WorkupT1T2PERSISTANCE_CHECK.py

#!/usr/bin/env python

from nipype.interfaces.base import CommandLine, CommandLineInputSpec, TraitedSpec, File, Directory
from nipype.interfaces.base import traits, isdefined, BaseInterface
from nipype.interfaces.utility import Merge, Split, Function, Rename, IdentityInterface
import nipype.interfaces.io as nio   # Data i/o
import nipype.pipeline.engine as pe  # pypeline engine

from SEMTools import *

"""
    from WorkupT1T2PERSISTANCE_CHECK import CreatePERSISTANCE_CHECKWorkflow
    myLocalPERSISTANCE_CHECKWF= CreatePERSISTANCE_CHECKWorkflow("999999_PersistanceCheckingWorkflow")
    PERSISTANCE_CHECKWF.connect(SplitAvgBABC,'avgBABCT1',myLocalPERSISTANCE_CHECKWF,'fixedVolume')
    PERSISTANCE_CHECKWF.connect(BABC,'outputLabels',myLocalPERSISTANCE_CHECKWF,'fixedBinaryVolume')
    PERSISTANCE_CHECKWF.connect(BAtlas,'template_t1',myLocalPERSISTANCE_CHECKWF,'movingVolume')
    PERSISTANCE_CHECKWF.connect(BAtlas,'template_brain',myLocalPERSISTANCE_CHECKWF,'movingBinaryVolume')
    PERSISTANCE_CHECKWF.connect(BLI,'outputTransformFilename',myLocalPERSISTANCE_CHECKWF,'initialTransform')
"""


def CreatePERSISTANCE_CHECKWorkflow(WFname):
    """ The purpose of this workflow is to debug the automatic deletion of files from the output directory.
    """
    PERSISTANCE_CHECKWF = pe.Workflow(name=WFname)

    inputsSpec = pe.Node(interface=IdentityInterface(fields=['fixedVolume', 'fixedBinaryVolume', 'movingVolume', 'movingBinaryVolume', 'initialTransform']), name='inputspec')
    PERSISTANCE_CHECKWF.connect(inputsSpec, 'subject_id', fs_reconall, 'subject_id')
    PERSISTANCE_CHECKWF.connect(inputsSpec, 'T1_files', fs_reconall, 'T1_files')

    print("DOING FILE PERSISTANCE CHECK")
    PERSISTANCE_CHECK = pe.Node(interface=BRAINSFit(), name="99999_PERSISTANCE_CHECK_PERSISTANCE_CHECK")
    PERSISTANCE_CHECK.inputs.costMetric = "MMI"
    PERSISTANCE_CHECK.inputs.debugLevel = 10
    PERSISTANCE_CHECK.inputs.maskProcessingMode = "ROI"
    PERSISTANCE_CHECK.inputs.numberOfSamples = 1000
    PERSISTANCE_CHECK.inputs.numberOfIterations = [1500]
    PERSISTANCE_CHECK.inputs.numberOfHistogramBins = 50
    PERSISTANCE_CHECK.inputs.maximumStepLength = 0.2
    PERSISTANCE_CHECK.inputs.minimumStepLength = [0.005]
    PERSISTANCE_CHECK.inputs.transformType = ["Affine"]
    PERSISTANCE_CHECK.inputs.maxBSplineDisplacement = 7
    PERSISTANCE_CHECK.inputs.maskInferiorCutOffFromCenter = 65
    PERSISTANCE_CHECK.inputs.splineGridSize = [28, 20, 24]
    PERSISTANCE_CHECK.inputs.outputVolume = "Trial_Initializer_Output.nii.gz"
    PERSISTANCE_CHECK.inputs.outputTransform = "Trial_Initializer_Output.h5"

    PERSISTANCE_CHECKWF.connect(inputsSpec, 'fixedVolume', PERSISTANCE_CHECK, 'fixedVolume')
    PERSISTANCE_CHECKWF.connect(inputsSpec, 'fixedBinaryVolume', PERSISTANCE_CHECK, 'fixedBinaryVolume')
    PERSISTANCE_CHECKWF.connect(inputsSpec, 'movingVolume', PERSISTANCE_CHECK, 'movingVolume')
    PERSISTANCE_CHECKWF.connect(inputsSpec, 'movingBinaryVolume', PERSISTANCE_CHECK, 'movingBinaryVolume')
    PERSISTANCE_CHECKWF.connect(inputsSpec, 'initialTransform', PERSISTANCE_CHECK, 'initialTransform')

    outputsSpec = pe.Node(interface=IdentityInterface(fields=['outputVolume', 'outputTransform']), name='outputspec')

    return PERSISTANCE_CHECKWF