Merge pull request #818 from hbraunDSP/ignore-bad-csa

Ignore unreadable siemens private headers

Author: effigies

nibabel-data/nitest-dicom

@@ -100,7 +100,8 @@ def read(csa_str):
     csa_dict['n_tags'], csa_dict['check'] = up_str.unpack('2I')
     if not 0 < csa_dict['n_tags'] <= MAX_CSA_ITEMS:
         raise CSAReadError('Number of tags `t` should be '
-                           '0 < t <= %d' % MAX_CSA_ITEMS)
+                           '0 < t <= %d. Instead found %d tags.'
+                           % (MAX_CSA_ITEMS, csa_dict['n_tags']))
     for tag_no in range(csa_dict['n_tags']):
         name, vm, vr, syngodt, n_items, last3 = \
             up_str.unpack('64si4s3i')

nibabel/nicom/csareader.py

@@ -80,7 +80,13 @@ def wrapper_from_data(dcm_data):
         return MultiframeWrapper(dcm_data)
     # Check for Siemens DICOM format types
     # Only Siemens will have data for the CSA header
-    csa = csar.get_csa_header(dcm_data)
+    try:
+        csa = csar.get_csa_header(dcm_data)
+    except csar.CSAReadError as e:
+        warnings.warn('Error while attempting to read CSA header: ' +
+                      str(e.args) +
+                      '\n Ignoring Siemens private (CSA) header info.')
+        csa = None
     if csa is None:
         return Wrapper(dcm_data)
     if csar.is_mosaic(csa):

nibabel/nicom/dicomwrappers.py

@@ -20,7 +20,7 @@
 from nose.tools import (assert_true, assert_false, assert_equal,
                         assert_not_equal, assert_raises)
 
-from numpy.testing import assert_array_equal, assert_array_almost_equal
+from numpy.testing import assert_array_equal, assert_array_almost_equal, assert_warns
 from ...tests.nibabel_data import get_nibabel_data, needs_nibabel_data
 
 IO_DATA_PATH = pjoin(dirname(__file__), 'data')
@@ -39,6 +39,8 @@
 DATA_FILE_EMPTY_ST = pjoin(IO_DATA_PATH, 'slicethickness_empty_string.dcm')
 DATA_FILE_4D_DERIVED = pjoin(get_nibabel_data(), 'nitest-dicom',
                              '4d_multiframe_with_derived.dcm')
+DATA_FILE_CT = pjoin(get_nibabel_data(), 'nitest-dicom',
+                     'siemens_ct_header_csa.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
@@ -633,6 +635,13 @@ def test_data_derived_shape(self):
         dw = didw.wrapper_from_file(DATA_FILE_4D_DERIVED)
         assert_equal(dw.image_shape, (96, 96, 60, 33))
 
+    @dicom_test
+    @needs_nibabel_data('nitest-dicom')
+    def test_data_unreadable_private_headers(self):
+        # Test CT image with unreadable CSA tags
+        dw = assert_warns(UserWarning, didw.wrapper_from_file, DATA_FILE_CT)
+        assert_equal(dw.image_shape, (512, 571))
+
     @dicom_test
     def test_data_fake(self):
         # Test algorithm for get_data