RF: Remove use of 'FunctionalGroupPointer' in determining 'StackID' axis

Author: embaker

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 pydicom
 
 class WrapperError(Exception):
     pass
@@ -463,27 +463,30 @@ def __init__(self, dcm_data):
     def image_shape(self):
         """The array shape as it will be returned by ``get_data()``
 
-        The shape is determined by the `Rows` DICOM attribute, `Columns`
+        The shape is determined by the *Rows* DICOM attribute, *Columns*
         DICOM attribute, and the set of frame indices given by the
-        `FrameContentSequence[0].DimensionIndexValues` DICOM attribute of each
-        element in the `PerFrameFunctionalGroupsSequence`.  The first two
+        *FrameContentSequence[0].DimensionIndexValues* DICOM attribute of each
+        element in the *PerFrameFunctionalGroupsSequence*.  The first two
         axes of the returned shape correspond to the rows, and columns
         respectively. The remaining axes correspond to those of the frame
         indices with order preserved.
 
         What each axis in the frame indices refers to is given by the
-        corresponding entry in the `DimensionIndexSequence` DICOM attribute.
-        WARNING, any axis refering to the `StackID` DICOM attribute will have 
-        been removed from the frame indices in determining the shape. This is
-        because only a file containing a single stack is currently allowed by
+        corresponding entry in the *DimensionIndexSequence* DICOM attribute.
+        **WARNING**: Any axis refering to the *StackID* DICOM attribute will
+        have been removed from the frame indices in determining the shape. This
+        is because only a file containing a single stack is currently allowed by
         this wrapper.
 
         References
         ----------
-        - C.7.6.17 Multi-frame Dimension Module of Supplement 49 of the DICOM
-        standard.
-        - C.7.6.16.2.2 Frame Content Macro of Supplement 49 of the DICOM
-        standard.
+
+        * `C.7.6.16 Multi-Frame Functional Groups Module
+        <http://dicom.nema.org/medical/dicom/current/output/pdf/part03.pdf#sect_C.7.6.16>_`
+
+        * `C.7.6.17 Multi-Frame Dimension Module
+        <http://dicom.nema.org/medical/dicom/current/output/pdf/part03.pdf#sect_C.7.6.17>_`
+
         """
         rows, cols = self.get('Rows'), self.get('Columns')
         if None in (rows, cols):
@@ -500,17 +503,14 @@ def image_shape(self):
         if len(stack_ids) > 1:
             raise WrapperError("File contains more than one StackID. "
                                "Cannot handle multi-stack files")
-        # Determine if one of the Dimension indices refers to the stack id
-        dim_seq = [(dim.DimensionIndexPointer, dim.FunctionalGroupPointer)
+        # Determine if one of the dimension indices refers to the stack id
+        dim_seq = [dim.DimensionIndexPointer
                    for dim in self.get('DimensionIndexSequence')]
-        # the pointer pair (StackID Dicom-tag, FrameContentSequence Dicom-tag)
-        # that indicates that the corresponding axis in the DimensionIndexValues
-        # attribute refers to the StackID
-        stack_id_dim_pointer = ((0x20, 0x9056), (0x20, 0x9111))
-        # remove superfluous stack id index if present
-        if stack_id_dim_pointer in dim_seq:
-            stack_dim_idx = dim_seq.index(stack_id_dim_pointer)
-            frame_indices = np.delete(frame_indices, stack_dim_idx, axis=1)
+        stackid_tag = pydicom.datadict.tag_for_name('StackID')
+        # remove the stack id axis if present
+        if stackid_tag in dim_seq:
+            stackid_dim_idx = dim_seq.index(stackid_tag)
+            frame_indices = np.delete(frame_indices, stackid_dim_idx, axis=1)
         # account for the 2 additional dimensions (row and column) not included
         # in the indices
         n_dim = frame_indices.shape[1] + 2

nibabel/nicom/tests/test_dicomwrappers.py

@@ -394,9 +394,10 @@ def fake_shape_dependents(div_seq, sid_seq=None, sid_dim=None):
         the index of the column in 'div_seq' to use as 'sid_seq'
     """
     class DimIdxSeqElem(object):
-        def __init__(self, dip=(0, 0), fgp=(0, 0)):
+        def __init__(self, dip=(0, 0), fgp=None):
             self.DimensionIndexPointer = dip
-            self.FunctionalGroupPointer = fgp
+            if fgp is not None:
+                self.FunctionalGroupPointer = fgp
     class FrmContSeqElem(object):
         def __init__(self, div, sid):
             self.DimensionIndexValues = div
@@ -415,7 +416,9 @@ def __init__(self, div, sid):
     dim_idx_seq = [DimIdxSeqElem()] * num_of_frames
     # add an entry for StackID into the DimensionIndexSequence
     if sid_dim is not None:
-        dim_idx_seq[sid_dim] = DimIdxSeqElem((0x20, 0x9056), (0x20, 0x9111))
+        sid_tag = pydicom.datadict.tag_for_name('StackID')
+        fcs_tag = pydicom.datadict.tag_for_name('FrameContentSequence')
+        dim_idx_seq[sid_dim] = DimIdxSeqElem(sid_tag, fcs_tag)
     # create the PerFrameFunctionalGroupsSequence
     frames = [PerFrmFuncGrpSeqElem(div, sid)
               for div, sid in zip(div_seq, sid_seq)]