nipype.interfaces.io module¶

class

>>> bg = BIDSDataGrabber() # doctest: +SKIP
>>> bg.inputs.base_dir = 'ds005/' # doctest: +SKIP
>>> bg.inputs.subject = '01' # doctest: +SKIP
>>> results = bg.run() # doctest: +SKIP

>>> bg = BIDSDataGrabber(infields = ['subject']) # doctest: +SKIP
>>> bg.inputs.base_dir = 'ds005/' # doctest: +SKIP
>>> bg.inputs.subject = '01' # doctest: +SKIP
>>> bg.inputs.output_query['dwi'] = dict(datatype='dwi') # doctest: +SKIP
>>> results = bg.run() # doctest: +SKIP

>>> from nipype.interfaces.io import DataFinder
>>> df = DataFinder()
>>> df.inputs.root_paths = '.'
>>> df.inputs.match_regex = r'.+/(?P<series_dir>.+(qT1|ep2d_fid_T1).+)/(?P<basename>.+)\.nii.gz'
>>> result = df.run() # doctest: +SKIP
>>> result.outputs.out_paths  # doctest: +SKIP
['./027-ep2d_fid_T1_Gd4/acquisition.nii.gz',
 './018-ep2d_fid_T1_Gd2/acquisition.nii.gz',
 './016-ep2d_fid_T1_Gd1/acquisition.nii.gz',
 './013-ep2d_fid_T1_pre/acquisition.nii.gz']
>>> result.outputs.series_dir  # doctest: +SKIP
['027-ep2d_fid_T1_Gd4',
 '018-ep2d_fid_T1_Gd2',
 '016-ep2d_fid_T1_Gd1',
 '013-ep2d_fid_T1_pre']
>>> result.outputs.basename  # doctest: +SKIP
['acquisition',
 'acquisition'
 'acquisition',
 'acquisition']

>>> from nipype.interfaces.io import DataGrabber

>>> dg = DataGrabber()
>>> dg.inputs.template = '*'

>>> dg.inputs.template = '%s/%s.dcm'
>>> dg.inputs.template_args['outfiles']=[['dicomdir','123456-1-1.dcm']]

>>> dg = DataGrabber(infields=['arg1','arg2'])
>>> dg.inputs.template = '%s/%s.nii'
>>> dg.inputs.arg1 = 'foo'
>>> dg.inputs.arg2 = 'foo'

>>> dg = DataGrabber(infields=['sid'], outfields=['func','struct','ref'])
>>> dg.inputs.base_directory = '.'
>>> dg.inputs.template = '%s/%s.nii'
>>> dg.inputs.template_args['func'] = [['sid',['f3','f5']]]
>>> dg.inputs.template_args['struct'] = [['sid',['struct']]]
>>> dg.inputs.template_args['ref'] = [['sid','ref']]
>>> dg.inputs.sid = 's1'

>>> dg.inputs.field_template = dict(struct='%s/struct.nii')
>>> dg.inputs.template_args['struct'] = [['sid']]

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'base_directory/container/parameterization/destloc/filename'

>>> ds = DataSink()
>>> ds.inputs.base_directory = 'results_dir'
>>> ds.inputs.container = 'subject'
>>> ds.inputs.structural = 'structural.nii'
>>> setattr(ds.inputs, 'contrasts.@con', ['cont1.nii', 'cont2.nii'])
>>> setattr(ds.inputs, 'contrasts.alt', ['cont1a.nii', 'cont2a.nii'])
>>> ds.run()  # doctest: +SKIP

>>> ds = DataSink(infields=['contasts.@con'])
>>> ds.inputs.base_directory = 'results_dir'
>>> ds.inputs.container = 'subject'
>>> ds.inputs.structural = 'structural.nii'
>>> setattr(ds.inputs, 'contrasts.@con', ['cont1.nii', 'cont2.nii'])
>>> setattr(ds.inputs, 'contrasts.alt', ['cont1a.nii', 'cont2a.nii'])
>>> ds.run()  # doctest: +SKIP

>>> from nipype.interfaces.io import ExportFile
>>> import os.path as op
>>> ef = ExportFile()
>>> ef.inputs.in_file = "T1.nii.gz"
>>> os.mkdir("output_folder")
>>> ef.inputs.out_file = op.abspath("output_folder/sub1_out.nii.gz")
>>> res = ef.run()
>>> os.path.exists(res.outputs.out_file)
True

>>> from nipype.interfaces.io import FreeSurferSource
>>> fs = FreeSurferSource()
>>> #fs.inputs.subjects_dir = '.'
>>> fs.inputs.subject_id = 'PWS04'
>>> res = fs.run() # doctest: +SKIP

>>> fs.inputs.hemi = 'lh'
>>> res = fs.run() # doctest: +SKIP

>>> import pprint
>>> from nipype.interfaces.io import JSONFileGrabber
>>> jsonSource = JSONFileGrabber()
>>> jsonSource.inputs.defaults = {'param1': 'overrideMe', 'param3': 1.0}
>>> res = jsonSource.run()
>>> pprint.pprint(res.outputs.get())
{'param1': 'overrideMe', 'param3': 1.0}
>>> jsonSource.inputs.in_file = os.path.join(datadir, 'jsongrabber.txt')
>>> res = jsonSource.run()
>>> pprint.pprint(res.outputs.get())  # doctest:, +ELLIPSIS
{'param1': 'exampleStr', 'param2': 4, 'param3': 1.0}

>>> jsonsink = JSONFileSink(input_names=['subject_id',
...                         'some_measurement'])
>>> jsonsink.inputs.subject_id = 's1'
>>> jsonsink.inputs.some_measurement = 11.4
>>> jsonsink.run() # doctest: +SKIP

