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ERROR: test_vessel_particles_mask_workflow.test_vessel_particles_mask_workflow
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Traceback (most recent call last):
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests/test_vessel_particles_mask_workflow.py", line 19, in test_vessel_particles_mask_workflow
wf.run()
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/engine/workflows.py", line 597, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 57, in run
report_nodes_not_run(notrun)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py", line 95, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. '
RuntimeError: Workflow did not execute cleanly. Check log for details
-------------------- >> begin captured logging << --------------------
workflow: INFO: ['check', 'execution', 'logging']
workflow: INFO: Running serially.
workflow: INFO: Executing node compute_feature_strength in dir: /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpqCxArD/VesselParticlesMaskWorkflow/compute_feature_strength
workflow: INFO: Running: ComputeFeatureStrength --C 245.000000 --alpha 0.630000 --alphase 0.250000 --beta 0.510000 --betase 0.100000 --feature RidgeLine --inFileName /Users/acil-user/Projects/CIP-build/CIP-build/Testing/Data/Input/vessel.nrrd --kappa 0.500000 --method Frangi --nu 0.000000 --outFileName /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpaqnFLU/vessel_strength.nhdr --ssm 1.000000 --std 0.7,4.0,7.0 --threads 0
interface: INFO: stdout 2016-12-09T23:05:38.925126: ComputeFeatureStrength [--returnparameterfile <std::string>]
interface: INFO: stdout 2016-12-09T23:05:38.925126: [--processinformationaddress <std::string>]
interface: INFO: stdout 2016-12-09T23:05:38.925126: [--xml] [--echo] [--betase <double>] [--kappa
interface: INFO: stdout 2016-12-09T23:05:38.925126: <double>] [--nu <double>] [--alphase <double>]
interface: INFO: stdout 2016-12-09T23:05:38.925126: [--C <double>] [--beta <double>] [--alpha
interface: INFO: stdout 2016-12-09T23:05:38.925126: <double>] [-f <RidgeLine|ValleyLine|RidgeSurface
interface: INFO: stdout 2016-12-09T23:05:38.925126: |ValleySurface>] [-m <Frangi|StrainEnergy
interface: INFO: stdout 2016-12-09T23:05:38.925126: |ModifiedKrissian|Descoteaux|FrangiXiao
interface: INFO: stdout 2016-12-09T23:05:38.925126: |DescoteauxXiao>] [--threads <int>]
interface: INFO: stdout 2016-12-09T23:05:38.925126: [--rescaleOff] [--ssm <0|1>] [--std
interface: INFO: stdout 2016-12-09T23:05:38.925126: <std::vector<double>>] [--outScaleFileName
interface: INFO: stdout 2016-12-09T23:05:38.925126: <std::string>] [-o <std::string>] [-i
interface: INFO: stdout 2016-12-09T23:05:38.925126: <std::string>] [--] [--version] [-h]
interface: INFO: stderr 2016-12-09T23:05:38.926011:PARSE ERROR: Argument: (--ssm)
interface: INFO: stderr 2016-12-09T23:05:38.926011: Couldn't read argument value from string '1.000000'
interface: INFO: stderr 2016-12-09T23:05:38.926011:
interface: INFO: stderr 2016-12-09T23:05:38.926011:Brief USAGE:
interface: INFO: stderr 2016-12-09T23:05:38.926011:
interface: INFO: stderr 2016-12-09T23:05:38.926011:For complete USAGE and HELP type:
interface: INFO: stderr 2016-12-09T23:05:38.926011: ComputeFeatureStrength --help
interface: INFO: stderr 2016-12-09T23:05:38.926011:
workflow: ERROR: ['Node compute_feature_strength failed to run on host bwh002376.bwh.harvard.edu.']
