def test_display_config(monkeypatch, dispnum):
"""Check that the display_variable option is used ($DISPLAY not set)"""
config._display = None
dispstr = ':%d' % dispnum
config.set('execution', 'display_variable', dispstr)
monkeypatch.delitem(os.environ, 'DISPLAY', raising=False)
assert config.get_display() == config.get('execution', 'display_variable')
# Test that it was correctly cached
assert config.get_display() == config.get('execution', 'display_variable')
def test_provenance_exists(tmpdir):
tmpdir.chdir()
from nipype import config
from nipype.interfaces.base import CommandLine
provenance_state = config.get('execution', 'write_provenance')
hash_state = config.get('execution', 'hash_method')
config.enable_provenance()
CommandLine('echo hello').run()
config.set('execution', 'write_provenance', provenance_state)
config.set('execution', 'hash_method', hash_state)
assert tmpdir.join('provenance.provn').check()
def test_provenance_exists(tmpdir):
tmpdir.chdir()
from nipype import config
from nipype.interfaces.base import CommandLine
provenance_state = config.get('execution', 'write_provenance')
hash_state = config.get('execution', 'hash_method')
config.enable_provenance()
CommandLine('echo hello').run()
config.set('execution', 'write_provenance', provenance_state)
config.set('execution', 'hash_method', hash_state)
assert tmpdir.join('provenance.provn').check()
def test_provenance_exists(tmpdir):
tmpdir.chdir()
from nipype import config
from nipype.interfaces.base import CommandLine
provenance_state = config.get("execution", "write_provenance")
hash_state = config.get("execution", "hash_method")
config.enable_provenance()
CommandLine("echo hello").run()
config.set("execution", "write_provenance", provenance_state)
config.set("execution", "hash_method", hash_state)
assert tmpdir.join("provenance.provn").check()
def test_provenance_exists(tmpdir):
tempdir = str(tmpdir)
os.chdir(tempdir)
from nipype import config
from nipype.interfaces.base import CommandLine
provenance_state = config.get('execution', 'write_provenance')
hash_state = config.get('execution', 'hash_method')
config.enable_provenance()
CommandLine('echo hello').run()
config.set('execution', 'write_provenance', provenance_state)
config.set('execution', 'hash_method', hash_state)
provenance_exists = os.path.exists(os.path.join(tempdir, 'provenance.provn'))
assert provenance_exists
def RunConnectivityWorkflow(path, outDir, workdir, conf_file=None):
if conf_file is not None:
res = open(conf_file, 'r').read()
conf = json.loads(res)
config.update_config(conf)
plugin = config.get("execution", "plugin")
plugin_args = config.get("execution", "plugin_args")
if plugin_args is not None:
plugin_args = eval(plugin_args)
wf = BuildConnectivityWorkflowSurface(path, outDir)
wf.base_dir = workdir
wf.run(plugin=plugin, plugin_args=plugin_args)
def test_provenance_exists(tmpdir):
tempdir = str(tmpdir)
os.chdir(tempdir)
from nipype import config
from nipype.interfaces.base import CommandLine
provenance_state = config.get('execution', 'write_provenance')
hash_state = config.get('execution', 'hash_method')
config.enable_provenance()
CommandLine('echo hello').run()
config.set('execution', 'write_provenance', provenance_state)
config.set('execution', 'hash_method', hash_state)
provenance_exists = os.path.exists(
os.path.join(tempdir, 'provenance.provn'))
assert provenance_exists
def enable_file_logging(self, filename):
"""
Hack to define a filename for the log file! It overloads the
'enable_file_logging' method in 'nipype/utils/logger.py' file.
"""
import logging
from logging.handlers import RotatingFileHandler as RFHandler
config = self._config
LOG_FILENAME = os.path.join(config.get('logging', 'log_directory'),
filename)
hdlr = RFHandler(LOG_FILENAME,
maxBytes=int(config.get('logging', 'log_size')),
backupCount=int(
config.get('logging', 'log_rotate')))
formatter = logging.Formatter(fmt=self.fmt, datefmt=self.datefmt)
hdlr.setFormatter(formatter)
self._logger.addHandler(hdlr)
self._fmlogger.addHandler(hdlr)
self._iflogger.addHandler(hdlr)
self._hdlr = hdlr
def _list_outputs(self):
"""Execute this module.
"""
# Init variables
outputs = self.output_spec().get()
out_files = []
# Use hardlink
use_hardlink = str2bool(
config.get('execution', 'try_hard_link_datasink'))
outdir = os.path.abspath(self.inputs.base_directory)
# Iterate through outputs attributes {key : path(s)}
for key, files in list(self.inputs._outputs.items()):
if not isdefined(files):
continue
files = ensure_list(files)
# flattening list
if isinstance(files, list):
if isinstance(files[0], list):
files = [item for sublist in files for item in sublist]
# Iterate through passed-in source files
for src in ensure_list(files):
# Format src and dst files
src = os.path.abspath(src)
if not os.path.isfile(src):
src = os.path.join(src, '')
dst = self._get_dst(src)
dst = os.path.join(outdir, dst)
# If src is a file, copy it to dst
if os.path.isfile(src):
copyfile(src,
dst,
copy=True,
hashmethod='content',
use_hardlink=use_hardlink)
out_files.append(dst)
# If src is a directory, copy entire contents to dst dir
elif os.path.isdir(src):
if os.path.exists(dst) and self.inputs.remove_dest_dir:
shutil.rmtree(dst)
copytree(src, dst)
out_files.append(dst)
# Return outputs dictionary
outputs['out_file'] = out_files
return outputs
sys.exit()
result_dir = os.path.abspath(args.output)
if not os.path.exists(result_dir):
os.mkdir(result_dir)
infosource = pe.Node(niu.IdentityInterface(
fields=['projects', 'subjects', 'experiments', 'scans']),
name='infosource',
synchronize=True)
infosource.iterables = [('projects', args.project), ('subjects', args.subject),
('experiments', args.experiment), ('scans', args.scan)]
r = pe.Workflow(name='xnat_downloader')
r.base_output_dir = 'xnat_grabber'
r.base_dir = config.get('logging', 'log_directory')
dg = pe.Node(interface=nio.XNATSource(
infields=['project', 'subject', 'experiment', 'scan'],
outfields=['output']),
name='dg')
if args.dicom:
resource = 'DICOM'
else:
resource = 'NIFTI'
dg.inputs.query_template = '/projects/%s/subjects/%s/experiments/%s/scans/%s/resources/' + resource
dg.inputs.query_template_args['output'] = [[
'project', 'subject', 'experiment', 'scan'
]]
def RunSubjectWorkflow(args):
"""
.-----------.
--- | Session 1 | ---> /project/subjectA/session1/phase/
/ *-----------*
.-----------. /
| Subject A | <
*-----------* \
\ .-----------.
--- | Session 2 | ---> /project/subjectA/session2/phase/
*-----------*
**** Replaces WorkflowT1T2.py ****
"""
database, start_time, subject, master_config = args
assert 'baseline' in master_config['components'] or 'longitudinal' in master_config['components'], "Baseline or Longitudinal is not in WORKFLOW_COMPONENTS!"
# HACK:
# To avoid a "sqlite3.ProgrammingError: Base Cursor.__init__ not called" error
# using multiprocessing.map_async(), re-instantiate database
# database.__init__(defaultDBName=database.dbName, subject_list=database.subjectList)
#
# END HACK
import time
from nipype import config, logging
config.update_config(master_config) # Set universal pipeline options
assert config.get('execution', 'plugin') == master_config['execution']['plugin']
# DEBUG
# config.enable_debug_mode()
# config.set('execution', 'stop_on_first_rerun', 'true')
# END DEBUG
logging.update_logging(config)
import nipype.pipeline.engine as pe
import nipype.interfaces.base as nbase
import nipype.interfaces.io as nio
from nipype.interfaces.utility import IdentityInterface, Function
import traits
from baw_exp import OpenSubjectDatabase
from SessionDB import SessionDB
from PipeLineFunctionHelpers import convertToList
from atlasNode import MakeAtlasNode
from utilities.misc import GenerateSubjectOutputPattern as outputPattern
from utilities.misc import GenerateWFName
while time.time() < start_time:
time.sleep(start_time - time.time() + 1)
print "Delaying start for {subject}".format(subject=subject)
print("===================== SUBJECT: {0} ===========================".format(subject))
subjectWorkflow = pe.Workflow(name="BAW_StandardWorkup_subject_{0}".format(subject))
subjectWorkflow.base_dir = config.get('logging', 'log_directory')
# subjectWorkflow.config['execution']['plugin'] = 'Linear' # Hardcodeded in WorkupT1T2.py - why?
# DEBUG
# subjectWorkflow.config['execution']['stop_on_first_rerun'] = 'true'
# END DEBUG
atlasNode = MakeAtlasNode(master_config['atlascache'], 'BAtlas')
sessionWorkflow = dict()
inputsSpec = dict()
sessions = database.getSessionsFromSubject(subject)
# print "These are the sessions: ", sessions
if 'baseline' in master_config['components']:
current_phase = 'baseline'
from baseline import create_baseline as create_wkfl
elif 'longitudinal' in master_config['components']:
current_phase = 'longitudinal'
from longitudinal import create_longitudial as create_wkfl
for session in sessions: # TODO (future): Replace with iterable inputSpec node and add Function node for getAllFiles()
project = database.getProjFromSession(session)
pname = "{0}_{1}".format(session, current_phase) # Long node names make graphs a pain to read/print
# pname = GenerateWFName(project, subject, session, current_phase)
print "Building session pipeline for {0}".format(session)
inputsSpec[session] = pe.Node(name='inputspec_{0}'.format(session),
interface=IdentityInterface(fields=['T1s', 'T2s', 'PDs', 'FLs', 'OTs']))
inputsSpec[session].inputs.T1s = database.getFilenamesByScantype(session, ['T1-15', 'T1-30'])
inputsSpec[session].inputs.T2s = database.getFilenamesByScantype(session, ['T2-15', 'T2-30'])
inputsSpec[session].inputs.PDs = database.getFilenamesByScantype(session, ['PD-15', 'PD-30'])
inputsSpec[session].inputs.FLs = database.getFilenamesByScantype(session, ['FL-15', 'FL-30'])
inputsSpec[session].inputs.OTs = database.getFilenamesByScantype(session, ['OTHER-15', 'OTHER-30'])
sessionWorkflow[session] = create_wkfl(project, subject, session, master_config,
interpMode='Linear', pipeline_name=pname)
subjectWorkflow.connect([(inputsSpec[session], sessionWorkflow[session], [('T1s', 'inputspec.T1s'),
('T2s', 'inputspec.T2s'),
('PDs', 'inputspec.PDs'),
('FLs', 'inputspec.FLs'),
('OTs', 'inputspec.OTHERs'),
]),
(atlasNode, sessionWorkflow[session], [('template_landmarks_50Lmks_fcsv',
'inputspec.atlasLandmarkFilename'),
('template_weights_50Lmks_wts',
'inputspec.atlasWeightFilename'),
('LLSModel_50Lmks_hdf5', 'inputspec.LLSModel'),
('T1_50Lmks_mdl', 'inputspec.inputTemplateModel')]),
])
if current_phase == 'baseline':
subjectWorkflow.connect([(atlasNode, sessionWorkflow[session], [('template_t1', 'inputspec.template_t1'),
('ExtendedAtlasDefinition_xml',
'inputspec.atlasDefinition')]),
])
else:
assert current_phase == 'longitudinal', "Phase value is unknown: {0}".format(current_phase)
from utils import run_workflow, print_workflow
if False:
print_workflow(template, plugin=master_config['execution']['plugin'], dotfilename='template')
return run_workflow(template, plugin=master_config['execution']['plugin'], plugin_args=master_config['plugin_args'])
def test_debug_mode():
from ... import logging
sofc_config = config.get("execution", "stop_on_first_crash")
ruo_config = config.get("execution", "remove_unnecessary_outputs")
ki_config = config.get("execution", "keep_inputs")
wf_config = config.get("logging", "workflow_level")
if_config = config.get("logging", "interface_level")
ut_config = config.get("logging", "utils_level")
wf_level = logging.getLogger("nipype.workflow").level
if_level = logging.getLogger("nipype.interface").level
ut_level = logging.getLogger("nipype.utils").level
config.enable_debug_mode()
# Check config is updated and logging levels, too
assert config.get("execution", "stop_on_first_crash") == "true"
assert config.get("execution", "remove_unnecessary_outputs") == "false"
assert config.get("execution", "keep_inputs") == "true"
assert config.get("logging", "workflow_level") == "DEBUG"
assert config.get("logging", "interface_level") == "DEBUG"
assert config.get("logging", "utils_level") == "DEBUG"
assert logging.getLogger("nipype.workflow").level == 10
assert logging.getLogger("nipype.interface").level == 10
assert logging.getLogger("nipype.utils").level == 10
# Restore config and levels
config.set("execution", "stop_on_first_crash", sofc_config)
config.set("execution", "remove_unnecessary_outputs", ruo_config)
config.set("execution", "keep_inputs", ki_config)
config.set("logging", "workflow_level", wf_config)
config.set("logging", "interface_level", if_config)
config.set("logging", "utils_level", ut_config)
logging.update_logging(config)
assert config.get("execution", "stop_on_first_crash") == sofc_config
assert config.get("execution", "remove_unnecessary_outputs") == ruo_config
assert config.get("execution", "keep_inputs") == ki_config
assert config.get("logging", "workflow_level") == wf_config
assert config.get("logging", "interface_level") == if_config
assert config.get("logging", "utils_level") == ut_config
assert logging.getLogger("nipype.workflow").level == wf_level
assert logging.getLogger("nipype.interface").level == if_level
assert logging.getLogger("nipype.utils").level == ut_level
def main(args):
subjects, master_config = args
import os
import sys
import traceback
# Set universal pipeline options
from nipype import config
config.update_config(master_config)
assert config.get('execution',
'plugin') == master_config['execution']['plugin']
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from nipype.interfaces.utility import IdentityInterface, Function
import nipype.interfaces.ants as ants
from template import MergeByExtendListElements, xml_filename
from PipeLineFunctionHelpers import mapPosteriorList
from atlasNode import GetAtlasNode, MakeNewAtlasTemplate
from utilities.misc import GenerateSubjectOutputPattern as outputPattern
from utilities.distributed import modify_qsub_args
template = pe.Workflow(name='SubjectAtlas_Template')
template.base_dir = master_config['logging']['log_directory']
BAtlas = GetAtlasNode(master_config['previouscache'], 'BAtlas')
inputspec = pe.Node(interface=IdentityInterface(fields=['subject']),
name='inputspec')
inputspec.iterables = ('subject', subjects)
baselineDG = pe.Node(nio.DataGrabber(infields=['subject'],
outfields=[
't1_average', 't2_average',
'pd_average', 'fl_average',
'outputLabels', 'posteriorImages'
]),
name='Baseline_DG')
baselineDG.inputs.base_directory = master_config['previousresult']
baselineDG.inputs.sort_filelist = True
baselineDG.inputs.raise_on_empty = False
baselineDG.inputs.template = '*/%s/*/Baseline/%s.nii.gz'
baselineDG.inputs.template_args['t1_average'] = [[
'subject', 't1_average_BRAINSABC'
]]
baselineDG.inputs.template_args['t2_average'] = [[
'subject', 't2_average_BRAINSABC'
]]
baselineDG.inputs.template_args['pd_average'] = [[
'subject', 'pd_average_BRAINSABC'
]]
baselineDG.inputs.template_args['fl_average'] = [[
'subject', 'fl_average_BRAINSABC'
]]
baselineDG.inputs.template_args['outputLabels'] = [[
'subject', 'brain_label_seg'
]]
baselineDG.inputs.field_template = {
'posteriorImages': '*/%s/*/TissueClassify/POSTERIOR_%s.nii.gz'
}
posterior_files = [
'AIR', 'BASAL', 'CRBLGM', 'CRBLWM', 'CSF', 'GLOBUS', 'HIPPOCAMPUS',
'NOTCSF', 'NOTGM', 'NOTVB', 'NOTWM', 'SURFGM', 'THALAMUS', 'VB', 'WM'
]
baselineDG.inputs.template_args['posteriorImages'] = [[
'subject', posterior_files
]]
MergeByExtendListElementsNode = pe.Node(
Function(
function=MergeByExtendListElements,
input_names=['t1s', 't2s', 'pds', 'fls', 'labels', 'posteriors'],
output_names=[
'ListOfImagesDictionaries', 'registrationImageTypes',
'interpolationMapping'
]),
run_without_submitting=True,
name="99_MergeByExtendListElements")
from PipeLineFunctionHelpers import WrapPosteriorImagesFromDictionaryFunction as wrapfunc
template.connect([(inputspec, baselineDG, [('subject', 'subject')]),
(baselineDG, MergeByExtendListElementsNode,
[('t1_average', 't1s'), ('t2_average', 't2s'),
('pd_average', 'pds'), ('fl_average', 'fls'),
('outputLabels', 'labels'),
(('posteriorImages', wrapfunc), 'posteriors')])])
myInitAvgWF = pe.Node(
interface=ants.AverageImages(),
name='Atlas_antsSimpleAverage') # was 'Phase1_antsSimpleAverage'
myInitAvgWF.inputs.dimension = 3
myInitAvgWF.inputs.normalize = True
template.connect(baselineDG, 't1_average', myInitAvgWF, "images")
####################################################################################################
# TEMPLATE_BUILD_RUN_MODE = 'MULTI_IMAGE'
# if numSessions == 1:
# TEMPLATE_BUILD_RUN_MODE = 'SINGLE_IMAGE'
####################################################################################################
from BAWantsRegistrationBuildTemplate import BAWantsRegistrationTemplateBuildSingleIterationWF as registrationWF
buildTemplateIteration1 = registrationWF('iteration01')
# buildTemplateIteration2 = buildTemplateIteration1.clone(name='buildTemplateIteration2')
buildTemplateIteration2 = registrationWF('Iteration02')
MakeNewAtlasTemplateNode = pe.Node(
interface=Function(
function=MakeNewAtlasTemplate,
input_names=[
't1_image', 'deformed_list', 'AtlasTemplate', 'outDefinition'
],
output_names=['outAtlasFullPath', 'clean_deformed_list']),
# This is a lot of work, so submit it run_without_submitting=True,
run_without_submitting=
True, # HACK: THIS NODE REALLY SHOULD RUN ON THE CLUSTER!
