def _build_nii(self, name):
kwargs = {}
if name.endswith('_meta'):
kwargs['embed_meta'] = True
name = name[:-5]
if name.endswith('_SAR'):
kwargs['voxel_order'] = 'SAR'
name = name[:-4]
if name == 'two_time_vol':
stack = dcmstack.DicomStack(time_order='EchoTime')
elif name == 'two_vector_vol':
stack = dcmstack.DicomStack(vector_order='EchoTime')
else:
stack = dcmstack.DicomStack()
stack.add_dcm(self.inputs[0])
if name == 'single_slice':
return stack.to_nifti(**kwargs)
stack.add_dcm(self.inputs[1])
if name == 'single_vol':
return stack.to_nifti(**kwargs)
stack.add_dcm(self.inputs[2])
stack.add_dcm(self.inputs[3])
if name in ('two_time_vol', 'two_vector_vol'):
return stack.to_nifti(**kwargs)
assert False # Unknown name
def multicoil_convert(self):
"""GE specific multicoil converesion. requires partial volume and missing slices check."""
log.debug('multicoil recon')
mr.partial_vol_check(self)
stacks = []
group_id = 0
for group in self._dcm_groups:
group_id += 1
log.debug('multicoil - %2s, %s dicom' %
(str(group_id), str(len(group))))
num_positions = len(set([d.SliceLocation for d in group]))
if num_positions != self.num_slices:
raise DicomError('coil %s has %s unique positions; expected %s' %
(group_id, num_positions, self.num_slices))
stack = dcmstack.DicomStack()
for dcm in group:
meta = MetaExtractor(dcm)
stack.add_dcm(dcm, meta)
nii_wrp = stack.to_nifti_wrapper()
stacks.append(nii_wrp)
try:
nii_wrp = dcmstack.dcmmeta.NiftiWrapper.from_sequence(stacks)
except dcmstack.InvalidStackError as e:
raise DicomError(
'cannot reconstruct %s: %s' %
(self.filepath, e)) # XXX FAIL! unexpected for recon to fail
# raise NIMSDicomError('cannot reconstruct %s: %s' % (self.filepath, e), log_level=logging.ERROR)
del self._dcm_groups, self._dcm_list, stacks, stack, dcm
nii = nii_wrp.nii_img
self.data = {'': nii.get_data()}
self.qto_xyz = nii.get_affine()
del nii_wrp, nii
mr.post_convert(self)
def fastcard_convert(self):
"""GE fast card conversion."""
log.debug('fast card')
stacks = []
group_id = 0
def _split_list(l, size):
return [l[i:i + size] for i in range(0, len(l), size)]
dcm_groups = _split_list(self._dcm_list, self.total_num_slices / 5)
for group in dcm_groups:
group_id += 1
num_positions = len(set([d.SliceLocation for d in group]))
if num_positions != self.num_slices:
raise DicomError('volume %s has %s unique positions; expected %s' %
(group_id, num_positions, self.num_slices))
stack = dcmstack.DicomStack()
for d in group:
meta = MetaExtractor(d)
stack.add_dcm(d, meta)
nii_wrp = stack.to_nifti_wrapper()
stacks.append(nii_wrp)
try:
nii_wrp = dcmstack.dcmmeta.NiftiWrapper.from_sequence(stacks)
except dcmstack.InvalidStackError as e:
raise DicomError('cannot reconstruct %s: %s' % (self.filepath, str(e)))
nii = nii_wrp.nii_img
self.data = {'': nii.get_data()}
self.qto_xyz = nii.get_affine()
mr.post_convert(self)
def test_single_slice(self):
stack = dcmstack.DicomStack()
stack.add_dcm(self.inputs[0])
data = stack.get_data()
eq_(data.shape, stack.get_shape())
eq_(sha256(data).hexdigest(),
'15cfa107ca73810a1c97f1c1872a7a4a05808ba6147e039cef3f63fa08735f5d')
def setUp(self):
dcm_path = path.join(test_dir, 'data', 'dcmstack', '2D_16Echo_qT2',
