.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.io
=============


.. _nipype.interfaces.io.DataGrabber:


.. index:: DataGrabber

DataGrabber
-----------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L347

Generic datagrabber module that wraps around glob in an
intelligent way for neuroimaging tasks to grab files


.. attention::

   Doesn't support directories currently

Examples
~~~~~~~~

>>> from nipype.interfaces.io import DataGrabber

Pick all files from current directory

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

Pick file foo/foo.nii from current directory

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

Same thing but with dynamically created fields

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

however this latter form can be used with iterables and iterfield in a
pipeline.

Dynamically created, user-defined input and output fields

>>> 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'

Change the template only for output field struct. The rest use the
general template

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

Inputs::

        [Mandatory]
        template: (a string)
                Layout used to get files. relative to base directory if defined

        [Optional]
        base_directory: (an existing directory name)
                Path to the base directory consisting of subject data.
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the interface fails to
                run
        raise_on_empty: (a boolean, nipype default value: True)
                Generate exception if list is empty for a given field
        sort_filelist: (a boolean, nipype default value: False)
                Sort the filelist that matches the template
        template_args: (a dictionary with keys which are a string and with values which are a
                 list of items which are a list of items which are any value)
                Information to plug into template

Outputs::

        None

.. _nipype.interfaces.io.DataSink:


.. index:: DataSink

DataSink
--------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L141

Generic datasink module to store structured outputs

Primarily for use within a workflow. This interface allows arbitrary
creation of input attributes. The names of these attributes define the
directory structure to create for storage of the files or directories.

The attributes take the following form:

string[[.[@]]string[[.[@]]string]] ...

where parts between [] are optional.

An attribute such as contrasts.@con will create a 'contrasts' directory
to store the results linked to the attribute. If the @ is left out, such
as in 'contrasts.con', a subdirectory 'con' will be created under
'contrasts'.

the general form of the output is::

   'base_directory/container/parameterization/destloc/filename'

   destloc = string[[.[@]]string[[.[@]]string]] and
   filename comesfrom the input to the connect statement.

.. warning::

    This is not a thread-safe node because it can write to a common
    shared location. It will not complain when it overwrites a file.

.. note::

    If both substitutions and regexp_substitutions are used, then
    substitutions are applied first followed by regexp_substitutions.

    This interface **cannot** be used in a MapNode as the inputs are
    defined only when the connect statement is executed.

Examples
~~~~~~~~

>>> 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

To use DataSink in a MapNode, its inputs have to be defined at the
time the interface is created.

>>> 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

Inputs::

        [Mandatory]

        [Optional]
        _outputs: (a dictionary with keys which are a string and with values which are any value,
                 nipype default value: {})
        base_directory: (a directory name)
                Path to the base directory for storing data.
        container: (a string)
                Folder within base directory in which to store output
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the interface fails to
                run
        parameterization: (a boolean, nipype default value: True)
                store output in parametrized structure
        regexp_substitutions: (a tuple of the form: (a string, a string))
                List of 2-tuples reflecting a pair of a Python regexp pattern and a replacement string.
                Invoked after string `substitutions`
        remove_dest_dir: (a boolean, nipype default value: False)
                remove dest directory when copying dirs
        strip_dir: (a directory name)
                path to strip out of filename
        substitutions: (a tuple of the form: (a string, a string))
                List of 2-tuples reflecting string to substitute and string to replace it with

Outputs::

        None

.. _nipype.interfaces.io.FreeSurferSource:


.. index:: FreeSurferSource

FreeSurferSource
----------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L593

