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Generate the registration resource in the parent workflow.
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FredLoney committed May 25, 2017
1 parent 03aee18 commit 3bc2cfa
Showing 1 changed file with 49 additions and 49 deletions.
98 changes: 49 additions & 49 deletions qipipe/pipeline/qipipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -372,17 +372,33 @@ def __init__(self, project, subject, session, scan, actions, **opts):
else:
self.collection = None

self.registration_resource = opts.pop('registration_resource', None)
# Capture the registration resource name, or generate if
# necessary. The registration resource name is created
# here rather than by the registration workflow, since
# it the registration time series is built and uploaded
# in the supervisory workflow.
reg_rsc_opt = opts.pop('registration_resource', None)
if reg_rsc_opt:
reg_rsc = reg_rsc_opt
elif 'register' in actions:
reg_rsc = registration.generate_resource_name()
self.logger.debug(
"Generated %s %s scan %d registration resource name %s." %
(subject, session, scan, reg_rsc)
)
else:
reg_rsc = None
self.registration_resource = reg_rsc
"""The registration resource name."""

reg_tech_opt = opts.pop('registration_technique', None)
reg_tech = reg_tech_opt.lower() if reg_tech_opt else None
if 'register' in actions and not reg_tech:
raise PipelineError('The registration technique was not'
' specified.')
self.registration_technique = reg_tech
"""The registration technique."""

if 'register' in actions and not self.registration_technique:
raise PipelineError('The registration technique was not specified.')

self.modeling_resource = opts.pop('modeling_resource', None)
"""The modeling XNAT resource name."""

Expand Down Expand Up @@ -490,53 +506,43 @@ def run_with_scan_download(self, project, subject, session, scan, actions):
" scan %d volumes" %
(project, subject, session, scan))

# If the registration resource already exists in XNAT, then
# partition the scan image file names into those which are
# already registered and those which need to be registered.
if self.registration_resource:
registered, unregistered = self._partition_registered(
xnat, project, subject, session, scan, scan_volumes
)
else:
registered = []
unregistered = scan_volumes
registered, unregistered = self._partition_registered(
xnat, project, subject, session, scan, scan_volumes
)

# Validate and log the partition.
if 'register' in actions:
if registered:
if unregistered:
self.logger.debug("Skipping registration of %d"
" previously registered %s %s %s"
" scan %d volumes:" %
(len(registered), project, subject,
session, scan))
self.logger.debug(
"Skipping registration of %d previously"
" registered %s %s scan %d volumes:" %
(len(registered), subject, session, scan)
)
self.logger.debug("%s" % registered)
else:
self.logger.debug("Skipping %s %s %s scan %d"
" registration, since all volumes"
" are already registered." %
(project, subject, session, scan))
self.logger.debug(
"Skipping %s %s scan %d registration, since"
" all volumes are already registered." %
(subject, session, scan)
)
if unregistered:
self.logger.debug("Registering %d %s %s %s scan %d"
" volumes:" %
(len(unregistered), project, subject,
session, scan))
self.logger.debug(
"Registering the following %d %s %s scan %d volumes:" %
(len(unregistered), subject, session, scan)
)
self.logger.debug("%s" % sorted(unregistered))
elif unregistered and self.registration_resource:
self.logger.error("The pipeline %s %s %s scan %d register"
" action is not specified but there are"
" %d unregistered volumes:" %
(project, subject, session, scan,
len(unregistered)))
self.logger.error(str(sorted(unregistered)))
raise ArgumentError("The pipeline %s %s %s scan %d register"
" action is not specified but there are"
" unregistered volumes" %
(project, subject, session, scan))
raise ArgumentError(
"The pipeline %s %s scan %d register action is not"
" specified but there are %d unregistered scan volumes"
" not in the %s registration resource" %
(subject, session, scan, len(unregistered),
self.registration_resource)
)
else:
self.logger.debug("Processing %d %s %s %s scan %d volumes:" %
(len(registered), project, subject, session,
scan))
self.logger.debug("Processing %d %s %s scan %d volumes:" %
(len(registered), subject, session, scan))
self.logger.debug("%s" % sorted(registered))

# Set the workflow input.
Expand Down Expand Up @@ -573,15 +579,10 @@ def _partition_registered(self, xnat, project, subject, session, scan,
# The XNAT registration object.
reg_obj = xnat.find_one(project, subject, session, scan=scan,
resource=self.registration_resource)
if not reg_obj:
raise ArgumentError("The %s %s scan %d registration resource"
" %s does not exist in XNAT" %
(subject, session, scan,
self.registration_resource))

# The realigned files.
registered = set(reg_obj.files().get())
# The unregistered volume numbers.
registered = set(reg_obj.files().get()) if reg_obj else []
# The unregistered files.
unregistered = set(files) - registered
self.logger.debug("The %s %s scan %d resource has %d registered volumes"
" and %d unregistered volumes." %
Expand Down Expand Up @@ -656,8 +657,7 @@ def _create_workflow(self, subject, session, scan, actions, **opts):
# parent, since Nipype Function arguments must be
# primitive.
reg_opts = self._child_options()
if self.registration_resource:
reg_opts['resource'] = self.registration_resource
reg_opts['resource'] = self.registration_resource
reg_opts['technique'] = self.registration_technique
if 'recursive_registration' in opts:
reg_opts['recursive'] = opts['recursive_registration']
Expand Down

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