name='99_MakeNewAtlasTemplate')
if master_config['execution'][
'plugin'] == 'SGE': # for some nodes, the qsub call needs to be modified on the cluster
MakeNewAtlasTemplateNode.plugin_args = {
'template': master_config['plugin_args']['template'],
'qsub_args': modify_qsub_args(master_config['queue'], '1000M', 1,
1),
'overwrite': True
}
for bt in [buildTemplateIteration1, buildTemplateIteration2]:
##################################################
# *** Hans, is this TODO already addressed? *** #
# ----> # TODO: Change these parameters <---- #
##################################################
BeginANTS = bt.get_node("BeginANTS")
BeginANTS.plugin_args = {
'template':
master_config['plugin_args']['template'],
'overwrite':
True,
'qsub_args':
modify_qsub_args(master_config['queue'],
'9000M',
4,
hard=False)
}
wimtdeformed = bt.get_node("wimtdeformed")
wimtdeformed.plugin_args = {
'template':
master_config['plugin_args']['template'],
'overwrite':
True,
'qsub_args':
modify_qsub_args(master_config['queue'], '2000M', 1, 2)
}
AvgAffineTransform = bt.get_node("AvgAffineTransform")
AvgAffineTransform.plugin_args = {
'template': master_config['plugin_args']['template'],
'overwrite': True,
'qsub_args': modify_qsub_args(master_config['queue'], '2000M',
1)
}
wimtPassivedeformed = bt.get_node("wimtPassivedeformed")
wimtPassivedeformed.plugin_args = {
'template':
master_config['plugin_args']['template'],
'overwrite':
True,
'qsub_args':
modify_qsub_args(master_config['queue'], '2000M', 1, 2)
}
template.connect([
(myInitAvgWF, buildTemplateIteration1, [('output_average_image',
'inputspec.fixed_image')]),
(MergeByExtendListElementsNode, buildTemplateIteration1,
[('ListOfImagesDictionaries', 'inputspec.ListOfImagesDictionaries'),
('registrationImageTypes', 'inputspec.registrationImageTypes'),
('interpolationMapping', 'inputspec.interpolationMapping')]),
(buildTemplateIteration1, buildTemplateIteration2,
[('outputspec.template', 'inputspec.fixed_image')]),
(MergeByExtendListElementsNode, buildTemplateIteration2,
[('ListOfImagesDictionaries', 'inputspec.ListOfImagesDictionaries'),
('registrationImageTypes', 'inputspec.registrationImageTypes'),
('interpolationMapping', 'inputspec.interpolationMapping')]),
(inputspec, MakeNewAtlasTemplateNode, [(('subject', xml_filename),
'outDefinition')]),
(BAtlas, MakeNewAtlasTemplateNode, [('ExtendedAtlasDefinition_xml_in',
'AtlasTemplate')]),
(buildTemplateIteration2, MakeNewAtlasTemplateNode,
[('outputspec.template', 't1_image'),
('outputspec.passive_deformed_templates', 'deformed_list')]),
])
# Create DataSinks
Atlas_DataSink = pe.Node(nio.DataSink(), name="Atlas_DS")
Atlas_DataSink.overwrite = master_config['ds_overwrite']
Atlas_DataSink.inputs.base_directory = master_config['resultdir']
Subject_DataSink = pe.Node(nio.DataSink(), name="Subject_DS")
Subject_DataSink.overwrite = master_config['ds_overwrite']
Subject_DataSink.inputs.base_directory = master_config['resultdir']
template.connect([
(inputspec, Atlas_DataSink, [('subject', 'container')]),
(buildTemplateIteration1, Atlas_DataSink,
[('outputspec.template', 'Atlas.iteration1')]), # Unnecessary
(MakeNewAtlasTemplateNode, Atlas_DataSink, [('outAtlasFullPath',
'Atlas.definitions')]),
(BAtlas, Atlas_DataSink,
[('template_landmarks_50Lmks_fcsv', 'Atlas.20111119_BCD.@fcsv'),
('template_weights_50Lmks_wts', 'Atlas.20111119_BCD.@wts'),
('LLSModel_50Lmks_hdf5', 'Atlas.20111119_BCD.@hdf5'),
('T1_50Lmks_mdl', 'Atlas.20111119_BCD.@mdl')]),
(inputspec, Subject_DataSink, [(('subject', outputPattern),
'regexp_substitutions')]),
(buildTemplateIteration2, Subject_DataSink,
[('outputspec.template', 'ANTSTemplate.@template')]),
(MakeNewAtlasTemplateNode, Subject_DataSink, [
('clean_deformed_list', 'ANTSTemplate.@passive_deformed_templates')
]),
])
from utils import run_workflow, print_workflow
if False:
print_workflow(template,
plugin=master_config['execution']['plugin'],
dotfilename='template')
return run_workflow(template,
plugin=master_config['execution']['plugin'],
plugin_args=master_config['plugin_args'])
def test_debug_mode():
from ... import logging
sofc_config = config.get('execution', 'stop_on_first_crash')
ruo_config = config.get('execution', 'remove_unnecessary_outputs')
ki_config = config.get('execution', 'keep_inputs')
wf_config = config.get('logging', 'workflow_level')
if_config = config.get('logging', 'interface_level')
ut_config = config.get('logging', 'utils_level')
wf_level = logging.getLogger('nipype.workflow').level
if_level = logging.getLogger('nipype.interface').level
ut_level = logging.getLogger('nipype.utils').level
config.enable_debug_mode()
# Check config is updated and logging levels, too
assert config.get('execution', 'stop_on_first_crash') == 'true'
assert config.get('execution', 'remove_unnecessary_outputs') == 'false'
assert config.get('execution', 'keep_inputs') == 'true'
assert config.get('logging', 'workflow_level') == 'DEBUG'
assert config.get('logging', 'interface_level') == 'DEBUG'
assert config.get('logging', 'utils_level') == 'DEBUG'
assert logging.getLogger('nipype.workflow').level == 10
assert logging.getLogger('nipype.interface').level == 10
assert logging.getLogger('nipype.utils').level == 10
# Restore config and levels
config.set('execution', 'stop_on_first_crash', sofc_config)
config.set('execution', 'remove_unnecessary_outputs', ruo_config)
config.set('execution', 'keep_inputs', ki_config)
config.set('logging', 'workflow_level', wf_config)
config.set('logging', 'interface_level', if_config)
config.set('logging', 'utils_level', ut_config)
logging.update_logging(config)
assert config.get('execution', 'stop_on_first_crash') == sofc_config
assert config.get('execution', 'remove_unnecessary_outputs') == ruo_config
assert config.get('execution', 'keep_inputs') == ki_config
assert config.get('logging', 'workflow_level') == wf_config
assert config.get('logging', 'interface_level') == if_config
assert config.get('logging', 'utils_level') == ut_config
assert logging.getLogger('nipype.workflow').level == wf_level
assert logging.getLogger('nipype.interface').level == if_level
assert logging.getLogger('nipype.utils').level == ut_level
def create_singleSession(dataDict, master_config, interpMode, pipeline_name):
"""
create singleSession workflow on a single session
This is the main function to call when processing a data set with T1 & T2
data. ExperimentBaseDirectoryPrefix is the base of the directory to place results, T1Images & T2Images
are the lists of images to be used in the auto-workup. atlas_fname_wpath is
the path and filename of the atlas to use.
"""
assert 'tissue_classify' in master_config['components'] or \
'auxlmk' in master_config['components'] or \
'segmentation' in master_config['components']
from nipype import config, logging
config.update_config(master_config) # Set universal pipeline options
assert config.get('execution', 'plugin') == master_config['execution']['plugin']
logging.update_logging(config)
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, Directory, traits, isdefined, BaseInterface
from nipype.interfaces.utility import Split, Rename, IdentityInterface, Function
from workflows.baseline import baseline_workflow as create_baseline
from PipeLineFunctionHelpers import convertToList
from utilities.misc import GenerateSubjectOutputPattern as outputPattern
from utilities.misc import GenerateWFName
from workflows.utils import run_workflow, print_workflow
from workflows.atlasNode import MakeAtlasNode
project = dataDict['project']
subject = dataDict['subject']
session = dataDict['session']
pname = "{0}_{1}_{2}".format(master_config['workflow_type'], subject, session)
sessionWorkflow = create_baseline(project, subject, session, master_config,
phase=master_config['workflow_type'],
interpMode=interpMode,
pipeline_name=pipeline_name)
sessionWorkflow.base_dir = master_config['cachedir']
inputsSpec = sessionWorkflow.get_node('inputspec')
inputsSpec.inputs.T1s = dataDict['T1s']
inputsSpec.inputs.T2s = dataDict['T2s']
inputsSpec.inputs.PDs = dataDict['PDs']
inputsSpec.inputs.FLs = dataDict['FLs']
inputsSpec.inputs.OTHERs = dataDict['OTs']
atlasNode = MakeAtlasNode(master_config['atlascache'], 'BAtlas_{0}'.format(session)) # TODO: input atlas csv
sessionWorkflow.connect([(atlasNode, inputsSpec, [('template_landmarks_50Lmks_fcsv',
'atlasLandmarkFilename'),
('template_weights_50Lmks_wts',
'atlasWeightFilename'),
('LLSModel_50Lmks_hdf5', 'LLSModel'),
('T1_50Lmks_mdl', 'inputTemplateModel')]),
])
if True: # FIXME: current_phase == 'baseline':
sessionWorkflow.connect([(atlasNode, inputsSpec, [('template_t1', 'template_t1'),
('ExtendedAtlasDefinition_xml',
'atlasDefinition')]),
])
else:
template_DG = pe.Node(interface=nio.DataGrabber(infields=['subject'],
outfields=['template_t1', 'outAtlasFullPath']),
name='Template_DG')
template_DG.inputs.base_directory = master_config['previousresult']
template_DG.inputs.subject = subject
template_DG.inputs.template = 'SUBJECT_TEMPLATES/%s/AVG_%s.nii.gz'
template_DG.inputs.template_args['template_t1'] = [['subject', 'T1']]
template_DG.inputs.field_template = {'outAtlasFullPath': 'Atlas/definitions/AtlasDefinition_%s.xml'}
template_DG.inputs.template_args['outAtlasFullPath'] = [['subject']]
template_DG.inputs.sort_filelist = True
template_DG.inputs.raise_on_empty = True
sessionWorkflow.connect([(template_DG, inputsSpec, [('outAtlasFullPath', 'atlasDefinition'),
('template_t1', 'template_t1')]),
])
if 'segmentation' in master_config['components']:
from workflows.segmentation import segmentation
from workflows.WorkupT1T2BRAINSCut import GenerateWFName
try:
bCutInputName = ".".join([GenerateWFName(project, subject, session, 'Segmentation'), 'inputspec'])
except:
print project, subject, session
raise
sname = 'segmentation'
onlyT1 = not(len(dataDict['T2s']) > 0)
segWF = segmentation(project, subject, session, master_config, onlyT1, pipeline_name=sname)
sessionWorkflow.connect([(atlasNode, segWF,
[('hncma-atlas', 'inputspec.hncma-atlas'),
('template_t1', 'inputspec.template_t1'),
('template_t1', bCutInputName + '.template_t1'),
('rho', bCutInputName + '.rho'),
('phi', bCutInputName + '.phi'),
('theta', bCutInputName + '.theta'),
('l_caudate_ProbabilityMap', bCutInputName + '.l_caudate_ProbabilityMap'),
('r_caudate_ProbabilityMap', bCutInputName + '.r_caudate_ProbabilityMap'),
('l_hippocampus_ProbabilityMap', bCutInputName + '.l_hippocampus_ProbabilityMap'),
('r_hippocampus_ProbabilityMap', bCutInputName + '.r_hippocampus_ProbabilityMap'),
('l_putamen_ProbabilityMap', bCutInputName + '.l_putamen_ProbabilityMap'),
('r_putamen_ProbabilityMap', bCutInputName + '.r_putamen_ProbabilityMap'),
('l_thalamus_ProbabilityMap', bCutInputName + '.l_thalamus_ProbabilityMap'),
('r_thalamus_ProbabilityMap', bCutInputName + '.r_thalamus_ProbabilityMap'),
('l_accumben_ProbabilityMap', bCutInputName + '.l_accumben_ProbabilityMap'),
('r_accumben_ProbabilityMap', bCutInputName + '.r_accumben_ProbabilityMap'),
('l_globus_ProbabilityMap', bCutInputName + '.l_globus_ProbabilityMap'),
('r_globus_ProbabilityMap', bCutInputName + '.r_globus_ProbabilityMap'),
('trainModelFile_txtD0060NT0060_gz',
bCutInputName + '.trainModelFile_txtD0060NT0060_gz')])])
outputSpec = sessionWorkflow.get_node('outputspec')
sessionWorkflow.connect([(outputSpec, segWF, [('t1_average', 'inputspec.t1_average'),
('LMIatlasToSubject_tx', 'inputspec.LMIatlasToSubject_tx'),
('outputLabels', 'inputspec.inputLabels'),
('posteriorImages', 'inputspec.posteriorImages'),
('tc_atlas2sessionInverse_tx',
'inputspec.TissueClassifyatlasToSubjectInverseTransform'),
('UpdatedPosteriorsList', 'inputspec.UpdatedPosteriorsList'),
('outputHeadLabels', 'inputspec.inputHeadLabels')])
])
if not onlyT1:
sessionWorkflow.connect([(outputSpec, segWF, [('t1_average', 'inputspec.t2_average')])])
return sessionWorkflow
def RunSubjectWorkflow(args):
"""
.-----------.
