Merge pull request #393 from moloney/missing-csa-fix

BF+TST: Skip over missing CSA header elem instead of raising.

Allows us to load data where the PrivateCreator is present but
the element containing the header info is not. Ran into this with
anonymized data.

Author: matthew-brett

nibabel/nicom/csareader.py

@@ -63,8 +63,11 @@ def get_csa_header(dcm_data, csa_type='image'):
     if section_start is None:
         return None
     element_no = section_start + element_offset
-    # Assume tag exists
-    tag = dcm_data[(0x29, element_no)]
+    try:
+        tag = dcm_data[(0x29, element_no)]
+    except KeyError:
+        # The element could be missing due to anonymization
+        return None
     return read(tag.value)
 
 

nibabel/nicom/tests/test_csareader.py

@@ -1,6 +1,8 @@
 """ Testing Siemens CSA header reader
 """
+import sys
 from os.path import join as pjoin
+from copy import deepcopy
 import gzip
 
 import numpy as np
@@ -10,9 +12,12 @@
 
 from nose.tools import (assert_true, assert_false, assert_equal, assert_raises)
 
+from numpy.testing.decorators import skipif
 
 from .test_dicomwrappers import (have_dicom, dicom_test,
                                  IO_DATA_PATH, DATA, DATA_FILE)
+if have_dicom:
+    from .test_dicomwrappers import pydicom
 
 CSA2_B0 = open(pjoin(IO_DATA_PATH, 'csa2_b0.bin'), 'rb').read()
 CSA2_B1000 = open(pjoin(IO_DATA_PATH, 'csa2_b1000.bin'), 'rb').read()
@@ -30,11 +35,7 @@ def test_csa_header_read():
     assert_true(csa.is_mosaic(hdr))
     # Get a shallow copy of the data, lacking the CSA marker
     # Need to do it this way because del appears broken in pydicom 0.9.7
-    try:
-        from dicom.dataset import Dataset
-    except ImportError:
-        from pydicom.dataset import Dataset
-    data2 = Dataset()
+    data2 = pydicom.dataset.Dataset()
     for element in DATA:
         if (element.tag.group, element.tag.elem) != (0x29, 0x10):
             data2.add(element)
@@ -128,3 +129,17 @@ def test_ice_dims():
         assert_equal(csa.get_ice_dims(csa_info),
                      ex_dims)
     assert_equal(csa.get_ice_dims({}), None)
+
+
+@dicom_test
+@skipif(sys.version_info < (2,7) and pydicom.__version__ < '1.0',
+        'Known issue for python 2.6 and pydicom < 1.0')
+def test_missing_csa_elem():
+    # Test that we get None instead of raising an Exception when the file has
+    # the PrivateCreator element for the CSA dict but not the element with the
+    # actual CSA header (perhaps due to anonymization)
+    dcm = deepcopy(DATA)
+    csa_tag = pydicom.dataset.Tag(0x29, 0x1010)
+    del dcm[csa_tag]
+    hdr = csa.get_csa_header(dcm, 'image')
+    assert_equal(hdr, None)