def gbm_datasource(sub_id, BASE_DIR):
sessions = [x for x in os.listdir(os.path.join(BASE_DIR, sub_id))
if 'REF' not in x and 'T10' not in x and 'RT_' not in x]
datasource = nipype.Node(
interface=nipype.DataGrabber(
infields=['sub_id', 'sessions', 'ref_ct', 'ref_t1'],
outfields=['t1', 'ct1', 't2', 'flair', 'reference', 't1_0']),
name='datasource')
datasource.inputs.base_directory = BASE_DIR
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.raise_on_empty = False
datasource.inputs.field_template = dict(t1='%s/%s/T1.nii.gz', ct1='%s/%s/CT1.nii.gz',
t2='%s/%s/T2.nii.gz', flair='%s/%s/FLAIR.nii.gz',
reference='%s/%s/CT.nii.gz',
t1_0='%s/%s/T1.nii.gz')
datasource.inputs.template_args = dict(t1=[['sub_id', 'sessions']],
ct1=[['sub_id', 'sessions']],
t2=[['sub_id', 'sessions']],
flair=[['sub_id', 'sessions']],
reference=[['sub_id', 'ref_ct']],
t1_0=[['sub_id', 'ref_t1']])
datasource.inputs.sub_id = sub_id
datasource.inputs.sessions = sessions
datasource.inputs.ref_ct = 'REF'
datasource.inputs.ref_t1 = 'T10'
return datasource, sessions
def single_tp_segmentation_datasource(sub_id, BASE_DIR):
sessions = [
x for x in os.listdir(os.path.join(BASE_DIR, sub_id))
if 'REF' not in x and 'T10' not in x and 'RT_' not in x
and os.path.isdir(os.path.join(BASE_DIR, sub_id, x))
]
ref_session = [
x for x in os.listdir(os.path.join(BASE_DIR, sub_id))
if x == 'REF' and os.path.isdir(os.path.join(BASE_DIR, sub_id, x))
]
if ref_session:
reference = True
else:
print('NO REFERENCE CT!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!')
reference = False
datasource = nipype.Node(interface=nipype.DataGrabber(
infields=['sub_id', 'sessions', 'ref_ct'],
outfields=[
't1', 'ct1', 't2', 'flair', 'reference', 'reg2t1_warp',
'reg2t1_mat', 'ct1_preproc', 'flair_preproc', 't1_preproc',
't2_preproc', 'regT12CT'
]),
name='datasource')
datasource.inputs.base_directory = BASE_DIR
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.raise_on_empty = False
datasource.inputs.field_template = dict(
t1='%s/%s/T1.nii.gz',
ct1='%s/%s/CT1.nii.gz',
t2='%s/%s/T2.nii.gz',
flair='%s/%s/FLAIR.nii.gz',
reference='%s/%s/CT.nii.gz',
regT12CT='%s/%s/reg2T1_ref.mat',
ct1_preproc='%s/%s/CT1_preproc.nii.gz',
t1_preproc='%s/%s/T1_preproc.nii.gz',
t2_preproc='%s/%s/T2_preproc.nii.gz',
flair_preproc='%s/%s/FLAIR_preproc.nii.gz')
datasource.inputs.template_args = dict(
t1=[['sub_id', 'sessions']],
ct1=[['sub_id', 'sessions']],
t2=[['sub_id', 'sessions']],
flair=[['sub_id', 'sessions']],
reference=[['sub_id', 'ref_ct']],
regT12CT=[['sub_id', 'sessions']],
ct1_preproc=[['sub_id', 'sessions']],
t1_preproc=[['sub_id', 'sessions']],
t2_preproc=[['sub_id', 'sessions']],
flair_preproc=[['sub_id', 'sessions']])
datasource.inputs.sub_id = sub_id
datasource.inputs.sessions = sessions
datasource.inputs.ref_ct = 'REF'
return datasource, sessions, reference
def create_datasource(self):
datasource = nipype.Node(interface=nipype.DataGrabber(
infields=['sub_id'], outfields=self.outfields),
name='datasource')
datasource.inputs.base_directory = self.input_dir
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.raise_on_empty = False
datasource.inputs.field_template = self.field_template