--- | Session 1 | ---> /project/subjectA/session1/phase/
/ *-----------*
.-----------. /
| Subject A | <
*-----------* \
\ .-----------.
--- | Session 2 | ---> /project/subjectA/session2/phase/
*-----------*
**** Replaces WorkflowT1T2.py ****
"""
start_time, subject, master_config = args
assert 'tissue_classify' in master_config['components'] or 'auxlmk' in master_config['components'] or 'segmentation' in master_config['components'], "Baseline or Longitudinal is not in WORKFLOW_COMPONENTS!"
import time
from nipype import config, logging
config.update_config(master_config) # Set universal pipeline options
assert config.get('execution', 'plugin') == master_config['execution']['plugin']
# DEBUG
# config.enable_debug_mode()
# config.set('execution', 'stop_on_first_rerun', 'true')
# END DEBUG
logging.update_logging(config)
import nipype.pipeline.engine as pe
import nipype.interfaces.base as nbase
import nipype.interfaces.io as nio
from nipype.interfaces.utility import IdentityInterface, Function
import traits
from baw_exp import OpenSubjectDatabase
from SessionDB import SessionDB
from PipeLineFunctionHelpers import convertToList
from atlasNode import MakeAtlasNode
from utilities.misc import GenerateSubjectOutputPattern as outputPattern
from utilities.misc import GenerateWFName
from utils import run_workflow, print_workflow
# while time.time() < start_time:
# time.sleep(start_time - time.time() + 1)
# print "Delaying start for {subject}".format(subject=subject)
# print("===================== SUBJECT: {0} ===========================".format(subject))
subjectWorkflow = pe.Workflow(name="BAW_StandardWorkup_subject_{0}".format(subject))
subjectWorkflow.base_dir = config.get('logging', 'log_directory')
# subjectWorkflow.config['execution']['plugin'] = 'Linear' # Hardcodeded in WorkupT1T2.py - why?
# DEBUG
# subjectWorkflow.config['execution']['stop_on_first_rerun'] = 'true'
# END DEBUG
sessionWorkflow = dict()
inputsSpec = dict()
# To avoid a "sqlite3.ProgrammingError: Base Cursor.__init__ not called" error
# using multiprocessing.map_async(), instantiate database here
database = OpenSubjectDatabase(master_config['cachedir'], [subject], master_config['prefix'], master_config['dbfile'])
# print database.getAllSessions()
database.open_connection()
sessions = database.getSessionsFromSubject(subject)
print "These are the sessions: ", sessions
# TODO: atlas input csv read
atlasNode = MakeAtlasNode(master_config['atlascache'], 'BAtlas')
# atlasNode = GetAtlasNode(master_config['previouscache'], 'BAtlas')
from singleSession import create_singleSession as create_wkfl
for session in sessions: # TODO (future): Replace with iterable inputSpec node and add Function node for getAllFiles()
project = database.getProjFromSession(session)
pname = "{0}_singleSession".format(session) # Long node names make graphs a pain to read/print
# pname = GenerateWFName(project, subject, session, 'singleSession')
print "Building session pipeline for {0}".format(session)
inputsSpec[session] = pe.Node(name='inputspec_{0}'.format(session),
interface=IdentityInterface(fields=['T1s', 'T2s', 'PDs', 'FLs', 'OTs']))
inputsSpec[session].inputs.T1s = database.getFilenamesByScantype(session, ['T1-15', 'T1-30'])
inputsSpec[session].inputs.T2s = database.getFilenamesByScantype(session, ['T2-15', 'T2-30'])
inputsSpec[session].inputs.PDs = database.getFilenamesByScantype(session, ['PD-15', 'PD-30'])
inputsSpec[session].inputs.FLs = database.getFilenamesByScantype(session, ['FL-15', 'FL-30'])
inputsSpec[session].inputs.OTs = database.getFilenamesByScantype(session, ['OTHER-15', 'OTHER-30'])
sessionWorkflow[session] = create_wkfl(project, subject, session, master_config,
interpMode='Linear', pipeline_name=pname)
subjectWorkflow.connect([(inputsSpec[session], sessionWorkflow[session], [('T1s', 'inputspec.T1s'),
('T2s', 'inputspec.T2s'),
('PDs', 'inputspec.PDs'),
('FLs', 'inputspec.FLs'),
('OTs', 'inputspec.OTHERs'),
]),
(atlasNode, sessionWorkflow[session], [('template_landmarks_50Lmks_fcsv',
'inputspec.atlasLandmarkFilename'),
('template_weights_50Lmks_wts',
'inputspec.atlasWeightFilename'),
('LLSModel_50Lmks_hdf5', 'inputspec.LLSModel'),
('T1_50Lmks_mdl', 'inputspec.inputTemplateModel')]),
])
if 'segmentation' in master_config['components']:
from WorkupT1T2BRAINSCut import GenerateWFName
try:
bCutInputName = ".".join(['segmentation', GenerateWFName(project, subject, session, 'Segmentation'), 'inputspec'])
except:
print project, subject, session
raise
subjectWorkflow.connect([(atlasNode, sessionWorkflow[session],
[('hncma-atlas', 'segmentation.inputspec.hncma-atlas'),
('template_t1', 'segmentation.inputspec.template_t1'),
('template_t1', bCutInputName + '.template_t1'),
('rho', bCutInputName + '.rho'),
('phi', bCutInputName + '.phi'),
('theta', bCutInputName + '.theta'),
('l_caudate_ProbabilityMap', bCutInputName + '.l_caudate_ProbabilityMap'),
('r_caudate_ProbabilityMap', bCutInputName + '.r_caudate_ProbabilityMap'),
('l_hippocampus_ProbabilityMap', bCutInputName + '.l_hippocampus_ProbabilityMap'),
('r_hippocampus_ProbabilityMap', bCutInputName + '.r_hippocampus_ProbabilityMap'),
('l_putamen_ProbabilityMap', bCutInputName + '.l_putamen_ProbabilityMap'),
('r_putamen_ProbabilityMap', bCutInputName + '.r_putamen_ProbabilityMap'),
('l_thalamus_ProbabilityMap', bCutInputName + '.l_thalamus_ProbabilityMap'),
('r_thalamus_ProbabilityMap', bCutInputName + '.r_thalamus_ProbabilityMap'),
('l_accumben_ProbabilityMap', bCutInputName + '.l_accumben_ProbabilityMap'),
('r_accumben_ProbabilityMap', bCutInputName + '.r_accumben_ProbabilityMap'),
('l_globus_ProbabilityMap', bCutInputName + '.l_globus_ProbabilityMap'),
('r_globus_ProbabilityMap', bCutInputName + '.r_globus_ProbabilityMap'),
('trainModelFile_txtD0060NT0060_gz',
bCutInputName + '.trainModelFile_txtD0060NT0060_gz')])])
if True: # FIXME: current_phase == 'baseline':
subjectWorkflow.connect([(atlasNode, sessionWorkflow[session], [('template_t1', 'inputspec.template_t1'),
('ExtendedAtlasDefinition_xml',
'inputspec.atlasDefinition')]),
])
else:
template_DG = pe.Node(interface=nio.DataGrabber(infields=['subject'],
outfields=['template_t1', 'outAtlasFullPath']),
name='Template_DG')
template_DG.inputs.base_directory = master_config['previousresult']
template_DG.inputs.subject = subject
template_DG.inputs.template = 'SUBJECT_TEMPLATES/%s/AVG_%s.nii.gz'
template_DG.inputs.template_args['template_t1'] = [['subject', 'T1']]
template_DG.inputs.field_template = {'outAtlasFullPath': 'Atlas/definitions/AtlasDefinition_%s.xml'}
template_DG.inputs.template_args['outAtlasFullPath'] = [['subject']]
template_DG.inputs.sort_filelist = True
template_DG.inputs.raise_on_empty = True
baw201.connect([(template_DG, sessionWorkflow[session], [('outAtlasFullPath', 'inputspec.atlasDefinition'),
('template_t1', 'inputspec.template_t1')]),
])
# HACK: only run first subject
break
# END HACK
if not True:
return print_workflow(subjectWorkflow,
plugin=master_config['execution']['plugin'], dotfilename='subjectWorkflow') #, graph2use='flat')
try:
return subjectWorkflow.run(plugin='SGEGraph', plugin_args=master_config['plugin_args'])
except:
return 1
def run_workflow(args, run=True):
"""Connect and execute the QAP Nipype workflow for one bundle of data.
- This function will update the resource pool with what is found in the
output directory (if it already exists). If the final expected output
of the pipeline is already found, the pipeline will not run and it
will move onto the next bundle. If the final expected output is not
present, the pipeline begins to build itself backwards.
:type args: tuple
:param args: A 7-element tuple of information comprising of the bundle's
resource pool, a list of participant info, the configuration
options, the pipeline ID run name and miscellaneous run args.
:rtype: dictionary
:return: A dictionary with information about the workflow run, its status,
and results.
"""
import os
import os.path as op
import nipype.interfaces.io as nio
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as niu
import qap
from qap_utils import read_json
import glob
import time
from time import strftime
from nipype import config as nyconfig
# unpack args
resource_pool_dict, sub_info_list, config, run_name, runargs, \
bundle_idx, num_bundles = args
# Read and apply general settings in config
keep_outputs = config.get('write_all_outputs', False)
# take date+time stamp for run identification purposes
pipeline_start_stamp = strftime("%Y-%m-%d_%H:%M:%S")
pipeline_start_time = time.time()
if "workflow_log_dir" not in config.keys():
config["workflow_log_dir"] = config["output_directory"]
bundle_log_dir = op.join(config["workflow_log_dir"],
'_'.join(["bundle", str(bundle_idx)]))
try:
os.makedirs(bundle_log_dir)
except:
if not op.isdir(bundle_log_dir):
err = "[!] Bundle log directory unable to be created.\n" \
"Path: %s\n\n" % bundle_log_dir
raise Exception(err)
else:
pass
# set up logging
nyconfig.update_config(
{'logging': {
'log_directory': bundle_log_dir,
'log_to_file': True
}})
logging.update_logging(nyconfig)
logger.info("QAP version %s" % qap.__version__)
logger.info("Pipeline start time: %s" % pipeline_start_stamp)
workflow = pe.Workflow(name=run_name)
workflow.base_dir = op.join(config["working_directory"])
# set up crash directory
workflow.config['execution'] = \
{'crashdump_dir': config["output_directory"]}
# create the one node all participants will start from
starter_node = pe.Node(niu.Function(input_names=['starter'],
output_names=['starter'],
function=starter_node_func),
name='starter_node')
# set a dummy variable
starter_node.inputs.starter = ""
new_outputs = 0
# iterate over each subject in the bundle
logger.info("Starting bundle %s out of %s.." %
(str(bundle_idx), str(num_bundles)))
# results dict
rt = {'status': 'Started', 'bundle_log_dir': bundle_log_dir}
for sub_info in sub_info_list:
resource_pool = resource_pool_dict[sub_info]
# in case we're dealing with string entries in the data dict
try:
resource_pool.keys()
except AttributeError:
continue
# resource pool check
invalid_paths = []
for resource in resource_pool.keys():
try:
if not op.isfile(
resource_pool[resource]) and resource != "site_name":
invalid_paths.append((resource, resource_pool[resource]))
except:
err = "\n\n[!]"
raise Exception(err)
if len(invalid_paths) > 0:
err = "\n\n[!] The paths provided in the subject list to the " \
"following resources are not valid:\n"
for path_tuple in invalid_paths:
err = "%s%s: %s\n" % (err, path_tuple[0], path_tuple[1])
err = "%s\n\n" % err
raise Exception(err)
# process subject info
sub_id = str(sub_info[0])
# for nipype
if "-" in sub_id:
sub_id = sub_id.replace("-", "_")
if "." in sub_id:
sub_id = sub_id.replace(".", "_")
if sub_info[1]:
session_id = str(sub_info[1])
# for nipype
if "-" in session_id:
session_id = session_id.replace("-", "_")
if "." in session_id:
session_id = session_id.replace(".", "_")
else:
session_id = "session_0"
if sub_info[2]:
scan_id = str(sub_info[2])
# for nipype
if "-" in scan_id:
scan_id = scan_id.replace("-", "_")
if "." in scan_id:
scan_id = scan_id.replace(".", "_")
else:
scan_id = "scan_0"
name = "_".join(["", sub_id, session_id, scan_id])
rt[name] = {
'id': sub_id,
'session': session_id,
'scan': scan_id,
'resource_pool': str(resource_pool)
}
logger.info("Participant info: %s" % name)
# set output directory
output_dir = op.join(config["output_directory"], run_name, sub_id,
session_id, scan_id)
try:
os.makedirs(output_dir)
except:
if not op.isdir(output_dir):
err = "[!] Output directory unable to be created.\n" \
"Path: %s\n\n" % output_dir
raise Exception(err)
else:
pass
# for QAP spreadsheet generation only
config.update({
"subject_id": sub_id,
"session_id": session_id,
"scan_id": scan_id,
"run_name": run_name
})
if "site_name" in resource_pool:
config.update({"site_name": resource_pool["site_name"]})
logger.info("Configuration settings:\n%s" % str(config))
qap_types = [
"anatomical_spatial", "functional_spatial", "functional_temporal"
]
# update that resource pool with what's already in the output
# directory
for resource in os.listdir(output_dir):
if (op.exists(op.join(output_dir, resource))
and resource not in resource_pool.keys()):
try:
resource_pool[resource] = \
glob.glob(op.join(output_dir, resource, "*"))[0]
except IndexError:
if ".json" in resource:
# load relevant json info into resource pool
json_file = op.join(output_dir, resource)
json_dict = read_json(json_file)
sub_json_dict = json_dict["%s %s %s" %
(sub_id, session_id,
scan_id)]
if "anatomical_header_info" in sub_json_dict.keys():
resource_pool["anatomical_header_info"] = \
sub_json_dict["anatomical_header_info"]
if "functional_header_info" in sub_json_dict.keys():
resource_pool["functional_header_info"] = \
sub_json_dict["functional_header_info"]
for qap_type in qap_types:
if qap_type in sub_json_dict.keys():
resource_pool["_".join(["qap",qap_type])] = \
sub_json_dict[qap_type]
except:
# a stray file in the sub-sess-scan output directory
pass
# create starter node which links all of the parallel workflows within
# the bundle together as a Nipype pipeline
resource_pool["starter"] = (starter_node, 'starter')
# individual workflow and logger setup
logger.info("Contents of resource pool for this participant:\n%s" %
str(resource_pool))
# start connecting the pipeline
qw = None
for qap_type in qap_types:
if "_".join(["qap", qap_type]) not in resource_pool.keys():
if qw is None:
from qap import qap_workflows as qw
wf_builder = \
getattr(qw, "_".join(["qap", qap_type, "workflow"]))
workflow, resource_pool = wf_builder(workflow, resource_pool,
config, name)
if ("anatomical_scan" in resource_pool.keys()) and \
("anatomical_header_info" not in resource_pool.keys()):
if qw is None:
from qap import qap_workflows as qw
workflow, resource_pool = \
qw.qap_gather_header_info(workflow, resource_pool, config,
name, "anatomical")
if ("functional_scan" in resource_pool.keys()) and \
("functional_header_info" not in resource_pool.keys()):
if qw is None:
from qap import qap_workflows as qw
workflow, resource_pool = \
qw.qap_gather_header_info(workflow, resource_pool, config,
name, "functional")
# set up the datasinks
out_list = []
for output in resource_pool.keys():
for qap_type in qap_types:
if qap_type in output:
out_list.append("_".join(["qap", qap_type]))
# write_all_outputs (writes everything to the output directory, not
# just the final JSON files)
if keep_outputs:
out_list = resource_pool.keys()
logger.info("Outputs we're keeping: %s" % str(out_list))
logger.info('Resource pool keys after workflow connection: '
'{}'.format(str(resource_pool.keys())))
# Save reports to out_dir if necessary
if config.get('write_report', False):
if ("qap_mosaic" in resource_pool.keys()) and \
("qap_mosaic" not in out_list):
out_list += ['qap_mosaic']
# The functional temporal also has an FD plot
if 'qap_functional_temporal' in resource_pool.keys():
if ("qap_fd" in resource_pool.keys()) and \
("qap_fd" not in out_list):
out_list += ['qap_fd']
for output in out_list:
# we use a check for len()==2 here to select those items in the
# resource pool which are tuples of (node, node_output), instead
# of the items which are straight paths to files
# resource pool items which are in the tuple format are the
# outputs that have been created in this workflow because they
# were not present in the subject list YML (the starting resource
# pool) and had to be generated
if (len(resource_pool[output]) == 2) and (output != "starter"):
ds = pe.Node(nio.DataSink(),
name='datasink_%s%s' % (output, name))
ds.inputs.base_directory = output_dir
node, out_file = resource_pool[output]
workflow.connect(node, out_file, ds, output)
new_outputs += 1
elif ".json" in resource_pool[output]:
new_outputs += 1
logger.info("New outputs: %s" % str(new_outputs))
# run the pipeline (if there is anything to do)
if new_outputs > 0:
if config.get('write_graph', False):
workflow.write_graph(dotfilename=op.join(
config["output_directory"], "".join([run_name, ".dot"])),
simple_form=False)
workflow.write_graph(graph2use="orig",
dotfilename=op.join(
config["output_directory"],
"".join([run_name, ".dot"])),
simple_form=False)
workflow.write_graph(graph2use="hierarchical",
dotfilename=op.join(
config["output_directory"],
"".join([run_name, ".dot"])),
simple_form=False)
if run:
try:
logger.info("Running with plugin %s" % runargs["plugin"])
logger.info("Using plugin args %s" % runargs["plugin_args"])
workflow.run(plugin=runargs["plugin"],
plugin_args=runargs["plugin_args"])
rt['status'] = 'finished'
logger.info("Workflow run finished for bundle %s." %
str(bundle_idx))
except Exception as e: # TODO We should be more specific here ...