'TE_20_SlcPos_-33.707626341697.dcm')
self.dcm = dicom.read_file(dcm_path)
self.stack = dcmstack.DicomStack()
self.stack.add_dcm(dcm)
def test_pix_overflow():
ds = make_dicom(pix_val=(2**16 - 1))
stack = dcmstack.DicomStack()
stack.add_dcm(ds)
data = stack.get_data()
eq_(np.max(data), (2**16 - 1))
eq_(data.dtype, np.uint16)
def test_vector_var_over_vol(self):
self.stack = dcmstack.DicomStack(vector_order='EchoTime')
self.stack.add_dcm(self.inputs[0])
self.stack.add_dcm(self.inputs[1])
self.stack.add_dcm(self.inputs[2])
self.stack.add_dcm(self.inputs[3])
self._chk()
def test_three_dim(self):
stack = dcmstack.DicomStack()
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
affine = stack.get_affine()
ref = np.load(path.join(self.data_dir, 'single_vol_aff.npy'))
ok_(np.allclose(affine, ref))
def test_image_collision():
dcm_path = path.join(test_dir, 'data', 'dcmstack', '2D_16Echo_qT2',
'TE_20_SlcPos_-33.707626341697.dcm')
dcm = dicom.read_file(dcm_path)
stack = dcmstack.DicomStack('EchoTime')
stack.add_dcm(dcm)
assert_raises(dcmstack.ImageCollisionError, stack.add_dcm, dcm)
def test_allow_dummy(self):
del self.inputs[0].Rows
del self.inputs[0].Columns
stack = dcmstack.DicomStack(allow_dummies=True)
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
shape = stack.get_shape()
eq_(shape, (192, 192, 2))
def test_two_time_vol(self, embed=False):
stack = dcmstack.DicomStack(time_order='EchoTime')
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
stack.add_dcm(self.inputs[2])
stack.add_dcm(self.inputs[3])
nii = stack.to_nifti()
self._chk(nii, 'two_time_vol')
def test_three_dim(self):
stack = dcmstack.DicomStack()
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
data = stack.get_data()
eq_(data.shape, stack.get_shape())
eq_(sha256(data).hexdigest(),
'ab5225fdbedceeea3442b2c9387e1abcbf398c71f525e0017251849c3cfbf49c')
def test_four_dim(self):
stack = dcmstack.DicomStack(time_order='EchoTime')
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
stack.add_dcm(self.inputs[2])
stack.add_dcm(self.inputs[3])
shape = stack.shape
eq_(shape, (192, 192, 2, 2))
def test_five_dim(self):
stack = dcmstack.DicomStack(vector_order='EchoTime')
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
stack.add_dcm(self.inputs[2])
stack.add_dcm(self.inputs[3])
shape = stack.get_shape()
eq_(shape, (192, 192, 2, 1, 2))
def test_single_slice(self):
stack = dcmstack.DicomStack()
stack.add_dcm(self.inputs[0])
affine = stack.get_affine()
ref = np.load(path.join(self.data_dir, 'single_slice_aff.npy'))
print affine
print ref
ok_(np.allclose(affine, ref))
def test_two_vector_vol(self):
stack = dcmstack.DicomStack(vector_order='EchoTime')
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
stack.add_dcm(self.inputs[2])
stack.add_dcm(self.inputs[3])
nii = stack.to_nifti()
self._chk(nii, 'two_vector_vol')
def test_allow_dummies(self):
del self.inputs[0].Rows
del self.inputs[0].Columns
stack = dcmstack.DicomStack(allow_dummies=True)
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
nii = stack.to_nifti()
data = nii.get_data()
ok_(np.all(data[:, :, 0] == np.iinfo(np.int16).max))
def test_fsl_hack():
ds = make_dicom({
