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 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 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 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 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 'baseline' in master_config['components'] or 'longitudinal' 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
if 'baseline' in master_config['components']:
current_phase = 'baseline'
atlasNode = MakeAtlasNode(master_config['atlascache'], 'BAtlas')
elif 'longitudinal' in master_config['components']:
current_phase = 'longitudinal'
atlasNode = GetAtlasNode(master_config['previouscache'], 'BAtlas')
from longitudinal import create_longitudinal 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 '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 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')]),
])
assert current_phase == 'longitudinal', "Phase value is unknown: {0}".format(current_phase)
if not True:
return print_workflow(subjectWorkflow,
plugin=master_config['execution']['plugin'], dotfilename='subjectWorkflow') #, graph2use='flat')
return run_workflow(subjectWorkflow, plugin=master_config['execution']['plugin'], plugin_args=master_config['plugin_args'])
