I am trying to replace our internal pipeline infrastructure with NiPype.
As a test, I want to connect to simple functions where the first gets an input and after some calculation returns an output which gets used for the second function as an input:
import numpy
import nipype.pipeline.engine as pe
from nipype.interfaces.utility import Function
from pipyTestWheels import *
def Connectivity( dtiVolume ):
print " CONNECTIVITY1::START"
print "reading dti Volume " + dtiVolume
print ">>> performing connectivity *nom*nom*nom*"
a = numpy.zeros( ( 1000, 1000 ) )
print " CONNECTIVITY1::END"
trkFile = 'another trk file'
return trkFile
def RegisterFibers( trkFile ):
print " REGISTERFIBERS::START"
print "reading trk File " + trkFile
print ">>> performing trkFile registration"
trkFileRegistered = '/tmp/tracksRegistered.trk'
print " REGISTERFIBERS::END"
return trkFileRegistered
def test():
ConnectivityNode = pe.Node( name='connectivity', interface=Function( function=Connectivity, input_names=['dtiVolume'], output_names=['trkFile'] ) )
RegisterFibersNode = pe.Node( name='registerFibers', interface=Function( function=RegisterFibers, input_names=['trkFile'], output_names=['trkFileRegistered'] ) )
pipeline = pe.Workflow( name='testWf' )
pipeline.add_nodes( [ConnectivityNode, RegisterFibersNode] )
pipeline.run( dtiVolume='safsafa' )
I get the following error:
Traceback (most recent call last):
File "pipyTestNipype.py", line 65, in <module>
test()
File "pipyTestNipype.py", line 46, in test
pipeline.run( dtiVolume='safsafa' )
TypeError: run() got an unexpected keyword argument 'dtiVolume'
If I just run pipeline.run(), then I get this error:
INFO:workflow:['execution', 'logging']
INFO:workflow:Running serially.
INFO:workflow:Executing node registerFibers in dir: /tmp/tmpxpW0lR/testWf/registerFibers
ERROR:workflow:['Node registerFibers failed to run on host ipmi.']
INFO:workflow:Saving crash info to /net/pretoria/local_mount/space/pretoria/2/chb/users/daniel.haehn/Projects/scripts/crash-20120215-101717-daniel.haehn-registerFibers.npz
INFO:workflow:Traceback (most recent call last):
File "/usr/lib/pymodules/python2.7/nipype/pipeline/plugins/linear.py", line 35, in run
node.run(updatehash=updatehash)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1141, in run
self._run_interface(execute=True)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1161, in _run_interface
self._result = self._run_command(execute)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1253, in _run_command
result = self._interface.run()
File "/usr/lib/pymodules/python2.7/nipype/interfaces/base.py", line 775, in run
runtime = self._run_interface(runtime)
File "/usr/lib/pymodules/python2.7/nipype/interfaces/utility.py", line 382, in _run_interface
out = function_handle(**args)
TypeError: RegisterFibers() takes exactly 1 argument (0 given)
Interface Function failed to run.
INFO:workflow:Executing node connectivity in dir: /tmp/tmptN84LP/testWf/connectivity
ERROR:workflow:['Node connectivity failed to run on host ipmi.']
INFO:workflow:Saving crash info to /net/pretoria/local_mount/space/pretoria/2/chb/users/daniel.haehn/Projects/scripts/crash-20120215-101717-daniel.haehn-connectivity.npz
INFO:workflow:Traceback (most recent call last):
File "/usr/lib/pymodules/python2.7/nipype/pipeline/plugins/linear.py", line 35, in run
node.run(updatehash=updatehash)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1141, in run
self._run_interface(execute=True)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1161, in _run_interface
self._result = self._run_command(execute)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 1253, in _run_command
result = self._interface.run()
File "/usr/lib/pymodules/python2.7/nipype/interfaces/base.py", line 775, in run
runtime = self._run_interface(runtime)
File "/usr/lib/pymodules/python2.7/nipype/interfaces/utility.py", line 382, in _run_interface
out = function_handle(**args)
TypeError: Connectivity() takes exactly 1 argument (0 given)
Interface Function failed to run.
INFO:workflow:***********************************
ERROR:workflow:could not run node: testWf.registerFibers
INFO:workflow:crashfile: /net/pretoria/local_mount/space/pretoria/2/chb/users/daniel.haehn/Projects/scripts/crash-20120215-101717-daniel.haehn-registerFibers.npz
ERROR:workflow:could not run node: testWf.connectivity
INFO:workflow:crashfile: /net/pretoria/local_mount/space/pretoria/2/chb/users/daniel.haehn/Projects/scripts/crash-20120215-101717-daniel.haehn-connectivity.npz
INFO:workflow:***********************************
Traceback (most recent call last):
File "pipyTestNipype.py", line 65, in <module>
test()
File "pipyTestNipype.py", line 46, in test
pipeline.run()
File "/usr/lib/pymodules/python2.7/nipype/pipeline/engine.py", line 467, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/plugins/linear.py", line 49, in run
report_nodes_not_run(notrun)
File "/usr/lib/pymodules/python2.7/nipype/pipeline/plugins/base.py", line 81, in report_nodes_not_run
raise RuntimeError('Workflow did not execute cleanly. Check log for details')
RuntimeError: Workflow did not execute cleanly. Check log for details
What shall I do?
Thanks!
Try this:
import nipype.pipeline.engine as pe
from nipype.interfaces.utility import Function
def Connectivity(dtiVolume):
import numpy
print " CONNECTIVITY1::START"
print "reading dti Volume " + dtiVolume
print ">>> performing connectivity *nom*nom*nom*"
a = numpy.zeros((1000, 1000))
print " CONNECTIVITY1::END"
trkFile = 'another trk file'
return trkFile
def RegisterFibers(trkFile):
print " REGISTERFIBERS::START"
print "reading trk File " + trkFile
print ">>> performing trkFile registration"
trkFileRegistered = '/tmp/tracksRegistered.trk'
print " REGISTERFIBERS::END"
return trkFileRegistered
def test():
ConnectivityNode = pe.Node(name='connectivity', interface=Function(function=Connectivity, input_names=['dtiVolume'], output_names=['trkFile']))
ConnectivityNode.inputs.dtiVolume = 'safsafa'
RegisterFibersNode = pe.Node(name='registerFibers', interface=Function(function=RegisterFibers, input_names=['trkFile'], output_names=['trkFileRegistered']))
pipeline = pe.Workflow(name='testWf')
pipeline.connect(ConnectivityNode, 'trkFile', RegisterFibersNode, 'trkFile')
pipeline.run()
Basically you did not connect the two nodes together and you were trying to set inputs as a parameter of the run() method instead of setting them at the node level. Hope this helps.