WIP: Adding a python wrapper for ICA_AROMA

nipype/interfaces/fsl/ICA_AROMA.py

@@ -0,0 +1,118 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""This commandline module provides classes for interfacing with the 
+`ICA-AROMA.py<https://github.com/rhr-pruim/ICA-AROMA>`_ command line tool. 
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname(os.path.realpath(__file__))
+    >>> datadir = os.path.realpath(os.path.join(filepath,
+    ...                            '../../testing/data'))
+    >>> os.chdir(datadir)
+"""
+from nipype.interfaces.base import (
+    TraitedSpec,
+    CommandLineInputSpec,
+    CommandLine,
+    File,
+    Directory,
+    traits,
+    OutputMultiPath
+)
+import os
+
+class ICA_AROMAInputSpec(CommandLineInputSpec):
+    feat_dir = Directory(exists=True, mandatory=True,
+                         argstr='-feat %s', 
+                         xor=['in_file', 'mat_file', 'fnirt_warp_file', 'motion_parameters'],
+                         desc='If a feat directory exists and temporal filtering '
+                         'has not been run yet, ICA_AROMA can use the files in '
+                         'this directory.')
+    in_file = File(exists=True, mandatory=True, 
+                   argstr='-i %s', xor=['feat_dir'], 
+                   desc='volume to be denoised')
+    out_dir = Directory('out', mandatory=True,
+                        argstr='-o %s',  
+                        desc='output directory')
+    mask = File(exists=True, argstr='-m %s', xor=['feat_dir'], 
+                desc='path/name volume mask')
+    dim = traits.Int(argstr='-dim %d',
+                     desc='Dimensionality reduction when running '
+                     'MELODIC (defualt is automatic estimation)')
+    TR = traits.Float(argstr='-tr %.3f',
+                      desc='TR in seconds. If this is not specified '
+                      'the TR will be extracted from the '
+                      'header of the fMRI nifti file.')
+    melodic_dir = Directory(exists=True, argstr='-meldir %s',
+                            desc='path to MELODIC directory if MELODIC has already been run')
+    mat_file = File(exists=True, argstr='-affmat %s', xor=['feat_dir'],
+                    desc='path/name of the mat-file describing the '
+                    'affine registration (e.g. FSL FLIRT) of the '
+                    'functional data to structural space (.mat file)')
+    fnirt_warp_file = File(exists=True, argstr='-warp %s', xor=['feat_dir'],
+                           desc='File name of the warp-file describing '
+                           'the non-linear registration (e.g. FSL FNIRT) '
+                           'of the structural data to MNI152 space (.nii.gz)')
+    motion_parameters = File(exists=True, mandatory=True,
+                             argstr='-mc %s', xor=['feat_dir'],
+                             desc='motion parameters file')
+    denoise_type = traits.Enum('nonaggr', 'aggr', 'both', 'no', usedefault=True,
+                               mandatory=True, argstr='-den %s',
+                               desc='Type of denoising strategy:\n'
+                               '-none: only classification, no denoising\n'
+                               '-nonaggr (default): non-aggresssive denoising, i.e. partial component regression\n'
+                               '-aggr: aggressive denoising, i.e. full component regression\n'
+                               '-both: both aggressive and non-aggressive denoising (two outputs)')
+
+class ICA_AROMAOutputSpec(TraitedSpec):
+    aggr_denoised_file = File(exists=True, 
+                              desc='if generated: aggressively denoised volume')
+    nonaggr_denoised_file = File(exists=True,
+                                 desc='if generated: non aggressively denoised volume' )
+    out_dir = Directory(exists=True, 
+                        desc='directory contains (in addition to the denoised files): '
+                        'melodic.ica + classified_motion_components + '
+                        'classification_overview + feature_scores + melodic_ic_mni)')
+
+class ICA_AROMA(CommandLine):
+    """
+    Interface for the ICA_AROMA.py script.
+
+    ICA-AROMA (i.e. 'ICA-based Automatic Removal Of Motion Artifacts') concerns 
+    a data-driven method to identify and remove motion-related independent
+    components from fMRI data. To that end it exploits a small, but robust
+    set of theoretically motivated features, preventing the need for classifier
+    re-training and therefore providing direct and easy applicability. 
+
+    See link for further documentation: https://github.com/rhr-pruim/ICA-AROMA
+
+    Example
+    -------
+
+    >>> from nipype.interfaces.fsl import ICA_AROMA 
+    >>> from nipype.testing import example_data
+    >>> AROMA_obj = ICA_AROMA.ICA_AROMA()
+    >>> AROMA_obj.inputs.in_file = 'functional.nii'
+    >>> AROMA_obj.inputs.mat_file = 'func_to_struct.mat'
+    >>> AROMA_obj.inputs.fnirt_warp_file = 'warpfield.nii'
+    >>> AROMA_obj.inputs.motion_parameters = 'fsl_mcflirt_movpar.txt'
+    >>> AROMA_obj.inputs.mask = 'mask.nii.gz'
+    >>> AROMA_obj.inputs.denoise_type = 'both'
+    >>> AROMA_obj.inputs.out_dir = 'ICA_testout'
+    >>> AROMA_obj.cmdline # doctest: +ALLOW_UNICODE
+    'ICA_AROMA.py -den both -warp warpfield.nii -i functional.nii -m mask.nii.gz -affmat func_to_struct.mat -mc fsl_mcflirt_movpar.txt -o ICA_testout'
+    """
+    _cmd = 'ICA_AROMA.py'
+    input_spec = ICA_AROMAInputSpec
+    output_spec = ICA_AROMAOutputSpec
+
+    def _list_outputs(self):
+        out_dir = os.path.abspath(self.inputs.out_dir)
+        outputs['out_dir'] = out_dir
+
+        if self.inputs.denoise_type in ('aggr', 'both'):
+            outputs['aggr_denoised_file'] = os.path.join(out_dir, 'denoised_func_data_aggr.nii.gz')
+        if self.inputs.denoise_type in ('nonaggr', 'both'):
+            outputs['nonaggr_denoised_file'] = os.path.join(out_dir, 'denoised_func_data_nonaggr.nii.gz')
+
+        return outputs