errmsg = e
rt.update({'status': 'failed'})
logger.info("Workflow run failed for bundle %s." %
str(bundle_idx))
# ... however this is run inside a pool.map: do not raise
# Exception
else:
return workflow
else:
rt['status'] = 'cached'
logger.info("\nEverything is already done for bundle %s." %
str(bundle_idx))
# Remove working directory when done
if not keep_outputs:
try:
work_dir = op.join(workflow.base_dir, scan_id)
if op.exists(work_dir):
import shutil
shutil.rmtree(work_dir)
except:
logger.warn("Couldn\'t remove the working directory!")
pass
if rt["status"] == "failed":
logger.error(errmsg)
else:
pipeline_end_stamp = strftime("%Y-%m-%d_%H:%M:%S")
pipeline_end_time = time.time()
logger.info("Elapsed time (minutes) since last start: %s" %
((pipeline_end_time - pipeline_start_time) / 60))
logger.info("Pipeline end time: %s" % pipeline_end_stamp)
return rt
def segmentation(projectid,
subjectid,
sessionid,
master_config,
BAtlas,
onlyT1=True,
pipeline_name=''):
import os.path
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from nipype.interfaces import ants
from nipype.interfaces.utility import IdentityInterface, Function, Merge
# Set universal pipeline options
from nipype import config
config.update_config(master_config)
assert config.get('execution',
'plugin') == master_config['execution']['plugin']
from PipeLineFunctionHelpers import ClipT1ImageWithBrainMask
from WorkupT1T2BRAINSCut import CreateBRAINSCutWorkflow
from utilities.distributed import modify_qsub_args
from SEMTools import BRAINSSnapShotWriter
baw200 = pe.Workflow(name=pipeline_name)
# HACK: print for debugging
for key, itme in master_config.items():
print "-" * 30
print key, ":", itme
print "-" * 30
#END HACK
inputsSpec = pe.Node(interface=IdentityInterface(fields=[
't1_average', 't2_average', 'LMIatlasToSubject_tx', 'inputLabels',
'inputHeadLabels', 'posteriorImages',
'TissueClassifyatlasToSubjectInverseTransform', 'UpdatedPosteriorsList'
]),
run_without_submitting=True,
name='inputspec')
# outputsSpec = pe.Node(interface=IdentityInterface(fields=[...]),
# run_without_submitting=True, name='outputspec')
currentClipT1ImageWithBrainMaskName = 'ClipT1ImageWithBrainMask_' + str(
subjectid) + "_" + str(sessionid)
ClipT1ImageWithBrainMaskNode = pe.Node(
interface=Function(
function=ClipT1ImageWithBrainMask,
input_names=['t1_image', 'brain_labels', 'clipped_file_name'],
output_names=['clipped_file']),
name=currentClipT1ImageWithBrainMaskName)
ClipT1ImageWithBrainMaskNode.inputs.clipped_file_name = 'clipped_from_BABC_labels_t1.nii.gz'
baw200.connect([(inputsSpec, ClipT1ImageWithBrainMaskNode,
[('t1_average', 't1_image'),
('inputLabels', 'brain_labels')])])
currentAtlasToSubjectantsRegistration = 'AtlasToSubjectANTsRegistration_' + str(
subjectid) + "_" + str(sessionid)
AtlasToSubjectantsRegistration = pe.Node(
interface=ants.Registration(),
name=currentAtlasToSubjectantsRegistration)
AtlasToSubjectantsRegistration.inputs.dimension = 3
AtlasToSubjectantsRegistration.inputs.transforms = ["Affine", "SyN"]
AtlasToSubjectantsRegistration.inputs.transform_parameters = [[0.1],
[
0.15,
3.0, 0.0
]]
AtlasToSubjectantsRegistration.inputs.metric = ['Mattes', 'CC']
AtlasToSubjectantsRegistration.inputs.sampling_strategy = ['Regular', None]
AtlasToSubjectantsRegistration.inputs.sampling_percentage = [1.0, 1.0]
AtlasToSubjectantsRegistration.inputs.metric_weight = [1.0, 1.0]
AtlasToSubjectantsRegistration.inputs.radius_or_number_of_bins = [32, 4]
AtlasToSubjectantsRegistration.inputs.number_of_iterations = [[
1000, 1000, 1000
], [10000, 500, 500, 200]]
AtlasToSubjectantsRegistration.inputs.convergence_threshold = [5e-7, 5e-7]
AtlasToSubjectantsRegistration.inputs.convergence_window_size = [25, 25]
AtlasToSubjectantsRegistration.inputs.use_histogram_matching = [True, True]
AtlasToSubjectantsRegistration.inputs.shrink_factors = [[4, 2, 1],
[5, 4, 2, 1]]
AtlasToSubjectantsRegistration.inputs.smoothing_sigmas = [[4, 2, 0],
[5, 4, 2, 0]]
AtlasToSubjectantsRegistration.inputs.sigma_units = ["vox", "vox"]
AtlasToSubjectantsRegistration.inputs.use_estimate_learning_rate_once = [
False, False
]
AtlasToSubjectantsRegistration.inputs.write_composite_transform = True
AtlasToSubjectantsRegistration.inputs.collapse_output_transforms = True
AtlasToSubjectantsRegistration.inputs.output_transform_prefix = 'AtlasToSubject_'
AtlasToSubjectantsRegistration.inputs.winsorize_lower_quantile = 0.025
AtlasToSubjectantsRegistration.inputs.winsorize_upper_quantile = 0.975
AtlasToSubjectantsRegistration.inputs.collapse_linear_transforms_to_fixed_image_header = False
AtlasToSubjectantsRegistration.inputs.output_warped_image = 'atlas2subject.nii.gz'
AtlasToSubjectantsRegistration.inputs.output_inverse_warped_image = 'subject2atlas.nii.gz'
baw200.connect([(inputsSpec, AtlasToSubjectantsRegistration,
[('LMIatlasToSubject_tx', 'initial_moving_transform'),
('t1_average', 'fixed_image')]),
(BAtlas, AtlasToSubjectantsRegistration,
[('template_t1', 'moving_image')])])
myLocalSegWF = CreateBRAINSCutWorkflow(projectid, subjectid, sessionid,
'Segmentation',
master_config['queue'],
master_config['long_q'], BAtlas,
onlyT1)
MergeStage2AverageImagesName = "99_mergeAvergeStage2Images_" + str(
sessionid)
MergeStage2AverageImages = pe.Node(interface=Merge(2),
run_without_submitting=True,
name=MergeStage2AverageImagesName)
baw200.connect([(inputsSpec, myLocalSegWF, [
('t1_average', 'inputspec.T1Volume'),
('posteriorImages', "inputspec.posteriorDictionary"),
('inputLabels', 'inputspec.RegistrationROI'),
]), (inputsSpec, MergeStage2AverageImages, [('t1_average', 'in1')]),
(AtlasToSubjectantsRegistration, myLocalSegWF,
[('composite_transform',
'inputspec.atlasToSubjectTransform')])])
if not onlyT1:
baw200.connect([
(inputsSpec, myLocalSegWF, [('t2_average', 'inputspec.T2Volume')]),
(inputsSpec, MergeStage2AverageImages, [('t2_average', 'in2')])
])
file_count = 15 # Count of files to merge into MergeSessionSubjectToAtlas
else:
file_count = 14 # Count of files to merge into MergeSessionSubjectToAtlas
## NOTE: Element 0 of AccumulatePriorsList is the accumulated GM tissue
# baw200.connect([(AccumulateLikeTissuePosteriorsNode, myLocalSegWF,
# [(('AccumulatePriorsList', getListIndex, 0), "inputspec.TotalGM")]),
# ])
### Now define where the final organized outputs should go.
DataSink = pe.Node(nio.DataSink(),
name="CleanedDenoisedSegmentation_DS_" +
str(subjectid) + "_" + str(sessionid))
DataSink.overwrite = master_config['ds_overwrite']
DataSink.inputs.base_directory = master_config['resultdir']
# DataSink.inputs.regexp_substitutions = GenerateOutputPattern(projectid, subjectid, sessionid,'BRAINSCut')
# DataSink.inputs.regexp_substitutions = GenerateBRAINSCutImagesOutputPattern(projectid, subjectid, sessionid)
DataSink.inputs.substitutions = [
('Segmentations',
os.path.join(projectid, subjectid, sessionid,
'CleanedDenoisedRFSegmentations')),
('subjectANNLabel_', ''), ('ANNContinuousPrediction', ''),
('subject.nii.gz', '.nii.gz'), ('_seg.nii.gz', '_seg.nii.gz'),
('.nii.gz', '_seg.nii.gz'), ('_seg_seg', '_seg')
]
baw200.connect([
(myLocalSegWF, DataSink,
[('outputspec.outputBinaryLeftCaudate', 'Segmentations.@LeftCaudate'),
('outputspec.outputBinaryRightCaudate',
'Segmentations.@RightCaudate'),
('outputspec.outputBinaryLeftHippocampus',
'Segmentations.@LeftHippocampus'),
('outputspec.outputBinaryRightHippocampus',
'Segmentations.@RightHippocampus'),
('outputspec.outputBinaryLeftPutamen', 'Segmentations.@LeftPutamen'),
('outputspec.outputBinaryRightPutamen',
'Segmentations.@RightPutamen'),
('outputspec.outputBinaryLeftThalamus',
'Segmentations.@LeftThalamus'),
('outputspec.outputBinaryRightThalamus',
'Segmentations.@RightThalamus'),
('outputspec.outputBinaryLeftAccumben',
'Segmentations.@LeftAccumben'),
('outputspec.outputBinaryRightAccumben',
'Segmentations.@RightAccumben'),
('outputspec.outputBinaryLeftGlobus', 'Segmentations.@LeftGlobus'),
('outputspec.outputBinaryRightGlobus', 'Segmentations.@RightGlobus'),
('outputspec.outputLabelImageName', 'Segmentations.@LabelImageName'),
('outputspec.outputCSVFileName', 'Segmentations.@CSVFileName')]),
# (myLocalSegWF, DataSink, [('outputspec.cleaned_labels', 'Segmentations.@cleaned_labels')])
])
MergeStage2BinaryVolumesName = "99_MergeStage2BinaryVolumes_" + str(
sessionid)
MergeStage2BinaryVolumes = pe.Node(interface=Merge(12),
run_without_submitting=True,
name=MergeStage2BinaryVolumesName)
baw200.connect([(myLocalSegWF, MergeStage2BinaryVolumes,
[('outputspec.outputBinaryLeftAccumben', 'in1'),
('outputspec.outputBinaryLeftCaudate', 'in2'),
('outputspec.outputBinaryLeftPutamen', 'in3'),
('outputspec.outputBinaryLeftGlobus', 'in4'),
('outputspec.outputBinaryLeftThalamus', 'in5'),
('outputspec.outputBinaryLeftHippocampus', 'in6'),
('outputspec.outputBinaryRightAccumben', 'in7'),
('outputspec.outputBinaryRightCaudate', 'in8'),
('outputspec.outputBinaryRightPutamen', 'in9'),
('outputspec.outputBinaryRightGlobus', 'in10'),
('outputspec.outputBinaryRightThalamus', 'in11'),
('outputspec.outputBinaryRightHippocampus', 'in12')])])
## SnapShotWriter for Segmented result checking:
SnapShotWriterNodeName = "SnapShotWriter_" + str(sessionid)
SnapShotWriter = pe.Node(interface=BRAINSSnapShotWriter(),
name=SnapShotWriterNodeName)
SnapShotWriter.inputs.outputFilename = 'snapShot' + str(
sessionid) + '.png' # output specification
SnapShotWriter.inputs.inputPlaneDirection = [2, 1, 1, 1, 1, 0, 0]
SnapShotWriter.inputs.inputSliceToExtractInPhysicalPoint = [
-3, -7, -3, 5, 7, 22, -22
]
baw200.connect([(MergeStage2AverageImages, SnapShotWriter,
[('out', 'inputVolumes')]),
(MergeStage2BinaryVolumes, SnapShotWriter,
[('out', 'inputBinaryVolumes')]),
(SnapShotWriter, DataSink,
[('outputFilename', 'Segmentations.@outputSnapShot')])])
currentAntsLabelWarpToSubject = 'AntsLabelWarpToSubject' + str(
subjectid) + "_" + str(sessionid)
AntsLabelWarpToSubject = pe.Node(interface=ants.ApplyTransforms(),
name=currentAntsLabelWarpToSubject)
AntsLabelWarpToSubject.inputs.dimension = 3
AntsLabelWarpToSubject.inputs.output_image = 'warped_hncma_atlas_seg.nii.gz'
AntsLabelWarpToSubject.inputs.interpolation = "MultiLabel"
baw200.connect([(AtlasToSubjectantsRegistration, AntsLabelWarpToSubject,
[('composite_transform', 'transforms')]),
(inputsSpec, AntsLabelWarpToSubject,
[('t1_average', 'reference_image')]),
(BAtlas, AntsLabelWarpToSubject, [('hncma-atlas',
'input_image')])])