datasource.inputs.template_args = self.template_args
datasource.inputs.sub_id = self.sub_id
return datasource
def create_datasource(self):
datasource = nipype.Node(interface=nipype.DataGrabber(
infields=['sub_id', 'sessions', 'ref_ct', 'ref_t1'],
outfields=self.outfields),
name='datasource')
datasource.inputs.base_directory = self.base_dir
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.raise_on_empty = False
datasource.inputs.field_template = self.field_template
datasource.inputs.template_args = self.template_args
datasource.inputs.sub_id = self.sub_id
datasource.inputs.sessions = self.sessions
datasource.inputs.ref_ct = 'REF'
datasource.inputs.ref_t1 = 'T10'
if self.rt is not None:
datasource.inputs.rt = self.rt['session']
if self.ct_sessions:
datasource.inputs.ct_session = self.ct_sessions
return datasource
for n, sub in enumerate(SUB_LIST):
for contrast in CONTRASTS:
sub_name = sub.split('/')[-1]
sessions = [x for x in sorted(glob.glob(os.path.join(sub, '*')))]
ct_tp = [i for i, s in enumerate(sessions) if CTS[n] in s]
sessions = [
x for x in sessions[ct_tp[0] + 1:]
if glob.glob(x + '/{}.nii.gz'.format(contrast))
]
if len(sessions) > 1:
ref_tp = sessions[0].split('/')[-1]
sessions.remove(sessions[0])
sessions = [x.split('/')[-1] for x in sessions]
datasource = nipype.Node(interface=nipype.DataGrabber(
infields=['contrasts', 'sub_id', 'sessions', 'ref_tp'],
outfields=['reference', 'to_reg']),
name='datasource')
datasource.inputs.base_directory = BASE_DIR
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.field_template = dict(
reference='%s/%s/%s.nii.gz', to_reg='%s/%s/%s.nii.gz')
datasource.inputs.template_args = dict(
to_reg=[['sub_id', 'sessions', 'contrasts']],
reference=[['sub_id', 'ref_tp', 'contrasts']])
datasource.inputs.raise_on_empty = False
datasource.inputs.contrasts = contrast
datasource.inputs.sub_id = sub.split('/')[-1]
datasource.inputs.sessions = sessions
datasource.inputs.ref_tp = ref_tp
from nipype.interfaces.dcm2nii import Dcm2niix
contrasts = ['T1KM', 'FLAIR', 'CT', 'ADC', 'T1', 'SWI', 'T2', 'T2KM']
rt_files = ['RTSTRUCT', 'RTDOSE', 'RTPLAN']
base_dir = '/media/fsforazz/portable_hdd/data_sorted/test/'
result_dir = '/mnt/sdb/Cinderella_FU_sorted_all_test2/'
cache_dir = '/mnt/sdb/sorted_data/sorting_cache2/'
inputnode = nipype.Node(
interface=util.IdentityInterface(fields=['contrasts']),
name='inputnode')
inputnode.iterables = ('contrasts', contrasts)
datasource = nipype.Node(
interface=nipype.DataGrabber(infields=['contrasts'], outfields=['directory']),
name='datasource')
datasource.inputs.base_directory = base_dir
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.field_template = dict(directory='*/*/%s/1-*')
inputnode_rt = nipype.Node(
interface=util.IdentityInterface(fields=['rt_files']),
name='inputnode_rt')
inputnode_rt.iterables = ('rt_files', rt_files)
datasource_rt = nipype.Node(
interface=nipype.DataGrabber(infields=['rt_files'], outfields=['directory']),
name='datasource_rt')
datasource_rt.inputs.base_directory = base_dir
data.append(os.path.join(sub_name, current_tp))
else:
previous = [x for x in data if sub_name in x][0]
