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FIX: Interpret empty string in SliceThickness DICOM field as missing (default to 1) #652

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Merged
merged 3 commits into from
Mar 21, 2019
Merged

FIX: Interpret empty string in SliceThickness DICOM field as missing (default to 1) #652

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9a91995
some dicom headers had an empty string in SliceThickness
mattcieslak Jul 24, 2018
57a7040
TEST: Add de-identified, compressed DICOM with empty string in SliceT…
effigies Mar 21, 2019
a06c005
Merge pull request #1 from effigies/enh/dicom_empty_string
mattcieslak Mar 21, 2019
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2 changes: 1 addition & 1 deletion nibabel/nicom/dicomwrappers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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Binary file added nibabel/nicom/tests/data/slicethickness_empty_string.dcm
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6 changes: 6 additions & 0 deletions nibabel/nicom/tests/test_dicomwrappers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
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