#####
### Now define where the final organized outputs should go.
AntsLabelWarpedToSubject_DSName = "AntsLabelWarpedToSubject_DS_" + str(
sessionid)
AntsLabelWarpedToSubject_DS = pe.Node(nio.DataSink(),
name=AntsLabelWarpedToSubject_DSName)
AntsLabelWarpedToSubject_DS.overwrite = master_config['ds_overwrite']
AntsLabelWarpedToSubject_DS.inputs.base_directory = master_config[
'resultdir']
AntsLabelWarpedToSubject_DS.inputs.substitutions = [
('AntsLabelWarpedToSubject',
os.path.join(projectid, subjectid, sessionid,
'AntsLabelWarpedToSubject'))
]
baw200.connect([(AntsLabelWarpToSubject, AntsLabelWarpedToSubject_DS,
[('output_image', 'AntsLabelWarpedToSubject')])])
MergeSessionSubjectToAtlasName = "99_MergeSessionSubjectToAtlas_" + str(
sessionid)
MergeSessionSubjectToAtlas = pe.Node(interface=Merge(file_count),
run_without_submitting=True,
name=MergeSessionSubjectToAtlasName)
baw200.connect([
(myLocalSegWF, MergeSessionSubjectToAtlas,
[('outputspec.outputBinaryLeftAccumben', 'in1'),
('outputspec.outputBinaryLeftCaudate', 'in2'),
('outputspec.outputBinaryLeftPutamen', 'in3'),
('outputspec.outputBinaryLeftGlobus', 'in4'),
('outputspec.outputBinaryLeftThalamus', 'in5'),
('outputspec.outputBinaryLeftHippocampus', 'in6'),
('outputspec.outputBinaryRightAccumben', 'in7'),
('outputspec.outputBinaryRightCaudate', 'in8'),
('outputspec.outputBinaryRightPutamen', 'in9'),
('outputspec.outputBinaryRightGlobus', 'in10'),
('outputspec.outputBinaryRightThalamus', 'in11'),
('outputspec.outputBinaryRightHippocampus', 'in12')]),
# (FixWMPartitioningNode, MergeSessionSubjectToAtlas, [('UpdatedPosteriorsList', 'in13')]),
(inputsSpec, MergeSessionSubjectToAtlas, [('UpdatedPosteriorsList',
'in13')]),
(inputsSpec, MergeSessionSubjectToAtlas, [('t1_average', 'in14')])
])
if not onlyT1:
assert file_count == 15
baw200.connect([(inputsSpec, MergeSessionSubjectToAtlas,
[('t2_average', 'in15')])])
LinearSubjectToAtlasANTsApplyTransformsName = 'LinearSubjectToAtlasANTsApplyTransforms_' + str(
sessionid)
LinearSubjectToAtlasANTsApplyTransforms = pe.MapNode(
interface=ants.ApplyTransforms(),
iterfield=['input_image'],
name=LinearSubjectToAtlasANTsApplyTransformsName)
LinearSubjectToAtlasANTsApplyTransforms.inputs.interpolation = 'Linear'
baw200.connect([
(AtlasToSubjectantsRegistration,
LinearSubjectToAtlasANTsApplyTransforms, [
('inverse_composite_transform', 'transforms')
]),
(BAtlas, LinearSubjectToAtlasANTsApplyTransforms,
[('template_t1', 'reference_image')]),
(MergeSessionSubjectToAtlas, LinearSubjectToAtlasANTsApplyTransforms,
[('out', 'input_image')])
])
MergeMultiLabelSessionSubjectToAtlasName = "99_MergeMultiLabelSessionSubjectToAtlas_" + str(
sessionid)
MergeMultiLabelSessionSubjectToAtlas = pe.Node(
interface=Merge(2),
run_without_submitting=True,
name=MergeMultiLabelSessionSubjectToAtlasName)
baw200.connect([(inputsSpec, MergeMultiLabelSessionSubjectToAtlas,
[('inputLabels', 'in1'), ('inputHeadLabels', 'in2')])])
### This is taking this sessions RF label map back into NAC atlas space.
#{
MultiLabelSubjectToAtlasANTsApplyTransformsName = 'MultiLabelSubjectToAtlasANTsApplyTransforms_' + str(
sessionid)
MultiLabelSubjectToAtlasANTsApplyTransforms = pe.MapNode(
interface=ants.ApplyTransforms(),
iterfield=['input_image'],
name=MultiLabelSubjectToAtlasANTsApplyTransformsName)
MultiLabelSubjectToAtlasANTsApplyTransforms.inputs.interpolation = 'MultiLabel'
baw200.connect([
(AtlasToSubjectantsRegistration,
MultiLabelSubjectToAtlasANTsApplyTransforms, [
('inverse_composite_transform', 'transforms')
]),
(BAtlas, MultiLabelSubjectToAtlasANTsApplyTransforms,
[('template_t1', 'reference_image')]),
(MergeMultiLabelSessionSubjectToAtlas,
MultiLabelSubjectToAtlasANTsApplyTransforms, [('out', 'input_image')])
])
#}
### Now we must take the sessions to THIS SUBJECTS personalized atlas.
#{
#}
### Now define where the final organized outputs should go.
Subj2Atlas_DSName = "SubjectToAtlas_DS_" + str(sessionid)
Subj2Atlas_DS = pe.Node(nio.DataSink(), name=Subj2Atlas_DSName)
Subj2Atlas_DS.overwrite = master_config['ds_overwrite']
Subj2Atlas_DS.inputs.base_directory = master_config['resultdir']
Subj2Atlas_DS.inputs.regexp_substitutions = [
(r'_LinearSubjectToAtlasANTsApplyTransforms_[^/]*',
r'' + sessionid + '/')
]
baw200.connect([(LinearSubjectToAtlasANTsApplyTransforms, Subj2Atlas_DS, [
('output_image', 'SubjectToAtlasWarped.@linear_output_images')
])])
Subj2AtlasTransforms_DSName = "SubjectToAtlasTransforms_DS_" + str(
sessionid)
Subj2AtlasTransforms_DS = pe.Node(nio.DataSink(),
name=Subj2AtlasTransforms_DSName)
Subj2AtlasTransforms_DS.overwrite = master_config['ds_overwrite']
Subj2AtlasTransforms_DS.inputs.base_directory = master_config['resultdir']
Subj2AtlasTransforms_DS.inputs.regexp_substitutions = [
(r'SubjectToAtlasWarped', r'SubjectToAtlasWarped/' + sessionid + '/')
]
baw200.connect([(AtlasToSubjectantsRegistration, Subj2AtlasTransforms_DS, [
('composite_transform', 'SubjectToAtlasWarped.@composite_transform'),
('inverse_composite_transform',
'SubjectToAtlasWarped.@inverse_composite_transform')
])])
# baw200.connect([(MultiLabelSubjectToAtlasANTsApplyTransforms, Subj2Atlas_DS, [('output_image', 'SubjectToAtlasWarped.@multilabel_output_images')])])
if master_config['execution'][
'plugin'] == 'SGE': # for some nodes, the qsub call needs to be modified on the cluster
AtlasToSubjectantsRegistration.plugin_args = {
'template':
master_config['plugin_args']['template'],
'overwrite':
True,
'qsub_args':
modify_qsub_args(master_config['queue'], '9000M', 4, hard=False)
}
SnapShotWriter.plugin_args = {
'template':
master_config['plugin_args']['template'],
'overwrite':
True,
'qsub_args':
modify_qsub_args(master_config['queue'], '1000M', 1, 1, hard=False)
}
LinearSubjectToAtlasANTsApplyTransforms.plugin_args = {
'template':
master_config['plugin_args']['template'],
'overwrite':
True,
'qsub_args':
modify_qsub_args(master_config['queue'], '1000M', 1, hard=True)
}
MultiLabelSubjectToAtlasANTsApplyTransforms.plugin_args = {
'template':
master_config['plugin_args']['template'],
'overwrite':
True,
'qsub_args':
modify_qsub_args(master_config['queue'], '1000M', 1, hard=True)
}
return baw200
def main(args):
subjects, master_config = args
import os
import sys
import traceback
# Set universal pipeline options
from nipype import config
config.update_config(master_config)
assert config.get('execution', 'plugin') == master_config['execution']['plugin']
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from nipype.interfaces.utility import IdentityInterface, Function
import nipype.interfaces.ants as ants
from template import MergeByExtendListElements, xml_filename
from PipeLineFunctionHelpers import mapPosteriorList
from atlasNode import GetAtlasNode, MakeNewAtlasTemplate
from utilities.misc import GenerateSubjectOutputPattern as outputPattern
from utilities.distributed import modify_qsub_args
template = pe.Workflow(name='SubjectAtlas_Template')
template.base_dir = master_config['logging']['log_directory']
if 'previouscache' in master_config:
# Running off previous baseline experiment
BAtlas = GetAtlasNode(master_config['previouscache'], 'BAtlas')
else:
# Running after previous baseline experiment
BAtlas = GetAtlasNode(os.path.dirname(master_config['atlascache']), 'BAtlas')
inputspec = pe.Node(interface=IdentityInterface(fields=['subject']), name='inputspec')
inputspec.iterables = ('subject', subjects)
baselineDG = pe.Node(nio.DataGrabber(infields=['subject'], outfields=['t1_average', 't2_average', 'pd_average',
'fl_average', 'outputLabels', 'posteriorImages']),
name='Baseline_DG')
if 'previousresult' in master_config:
baselineDG.inputs.base_directory = master_config['previousresult']
else:
baselineDG.inputs.base_directory = master_config['resultdir']
baselineDG.inputs.sort_filelist = True
baselineDG.inputs.raise_on_empty = False
baselineDG.inputs.template = '*/%s/*/Baseline/%s.nii.gz'
baselineDG.inputs.template_args['t1_average'] = [['subject', 't1_average_BRAINSABC']]
baselineDG.inputs.template_args['t2_average'] = [['subject', 't2_average_BRAINSABC']]
baselineDG.inputs.template_args['pd_average'] = [['subject', 'pd_average_BRAINSABC']]
baselineDG.inputs.template_args['fl_average'] = [['subject', 'fl_average_BRAINSABC']]
baselineDG.inputs.template_args['outputLabels'] = [['subject', 'brain_label_seg']]
baselineDG.inputs.field_template = {'posteriorImages':'*/%s/*/TissueClassify/POSTERIOR_%s.nii.gz'}
posterior_files = ['AIR', 'BASAL', 'CRBLGM', 'CRBLWM', 'CSF', 'GLOBUS', 'HIPPOCAMPUS', 'NOTCSF', 'NOTGM', 'NOTVB', 'NOTWM',
'SURFGM', 'THALAMUS', 'VB', 'WM']
baselineDG.inputs.template_args['posteriorImages'] = [['subject', posterior_files]]
MergeByExtendListElementsNode = pe.Node(Function(function=MergeByExtendListElements,
input_names=['t1s', 't2s',
'pds', 'fls',
'labels', 'posteriors'],
output_names=['ListOfImagesDictionaries', 'registrationImageTypes',
'interpolationMapping']),
run_without_submitting=True, name="99_MergeByExtendListElements")
from PipeLineFunctionHelpers import WrapPosteriorImagesFromDictionaryFunction as wrapfunc
template.connect([(inputspec, baselineDG, [('subject', 'subject')]),
(baselineDG, MergeByExtendListElementsNode, [('t1_average', 't1s'),
('t2_average', 't2s'),
('pd_average', 'pds'),
('fl_average', 'fls'),
('outputLabels', 'labels'),
(('posteriorImages', wrapfunc), 'posteriors')])
])
myInitAvgWF = pe.Node(interface=ants.AverageImages(), name='Atlas_antsSimpleAverage') # was 'Phase1_antsSimpleAverage'
myInitAvgWF.inputs.dimension = 3
myInitAvgWF.inputs.normalize = True
template.connect(baselineDG, 't1_average', myInitAvgWF, "images")
####################################################################################################
# TEMPLATE_BUILD_RUN_MODE = 'MULTI_IMAGE'
# if numSessions == 1:
# TEMPLATE_BUILD_RUN_MODE = 'SINGLE_IMAGE'
####################################################################################################
from BAWantsRegistrationBuildTemplate import BAWantsRegistrationTemplateBuildSingleIterationWF as registrationWF
buildTemplateIteration1 = registrationWF('iteration01')
# buildTemplateIteration2 = buildTemplateIteration1.clone(name='buildTemplateIteration2')
buildTemplateIteration2 = registrationWF('Iteration02')
MakeNewAtlasTemplateNode = pe.Node(interface=Function(function=MakeNewAtlasTemplate,
input_names=['t1_image', 'deformed_list', 'AtlasTemplate', 'outDefinition'],
output_names=['outAtlasFullPath', 'clean_deformed_list']),
# This is a lot of work, so submit it run_without_submitting=True,
run_without_submitting=True, # HACK: THIS NODE REALLY SHOULD RUN ON THE CLUSTER!
name='99_MakeNewAtlasTemplate')
if master_config['execution']['plugin'] == 'SGE': # for some nodes, the qsub call needs to be modified on the cluster
MakeNewAtlasTemplateNode.plugin_args = {'template': master_config['plugin_args']['template'],
'qsub_args': modify_qsub_args(master_config['queue'], '1000M', 1, 1),
'overwrite': True}
for bt in [buildTemplateIteration1, buildTemplateIteration2]:
##################################################
# *** Hans, is this TODO already addressed? *** #
# ----> # TODO: Change these parameters <---- #
##################################################
BeginANTS = bt.get_node("BeginANTS")
BeginANTS.plugin_args = {'template': master_config['plugin_args']['template'], 'overwrite': True,
'qsub_args': modify_qsub_args(master_config['queue'], '9000M', 4, hard=False)}
wimtdeformed = bt.get_node("wimtdeformed")
wimtdeformed.plugin_args = {'template': master_config['plugin_args']['template'], 'overwrite': True,
'qsub_args': modify_qsub_args(master_config['queue'], '2000M', 1, 2)}
AvgAffineTransform = bt.get_node("AvgAffineTransform")
AvgAffineTransform.plugin_args = {'template': master_config['plugin_args']['template'], 'overwrite': True,
'qsub_args': modify_qsub_args(master_config['queue'], '2000M', 1)}
wimtPassivedeformed = bt.get_node("wimtPassivedeformed")
wimtPassivedeformed.plugin_args = {'template': master_config['plugin_args']['template'], 'overwrite': True,
'qsub_args': modify_qsub_args(master_config['queue'], '2000M', 1, 2)}
template.connect([(myInitAvgWF, buildTemplateIteration1, [('output_average_image', 'inputspec.fixed_image')]),
(MergeByExtendListElementsNode, buildTemplateIteration1, [('ListOfImagesDictionaries', 'inputspec.ListOfImagesDictionaries'),
('registrationImageTypes', 'inputspec.registrationImageTypes'),
('interpolationMapping','inputspec.interpolationMapping')]),
(buildTemplateIteration1, buildTemplateIteration2, [('outputspec.template', 'inputspec.fixed_image')]),
(MergeByExtendListElementsNode, buildTemplateIteration2, [('ListOfImagesDictionaries', 'inputspec.ListOfImagesDictionaries'),
('registrationImageTypes','inputspec.registrationImageTypes'),
('interpolationMapping', 'inputspec.interpolationMapping')]),
(inputspec, MakeNewAtlasTemplateNode, [(('subject', xml_filename), 'outDefinition')]),
(BAtlas, MakeNewAtlasTemplateNode, [('ExtendedAtlasDefinition_xml_in', 'AtlasTemplate')]),
(buildTemplateIteration2, MakeNewAtlasTemplateNode, [('outputspec.template', 't1_image'),
('outputspec.passive_deformed_templates', 'deformed_list')]),
])
# Create DataSinks
Atlas_DataSink = pe.Node(nio.DataSink(), name="Atlas_DS")
Atlas_DataSink.overwrite = master_config['ds_overwrite']
Atlas_DataSink.inputs.base_directory = master_config['resultdir']
Subject_DataSink = pe.Node(nio.DataSink(), name="Subject_DS")
Subject_DataSink.overwrite = master_config['ds_overwrite']
Subject_DataSink.inputs.base_directory = master_config['resultdir']
template.connect([(inputspec, Atlas_DataSink, [('subject', 'container')]),
(buildTemplateIteration1, Atlas_DataSink, [('outputspec.template', 'Atlas.iteration1')]), # Unnecessary
(MakeNewAtlasTemplateNode, Atlas_DataSink, [('outAtlasFullPath', 'Atlas.definitions')]),
(BAtlas, Atlas_DataSink, [('template_landmarks_50Lmks_fcsv', 'Atlas.20111119_BCD.@fcsv'),
('template_weights_50Lmks_wts', 'Atlas.20111119_BCD.@wts'),
('LLSModel_50Lmks_hdf5', 'Atlas.20111119_BCD.@hdf5'),
('T1_50Lmks_mdl', 'Atlas.20111119_BCD.@mdl')]),
(inputspec, Subject_DataSink, [(('subject', outputPattern), 'regexp_substitutions')]),
(buildTemplateIteration2, Subject_DataSink, [('outputspec.template', 'ANTSTemplate.@template')]),
(MakeNewAtlasTemplateNode, Subject_DataSink, [('clean_deformed_list', 'ANTSTemplate.@passive_deformed_templates')]),
])
from utils import run_workflow, print_workflow
if False:
print_workflow(template, plugin=master_config['execution']['plugin'], dotfilename='template')
return run_workflow(template, plugin=master_config['execution']['plugin'], plugin_args=master_config['plugin_args'])
def run_workflow(args, run=True):
"""Connect and execute the QAP Nipype workflow for one bundle of data.
