如何使用NiPype連接兩個簡單的函數？

Question

我試圖用NiPype替換我們的內部管道基礎設施。

作爲測試，我想連接到簡單的功能，其中所述第一獲取的輸入端和一些計算之後返回其被用於第二功能的輸入的輸出：

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') 

我得到以下錯誤：

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' 

如果我只是運行pipeline.run（），然後我得到這個錯誤：

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 

我該怎麼辦？

謝謝！

Answer 1

試試這個：

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() 

基本上你沒有這兩個節點連接在一起，你想設置的輸入爲run（）方法的參數，而不是在節點級別設置它們的。希望這可以幫助。