nipype/interfaces/fsl/tests/test_auto_ICA_AROMA.py

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+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..ICA_AROMA import ICA_AROMA
+
+
+def test_ICA_AROMA_inputs():
+    input_map = dict(TR=dict(argstr='-tr %.3f',
+    ),
+    args=dict(argstr='%s',
+    ),
+    denoise_type=dict(argstr='-den %s',
+    mandatory=True,
+    usedefault=True,
+    ),
+    dim=dict(argstr='-dim %d',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    feat_dir=dict(argstr='-feat %s',
+    mandatory=True,
+    xor=['in_file', 'mat_file', 'fnirt_warp_file', 'motion_parameters'],
+    ),
+    fnirt_warp_file=dict(argstr='-warp %s',
+    xor=['feat_dir'],
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-i %s',
+    mandatory=True,
+    xor=['feat_dir'],
+    ),
+    mask=dict(argstr='-m %s',
+    xor=['feat_dir'],
+    ),
+    mat_file=dict(argstr='-affmat %s',
+    xor=['feat_dir'],
+    ),
+    melodic_dir=dict(argstr='-meldir %s',
+    ),
+    motion_parameters=dict(argstr='-mc %s',
+    mandatory=True,
+    xor=['feat_dir'],
+    ),
+    out_dir=dict(argstr='-o %s',
+    mandatory=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = ICA_AROMA.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_ICA_AROMA_outputs():
+    output_map = dict(aggr_denoised_file=dict(),
+    nonaggr_denoised_file=dict(),
+    out_dir=dict(),
+    )
+    outputs = ICA_AROMA.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value