Ejemplos de sub en Python

Ejemplo n.º 1

Archivo: WorkupT1T2.py Proyecto: gec1/BRAINSStandAlone

def GenerateSubjectOutputPattern(subjectid):
    """ This function generates output path substitutions for workflows and nodes that conform to a common standard.
HACK:  [('ANTSTemplate/Iteration02_Reshaped.nii.gz', 'SUBJECT_TEMPLATES/0668/T1_RESHAPED.nii.gz'),
('ANTSTemplate/_ReshapeAveragePassiveImageWithShapeUpdate[0-9]*', 'SUBJECT_TEMPLATES/0668')]
subs=r'test/\g<project>/\g<subject>/\g<session>'
pe.sub(subs,test)
pat=r'foo/_uid_(?P<project>PHD_[0-9][0-9][0-9])_(?P<subject>[0-9][0-9][0-9][0-9])_(?P<session>[0-9][0-9][0-9][0-9][0-9])'
pe=re.compile(pat)
pe.sub(subs,test)
test
test='foo/_uid_PHD_024_0003_12345'
pe.sub(subs,test)
pat=r'(?P<modulename>[^/]*)/_uid_(?P<project>PHD_[0-9][0-9][0-9])_(?P<subject>[0-9][0-9][0-9][0-9])_(?P<session>[0-9][0-9][0-9][0-9][0-9])'
subs=r'test/\g<project>/\g<subject>/\g<session>/\g<modulename>'
pe.sub(subs,test)
pe=re.compile(pat)
pe.sub(subs,test)

"""
    patternList=[]

    find_pat=os.path.join('ANTSTemplate','Iteration02_Reshaped.nii.gz')
    replace_pat=os.path.join('SUBJECT_TEMPLATES',subjectid,r'AVG_T1.nii.gz')
    patternList.append( (find_pat,replace_pat) )

    find_pat=os.path.join('ANTSTemplate',r'_ReshapeAveragePassiveImageWithShapeUpdate[0-9]*/AVG_[A-Z0-9]*WARP_(?P<structure>AVG_[A-Z0-9]*.nii.gz)')
    replace_pat=os.path.join('SUBJECT_TEMPLATES',subjectid,r'\g<structure>')
    patternList.append( (find_pat,replace_pat) )

    find_pat=os.path.join('ANTSTemplate',r'CLIPPED_AVG_[A-Z]*WARP_(?P<structure>AVG_[A-Z]*.nii.gz)')
    replace_pat=os.path.join('SUBJECT_TEMPLATES',subjectid,r'\g<structure>')
    patternList.append( (find_pat,replace_pat) )

    print "HACK: ", patternList
    return patternList

Ejemplo n.º 2

def GenerateSubjectOutputPattern(subjectid):
    """ This function generates output path substitutions for workflows and nodes that conform to a common standard.
HACK:  [('ANTSTemplate/Iteration02_Reshaped.nii.gz', 'SUBJECT_TEMPLATES/0668/T1_RESHAPED.nii.gz'),
('ANTSTemplate/_ReshapeAveragePassiveImageWithShapeUpdate[0-9]*', 'SUBJECT_TEMPLATES/0668')]
subs=r'test/\g<project>/\g<subject>/\g<session>'
pe.sub(subs,test)
pat=r'foo/_uid_(?P<project>PHD_[0-9][0-9][0-9])_(?P<subject>[0-9][0-9][0-9][0-9])_(?P<session>[0-9][0-9][0-9][0-9][0-9])'
pe=re.compile(pat)
pe.sub(subs,test)
test
test='foo/_uid_PHD_024_0003_12345'
pe.sub(subs,test)
pat=r'(?P<modulename>[^/]*)/_uid_(?P<project>PHD_[0-9][0-9][0-9])_(?P<subject>[0-9][0-9][0-9][0-9])_(?P<session>[0-9][0-9][0-9][0-9][0-9])'
subs=r'test/\g<project>/\g<subject>/\g<session>/\g<modulename>'
pe.sub(subs,test)
pe=re.compile(pat)
pe.sub(subs,test)

