ENH: Support for Philips DICOMs w/ derived volume

nibabel/nicom/dicomwrappers.py

@@ -21,7 +21,7 @@
 from .dwiparams import B2q, nearest_pos_semi_def, q2bg
 from ..openers import ImageOpener
 from ..onetime import setattr_on_read as one_time
-from ..pydicom_compat import tag_for_keyword
+from ..pydicom_compat import tag_for_keyword, Sequence
 
 
 class WrapperError(Exception):
@@ -461,10 +461,23 @@ def __init__(self, dcm_data):
         Wrapper.__init__(self, dcm_data)
         self.dcm_data = dcm_data
         self.frames = dcm_data.get('PerFrameFunctionalGroupsSequence')
+        self._nframes = self.get('NumberOfFrames')
         try:
             self.frames[0]
         except TypeError:
             raise WrapperError("PerFrameFunctionalGroupsSequence is empty.")
+        try:
+            # DWI image where derived isotropic, ADC or trace volume
+            # was appended to the series
+            if self.frames[0].get([0x18, 0x9117], None):
+                self.frames = Sequence(
+                    frame for frame in self.frames if
+                    frame.get([0x18, 0x9117])[0].get([0x18, 0x9075]).value
+                    != 'ISOTROPIC'
+                    )
+                self._nframes = len(self.frames)
+        except AttributeError:
+            pass
         try:
             self.shared = dcm_data.get('SharedFunctionalGroupsSequence')[0]
         except TypeError:
@@ -503,8 +516,7 @@ def image_shape(self):
         if None in (rows, cols):
             raise WrapperError("Rows and/or Columns are empty.")
         # Check number of frames
-        n_frames = self.get('NumberOfFrames')
-        assert len(self.frames) == n_frames
+        assert len(self.frames) == self._nframes
         frame_indices = np.array(
             [frame.FrameContentSequence[0].DimensionIndexValues
              for frame in self.frames])
@@ -528,12 +540,15 @@ def image_shape(self):
         # Store frame indices
         self._frame_indices = frame_indices
         if n_dim < 4:  # 3D volume
-            return rows, cols, n_frames
+            return rows, cols, self._nframes
         # More than 3 dimensions
         ns_unique = [len(np.unique(row)) for row in self._frame_indices.T]
+        if len(ns_unique) == 3:
+            # derived volume is included
+            ns_unique.pop(1)
         shape = (rows, cols) + tuple(ns_unique)
         n_vols = np.prod(shape[3:])
-        if n_frames != n_vols * shape[2]:
+        if self._nframes != n_vols * shape[2]:
             raise WrapperError("Calculated shape does not match number of "
                                "frames.")
         return tuple(shape)

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_4D_DERIVED = pjoin(IO_DATA_PATH, '4d_multiframe_with_derived.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 +617,13 @@ def test_data_real(self):
         assert_equal(sha1(dat_str).hexdigest(),
                      '149323269b0af92baa7508e19ca315240f77fa8c')
 
+    @dicom_test
+    def test_data_derived_shape(self):
+        # Test 4D diffusion data with an additional trace volume included
+        # Excludes the trace volume and generates the correct shape
+        dw = didw.wrapper_from_file(DATA_FILE_4D_DERIVED)
+        assert_equal(dw.image_shape, (96, 96, 60, 33))
+
     @dicom_test
     def test_data_fake(self):
         # Test algorithm for get_data

nibabel/pydicom_compat.py

@@ -21,19 +21,21 @@
 import numpy as np
 
 have_dicom = True
-pydicom = read_file = tag_for_keyword = None
+pydicom = read_file = tag_for_keyword = Sequence = None
 
 try:
     import dicom as pydicom
     # Values not imported by default
     import dicom.values
+    from dicom.sequence import Sequence
 except ImportError:
     try:
         import pydicom
     except ImportError:
         have_dicom = False
     else:  # pydicom module available
         from pydicom.dicomio import read_file
+        from pydicom.sequence import Sequence
         # Values not imported by default
         import pydicom.values
 else:  # dicom module available