work_dir = os.path.join(os.getcwd(), 'working')
wf.base_dir = work_dir
datasink.inputs.base_directory = os.path.join(work_dir, 'output')
wf.config['execution'] = dict(crashdump_dir=os.path.join(work_dir,
'crashdumps'),
stop_on_first_crash=True)
#wf.run('MultiProc', plugin_args={'n_procs': 4})
eg = wf.run('Linear')
wf.export('openfmri.py')
wf.write_graph(dotfilename='hgraph.dot', graph2use='hierarchical')
wf.write_graph(dotfilename='egraph.dot', graph2use='exec')
wf.write_graph(dotfilename='fgraph.dot', graph2use='flat')
wf.write_graph(dotfilename='ograph.dot', graph2use='orig')
return eg
if __name__ == '__main__':
import argparse
parser = argparse.ArgumentParser(prog='fmri_openfmri.py',
description=__doc__)
parser.add_argument('-d', '--datasetdir', required=True)
parser.add_argument('-s', '--subject', default=None)
parser.add_argument('-m', '--model', default=1)
parser.add_argument('-t', '--task', default=1)
args = parser.parse_args()
eg = analyze_openfmri_dataset(data_dir=os.path.abspath(args.datasetdir),
subject=args.subject,
model_id=int(args.model),
task_id=int(args.task))
from nipype.pipeline.utils import write_prov
g = write_prov(eg, format='turtle')
return
if 'shouldfail' in testspec and testspec['shouldfail'] == True:
self.assertThat(e,
Annotate("an expected failure did not occur in test '%s': %s (%s)"
% (testid, str(e), e.__class__.__name__),
Equals(None)))
finally:
execinfo['stdout'] = capture_stdout.getvalue()
execinfo['stderr'] = capture_stderr.getvalue()
sys.stdout = rescue_stdout
sys.stderr = rescue_stderr
# try dumping provenance info
try:
from nipype.pipeline.utils import write_prov
write_prov(exec_graph,
filename=opj(workflow.base_dir, 'provenance.json'))
except ImportError:
lgr.debug("local nipype version doesn't support provenance capture")
def _check_output_presence(self, spec):
outspec = spec.get('outputs', {})
unmatched_output = []
for ospec_id in outspec:
ospec = outspec[ospec_id]
ospectype = ospec['type']
if ospectype == 'file':
self.assertThat(
ospec['value'],
Annotate('expected output file missing', FileExists()))
elif ospectype == 'directory':
self.assertThat(
e,
Annotate(
"an expected failure did not occur in test '%s': %s (%s)"
% (testid, str(e), e.__class__.__name__),
Equals(None)))
finally:
execinfo['stdout'] = capture_stdout.getvalue()
execinfo['stderr'] = capture_stderr.getvalue()
sys.stdout = rescue_stdout
sys.stderr = rescue_stderr
# try dumping provenance info
try:
from nipype.pipeline.utils import write_prov
write_prov(exec_graph,
filename=opj(workflow.base_dir, 'provenance.json'))
except ImportError:
lgr.debug(
"local nipype version doesn't support provenance capture")
def _check_output_presence(self, spec):
outspec = spec.get('outputs', {})
unmatched_output = []
for ospec_id in outspec:
ospec = outspec[ospec_id]
ospectype = ospec['type']
if ospectype == 'file':
self.assertThat(
ospec['value'],
Annotate('expected output file missing', FileExists()))
elif ospectype == 'directory':
def _execute_nipype_test(self, testid, testspec):
# TODO merge/refactor this one with the plain python code method
from cStringIO import StringIO
import sys
execinfo = self._details['exec_info'][testid]
try:
import nipype
except ImportError:
self.skipTest("Nipype not found, skipping test")
# where is the workflow
if 'file' in testspec:
testwffilepath = testspec['file']
lgr.debug("using custom workflow file name '%s'" % testwffilepath)
else:
testwffilepath = 'workflow.py'
lgr.debug("using default workflow file name '%s'" % testwffilepath)
# execute the script and extract the workflow
locals = dict()
try:
execfile(testwffilepath, dict(), locals)
except Exception as e:
lgr.error("%s: %s" % (e.__class__.__name__, str(e)))
self.assertThat(e,
Annotate("test workflow setup failed: %s (%s)"
% (e.__class__.__name__, str(e)), Equals(None)))
self.assertThat(locals,
Annotate("test workflow script create expected workflow object",
Contains('test_workflow')))
workflow = locals['test_workflow']
# make sure nipype executes it in the right place
workflow.base_dir=os.path.abspath(opj(os.curdir, '_workflow_exec'))
# we want content, not time based hashing
if 'execution' in workflow.config:
workflow.config['execution']['hash_method'] = "content"
else:
workflow.config['execution'] = dict(hash_method="content")
# execution
try:
rescue_stdout = sys.stdout
rescue_stderr = sys.stderr
sys.stdout = capture_stdout = StringIO()
sys.stderr = capture_stderr = StringIO()
try:
exec_graph = workflow.run()
except Exception as e:
execinfo['exception'] = dict(type=e.__class__.__name__,
info=str(e))
if not 'shouldfail' in testspec or testspec['shouldfail'] == False:
lgr.error("%s: %s" % (e.__class__.__name__, str(e)))
self.assertThat(e,
Annotate("exception occured while executing Nipype workflow in test '%s': %s (%s)"
% (testid, str(e), e.__class__.__name__),
Equals(None)))
return
if 'shouldfail' in testspec and testspec['shouldfail'] == True:
self.assertThat(e,
Annotate("an expected failure did not occur in test '%s': %s (%s)"
% (testid, str(e), e.__class__.__name__),
Equals(None)))
finally:
execinfo['stdout'] = capture_stdout.getvalue()
execinfo['stderr'] = capture_stderr.getvalue()
sys.stdout = rescue_stdout
sys.stderr = rescue_stderr
# try dumping provenance info
try:
from nipype.pipeline.utils import write_prov
write_prov(exec_graph,
filename=opj(workflow.base_dir, 'provenance.json'))
except ImportError:
lgr.debug("local nipype version doesn't support provenance capture")