def __init__(self, project_info):
self.stages = {
'Segmentation': SegmentationStage(),
'Parcellation': ParcellationStage(pipeline_mode="Diffusion"),
'Preprocessing': PreprocessingStage(),
'Registration': RegistrationStage(pipeline_mode="Diffusion"),
'Diffusion': DiffusionStage(),
'MRTrixConnectome': MRTrixConnectomeStage()
}
Pipeline.__init__(self, project_info)
self.diffusion_imaging_model = project_info.diffusion_imaging_model
self.subject = project_info.subject
self.global_conf.subjects = project_info.subjects
self.global_conf.subject = self.subject
self.subject_directory = os.path.join(self.base_directory,
self.subject)
self.derivatives_directory = os.path.join(self.base_directory,
'derivatives')
self.stages['Segmentation'].config.on_trait_change(
self.update_parcellation, 'seg_tool')
self.stages['Parcellation'].config.on_trait_change(
self.update_segmentation, 'parcellation_scheme')
def __init__(self, bids_dir, output_dir):
"""Constructor of the SegmentationStageUI class.
Parameters
-----------
bids_dir : path
BIDS root directory
output_dir : path
Output directory
See also
---------
cmp.stages.segmentation.segmentation.SegmentationStage.__init_
cmp.cmpbidsappmanager.stages.segmentation.segmentation.SegmentationStageUI
"""
SegmentationStage.__init__(self, bids_dir, output_dir)
self.config = SegmentationConfigUI()
def __init__(self, project_info):
self.stages = {
'Preprocessing': PreprocessingStage(),
'Segmentation': SegmentationStage(),
'Parcellation': ParcellationStage(pipeline_mode="Diffusion"),
'Registration': RegistrationStage(pipeline_mode="Diffusion"),
'Diffusion': DiffusionStage(),
'Connectome': ConnectomeStage()
}
Pipeline.__init__(self, project_info)
self.stages['Segmentation'].config.on_trait_change(
self.update_parcellation, 'seg_tool')
self.stages['Parcellation'].config.on_trait_change(
self.update_segmentation, 'parcellation_scheme')
def __init__(self, project_info):
"""Constructor of an `AnatomicalPipeline` object.
Parameters
----------
project_info : cmp.project.CMP_Project_Info
Instance of `CMP_Project_Info` object.
See Also
--------
cmp.project.CMP_Project_Info
"""
self.global_conf.subjects = project_info.subjects
self.global_conf.subject = self.subject
if len(project_info.subject_sessions) > 0:
self.global_conf.subject_session = project_info.subject_session
self.subject_directory = os.path.join(project_info.base_directory,
project_info.subject,
project_info.subject_session)
subject_id = "_".join((self.subject, self.global_conf.subject_session))
else:
self.global_conf.subject_session = ''
self.subject_directory = os.path.join(project_info.base_directory, project_info.subject)
subject_id = self.subject
self.derivatives_directory = os.path.abspath(project_info.output_directory)
self.output_directory = os.path.abspath(project_info.output_directory)
self.stages = {'Segmentation': SegmentationStage(bids_dir=project_info.base_directory,
output_dir=self.output_directory),
'Parcellation': ParcellationStage(pipeline_mode="Diffusion",
bids_dir=project_info.base_directory,
output_dir=self.output_directory)}
cmp_common.Pipeline.__init__(self, project_info)
self.subject = project_info.subject
self.stages['Segmentation'].config.freesurfer_subjects_dir = os.path.join(self.output_directory,
'freesurfer')
self.stages['Segmentation'].config.freesurfer_subject_id = os.path.join(self.output_directory,
'freesurfer', subject_id)
self.stages['Segmentation'].config.on_trait_change(self.update_parcellation, 'seg_tool')
self.stages['Parcellation'].config.on_trait_change(self.update_segmentation, 'parcellation_scheme')
self.stages['Parcellation'].config.on_trait_change(self.update_parcellation_scheme, 'parcellation_scheme')
def __init__(self, project_info):
# super(Pipeline, self).__init__(project_info)
self.subject = project_info.subject
self.last_date_processed = project_info.anat_last_date_processed
self.global_conf.subjects = project_info.subjects
self.global_conf.subject = self.subject