'BitsStored': 14,
}, 2**14 - 1)
stack = dcmstack.DicomStack()
stack.add_dcm(ds)
data = stack.get_data()
eq_(np.max(data), (2**14 - 1))
eq_(data.dtype, np.int16)
def test_only_dummy(self):
self.stack = dcmstack.DicomStack(allow_dummies=True)
del self.inputs[0].Rows
del self.inputs[0].Columns
del self.inputs[1].Rows
del self.inputs[1].Columns
self.stack.add_dcm(self.inputs[0])
self.stack.add_dcm(self.inputs[1])
self._chk()
def test_three_dim(self):
stack = dcmstack.DicomStack()
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
data = stack.get_data()
eq_(data.shape, stack.get_shape())
eq_(
sha256(data).hexdigest(),
'ec60d148734916bb05aa7d73cc76bd0777560518da86d1ac5aa93c8f151cf73f')
def get_data_from_dicom(alldic, Ei):
#Ei = Exam_info.Exam_info()
mf = dcmstack.make_key_regex_filter(['nothingtoremove'])
pg, dicom_file_size, n_ommited = Ei.get_group_stack_from_dic(alldic)
all_stack = []
dicom_ok = True
for v in pg.itervalues():
my_stack = dcmstack.DicomStack(meta_filter=mf,
time_order='InstanceNumber')
n_ommited = 0
n_repeat = 0
for vol in v: #vol[0] champs de pydicom vol[1] ordererd dict
try:
my_stack.add_dcm(vol[0], meta=vol[1])
except dcmstack.IncongruentImageError:
n_ommited += 1
dicom_ok = False
except dcmstack.ImageCollisionError:
n_repeat += 1
dicom_ok = False
except Exception as e:
log.info("oups dic %s because expection" % (vol[2]))
print e
n_ommited += 1
dicom_ok = False
# dicom_file_size += os.path.getsize(vol[2])
if n_repeat > 0:
log.info("Found %d duplicate dicom file", n_repeat)
if n_ommited > 0:
log.info("Found %d stack incongruent dicom file", n_ommited)
try:
all_stack.append(
my_stack.to_nifti(voxel_order='LAS', embed_meta=True))
except (dcmstack.InvalidStackError,
dcmstack.IncongruentImageError) as detail:
log.info("INVALIDE STACK because %s ", detail)
dicom_ok = False
except Exception:
log.info("STACK error")
dicom_ok = False
alldata = []
for nii in all_stack:
data = nii.get_data()
alldata.append(data)
return alldata, dicom_ok
def test_five_dim(self):
stack = dcmstack.DicomStack(vector_order='EchoTime')
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
stack.add_dcm(self.inputs[2])
stack.add_dcm(self.inputs[3])
data = stack.get_data()
eq_(data.shape, stack.get_shape())
eq_(sha256(data).hexdigest(),
'bb3639a6ece13dc9a11d65f1b09ab3ccaed63b22dcf0f96fb5d3dd8805cc7b8a')
def test_wrong_guess_first(self):
#Test situations where the initial guesses are wrong
stack = dcmstack.DicomStack()
for key in dcmstack.DicomStack.sort_guesses[:-1]:
for in_dcm in self.inputs:
setattr(in_dcm, key, 0)
for idx, in_dcm in enumerate(self.inputs):
setattr(in_dcm, dcmstack.DicomStack.sort_guesses[-1], idx)
stack.add_dcm(in_dcm)
eq_(stack.get_shape(), (192, 192, 2, 2))
def test_single_guess(self):
#Test situations where there is only one possible correct guess
for key in dcmstack.DicomStack.sort_guesses:
stack = dcmstack.DicomStack()
for idx, in_dcm in enumerate(self.inputs):
setattr(in_dcm, key, self._get_vr_ord(key, idx))
stack.add_dcm(in_dcm)
eq_(stack.get_shape(), (192, 192, 2, 2))
for in_dcm in self.inputs:
delattr(in_dcm, key)
def test_allow_dummy(self):
del self.inputs[0].Rows
del self.inputs[0].Columns
