort(_slice_sorter)
+            vol_list.sort(key=_slice_sorter)
             zs = [s.slice_indicator for s in vol_list]
             if len(set(zs)) < len(zs):  # not unique zs
                 # third pass
@@ -163,12 +163,12 @@ def slices_to_series(wrappers):
     return out_vol_lists
 
 
-def _slice_sorter(s1, s2):
-    return cmp(s1.slice_indicator, s2.slice_indicator)
+def _slice_sorter(s):
+    return s.slice_indicator
 
 
-def _instance_sorter(s1, s2):
-    return cmp(s1.instance_number, s2.instance_number)
+def _instance_sorter(s):
+    return s.instance_number
 
 
 def _third_pass(wrappers):
@@ -182,9 +182,9 @@ def _third_pass(wrappers):
                              'missing InstanceNumber')
     if len(set(inos)) < len(inos):
         raise DicomReadError(msg_fmt % 'some or all slices with '
-                             'the sane InstanceNumber')
+                             'the same InstanceNumber')
     # sort by instance number
-    wrappers.sort(_instance_sorter)
+    wrappers.sort(key=_instance_sorter)
     # start loop, in which we start a new volume, each time we see a z
     # we've seen already in the current volume
     dw = wrappers[0]
diff --git a/nibabel/nicom/dicomwrappers.py b/nibabel/nicom/dicomwrappers.py
@@ -201,7 +201,7 @@ def voxel_sizes(self):
         zs = self.get('SpacingBetweenSlices')
         if zs is None:
             zs = self.get('SliceThickness')
-            if zs is None:
+            if zs is None or zs == '':
                 zs = 1
         # Protect from python decimals in pydicom 0.9.7
         zs = float(zs)
diff --git a/nibabel/nicom/tests/data/0.dcm b/nibabel/nicom/tests/data/0.dcm
diff --git a/nibabel/nicom/tests/data/1.dcm b/nibabel/nicom/tests/data/1.dcm
diff --git a/nibabel/nicom/tests/data/slicethickness_empty_string.dcm b/nibabel/nicom/tests/data/slicethickness_empty_string.dcm
diff --git a/nibabel/nicom/tests/test_dicomreaders.py b/nibabel/nicom/tests/test_dicomreaders.py
@@ -2,6 +2,8 @@
 
 """
 
+from os.path import join as pjoin, abspath
+
 import numpy as np
 
 from .. import dicomreaders as didr
@@ -68,3 +70,12 @@ def test_passing_kwds():
                       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]
+    series = didr.slices_to_series(wrappers)
+    assert_equal(len(series), 1)
+    assert_equal(len(series[0]), 2)
+
diff --git a/nibabel/nicom/tests/test_dicomwrappers.py b/nibabel/nicom/tests/test_dicomwrappers.py
@@ -35,6 +35,7 @@
 DATA_FILE_SLC_NORM = pjoin(IO_DATA_PATH, 'csa_slice_norm.dcm')
 DATA_FILE_DEC_RSCL = pjoin(IO_DATA_PATH, 'decimal_rescale.dcm')
 DATA_FILE_4D = pjoin(IO_DATA_PATH, '4d_multiframe_test.dcm')
+DATA_FILE_EMPTY_ST = pjoin(IO_DATA_PATH, 'slicethickness_empty_string.dcm')
 
 # This affine from our converted image was shown to match our image spatially
 # with an image from SPM DICOM conversion. We checked the matching with SPM
@@ -616,6 +617,11 @@ def test_data_real(self):
         assert_equal(sha1(dat_str).hexdigest(),
                      '149323269b0af92baa7508e19ca315240f77fa8c')
 
+    @dicom_test
+    def test_slicethickness_fallback(self):
+        dw = didw.wrapper_from_file(DATA_FILE_EMPTY_ST)
+        assert_equal(dw.voxel_sizes[2], 1.0)
+
     @dicom_test
     def test_data_fake(self):
         # Test algorithm for get_data
diff --git a/nibabel/nifti1.py b/nibabel/nifti1.py
@@ -125,7 +125,9 @@
     (1, 'scanner', "NIFTI_XFORM_SCANNER_ANAT"),
     (2, 'aligned', "NIFTI_XFORM_ALIGNED_ANAT"),
     (3, 'talairach', "NIFTI_XFORM_TALAIRACH"),
-    (4, 'mni', "NIFTI_XFORM_MNI_152")), fields=('code', 'label', 'niistring'))
+    (4, 'mni', "NIFTI_XFORM_MNI_152"),
+    (5, 'template', "NIFTI_XFORM_TEMPLATE_OTHER"),
+    ), fields=('code', 'label', 'niistring'))
 
 # unit codes
 unit_codes = Recoder((  # code, label
@@ -2014,13 +2016,9 @@ def as_reoriented(self, ornt):
             return img
 
         # Also apply the transform to the dim_info fields
-        new_dim = list(img.header.get_dim_info())
-        for idx, value in enumerate(new_dim):
-            # For each value, leave as None if it was that way,
-            # otherwise check where we have mapped it to
-            if value is None:
-                continue
-            new_dim[idx] = np.where(ornt[:, 0] == idx)[0]
+        new_dim = [
+            None if orig_dim is None else int(ornt[orig_dim, 0])
+            for orig_dim in img.header.get_dim_info()]
 
         img.header.set_dim_info(*new_dim)
 
diff --git a/nibabel/tests/test_nifti1.py b/nibabel/tests/test_nifti1.py
@@ -28,8 +28,10 @@
 from nibabel.spatialimages import HeaderDataError
 from nibabel.tmpdirs import InTemporaryDirectory
 from ..freesurfer import load as mghload
+from ..orientations import aff2axcodes
 
 from .test_arraywriters import rt_err_estimate, IUINT_TYPES
+from .test_orientations import ALL_ORNTS
 from .test_helpers import bytesio_filemap, bytesio_round_trip
 from .nibabel_data import get_nibabel_data, needs_nibabel_data
 