workflow: INFO: Saving crash info to /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests/crash-20161209-230539-acil-user-compute_feature_strength-63636d80-4efc-4773-bd68-d36c3a8c4cd9.pklz
workflow: INFO: Traceback (most recent call last):
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 39, in run
node.run(updatehash=updatehash)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 394, in run
self._run_interface()
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 504, in _run_interface
self._result = self._run_command(execute)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/pipeline/engine/nodes.py", line 630, in _run_command
result = self._interface.run()
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
runtime = self._run_wrapper(runtime)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper
runtime = self._run_interface(runtime)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface
self.raise_exception(runtime)
File "/Users/acil-user/Projects/CIP-build/CIPPython-install/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception
raise RuntimeError(message)
RuntimeError: Command:
ComputeFeatureStrength --C 245.000000 --alpha 0.630000 --alphase 0.250000 --beta 0.510000 --betase 0.100000 --feature RidgeLine --inFileName /Users/acil-user/Projects/CIP-build/CIP-build/Testing/Data/Input/vessel.nrrd --kappa 0.500000 --method Frangi --nu 0.000000 --outFileName /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpaqnFLU/vessel_strength.nhdr --ssm 1.000000 --std 0.7,4.0,7.0 --threads 0
Standard output:
ComputeFeatureStrength [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>]
[--xml] [--echo] [--betase <double>] [--kappa
<double>] [--nu <double>] [--alphase <double>]
[--C <double>] [--beta <double>] [--alpha
<double>] [-f <RidgeLine|ValleyLine|RidgeSurface
|ValleySurface>] [-m <Frangi|StrainEnergy
|ModifiedKrissian|Descoteaux|FrangiXiao
|DescoteauxXiao>] [--threads <int>]
[--rescaleOff] [--ssm <0|1>] [--std
<std::vector<double>>] [--outScaleFileName
<std::string>] [-o <std::string>] [-i
<std::string>] [--] [--version] [-h]
Standard error:
PARSE ERROR: Argument: (--ssm)
Couldn't read argument value from string '1.000000'
Brief USAGE:
For complete USAGE and HELP type:
ComputeFeatureStrength --help
Return code: 1
Interface ComputeFeatureStrength failed to run.
workflow: INFO: Executing node compute_distance_transform in dir: /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpHYBWRd/VesselParticlesMaskWorkflow/compute_distance_transform
workflow: INFO: Running: ComputeDistanceMap --distanceMap /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpaqnFLU/vessel_distanceMap.nhdr --labelMap /Users/acil-user/Projects/CIP-build/CIP-build/Testing/Data/Input/vessel_volumeMask.nrrd
interface: INFO: stdout 2016-12-09T23:05:39.974522:Reading label map...
interface: INFO: stdout 2016-12-09T23:05:39.974522:Skipping downsampling...
interface: INFO: stdout 2016-12-09T23:05:39.974522:Computing distance map...
interface: INFO: stdout 2016-12-09T23:05:39.974522:Writing to file...
interface: INFO: stdout 2016-12-09T23:05:39.974522:DONE.
workflow: INFO: Executing node unu_2op_lt in dir: /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpMEhsco/VesselParticlesMaskWorkflow/unu_2op_lt
workflow: INFO: Running: unu 2op lt /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpaqnFLU/vessel_distanceMap.nhdr -2.000000 --output /var/folders/gj/9q4d_d3s3r34xj5yqjvfh_s00000gp/T/tmpaqnFLU/vessel_featureMask.nhdr --type short
workflow: INFO: ***********************************
workflow: ERROR: could not run node: VesselParticlesMaskWorkflow.compute_feature_strength
workflow: INFO: crashfile: /Users/acil-user/Projects/CIP-build/CIP-build/cip_python/nipype/workflows/tests/crash-20161209-230539-acil-user-compute_feature_strength-63636d80-4efc-4773-bd68-d36c3a8c4cd9.pklz
workflow: INFO: ***********************************
--------------------- >> end captured logging << ---------------------
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Ran 1 test in 3.169s
FAILED (errors=1)