Generates freesurfer subject info from their directories

Examples
~~~~~~~~

>>> 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

Inputs::

        [Mandatory]
        subject_id: (a string)
                Subject name for whom to retrieve data
        subjects_dir: (a directory name)
                Freesurfer subjects directory.

        [Optional]
        hemi: ('both' or 'lh' or 'rh', nipype default value: both)
                Selects hemisphere specific outputs
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the interface fails to
                run

Outputs::

        BA_stats: (an existing file name)
                Brodmann Area statistics files
        T1: (an existing file name)
                Intensity normalized whole-head volume
        annot: (an existing file name)
                Surface annotation files
        aparc_a2009s_stats: (an existing file name)
                Aparc a2009s parcellation statistics files
        aparc_aseg: (an existing file name)
                Aparc parcellation projected into aseg volume
        aparc_stats: (an existing file name)
                Aparc parcellation statistics files
        aseg: (an existing file name)
                Volumetric map of regions from automatic segmentation
        aseg_stats: (an existing file name)
                Automated segmentation statistics file
        brain: (an existing file name)
                Intensity normalized brain-only volume
        brainmask: (an existing file name)
                Skull-stripped (brain-only) volume
        curv: (an existing file name)
                Maps of surface curvature
        curv_stats: (an existing file name)
                Curvature statistics files
        entorhinal_exvivo_stats: (an existing file name)
                Entorhinal exvivo statistics files
        filled: (an existing file name)
                Subcortical mass volume
        inflated: (an existing file name)
                Inflated surface meshes
        label: (an existing file name)
                Volume and surface label files
        norm: (an existing file name)
                Normalized skull-stripped volume
        nu: (an existing file name)
                Non-uniformity corrected whole-head volume
        orig: (an existing file name)
                Base image conformed to Freesurfer space
        pial: (an existing file name)
                Gray matter/pia mater surface meshes
        rawavg: (an existing file name)
                Volume formed by averaging input images
        ribbon: (an existing file name)
                Volumetric maps of cortical ribbons
        smoothwm: (an existing file name)
                Smoothed original surface meshes
        sphere: (an existing file name)
                Spherical surface meshes
        sphere_reg: (an existing file name)
                Spherical registration file
        sulc: (an existing file name)
                Surface maps of sulcal depth
        thickness: (an existing file name)
                Surface maps of cortical thickness
        volume: (an existing file name)
                Surface maps of cortical volume
        white: (an existing file name)
                White/gray matter surface meshes
        wm: (an existing file name)
                Segmented white-matter volume
        wmparc: (an existing file name)
                Aparc parcellation projected into subcortical white matter
        wmparc_stats: (an existing file name)
                White matter parcellation statistics file

.. _nipype.interfaces.io.IOBase:


.. index:: IOBase

IOBase
------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L96

Inputs::

        [Mandatory]

        [Optional]
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the interface fails to
                run

Outputs::

        None

.. _nipype.interfaces.io.SQLiteSink:


.. index:: SQLiteSink

SQLiteSink
----------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L1120

Very simple frontend for storing values into SQLite database.

.. warning::

    This is not a thread-safe node because it can write to a common
    shared location. It will not complain when it overwrites a file.

Examples
~~~~~~~~

>>> 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

Inputs::

        [Mandatory]
        database_file: (an existing file name)
        table_name: (a string)

        [Optional]
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the interface fails to
                run

Outputs::

        None

.. _nipype.interfaces.io.XNATSink:


.. index:: XNATSink

XNATSink
--------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L916

Generic datasink module that takes a directory containing a
list of nifti files and provides a set of structured output
fields.

Inputs::

        [Mandatory]
        config: (a file name)
                mutually_exclusive: server
        experiment_id: (a string)
                Set to workflow name
        project_id: (a string)
                Project in which to store the outputs
        server: (a string)
                mutually_exclusive: config
                requires: user, pwd
        subject_id: (a string)
                Set to subject id

        [Optional]
        _outputs: (a dictionary with keys which are a string and with values which are any value,
                 nipype default value: {})
        cache_dir: (a directory name)
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the interface fails to
                run
        pwd: (a string)
        user: (a string)

Outputs::

        None

.. _nipype.interfaces.io.XNATSource:


.. index:: XNATSource

XNATSource
----------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L676

Generic XNATSource module that wraps around the pyxnat module in
an intelligent way for neuroimaging tasks to grab files and data
from an XNAT server.

Examples
~~~~~~~~

>>> from nipype.interfaces.io import XNATSource

Pick all files from current directory

>>> 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'

Inputs::

        [Mandatory]
        config: (a file name)
                mutually_exclusive: server
        query_template: (a string)
                Layout used to get files. Relative to base directory if defined
        server: (a string)
                mutually_exclusive: config
                requires: user, pwd

        [Optional]
        cache_dir: (a directory name)
                Cache directory
        ignore_exception: (a boolean, nipype default value: False)
                Print an error message instead of throwing an exception in case the interface fails to
                run
        pwd: (a string)
        query_template_args: (a dictionary with keys which are a string and with values which are
                 a list of items which are a list of items which are any value, nipype default value:
                 {'outfiles': []})
                Information to plug into template
        user: (a string)

Outputs::

        None

.. module:: nipype.interfaces.io


.. _nipype.interfaces.io.add_traits:

:func:`add_traits`
------------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L79



Add traits to a traited class.

All traits are set to Undefined by default


.. _nipype.interfaces.io.copytree:

:func:`copytree`
----------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L45



Recursively copy a directory tree using
nipype.utils.filemanip.copyfile()

This is not a thread-safe routine. However, in the case of creating new
directories, it checks to see if a particular directory has already been
created by another process.


.. _nipype.interfaces.io.push_file:

:func:`push_file`
-----------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L1033






.. _nipype.interfaces.io.quote_id:

:func:`quote_id`
----------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L1027






.. _nipype.interfaces.io.unquote_id:

:func:`unquote_id`
------------------

Code: http://github.com/nipy/nipype/blob/master/nipype/interfaces/io.py#L1030