if len(project_info.subject_sessions) > 0:
self.global_conf.subject_session = project_info.subject_session
self.subject_directory = os.path.join(
self.base_directory, self.subject,
self.global_conf.subject_session)
else:
self.global_conf.subject_session = ''
self.subject_directory = os.path.join(self.base_directory,
self.subject)
self.derivatives_directory = os.path.abspath(
project_info.output_directory)
self.output_directory = os.path.abspath(project_info.output_directory)
self.stages = {
'Segmentation':
SegmentationStage(bids_dir=project_info.base_directory,
output_dir=self.output_directory),
'Parcellation':
ParcellationStage(pipeline_mode="Diffusion",
bids_dir=project_info.base_directory,
output_dir=self.output_directory)
}
cmp_common.Pipeline.__init__(self, project_info)
self.stages['Segmentation'].config.on_trait_change(
self.update_parcellation, 'seg_tool')
self.stages['Parcellation'].config.on_trait_change(
self.update_segmentation, 'parcellation_scheme')
self.stages['Parcellation'].config.on_trait_change(
self.update_parcellation_scheme, 'parcellation_scheme')
def __init__(self, project_info):
self.stages = {
'Preprocessing': PreprocessingStage(),
'Segmentation': SegmentationStage(),
'Parcellation': ParcellationStage(pipeline_mode="fMRI"),
'Registration': RegistrationStage(pipeline_mode="fMRI"),
'Functional': FunctionalStage(),
'Connectome': ConnectomeStage()
}
Pipeline.__init__(self, project_info)
self.stages['Segmentation'].config.on_trait_change(
self.update_parcellation, 'seg_tool')
self.stages['Parcellation'].config.on_trait_change(
self.update_segmentation, 'parcellation_scheme')
self.stages['Functional'].config.on_trait_change(
self.update_nuisance_requirements, 'global_nuisance')
self.stages['Functional'].config.on_trait_change(
self.update_nuisance_requirements, 'csf')
self.stages['Functional'].config.on_trait_change(
self.update_nuisance_requirements, 'wm')
self.stages['Connectome'].config.on_trait_change(
self.update_scrubbing, 'apply_scrubbing')
def __init__(self, bids_dir, output_dir):
SegmentationStage.__init__(self, bids_dir, output_dir)
self.config = SegmentationConfigUI()
def __init__(self, project_info):
"""Constructor of an `AnatomicalPipeline` object.
Parameters
----------
project_info : cmp.project.ProjectInfo
Instance of `CMP_Project_Info` object.
See Also
--------
cmp.project.CMP_Project_Info
"""
self.global_conf.subjects = project_info.subjects
self.global_conf.subject = project_info.subject
if len(project_info.subject_sessions) > 0:
self.global_conf.subject_session = project_info.subject_session
self.subject_directory = os.path.join(
project_info.base_directory,
project_info.subject,
project_info.subject_session,
)
subject_id = "_".join(
(self.global_conf.subject, self.global_conf.subject_session))
else:
self.global_conf.subject_session = ""
self.subject_directory = os.path.join(project_info.base_directory,
self.global_conf.subject)
subject_id = self.global_conf.subject
self.derivatives_directory = os.path.abspath(
project_info.output_directory)
self.output_directory = os.path.abspath(project_info.output_directory)
self.stages = {
"Segmentation":
SegmentationStage(subject=self.global_conf.subject,
session=self.global_conf.subject_session,
bids_dir=project_info.base_directory,
output_dir=self.output_directory),
"Parcellation":
ParcellationStage(
pipeline_mode="Diffusion",
subject=self.global_conf.subject,
session=self.global_conf.subject_session,
bids_dir=project_info.base_directory,
output_dir=self.output_directory,
),
}
cmp_common.Pipeline.__init__(self, project_info)
self.subject = project_info.subject
self.stages[
"Segmentation"].config.freesurfer_subjects_dir = os.path.join(
self.output_directory, __freesurfer_directory__)
self.stages[
"Segmentation"].config.freesurfer_subject_id = os.path.join(
self.output_directory, __freesurfer_directory__, subject_id)
self.stages["Parcellation"].config.on_trait_change(
self._update_parcellation_scheme, "parcellation_scheme")