stack = dcmstack.DicomStack(allow_dummies=True)
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
data = stack.get_data()
eq_(data.shape, stack.get_shape())
ok_(np.all(data[:, :, -1] == np.iinfo(np.int16).max))
eq_(sha256(data).hexdigest(),
'7d85fbcb60a5021a45df3975613dcb7ac731830e0a268590cc798dc39897c04b')
def test_allow_dummy(self):
del self.inputs[0].Rows
del self.inputs[0].Columns
stack = dcmstack.DicomStack(allow_dummies=True)
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
data = stack.get_data()
eq_(data.shape, stack.get_shape())
eq_(
sha256(data).hexdigest(),
'ed14cb8694f1c0d542562fecc6fd71bced3810df4fcb857a091c8e8525fbdda6')
def test_five_dim(self):
stack = dcmstack.DicomStack(vector_order='EchoTime')
stack.add_dcm(self.inputs[0])
stack.add_dcm(self.inputs[1])
stack.add_dcm(self.inputs[2])
stack.add_dcm(self.inputs[3])
data = stack.get_data()
eq_(data.shape, stack.get_shape())
eq_(
sha256(data).hexdigest(),
'c14d3a8324bdf4b85be05d765c0864b4e2661d7aa716adaf85a28b4102e1992b')
def _run_interface(self, runtime):
src_paths = self._get_filelist(self.inputs.dicom_files)
include_regexes = dcmstack.default_key_incl_res
if isdefined(self.inputs.include_regexes):
include_regexes += self.inputs.include_regexes
exclude_regexes = dcmstack.default_key_excl_res
if isdefined(self.inputs.exclude_regexes):
exclude_regexes += self.inputs.exclude_regexes
meta_filter = dcmstack.make_key_regex_filter(exclude_regexes,
include_regexes)
stack = dcmstack.DicomStack(meta_filter=meta_filter)
for src_path in src_paths:
src_dcm = dicom.read_file(src_path, force=True)
stack.add_dcm(src_dcm)
nii = stack.to_nifti(embed_meta=True)
nw = NiftiWrapper(nii)
self.out_path = \
self._get_out_path(nw.meta_ext.get_class_dict(('global', 'const')))
if not self.inputs.embed_meta:
nw.remove_extension()
nb.save(nii, self.out_path)
return runtime
def test_pix_overflow():
ds = make_dicom(pix_val=(2**16 - 1))
# ds = pydicom.dataset.Dataset()
# ds.file_meta = pydicom.dataset.Dataset()
# ds.file_meta.TransferSyntaxUID = ExplicitVRLittleEndian
# ds.is_little_endian = True
# ds.ImagePositionPatient = [0.0, 0.0, 0.0]
# ds.ImageOrientationPatient = [1.0, 0.0, 0.0, 0.0, 1.0, 0.0]
# ds.PixelSpacing = [1.0, 1.0]
# ds.SliceThickness = 1.0
# ds.Rows = 16
# ds.Columns = 16
# ds.BitsAllocated = 16
# ds.BitsStored = 16
# ds.PixelRepresentation = 0
# ds.SamplesPerPixel = 1
# ds.PixelData = (np.ones((16, 16), np.uint16) * (2**16 - 1)).tostring()
stack = dcmstack.DicomStack()
stack.add_dcm(ds)
data = stack.get_data()
eq_(np.max(data), (2**16 - 1))
eq_(data.dtype, np.uint16)
def standard_convert(self):
"""Standard reconstruction, works for most manufacturers and scans."""
log.debug('standard recon')
partial_vol_check(self)
stack = dcmstack.DicomStack()
for dcm in self._dcm_list:
stack.add_dcm(dcm, MetaExtractor(dcm))
try:
nii_wrp = stack.to_nifti_wrapper()
except dcmstack.InvalidStackError as e:
raise DicomError(
'cannot reconstruct %s: %s' %
(self.filepath, e)) # XXX FAIL! unexpect for recon to fail
del self._dcm_list, stack, dcm
nii = nii_wrp.nii_img
self.data = {'': nii.get_data()}
self.qto_xyz = nii.get_affine()
del nii_wrp, nii
post_convert(self)