previous_tp = previous.split('/')[-1]
if current_tp > previous_tp:
data.remove(previous)
data.append(os.path.join(sub_name, current_tp))
return data
base_dir = '/mnt/sdb/anal_sorted/'
cache_dir = '/mnt/sdb/feat_cache'
result_dir = '/mnt/sdb/anal_fe'
sub_list = creste_sub_list(base_dir)
datasource = nipype.Node(interface=nipype.DataGrabber(
infields=['sub_id'], outfields=['ct', 'rtstruct']),
name='datasource')
datasource.inputs.base_directory = base_dir
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.field_template = dict(ct='%s/CT.nii.gz',
rtstruct='%s/RTSTRUCT/*.dcm')
datasource.inputs.template_args = dict(ct=[['sub_id']], rtstruct=[['sub_id']])
datasource.inputs.raise_on_empty = False
datasource.inputs.sub_id = sub_list
voxelizer = nipype.MapNode(interface=Voxelizer(),
iterfield=['reference', 'struct_file'],
name='voxelizer')
voxelizer.inputs.regular_expression = '.*PTV.*'
voxelizer.inputs.multi_structs = True
# contrasts = ['T1KM', 'FLAIR', 'CT', 'ADC', 'T1', 'SWI', 'T2', 'T2KM']
contrasts = ['T1', 'FLAIR', 'CT1', 'T2']
rt_files = ['RTCT', 'RTSTRUCT', 'RTDOSE', 'RTPLAN']
ct_files = ['CT']
base_dir = '/mnt/sdb/debugging_workflow'
result_dir = '/mnt/sdb/debugging_workflow_out'
cache_dir = '/mnt/sdb/debugging_workflow_cache'
if not os.path.isdir(result_dir):
os.mkdir(result_dir)
inputnode = nipype.Node(interface=util.IdentityInterface(fields=['contrasts']),
name='inputnode')
inputnode.iterables = ('contrasts', contrasts)
datasource = nipype.Node(interface=nipype.DataGrabber(infields=['contrasts'],
outfields=['directory']),
name='datasource')
datasource.inputs.base_directory = base_dir
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.field_template = dict(directory='*/*/%s')
datasource_ct = nipype.Node(interface=nipype.DataGrabber(
infields=['name'], outfields=['directory']),
name='datasource_ct')
datasource_ct.inputs.base_directory = base_dir
datasource_ct.inputs.template = '*'
datasource_ct.inputs.sort_filelist = True
datasource_ct.inputs.field_template = dict(directory='*/*/%s')
datasource_ct.inputs.name = 'CT'
CLEAN_CACHE = ARGS.clean_cache
sequences = ['t1', 'ct1', 't2', 'flair']
sub_list = os.listdir(BASE_DIR)
if not os.path.isdir(WORKFLOW_CACHE):
os.makedirs(WORKFLOW_CACHE)
for sub_id in sub_list:
NIPYPE_CACHE = os.path.join(NIPYPE_CACHE_BASE, sub_id)
sessions = [x for x in os.listdir(os.path.join(BASE_DIR, sub_id))
if 'REF' not in x and 'T10' not in x and 'RT_' not in x]
datasource = nipype.Node(
interface=nipype.DataGrabber(
infields=['sub_id', 'sessions', 'ref_ct', 'ref_t1'],
outfields=['t1', 'ct1', 't2', 'flair', 'reference', 't1_0']),
name='datasource')
datasource.inputs.base_directory = BASE_DIR
datasource.inputs.template = '*'
datasource.inputs.sort_filelist = True
datasource.inputs.raise_on_empty = False
datasource.inputs.field_template = dict(t1='%s/%s/T1.nii.gz', ct1='%s/%s/CT1.nii.gz',
t2='%s/%s/T2.nii.gz', flair='%s/%s/FLAIR.nii.gz',
reference='%s/%s/CT.nii.gz',
t1_0='%s/%s/T1.nii.gz')
datasource.inputs.template_args = dict(t1=[['sub_id', 'sessions']],
ct1=[['sub_id', 'sessions']],
t2=[['sub_id', 'sessions']],
flair=[['sub_id', 'sessions']],
reference=[['sub_id', 'ref_ct']],