def test_key_regex_filter():
filt = dcmstack.make_key_regex_filter(["test", "another"], ["2", "another test"])
ok_(filt("test", 1))
ok_(filt("test another", 1))
ok_(filt("another tes", 1))
ok_(not filt("test2", 1))
ok_(not filt("2 another", 1))
ok_(not filt("another test", 1))
def test_key_regex_filter():
filt = dcmstack.make_key_regex_filter(['test', 'another'],
['2', 'another test'])
ok_(filt('test', 1))
ok_(filt('test another', 1))
ok_(filt('another tes', 1))
ok_(not filt('test2', 1))
ok_(not filt('2 another', 1))
ok_(not filt('another test', 1))
def test_key_regex_filter():
filt = dcmstack.make_key_regex_filter(['test', 'another'],
['2', 'another test'])
ok_(filt('test', 1))
ok_(filt('test another', 1))
ok_(filt('another tes', 1))
ok_(not filt('test2', 1))
ok_(not filt('2 another', 1))
ok_(not filt('another test', 1))
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 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 _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 _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