"""
    patternList = []

    find_pat = os.path.join('ANTSTemplate', 'Iteration02_Reshaped.nii.gz')
    replace_pat = os.path.join('SUBJECT_TEMPLATES', subjectid,
                               r'AVG_T1.nii.gz')
    patternList.append((find_pat, replace_pat))

    find_pat = os.path.join(
        'ANTSTemplate',
        r'_ReshapeAveragePassiveImageWithShapeUpdate[0-9]*/AVG_[A-Z0-9]*WARP_(?P<structure>AVG_[A-Z0-9]*.nii.gz)'
    )
    replace_pat = os.path.join('SUBJECT_TEMPLATES', subjectid,
                               r'\g<structure>')
    patternList.append((find_pat, replace_pat))

    find_pat = os.path.join(
        'ANTSTemplate',
        r'CLIPPED_AVG_[A-Z]*WARP_(?P<structure>AVG_[A-Z]*.nii.gz)')
    replace_pat = os.path.join('SUBJECT_TEMPLATES', subjectid,
                               r'\g<structure>')
    patternList.append((find_pat, replace_pat))

    print "HACK: ", patternList
    return patternList

Ejemplo n.º 3

Archivo: WorkupT1T2SingleSubjectPhaseII.py Proyecto: aghayoor/BRAINSTools

        T1T2WorkupSingle.write_graph()
    except:
        pass
    """

    return T1T2WorkupSingle

#############
## The following are just notes, and not really part of this script.
##
        # T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputLandmarksInACPCAlignedSpace', T1T2WorkupSingleDataSink,'foo.@outputLandmarksInACPCAlignedSpace')
        # T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputResampledVolume', T1T2WorkupSingleDataSink,'foo.@outputResampledVolume')
        # T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputLandmarksInInputSpace', T1T2WorkupSingleDataSink,'foo.@outputLandmarksInInputSpace')
        # T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputTransform', T1T2WorkupSingleDataSink,'foo.@outputTransform')
        # T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputMRML', T1T2WorkupSingleDataSink,'foo.@outputMRML')
"""
    subs=r'test/\g<project>/\g<subject>/\g<session>'
pe.sub(subs,test)
pat=r'foo/_uid_(?P<project>PHD_[0-9][0-9][0-9])_(?P<subject>[0-9][0-9][0-9][0-9])_(?P<session>[0-9][0-9][0-9][0-9][0-9])'
pe=re.compile(pat)
pe.sub(subs,test)
test
test='foo/_uid_PHD_024_0003_12345'
pe.sub(subs,test)
pat=r'(?P<modulename>[^/]*)/_uid_(?P<project>PHD_[0-9][0-9][0-9])_(?P<subject>[0-9][0-9][0-9][0-9])_(?P<session>[0-9][0-9][0-9][0-9][0-9])'
subs=r'test/\g<project>/\g<subject>/\g<session>/\g<modulename>'
pe.sub(subs,test)
pe=re.compile(pat)
pe.sub(subs,test)

"""

Ejemplo n.º 4

Archivo: WorkupT1T2SingleSubjectPhaseII.py Proyecto: pieper/BRAINSTools

    except:
        pass
    """

    return T1T2WorkupSingle


#############
## The following are just notes, and not really part of this script.
##
# T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputLandmarksInACPCAlignedSpace', T1T2WorkupSingleDataSink,'foo.@outputLandmarksInACPCAlignedSpace')
# T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputResampledVolume', T1T2WorkupSingleDataSink,'foo.@outputResampledVolume')
# T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputLandmarksInInputSpace', T1T2WorkupSingleDataSink,'foo.@outputLandmarksInInputSpace')
# T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputTransform', T1T2WorkupSingleDataSink,'foo.@outputTransform')
# T1T2WorkupSingle.connect(myLocalLMIWF, 'outputspec.outputMRML', T1T2WorkupSingleDataSink,'foo.@outputMRML')
"""
    subs=r'test/\g<project>/\g<subject>/\g<session>'
pe.sub(subs,test)
pat=r'foo/_uid_(?P<project>PHD_[0-9][0-9][0-9])_(?P<subject>[0-9][0-9][0-9][0-9])_(?P<session>[0-9][0-9][0-9][0-9][0-9])'
pe=re.compile(pat)
pe.sub(subs,test)
test
test='foo/_uid_PHD_024_0003_12345'
pe.sub(subs,test)
pat=r'(?P<modulename>[^/]*)/_uid_(?P<project>PHD_[0-9][0-9][0-9])_(?P<subject>[0-9][0-9][0-9][0-9])_(?P<session>[0-9][0-9][0-9][0-9][0-9])'
subs=r'test/\g<project>/\g<subject>/\g<session>/\g<modulename>'
pe.sub(subs,test)
pe=re.compile(pat)
pe.sub(subs,test)

"""