- This function will update the resource pool with what is found in the
output directory (if it already exists). If the final expected output
of the pipeline is already found, the pipeline will not run and it
will move onto the next bundle. If the final expected output is not
present, the pipeline begins to build itself backwards.
:type args: tuple
:param args: A 7-element tuple of information comprising of the bundle's
resource pool, a list of participant info, the configuration
options, the pipeline ID run name and miscellaneous run args.
:rtype: dictionary
:return: A dictionary with information about the workflow run, its status,
and results.
"""
import os
import os.path as op
import nipype.interfaces.io as nio
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as niu
import qap
from qap_utils import read_json
import glob
import time
from time import strftime
from nipype import config as nyconfig
# unpack args
resource_pool_dict, sub_info_list, config, run_name, runargs, \
bundle_idx, num_bundles = args
# Read and apply general settings in config
keep_outputs = config.get('write_all_outputs', False)
# take date+time stamp for run identification purposes
pipeline_start_stamp = strftime("%Y-%m-%d_%H:%M:%S")
pipeline_start_time = time.time()
if "workflow_log_dir" not in config.keys():
config["workflow_log_dir"] = config["output_directory"]
bundle_log_dir = op.join(config["workflow_log_dir"],
'_'.join(["bundle", str(bundle_idx)]))
try:
os.makedirs(bundle_log_dir)
except:
if not op.isdir(bundle_log_dir):
err = "[!] Bundle log directory unable to be created.\n" \
"Path: %s\n\n" % bundle_log_dir
raise Exception(err)
else:
pass
# set up logging
nyconfig.update_config(
{'logging': {'log_directory': bundle_log_dir, 'log_to_file': True}})
logging.update_logging(nyconfig)
logger.info("QAP version %s" % qap.__version__)
logger.info("Pipeline start time: %s" % pipeline_start_stamp)
workflow = pe.Workflow(name=run_name)
workflow.base_dir = op.join(config["working_directory"])
# set up crash directory
workflow.config['execution'] = \
{'crashdump_dir': config["output_directory"]}
# create the one node all participants will start from
starter_node = pe.Node(niu.Function(input_names=['starter'],
output_names=['starter'],
function=starter_node_func),
name='starter_node')
# set a dummy variable
starter_node.inputs.starter = ""
new_outputs = 0
# iterate over each subject in the bundle
logger.info("Starting bundle %s out of %s.." % (str(bundle_idx),
str(num_bundles)))
# results dict
rt = {'status': 'Started', 'bundle_log_dir': bundle_log_dir}
for sub_info in sub_info_list:
resource_pool = resource_pool_dict[sub_info]
# in case we're dealing with string entries in the data dict
try:
resource_pool.keys()
except AttributeError:
continue
# resource pool check
invalid_paths = []
for resource in resource_pool.keys():
try:
if not op.isfile(resource_pool[resource]) and resource != "site_name":
invalid_paths.append((resource, resource_pool[resource]))
except:
err = "\n\n[!]"
raise Exception(err)
if len(invalid_paths) > 0:
err = "\n\n[!] The paths provided in the subject list to the " \
"following resources are not valid:\n"
for path_tuple in invalid_paths:
err = "%s%s: %s\n" % (err, path_tuple[0], path_tuple[1])
err = "%s\n\n" % err
raise Exception(err)
# process subject info
sub_id = str(sub_info[0])
# for nipype
if "-" in sub_id:
sub_id = sub_id.replace("-","_")
if "." in sub_id:
sub_id = sub_id.replace(".","_")
if sub_info[1]:
session_id = str(sub_info[1])
# for nipype
if "-" in session_id:
session_id = session_id.replace("-","_")
if "." in session_id:
session_id = session_id.replace(".","_")
else:
session_id = "session_0"
if sub_info[2]:
scan_id = str(sub_info[2])
# for nipype
if "-" in scan_id:
scan_id = scan_id.replace("-","_")
if "." in scan_id:
scan_id = scan_id.replace(".","_")
else:
scan_id = "scan_0"
name = "_".join(["", sub_id, session_id, scan_id])
rt[name] = {'id': sub_id, 'session': session_id, 'scan': scan_id,
'resource_pool': str(resource_pool)}
logger.info("Participant info: %s" % name)
# set output directory
output_dir = op.join(config["output_directory"], run_name,
sub_id, session_id, scan_id)
try:
os.makedirs(output_dir)
except:
if not op.isdir(output_dir):
err = "[!] Output directory unable to be created.\n" \
"Path: %s\n\n" % output_dir
raise Exception(err)
else:
pass
# for QAP spreadsheet generation only
config.update({"subject_id": sub_id, "session_id": session_id,
"scan_id": scan_id, "run_name": run_name})
if "site_name" in resource_pool:
config.update({"site_name": resource_pool["site_name"]})
logger.info("Configuration settings:\n%s" % str(config))
qap_types = ["anatomical_spatial",
"functional_spatial",
"functional_temporal"]
# update that resource pool with what's already in the output
# directory
for resource in os.listdir(output_dir):
if (op.exists(op.join(output_dir, resource)) and
resource not in resource_pool.keys()):
try:
resource_pool[resource] = \
glob.glob(op.join(output_dir, resource, "*"))[0]
except IndexError:
if ".json" in resource:
# load relevant json info into resource pool
json_file = op.join(output_dir, resource)
json_dict = read_json(json_file)
sub_json_dict = json_dict["%s %s %s" % (sub_id,
session_id,
scan_id)]
if "anatomical_header_info" in sub_json_dict.keys():
resource_pool["anatomical_header_info"] = \
sub_json_dict["anatomical_header_info"]
if "functional_header_info" in sub_json_dict.keys():
resource_pool["functional_header_info"] = \
sub_json_dict["functional_header_info"]
for qap_type in qap_types:
if qap_type in sub_json_dict.keys():
resource_pool["_".join(["qap",qap_type])] = \
sub_json_dict[qap_type]
except:
# a stray file in the sub-sess-scan output directory
pass
# create starter node which links all of the parallel workflows within
# the bundle together as a Nipype pipeline
resource_pool["starter"] = (starter_node, 'starter')
# individual workflow and logger setup
logger.info("Contents of resource pool for this participant:\n%s"
% str(resource_pool))
# start connecting the pipeline
qw = None
for qap_type in qap_types:
if "_".join(["qap", qap_type]) not in resource_pool.keys():
if qw is None:
from qap import qap_workflows as qw
wf_builder = \
getattr(qw, "_".join(["qap", qap_type, "workflow"]))
workflow, resource_pool = wf_builder(workflow, resource_pool,
config, name)
if ("anatomical_scan" in resource_pool.keys()) and \
("anatomical_header_info" not in resource_pool.keys()):
if qw is None:
from qap import qap_workflows as qw
workflow, resource_pool = \
qw.qap_gather_header_info(workflow, resource_pool, config,
name, "anatomical")
if ("functional_scan" in resource_pool.keys()) and \
("functional_header_info" not in resource_pool.keys()):
if qw is None:
from qap import qap_workflows as qw
workflow, resource_pool = \
qw.qap_gather_header_info(workflow, resource_pool, config,
name, "functional")
# set up the datasinks
out_list = []
for output in resource_pool.keys():
for qap_type in qap_types:
if qap_type in output:
out_list.append("_".join(["qap", qap_type]))
# write_all_outputs (writes everything to the output directory, not
# just the final JSON files)
if keep_outputs:
out_list = resource_pool.keys()
logger.info("Outputs we're keeping: %s" % str(out_list))
logger.info('Resource pool keys after workflow connection: '
'{}'.format(str(resource_pool.keys())))
# Save reports to out_dir if necessary
if config.get('write_report', False):
if ("qap_mosaic" in resource_pool.keys()) and \
("qap_mosaic" not in out_list):
out_list += ['qap_mosaic']
# The functional temporal also has an FD plot
if 'qap_functional_temporal' in resource_pool.keys():
if ("qap_fd" in resource_pool.keys()) and \
("qap_fd" not in out_list):
out_list += ['qap_fd']
for output in out_list:
# we use a check for len()==2 here to select those items in the
# resource pool which are tuples of (node, node_output), instead
# of the items which are straight paths to files
# resource pool items which are in the tuple format are the
# outputs that have been created in this workflow because they
# were not present in the subject list YML (the starting resource
# pool) and had to be generated
if (len(resource_pool[output]) == 2) and (output != "starter"):
ds = pe.Node(nio.DataSink(), name='datasink_%s%s'
% (output,name))
ds.inputs.base_directory = output_dir
node, out_file = resource_pool[output]
workflow.connect(node, out_file, ds, output)
new_outputs += 1
elif ".json" in resource_pool[output]:
new_outputs += 1
logger.info("New outputs: %s" % str(new_outputs))
# run the pipeline (if there is anything to do)
if new_outputs > 0:
if config.get('write_graph', False):
workflow.write_graph(
dotfilename=op.join(config["output_directory"],
"".join([run_name, ".dot"])),
simple_form=False)
workflow.write_graph(
graph2use="orig",
dotfilename=op.join(config["output_directory"],
"".join([run_name, ".dot"])),
simple_form=False)
workflow.write_graph(
graph2use="hierarchical",
dotfilename=op.join(config["output_directory"],
"".join([run_name, ".dot"])),
simple_form=False)
if run:
try:
logger.info("Running with plugin %s" % runargs["plugin"])
logger.info("Using plugin args %s" % runargs["plugin_args"])
workflow.run(plugin=runargs["plugin"],
plugin_args=runargs["plugin_args"])
rt['status'] = 'finished'
logger.info("Workflow run finished for bundle %s."
% str(bundle_idx))
except Exception as e: # TODO We should be more specific here ...
errmsg = e
rt.update({'status': 'failed'})
logger.info("Workflow run failed for bundle %s."
% str(bundle_idx))
# ... however this is run inside a pool.map: do not raise
# Exception
else:
return workflow
else:
rt['status'] = 'cached'
logger.info("\nEverything is already done for bundle %s."
% str(bundle_idx))
# Remove working directory when done
if not keep_outputs:
try:
work_dir = op.join(workflow.base_dir, scan_id)
if op.exists(work_dir):
import shutil
shutil.rmtree(work_dir)
except:
logger.warn("Couldn\'t remove the working directory!")
pass
if rt["status"] == "failed":
logger.error(errmsg)
else:
pipeline_end_stamp = strftime("%Y-%m-%d_%H:%M:%S")
pipeline_end_time = time.time()
logger.info("Elapsed time (minutes) since last start: %s"
% ((pipeline_end_time - pipeline_start_time) / 60))
logger.info("Pipeline end time: %s" % pipeline_end_stamp)
return rt
def _list_outputs(self):
"""Execute this module.
"""
# Init variables
outputs = self.output_spec().get()
out_files = []
# Use hardlink
use_hardlink = str2bool(
config.get('execution', 'try_hard_link_datasink'))
# Set local output directory if specified
if isdefined(self.inputs.local_copy):
outdir = self.inputs.local_copy
else:
outdir = self.inputs.base_directory
# If base directory isn't given, assume current directory
if not isdefined(outdir):
outdir = '.'