>>> dictsink = JSONFileSink()
>>> dictsink.inputs.in_dict = {'subject_id': 's1',
...                            'some_measurement': 11.4}
>>> dictsink.run() # doctest: +SKIP

>>> sql = MySQLSink(input_names=['subject_id', 'some_measurement'])
>>> sql.inputs.database_name = 'my_database'
>>> sql.inputs.table_name = 'experiment_results'
>>> sql.inputs.username = 'root'
>>> sql.inputs.password = 'secret'
>>> sql.inputs.subject_id = 's1'
>>> sql.inputs.some_measurement = 11.4
>>> sql.run() # doctest: +SKIP

>>> s3grab = S3DataGrabber(infields=['subj_id'], outfields=["func", "anat"])
>>> s3grab.inputs.bucket = 'openneuro'
>>> s3grab.inputs.sort_filelist = True
>>> s3grab.inputs.template = '*'
>>> s3grab.inputs.anon = True
>>> s3grab.inputs.bucket_path = 'ds000101/ds000101_R2.0.0/uncompressed/'
>>> s3grab.inputs.local_directory = '/tmp'
>>> s3grab.inputs.field_template = {'anat': '%s/anat/%s_T1w.nii.gz',
...                                 'func': '%s/func/%s_task-simon_run-1_bold.nii.gz'}
>>> s3grab.inputs.template_args = {'anat': [['subj_id', 'subj_id']],
...                                'func': [['subj_id', 'subj_id']]}
>>> s3grab.inputs.subj_id = 'sub-01'
>>> s3grab.run()  # doctest: +SKIP

>>> sql = SQLiteSink(input_names=['subject_id', 'some_measurement'])
>>> sql.inputs.database_file = 'my_database.db'
>>> sql.inputs.table_name = 'experiment_results'
>>> sql.inputs.subject_id = 's1'
>>> sql.inputs.some_measurement = 11.4
>>> sql.run() # doctest: +SKIP

>>> from nipype.interfaces.io import SSHDataGrabber
>>> dg = SSHDataGrabber()
>>> dg.inputs.hostname = 'test.rebex.net'
>>> dg.inputs.user = 'demo'
>>> dg.inputs.password = 'password'
>>> dg.inputs.base_directory = 'pub/example'

>>> dg.inputs.template = '*'

>>> dg.inputs.template_expression = 'regexp'
>>> dg.inputs.template = 'pop[0-9].*'

>>> dg = SSHDataGrabber(infields=['arg1','arg2'])
>>> dg.inputs.hostname = 'test.rebex.net'
>>> dg.inputs.user = 'demo'
>>> dg.inputs.password = 'password'
>>> dg.inputs.base_directory = 'pub'
>>> dg.inputs.template = '%s/%s.txt'
>>> dg.inputs.arg1 = 'example'
>>> dg.inputs.arg2 = 'foo'

>>> dg = SSHDataGrabber(infields=['sid'], outfields=['func','struct','ref'])
>>> dg.inputs.hostname = 'myhost.com'
>>> dg.inputs.base_directory = '/main_folder/my_remote_dir'
>>> dg.inputs.template_args['func'] = [['sid',['f3','f5']]]
>>> dg.inputs.template_args['struct'] = [['sid',['struct']]]
>>> dg.inputs.template_args['ref'] = [['sid','ref']]
>>> dg.inputs.sid = 's1'

>>> dg.inputs.field_template = dict(struct='%s/struct.nii')
>>> dg.inputs.template_args['struct'] = [['sid']]

>>> import pprint
>>> from nipype import SelectFiles, Node
>>> templates={"T1": "{subject_id}/struct/T1.nii",
...            "epi": "{subject_id}/func/f[0,1].nii"}
>>> dg = Node(SelectFiles(templates), "selectfiles")
>>> dg.inputs.subject_id = "subj1"
>>> pprint.pprint(dg.outputs.get())  # doctest:
{'T1': <undefined>, 'epi': <undefined>}

>>> templates["epi"] = "{subject_id}/func/f{run}.nii"
>>> dg = Node(SelectFiles(templates), "selectfiles")
>>> dg.inputs.subject_id = "subj1"
>>> dg.inputs.run = [10, 11]

>>> dg = XNATSource()
>>> dg.inputs.template = '*'

>>> dg = XNATSource(infields=['project','subject','experiment','assessor','inout'])
>>> dg.inputs.query_template = '/projects/%s/subjects/%s/experiments/%s'                '/assessors/%s/%s_resources/files'
>>> dg.inputs.project = 'IMAGEN'
>>> dg.inputs.subject = 'IMAGEN_000000001274'
>>> dg.inputs.experiment = '*SessionA*'
>>> dg.inputs.assessor = '*ADNI_MPRAGE_nii'
>>> dg.inputs.inout = 'out'

>>> dg = XNATSource(infields=['sid'],outfields=['struct','func'])
>>> dg.inputs.query_template = '/projects/IMAGEN/subjects/%s/experiments/*SessionA*'                '/assessors/*%s_nii/out_resources/files'
>>> dg.inputs.query_template_args['struct'] = [['sid','ADNI_MPRAGE']]
>>> dg.inputs.query_template_args['func'] = [['sid','EPI_faces']]
>>> dg.inputs.sid = 'IMAGEN_000000001274'

Release	Devel
1.6.0	1.6.0
Download	Github

Table of Contents

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nipype.interfaces.io module¶

BIDSDataGrabber¶

DataFinder¶

DataGrabber¶

DataSink¶

ExportFile¶

FreeSurferSource¶

IOBase¶

JSONFileGrabber¶

JSONFileSink¶

MySQLSink¶

S3DataGrabber¶

SQLiteSink¶

SSHDataGrabber¶

SelectFiles¶

XNATSink¶

XNATSource¶