@@ -226,6 +228,21 @@ def test_nifti_qsform_checks(self):
         assert_equal(message,
                      'sform_code -1 not valid; setting to 0')
 
+    def test_nifti_xform_codes(self):
+        # Verify that all xform codes can be set in both qform and sform
+        hdr = self.header_class()
+        affine = np.eye(4)
+        for code in nifti1.xform_codes.keys():
+            hdr.set_qform(affine, code)
+            assert_equal(hdr['qform_code'], nifti1.xform_codes[code])
+            hdr.set_sform(affine, code)
+            assert_equal(hdr['sform_code'], nifti1.xform_codes[code])
+
+        # Raise KeyError on unknown code
+        for bad_code in (-1, 6, 10):
+            assert_raises(KeyError, hdr.set_qform, affine, bad_code)
+            assert_raises(KeyError, hdr.set_sform, affine, bad_code)
+
     def test_magic_offset_checks(self):
         # magic and offset
         HC = self.header_class
@@ -1403,6 +1420,36 @@ def test_rt_bias(self):
                 bias_thresh = np.max([max_miss / np.sqrt(count), eps])
                 assert_true(np.abs(bias) < bias_thresh)
 
+    def test_reoriented_dim_info(self):
+        # Check that dim_info is reoriented correctly
+        arr = np.arange(24).reshape((2, 3, 4))
+        # Start as RAS
+        aff = np.diag([2, 3, 4, 1])
+        simg = self.single_class(arr, aff)
+        for freq, phas, slic in ((0, 1, 2),
+                                 (0, 2, 1),
+                                 (1, 0, 2),
+                                 (2, 0, 1),
+                                 (None, None, None),
+                                 (0, 2, None),
+                                 (0, None, None),
+                                 (None, 2, 1),
+                                 (None, None, 1),
+                                 ):
+            simg.header.set_dim_info(freq, phas, slic)
+            fdir = 'RAS'[freq] if freq is not None else None
+            pdir = 'RAS'[phas] if phas is not None else None
+            sdir = 'RAS'[slic] if slic is not None else None
+            for ornt in ALL_ORNTS:
+                rimg = simg.as_reoriented(np.array(ornt))
+                axcode = aff2axcodes(rimg.affine)
+                dirs = ''.join(axcode).replace('P', 'A').replace('I', 'S').replace('L', 'R')
+                new_freq, new_phas, new_slic = rimg.header.get_dim_info()
+                new_fdir = dirs[new_freq] if new_freq is not None else None
+                new_pdir = dirs[new_phas] if new_phas is not None else None
+                new_sdir = dirs[new_slic] if new_slic is not None else None
+                assert_equal((new_fdir, new_pdir, new_sdir), (fdir, pdir, sdir))
+
 
 @runif_extra_has('slow')
 def test_large_nifti1():
diff --git a/nibabel/tests/test_orientations.py b/nibabel/tests/test_orientations.py
@@ -83,6 +83,18 @@
 OUT_ORNTS = [np.array(ornt) for ornt in OUT_ORNTS]
 
 
+_LABELS = ['RL', 'AP', 'SI']
+ALL_AXCODES = [(_LABELS[i0][j0], _LABELS[i1][j1], _LABELS[i2][j2])
+               for i0 in range(3) for i1 in range(3) for i2 in range(3)
+               if i0 != i1 != i2 != i0
+               for j0 in range(2) for j1 in range(2) for j2 in range(2)]
+
+ALL_ORNTS = [[[i0, j0], [i1, j1], [i2, j2]]
+             for i0 in range(3) for i1 in range(3) for i2 in range(3)
+             if i0 != i1 != i2 != i0
+             for j0 in [1, -1] for j1 in [1, -1] for j2 in [1, -1]]
+
+
 def same_transform(taff, ornt, shape):
     # Applying transformations implied by `ornt` to a made-up array
     # ``arr`` of shape `shape`, results in ``t_arr``. When the point
@@ -125,6 +137,10 @@ def test_apply():
                   apply_orientation,
                   a,
                   [[0, 1], [np.nan, np.nan], [2, 1]])
+    shape = np.array(a.shape)
+    for ornt in ALL_ORNTS:
+        t_arr = apply_orientation(a, ornt)
+        assert_array_equal(a.shape, np.array(t_arr.shape)[np.array(ornt)[:, 0]])
 
 
 def test_flip_axis():
@@ -282,6 +298,9 @@ def test_ornt2axcodes():
     # As do directions not in range
     assert_raises(ValueError, ornt2axcodes, [[0, 0]])
 
+    for axcodes, ornt in zip(ALL_AXCODES, ALL_ORNTS):
+        assert_equal(ornt2axcodes(ornt), axcodes)
+
 
 def test_axcodes2ornt():
     # Go from axcodes back to orientations
@@ -340,6 +359,9 @@ def test_axcodes2ornt():
     assert_raises(ValueError, axcodes2ornt, 'blD', ('SD', 'BF', 'lD'))
     assert_raises(ValueError, axcodes2ornt, 'blD', ('SD', 'SF', 'lD'))
 
+    for axcodes, ornt in zip(ALL_AXCODES, ALL_ORNTS):
+        assert_array_equal(axcodes2ornt(axcodes), ornt)
+
 
 def test_aff2axcodes():
     assert_equal(aff2axcodes(np.eye(4)), tuple('RAS'))