# Check if base directory reflects S3 bucket upload
s3_flag, bucket_name = self._check_s3_base_dir()
if s3_flag:
s3dir = self.inputs.base_directory
# If user overrides bucket object, use that
if self.inputs.bucket:
bucket = self.inputs.bucket
# Otherwise fetch bucket object using name
else:
try:
bucket = self._fetch_bucket(bucket_name)
# If encountering an exception during bucket access, set output
# base directory to a local folder
except Exception as exc:
s3dir = '<N/A>'
if not isdefined(self.inputs.local_copy):
local_out_exception = os.path.join(
os.path.expanduser('~'),
's3_datasink_' + bucket_name)
outdir = local_out_exception
# Log local copying directory
iflogger.info(
'Access to S3 failed! Storing outputs locally at: '
'%s\nError: %s', outdir, exc)
else:
s3dir = '<N/A>'
# If container input is given, append that to outdir
if isdefined(self.inputs.container):
outdir = os.path.join(outdir, self.inputs.container)
s3dir = os.path.join(s3dir, self.inputs.container)
# If sinking to local folder
if outdir != s3dir:
outdir = os.path.abspath(outdir)
# Create the directory if it doesn't exist
if not os.path.exists(outdir):
try:
os.makedirs(outdir)
except OSError as inst:
if 'File exists' in inst.strerror:
pass
else:
raise (inst)
# Iterate through outputs attributes {key : path(s)}
for key, files in list(self.inputs._outputs.items()):
if not isdefined(files):
continue
iflogger.debug("key: %s files: %s", key, str(files))
files = ensure_list(files if files else [])
tempoutdir = outdir
if s3_flag:
s3tempoutdir = s3dir
for d in key.split('.'):
if d[0] == '@':
continue
tempoutdir = os.path.join(tempoutdir, d)
if s3_flag:
s3tempoutdir = os.path.join(s3tempoutdir, d)
# flattening list
if files and isinstance(files, list):
if isinstance(files[0], list):
files = [item for sublist in files for item in sublist]
# Iterate through passed-in source files
for src in ensure_list(files):
# Format src and dst files
src = os.path.abspath(src)
if not os.path.isfile(src):
src = os.path.join(src, '')
dst = self._get_dst(src)
if s3_flag:
s3dst = os.path.join(s3tempoutdir, dst)
s3dst = self._substitute(s3dst)
dst = os.path.join(tempoutdir, dst)
dst = self._substitute(dst)
path, _ = os.path.split(dst)
# If we're uploading to S3
if s3_flag:
self._upload_to_s3(bucket, src, s3dst)
out_files.append(s3dst)
# Otherwise, copy locally src -> dst
if not s3_flag or isdefined(self.inputs.local_copy):
# Create output directory if it doesn't exist
if not os.path.exists(path):
try:
os.makedirs(path)
except OSError as inst:
if 'File exists' in inst.strerror:
pass
else:
raise (inst)
# If src == dst, it's already home
if (not os.path.exists(dst)) or (os.stat(src) !=
os.stat(dst)):
# If src is a file, copy it to dst
if os.path.isfile(src):
iflogger.debug(f'copyfile: {src} {dst}')
copyfile(src,
dst,
copy=True,
hashmethod='content',
use_hardlink=use_hardlink)
# If src is a directory, copy
# entire contents to dst dir
elif os.path.isdir(src):
if (os.path.exists(dst)
and self.inputs.remove_dest_dir):
iflogger.debug('removing: %s', dst)
shutil.rmtree(dst)
iflogger.debug('copydir: %s %s', src, dst)
copytree(src, dst)
out_files.append(dst)
# Return outputs dictionary
outputs['out_file'] = out_files
return outputs
from IPython.display import Image
from nipype.interfaces.base import (
traits,
TraitedSpec,
CommandLineInputSpec,
CommandLine,
File,
isdefined
)
from nipype.utils.filemanip import fname_presuffix
from nipype import config
config.set('execution', 'display_variable', os.environ['DISPLAY'])
print config.get('execution', 'display_variable')
class MP2RageSkullStripInputSpec(CommandLineInputSpec):
in_filter_image = traits.File(mandatory=False, argstr='-inFilter %s', desc=' Filter Image')
in_inv2 = traits.File(exists=True, argstr='-inInv2 %s', desc='Inv2 Image')
in_t1 = traits.File(exists=True, argstr='-inT1 %s', desc='T1 Map image')
int_t1_weighted = traits.File(exists=True, argstr='-inT1weighted %s', desc='T1-Weighted Image')
out_brain_mask = traits.File('brain_mask.nii.gz', usedefault=True, argstr='-outBrain %s', desc='Path/name of brain mask')
out_masked_t1 = traits.File(argstr='-outMasked %s', desc='Create masked T1')
out_masked_t1_weighted = traits.Bool(argstr='-outMasked2 %s', desc='Path/name of masked T1-weighted image')
out_masked_filter_image = traits.Bool(argstr='-outMasked3 %s', desc='Path/name of masked Filter image')
class MP2RageSkullStripOutputSpec(TraitedSpec):
brain_mask = traits.File()
masked_t1 = traits.File()
def RunSubjectWorkflow(args):
"""
.-----------.
--- | Session 1 | ---> /project/subjectA/session1/phase/
/ *-----------*
.-----------. /
| Subject A | <
*-----------* \
\ .-----------.
--- | Session 2 | ---> /project/subjectA/session2/phase/
*-----------*
**** Replaces WorkflowT1T2.py ****
"""
database, start_time, subject, master_config = args
assert 'baseline' in master_config[
'components'] or 'longitudinal' in master_config[
'components'], "Baseline or Longitudinal is not in WORKFLOW_COMPONENTS!"
# HACK:
# To avoid a "sqlite3.ProgrammingError: Base Cursor.__init__ not called" error
# using multiprocessing.map_async(), re-instantiate database
# database.__init__(defaultDBName=database.dbName, subject_list=database.subjectList)
#
# END HACK
import time
from nipype import config, logging
config.update_config(master_config) # Set universal pipeline options
assert config.get('execution',
'plugin') == master_config['execution']['plugin']
# DEBUG
# config.enable_debug_mode()
# config.set('execution', 'stop_on_first_rerun', 'true')
# END DEBUG
logging.update_logging(config)
import nipype.pipeline.engine as pe
import nipype.interfaces.base as nbase
import nipype.interfaces.io as nio
from nipype.interfaces.utility import IdentityInterface, Function
import traits
from baw_exp import OpenSubjectDatabase
from SessionDB import SessionDB
from PipeLineFunctionHelpers import convertToList
from atlasNode import MakeAtlasNode
from utilities.misc import GenerateSubjectOutputPattern as outputPattern
from utilities.misc import GenerateWFName
while time.time() < start_time:
time.sleep(start_time - time.time() + 1)
print "Delaying start for {subject}".format(subject=subject)
print("===================== SUBJECT: {0} ===========================".
format(subject))
subjectWorkflow = pe.Workflow(
name="BAW_StandardWorkup_subject_{0}".format(subject))
subjectWorkflow.base_dir = config.get('logging', 'log_directory')
# subjectWorkflow.config['execution']['plugin'] = 'Linear' # Hardcodeded in WorkupT1T2.py - why?
# DEBUG
# subjectWorkflow.config['execution']['stop_on_first_rerun'] = 'true'
# END DEBUG
atlasNode = MakeAtlasNode(master_config['atlascache'], 'BAtlas')
sessionWorkflow = dict()
inputsSpec = dict()
sessions = database.getSessionsFromSubject(subject)
# print "These are the sessions: ", sessions
if 'baseline' in master_config['components']:
current_phase = 'baseline'
from baseline import create_baseline as create_wkfl
elif 'longitudinal' in master_config['components']:
current_phase = 'longitudinal'
from longitudinal import create_longitudial as create_wkfl
for session in sessions: # TODO (future): Replace with iterable inputSpec node and add Function node for getAllFiles()
project = database.getProjFromSession(session)
pname = "{0}_{1}".format(
session,
current_phase) # Long node names make graphs a pain to read/print
# pname = GenerateWFName(project, subject, session, current_phase)
print "Building session pipeline for {0}".format(session)
inputsSpec[session] = pe.Node(
name='inputspec_{0}'.format(session),
interface=IdentityInterface(
fields=['T1s', 'T2s', 'PDs', 'FLs', 'OTs']))
inputsSpec[session].inputs.T1s = database.getFilenamesByScantype(
session, ['T1-15', 'T1-30'])
inputsSpec[session].inputs.T2s = database.getFilenamesByScantype(
session, ['T2-15', 'T2-30'])
inputsSpec[session].inputs.PDs = database.getFilenamesByScantype(
session, ['PD-15', 'PD-30'])
inputsSpec[session].inputs.FLs = database.getFilenamesByScantype(
session, ['FL-15', 'FL-30'])
inputsSpec[session].inputs.OTs = database.getFilenamesByScantype(
session, ['OTHER-15', 'OTHER-30'])
sessionWorkflow[session] = create_wkfl(project,
subject,
session,
master_config,
interpMode='Linear',
pipeline_name=pname)
subjectWorkflow.connect([
(inputsSpec[session], sessionWorkflow[session], [
('T1s', 'inputspec.T1s'),
('T2s', 'inputspec.T2s'),
('PDs', 'inputspec.PDs'),
('FLs', 'inputspec.FLs'),
('OTs', 'inputspec.OTHERs'),
]),
(atlasNode, sessionWorkflow[session],
[('template_landmarks_50Lmks_fcsv',
'inputspec.atlasLandmarkFilename'),
('template_weights_50Lmks_wts', 'inputspec.atlasWeightFilename'),
('LLSModel_50Lmks_hdf5', 'inputspec.LLSModel'),
('T1_50Lmks_mdl', 'inputspec.inputTemplateModel')]),
])
if current_phase == 'baseline':
subjectWorkflow.connect([
(atlasNode, sessionWorkflow[session],
[('template_t1', 'inputspec.template_t1'),
('ExtendedAtlasDefinition_xml', 'inputspec.atlasDefinition')
]),
])
else:
assert current_phase == 'longitudinal', "Phase value is unknown: {0}".format(
current_phase)
from utils import run_workflow, print_workflow
if False:
print_workflow(template,
plugin=master_config['execution']['plugin'],
dotfilename='template')
return run_workflow(template,
plugin=master_config['execution']['plugin'],
plugin_args=master_config['plugin_args'])
def test_debug_mode():
from ... import logging
sofc_config = config.get('execution', 'stop_on_first_crash')
ruo_config = config.get('execution', 'remove_unnecessary_outputs')
ki_config = config.get('execution', 'keep_inputs')
wf_config = config.get('logging', 'workflow_level')
if_config = config.get('logging', 'interface_level')
ut_config = config.get('logging', 'utils_level')
wf_level = logging.getLogger('nipype.workflow').level
if_level = logging.getLogger('nipype.interface').level
ut_level = logging.getLogger('nipype.utils').level
config.enable_debug_mode()
# Check config is updated and logging levels, too
assert config.get('execution', 'stop_on_first_crash') == 'true'
assert config.get('execution', 'remove_unnecessary_outputs') == 'false'
assert config.get('execution', 'keep_inputs') == 'true'
assert config.get('logging', 'workflow_level') == 'DEBUG'
assert config.get('logging', 'interface_level') == 'DEBUG'
assert config.get('logging', 'utils_level') == 'DEBUG'
assert logging.getLogger('nipype.workflow').level == 10
assert logging.getLogger('nipype.interface').level == 10
assert logging.getLogger('nipype.utils').level == 10
# Restore config and levels
config.set('execution', 'stop_on_first_crash', sofc_config)
config.set('execution', 'remove_unnecessary_outputs', ruo_config)
config.set('execution', 'keep_inputs', ki_config)
config.set('logging', 'workflow_level', wf_config)
config.set('logging', 'interface_level', if_config)
config.set('logging', 'utils_level', ut_config)
logging.update_logging(config)
assert config.get('execution', 'stop_on_first_crash') == sofc_config
assert config.get('execution', 'remove_unnecessary_outputs') == ruo_config
assert config.get('execution', 'keep_inputs') == ki_config
assert config.get('logging', 'workflow_level') == wf_config
assert config.get('logging', 'interface_level') == if_config
assert config.get('logging', 'utils_level') == ut_config
assert logging.getLogger('nipype.workflow').level == wf_level
assert logging.getLogger('nipype.interface').level == if_level
assert logging.getLogger('nipype.utils').level == ut_level
def segmentation(projectid, subjectid, sessionid, master_config, onlyT1=True, pipeline_name=''):
import os.path
import nipype.pipeline.engine as pe
import nipype.interfaces.io as nio
from nipype.interfaces import ants
from nipype.interfaces.utility import IdentityInterface, Function, Merge
# Set universal pipeline options
from nipype import config
config.update_config(master_config)
assert config.get('execution', 'plugin') == master_config['execution']['plugin']
from PipeLineFunctionHelpers import ClipT1ImageWithBrainMask
from WorkupT1T2BRAINSCut import CreateBRAINSCutWorkflow
from utilities.distributed import modify_qsub_args
from SEMTools import BRAINSSnapShotWriter
baw200 = pe.Workflow(name=pipeline_name)
# HACK: print for debugging
for key, itme in master_config.items():
print "-" * 30
print key, ":", itme
print "-" * 30
#END HACK
inputsSpec = pe.Node(interface=IdentityInterface(fields=['t1_average',
't2_average',
'template_t1',
'hncma-atlas',
'LMIatlasToSubject_tx',
'inputLabels',
'inputHeadLabels',
'posteriorImages',
'TissueClassifyatlasToSubjectInverseTransform',
'UpdatedPosteriorsList']),
run_without_submitting=True, name='inputspec')
# outputsSpec = pe.Node(interface=IdentityInterface(fields=[...]),
# run_without_submitting=True, name='outputspec')
currentClipT1ImageWithBrainMaskName = 'ClipT1ImageWithBrainMask_' + str(subjectid) + "_" + str(sessionid)
ClipT1ImageWithBrainMaskNode = pe.Node(interface=Function(function=ClipT1ImageWithBrainMask,
input_names=['t1_image', 'brain_labels',
'clipped_file_name'],
output_names=['clipped_file']),
name=currentClipT1ImageWithBrainMaskName)
ClipT1ImageWithBrainMaskNode.inputs.clipped_file_name = 'clipped_from_BABC_labels_t1.nii.gz'
baw200.connect([(inputsSpec, ClipT1ImageWithBrainMaskNode, [('t1_average', 't1_image'),
('inputLabels', 'brain_labels')])])
currentAtlasToSubjectantsRegistration = 'AtlasToSubjectANTsRegistration_' + str(subjectid) + "_" + str(sessionid)
AtlasToSubjectantsRegistration = pe.Node(interface=ants.Registration(), name=currentAtlasToSubjectantsRegistration)
AtlasToSubjectantsRegistration.inputs.dimension = 3
AtlasToSubjectantsRegistration.inputs.transforms = ["Affine", "SyN"]
AtlasToSubjectantsRegistration.inputs.transform_parameters = [[0.1], [0.15, 3.0, 0.0]]
AtlasToSubjectantsRegistration.inputs.metric = ['Mattes', 'CC']
AtlasToSubjectantsRegistration.inputs.sampling_strategy = ['Regular', None]
AtlasToSubjectantsRegistration.inputs.sampling_percentage = [1.0, 1.0]
AtlasToSubjectantsRegistration.inputs.metric_weight = [1.0, 1.0]
AtlasToSubjectantsRegistration.inputs.radius_or_number_of_bins = [32, 4]
AtlasToSubjectantsRegistration.inputs.number_of_iterations = [[1000, 1000, 1000], [10000, 500, 500, 200]]
AtlasToSubjectantsRegistration.inputs.convergence_threshold = [5e-7, 5e-7]
AtlasToSubjectantsRegistration.inputs.convergence_window_size = [25, 25]
AtlasToSubjectantsRegistration.inputs.use_histogram_matching = [True, True]
AtlasToSubjectantsRegistration.inputs.shrink_factors = [[4, 2, 1], [5, 4, 2, 1]]
AtlasToSubjectantsRegistration.inputs.smoothing_sigmas = [[4, 2, 0], [5, 4, 2, 0]]
AtlasToSubjectantsRegistration.inputs.sigma_units = ["vox","vox"]
AtlasToSubjectantsRegistration.inputs.use_estimate_learning_rate_once = [False, False]
AtlasToSubjectantsRegistration.inputs.write_composite_transform = True
AtlasToSubjectantsRegistration.inputs.collapse_output_transforms = True
AtlasToSubjectantsRegistration.inputs.output_transform_prefix = 'AtlasToSubject_'
AtlasToSubjectantsRegistration.inputs.winsorize_lower_quantile = 0.025
AtlasToSubjectantsRegistration.inputs.winsorize_upper_quantile = 0.975
AtlasToSubjectantsRegistration.inputs.collapse_linear_transforms_to_fixed_image_header = False
AtlasToSubjectantsRegistration.inputs.output_warped_image = 'atlas2subject.nii.gz'
AtlasToSubjectantsRegistration.inputs.output_inverse_warped_image = 'subject2atlas.nii.gz'
baw200.connect([(inputsSpec, AtlasToSubjectantsRegistration, [('LMIatlasToSubject_tx', 'initial_moving_transform'),
('t1_average', 'fixed_image'),
('template_t1', 'moving_image')])
])
myLocalSegWF = CreateBRAINSCutWorkflow(projectid,
subjectid,
sessionid,
master_config['queue'],
master_config['long_q'],
t1Only=onlyT1)
MergeStage2AverageImagesName = "99_mergeAvergeStage2Images_" + str(sessionid)
MergeStage2AverageImages = pe.Node(interface=Merge(2), run_without_submitting=True,
name=MergeStage2AverageImagesName)
baw200.connect([(inputsSpec, myLocalSegWF, [('t1_average', 'inputspec.T1Volume'),
('posteriorImages', "inputspec.posteriorDictionary"),
('inputLabels', 'inputspec.RegistrationROI'),]),
(inputsSpec, MergeStage2AverageImages, [('t1_average', 'in1')]),
(AtlasToSubjectantsRegistration, myLocalSegWF, [('composite_transform',
'inputspec.atlasToSubjectTransform')])
])
if not onlyT1:
baw200.connect([(inputsSpec, myLocalSegWF, [('t2_average', 'inputspec.T2Volume')]),
(inputsSpec, MergeStage2AverageImages, [('t2_average', 'in2')])])
file_count = 15 # Count of files to merge into MergeSessionSubjectToAtlas
else:
