Skip to content

ENH: Support for Philips DICOMs w/ derived volume #727

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 12 commits into from
Mar 19, 2019
Merged

ENH: Support for Philips DICOMs w/ derived volume #727

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
3a985f5
enh+wip: support for philips dcm w/ derived volume
mgxd Feb 20, 2019
bbd420a
fix: (py)dicom import
mgxd Feb 20, 2019
b7ef629
fix: set missing import to None, ensure first frame exists before fet…
mgxd Feb 20, 2019
6ec7b0a
fix: skip if frame does not have get attribute
mgxd Feb 20, 2019
039d4f0
sty: import specifics separately
mgxd Feb 27, 2019
2af8950
fix: allow non-diffusion 5D
mgxd Feb 27, 2019
c59b30b
fix: remove unnecessary check
mgxd Mar 1, 2019
f95d716
rf: better error handling, reflect change on frame_indices
mgxd Mar 14, 2019
469f623
add: warn if frames were altered
mgxd Mar 14, 2019
5409f50
Merge branch 'master' of https://github.com/nipy/nibabel into fix/trace
mgxd Mar 18, 2019
dfd93e1
rf: condense frame checking try block
mgxd Mar 18, 2019
5181407
fix: ensure derived index is removed
mgxd Mar 18, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 16 additions & 5 deletions nibabel/nicom/dicomwrappers.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down Expand Up @@ -461,10 +461,19 @@ 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.")
# DWI image where derived isotropic, ADC or trace volume was appended to the series
if self.frames[0].get([0x18, 0x9117]):
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)
try:
self.shared = dcm_data.get('SharedFunctionalGroupsSequence')[0]
except TypeError:
Expand Down Expand Up @@ -503,8 +512,7 @@ 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])
Expand All @@ -528,12 +536,15 @@ 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)
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I don't really follow this guard. Can you elaborate?

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I'm not sure this addresses the problem properly / gracefully, but I'm unsure how to proceed. I've come across a derived image included in the diffusion DICOM, which is currently not properly handled. I thought this meant 5D data wasn't yet handled, but in fact there is a test specifically for this introduced in 3f04e3c (maybe @matthew-brett can share some wisdom)

nibabel/nibabel/nicom/tests/test_dicomwrappers.py

Lines 656 to 682 in ad0b13f

# 5D!
dim_idxs = [
[1, 4, 2, 1],
[1, 2, 2, 1],
[1, 3, 2, 1],
[1, 1, 2, 1],
[1, 4, 2, 2],
[1, 2, 2, 2],
[1, 3, 2, 2],
[1, 1, 2, 2],
[1, 4, 1, 1],
[1, 2, 1, 1],
[1, 3, 1, 1],
[1, 1, 1, 1],
[1, 4, 1, 2],
[1, 2, 1, 2],
[1, 3, 1, 2],
[1, 1, 1, 2]]
fake_mf.update(fake_shape_dependents(dim_idxs, sid_dim=0))
shape = (2, 3, 4, 2, 2)
data = np.arange(np.prod(shape)).reshape(shape)
sorted_data = data.reshape(shape[:2] + (-1,), order='F')
order = [11, 9, 10, 8, 3, 1, 2, 0,
15, 13, 14, 12, 7, 5, 6, 4]
sorted_data = sorted_data[..., np.argsort(order)]
fake_mf['pixel_array'] = np.rollaxis(sorted_data, 2)
assert_array_equal(MFW(fake_mf).get_data(), data * 2.0 - 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)
Expand Down
Binary file added nibabel/nicom/tests/data/4d_multiframe_with_derived.dcm
View file
Open in desktop
Binary file not shown.
8 changes: 8 additions & 0 deletions nibabel/nicom/tests/test_dicomwrappers.py
View file
Open in desktop
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_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
Expand Down Expand Up @@ -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
Expand Down
1 change: 1 addition & 0 deletions nibabel/pydicom_compat.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@
read_file = pydicom.read_file

if have_dicom:
from pydicom.sequence import Sequence
try:
# Versions >= 1.0
tag_for_keyword = pydicom.datadict.tag_for_keyword
Expand Down