file_count = 14 # Count of files to merge into MergeSessionSubjectToAtlas
## NOTE: Element 0 of AccumulatePriorsList is the accumulated GM tissue
# baw200.connect([(AccumulateLikeTissuePosteriorsNode, myLocalSegWF,
# [(('AccumulatePriorsList', getListIndex, 0), "inputspec.TotalGM")]),
# ])
### Now define where the final organized outputs should go.
DataSink = pe.Node(nio.DataSink(), name="CleanedDenoisedSegmentation_DS_" + str(subjectid) + "_" + str(sessionid))
DataSink.overwrite = master_config['ds_overwrite']
DataSink.inputs.base_directory = master_config['resultdir']
# DataSink.inputs.regexp_substitutions = GenerateOutputPattern(projectid, subjectid, sessionid,'BRAINSCut')
# DataSink.inputs.regexp_substitutions = GenerateBRAINSCutImagesOutputPattern(projectid, subjectid, sessionid)
DataSink.inputs.substitutions = [('Segmentations', os.path.join(projectid, subjectid, sessionid, 'CleanedDenoisedRFSegmentations')),
('subjectANNLabel_', ''),
('ANNContinuousPrediction', ''),
('subject.nii.gz', '.nii.gz'),
('_seg.nii.gz', '_seg.nii.gz'),
('.nii.gz', '_seg.nii.gz'),
('_seg_seg', '_seg')]
baw200.connect([(myLocalSegWF, DataSink, [('outputspec.outputBinaryLeftCaudate', 'Segmentations.@LeftCaudate'),
('outputspec.outputBinaryRightCaudate', 'Segmentations.@RightCaudate'),
('outputspec.outputBinaryLeftHippocampus', 'Segmentations.@LeftHippocampus'),
('outputspec.outputBinaryRightHippocampus', 'Segmentations.@RightHippocampus'),
('outputspec.outputBinaryLeftPutamen', 'Segmentations.@LeftPutamen'),
('outputspec.outputBinaryRightPutamen', 'Segmentations.@RightPutamen'),
('outputspec.outputBinaryLeftThalamus', 'Segmentations.@LeftThalamus'),
('outputspec.outputBinaryRightThalamus', 'Segmentations.@RightThalamus'),
('outputspec.outputBinaryLeftAccumben', 'Segmentations.@LeftAccumben'),
('outputspec.outputBinaryRightAccumben', 'Segmentations.@RightAccumben'),
('outputspec.outputBinaryLeftGlobus', 'Segmentations.@LeftGlobus'),
('outputspec.outputBinaryRightGlobus', 'Segmentations.@RightGlobus'),
('outputspec.outputLabelImageName', 'Segmentations.@LabelImageName'),
('outputspec.outputCSVFileName', 'Segmentations.@CSVFileName')]),
# (myLocalSegWF, DataSink, [('outputspec.cleaned_labels', 'Segmentations.@cleaned_labels')])
])
MergeStage2BinaryVolumesName = "99_MergeStage2BinaryVolumes_" + str(sessionid)
MergeStage2BinaryVolumes = pe.Node(interface=Merge(12), run_without_submitting=True,
name=MergeStage2BinaryVolumesName)
baw200.connect([(myLocalSegWF, MergeStage2BinaryVolumes, [('outputspec.outputBinaryLeftAccumben', 'in1'),
('outputspec.outputBinaryLeftCaudate', 'in2'),
('outputspec.outputBinaryLeftPutamen', 'in3'),
('outputspec.outputBinaryLeftGlobus', 'in4'),
('outputspec.outputBinaryLeftThalamus', 'in5'),
('outputspec.outputBinaryLeftHippocampus', 'in6'),
('outputspec.outputBinaryRightAccumben', 'in7'),
('outputspec.outputBinaryRightCaudate', 'in8'),
('outputspec.outputBinaryRightPutamen', 'in9'),
('outputspec.outputBinaryRightGlobus', 'in10'),
('outputspec.outputBinaryRightThalamus', 'in11'),
('outputspec.outputBinaryRightHippocampus', 'in12')])
])
## SnapShotWriter for Segmented result checking:
SnapShotWriterNodeName = "SnapShotWriter_" + str(sessionid)
SnapShotWriter = pe.Node(interface=BRAINSSnapShotWriter(), name=SnapShotWriterNodeName)
SnapShotWriter.inputs.outputFilename = 'snapShot' + str(sessionid) + '.png' # output specification
SnapShotWriter.inputs.inputPlaneDirection = [2, 1, 1, 1, 1, 0, 0]
SnapShotWriter.inputs.inputSliceToExtractInPhysicalPoint = [-3, -7, -3, 5, 7, 22, -22]
baw200.connect([(MergeStage2AverageImages, SnapShotWriter, [('out', 'inputVolumes')]),
(MergeStage2BinaryVolumes, SnapShotWriter, [('out', 'inputBinaryVolumes')]),
(SnapShotWriter, DataSink, [('outputFilename', 'Segmentations.@outputSnapShot')])
])
currentAntsLabelWarpToSubject = 'AntsLabelWarpToSubject' + str(subjectid) + "_" + str(sessionid)
AntsLabelWarpToSubject = pe.Node(interface=ants.ApplyTransforms(), name=currentAntsLabelWarpToSubject)
AntsLabelWarpToSubject.inputs.dimension = 3
AntsLabelWarpToSubject.inputs.output_image = 'warped_hncma_atlas_seg.nii.gz'
AntsLabelWarpToSubject.inputs.interpolation = "MultiLabel"
baw200.connect([(AtlasToSubjectantsRegistration, AntsLabelWarpToSubject, [('composite_transform', 'transforms')]),
(inputsSpec, AntsLabelWarpToSubject, [('t1_average', 'reference_image'),
('hncma-atlas', 'input_image')])
])
#####
### Now define where the final organized outputs should go.
AntsLabelWarpedToSubject_DSName = "AntsLabelWarpedToSubject_DS_" + str(sessionid)
AntsLabelWarpedToSubject_DS = pe.Node(nio.DataSink(), name=AntsLabelWarpedToSubject_DSName)
AntsLabelWarpedToSubject_DS.overwrite = master_config['ds_overwrite']
AntsLabelWarpedToSubject_DS.inputs.base_directory = master_config['resultdir']
AntsLabelWarpedToSubject_DS.inputs.substitutions = [('AntsLabelWarpedToSubject', os.path.join(projectid, subjectid, sessionid, 'AntsLabelWarpedToSubject'))]
baw200.connect([(AntsLabelWarpToSubject, AntsLabelWarpedToSubject_DS, [('output_image', 'AntsLabelWarpedToSubject')])])
MergeSessionSubjectToAtlasName = "99_MergeSessionSubjectToAtlas_" + str(sessionid)
MergeSessionSubjectToAtlas = pe.Node(interface=Merge(file_count), run_without_submitting=True,
name=MergeSessionSubjectToAtlasName)
baw200.connect([(myLocalSegWF, MergeSessionSubjectToAtlas, [('outputspec.outputBinaryLeftAccumben', 'in1'),
('outputspec.outputBinaryLeftCaudate', 'in2'),
('outputspec.outputBinaryLeftPutamen', 'in3'),
('outputspec.outputBinaryLeftGlobus', 'in4'),
('outputspec.outputBinaryLeftThalamus', 'in5'),
('outputspec.outputBinaryLeftHippocampus', 'in6'),
('outputspec.outputBinaryRightAccumben', 'in7'),
('outputspec.outputBinaryRightCaudate', 'in8'),
('outputspec.outputBinaryRightPutamen', 'in9'),
('outputspec.outputBinaryRightGlobus', 'in10'),
('outputspec.outputBinaryRightThalamus', 'in11'),
('outputspec.outputBinaryRightHippocampus', 'in12')]),
# (FixWMPartitioningNode, MergeSessionSubjectToAtlas, [('UpdatedPosteriorsList', 'in13')]),
(inputsSpec, MergeSessionSubjectToAtlas, [('UpdatedPosteriorsList', 'in13')]),
(inputsSpec, MergeSessionSubjectToAtlas, [('t1_average', 'in14')])
])
if not onlyT1:
assert file_count == 15
baw200.connect([(inputsSpec, MergeSessionSubjectToAtlas, [('t2_average', 'in15')])])
LinearSubjectToAtlasANTsApplyTransformsName = 'LinearSubjectToAtlasANTsApplyTransforms_' + str(sessionid)
LinearSubjectToAtlasANTsApplyTransforms = pe.MapNode(interface=ants.ApplyTransforms(), iterfield=['input_image'],
name=LinearSubjectToAtlasANTsApplyTransformsName)
LinearSubjectToAtlasANTsApplyTransforms.inputs.interpolation = 'Linear'
baw200.connect([(AtlasToSubjectantsRegistration, LinearSubjectToAtlasANTsApplyTransforms, [('inverse_composite_transform',
'transforms')]),
(inputsSpec, LinearSubjectToAtlasANTsApplyTransforms, [('template_t1', 'reference_image')]),
(MergeSessionSubjectToAtlas, LinearSubjectToAtlasANTsApplyTransforms, [('out', 'input_image')])
])
MergeMultiLabelSessionSubjectToAtlasName = "99_MergeMultiLabelSessionSubjectToAtlas_" + str(sessionid)
MergeMultiLabelSessionSubjectToAtlas = pe.Node(interface=Merge(2), run_without_submitting=True,
name=MergeMultiLabelSessionSubjectToAtlasName)
baw200.connect([(inputsSpec, MergeMultiLabelSessionSubjectToAtlas, [('inputLabels', 'in1'),
('inputHeadLabels', 'in2')])
])
### This is taking this sessions RF label map back into NAC atlas space.
#{
MultiLabelSubjectToAtlasANTsApplyTransformsName = 'MultiLabelSubjectToAtlasANTsApplyTransforms_' + str(sessionid) + '_map'
MultiLabelSubjectToAtlasANTsApplyTransforms = pe.MapNode(interface=ants.ApplyTransforms(), iterfield=['input_image'],
name=MultiLabelSubjectToAtlasANTsApplyTransformsName)
MultiLabelSubjectToAtlasANTsApplyTransforms.inputs.interpolation = 'MultiLabel'
baw200.connect([(AtlasToSubjectantsRegistration, MultiLabelSubjectToAtlasANTsApplyTransforms,
[('inverse_composite_transform', 'transforms')]),
(inputsSpec, MultiLabelSubjectToAtlasANTsApplyTransforms, [('template_t1', 'reference_image')]),
(MergeMultiLabelSessionSubjectToAtlas, MultiLabelSubjectToAtlasANTsApplyTransforms,
[('out', 'input_image')])
])
#}
### Now we must take the sessions to THIS SUBJECTS personalized atlas.
#{
#}
### Now define where the final organized outputs should go.
Subj2Atlas_DSName = "SubjectToAtlas_DS_" + str(sessionid)
Subj2Atlas_DS = pe.Node(nio.DataSink(), name=Subj2Atlas_DSName)
Subj2Atlas_DS.overwrite = master_config['ds_overwrite']
Subj2Atlas_DS.inputs.base_directory = master_config['resultdir']
Subj2Atlas_DS.inputs.regexp_substitutions = [(r'_LinearSubjectToAtlasANTsApplyTransforms_[^/]*',
r'' + sessionid + '/')]
baw200.connect([(LinearSubjectToAtlasANTsApplyTransforms, Subj2Atlas_DS,
[('output_image', 'SubjectToAtlasWarped.@linear_output_images')])])
Subj2AtlasTransforms_DSName = "SubjectToAtlasTransforms_DS_" + str(sessionid)
Subj2AtlasTransforms_DS = pe.Node(nio.DataSink(), name=Subj2AtlasTransforms_DSName)
Subj2AtlasTransforms_DS.overwrite = master_config['ds_overwrite']
Subj2AtlasTransforms_DS.inputs.base_directory = master_config['resultdir']
Subj2AtlasTransforms_DS.inputs.regexp_substitutions = [(r'SubjectToAtlasWarped',
r'SubjectToAtlasWarped/' + sessionid + '/')]
baw200.connect([(AtlasToSubjectantsRegistration, Subj2AtlasTransforms_DS,
[('composite_transform', 'SubjectToAtlasWarped.@composite_transform'),
('inverse_composite_transform', 'SubjectToAtlasWarped.@inverse_composite_transform')])])
# baw200.connect([(MultiLabelSubjectToAtlasANTsApplyTransforms, Subj2Atlas_DS, [('output_image', 'SubjectToAtlasWarped.@multilabel_output_images')])])
if master_config['execution']['plugin'] == 'SGE': # for some nodes, the qsub call needs to be modified on the cluster
AtlasToSubjectantsRegistration.plugin_args = {'template': master_config['plugin_args']['template'], 'overwrite': True,
'qsub_args': modify_qsub_args(master_config['queue'], '9000M', 4,
hard=False)}
SnapShotWriter.plugin_args = {'template': master_config['plugin_args']['template'], 'overwrite': True,
'qsub_args': modify_qsub_args(master_config['queue'], '1000M', 1, 1, hard=False)}
LinearSubjectToAtlasANTsApplyTransforms.plugin_args = {'template': master_config['plugin_args']['template'],
'overwrite': True,
'qsub_args': modify_qsub_args(master_config['queue'], '1000M',
1, hard=True)}
MultiLabelSubjectToAtlasANTsApplyTransforms.plugin_args = {'template': master_config['plugin_args']['template'],
'overwrite': True,
'qsub_args': modify_qsub_args(master_config['queue'], '1000M',
1, hard=True)}
return baw200
outputs["resized_file"] = self._gen_filename(self.inputs.in_file)
else:
outputs["resized_file"] = os.path.abspath(self.inputs.out_file)
return outputs
def _gen_filename(self, name):
pth, fn, ext = filemanip.split_filename(self.inputs.in_file)
return os.path.join(os.getcwd(), fn + "_resized" + ext)
from nipype.utils.filemanip import fname_presuffix
from nipype import config
config.set("execution", "display_variable", os.environ["DISPLAY"])
print config.get("execution", "display_variable")
class MP2RageSkullStripInputSpec(CommandLineInputSpec):
in_filter_image = traits.File(mandatory=False, argstr="-inFilter %s", desc=" Filter Image")
in_inv2 = traits.File(exists=True, argstr="-inInv2 %s", desc="Inv2 Image")
in_t1 = traits.File(exists=True, argstr="-inT1 %s", desc="T1 Map image")
in_t1_weighted = traits.File(exists=True, argstr="-inT1weighted %s", desc="T1-Weighted Image")
out_brain_mask = traits.File(
"brain_mask.nii.gz", usedefault=True, argstr="-outBrain %s", desc="Path/name of brain mask"
)
out_masked_t1 = traits.Bool(True, usedefault=True, argstr="-outMasked %s", desc="Create masked T1")
out_masked_t1_weighted = traits.Bool(
True, usedefault=True, argstr="-outMasked2 %s", desc="Path/name of masked T1-weighted image"
)
out_masked_filter_image = traits.Bool(
