added this now to new fork of repo

Author: wmpauli

nipype/interfaces/fsl/fix.py

@@ -0,0 +1,110 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""The fix module provides classes for interfacing with the `FSL FIX
+<http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/index.html>`_ command line tools.  
+This was written to work with FSL version v5.0
+    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,
+    Directory,
+    InputMultiPath,
+    traits,
+    File
+)
+import os
+
+class FIXInputSpec(CommandLineInputSpec):
+    mel_ica = InputMultiPath(Directory(exists=True), copyfile=False,
+                              desc='Melodic output directory or directories',
+                              argstr='%s', position=-1)
+
+
+    # Different modes of operation, which are pretty much mutually exclusive
+    _xor_inputs = ('extract_features', 'classify', 'apply_cleanup', 'train', 'test_accuracy')
+    
+    # /usr/local/fix/fix -f <mel.ica>
+    extract_features = traits.Bool(desc='Extract features (for later training and/or classifying)',
+                                   argstr='-f', xor=_xor_inputs, requires='mel_ica')
+
+    # /usr/local/fix/fix -c <mel.ica> <training.RData> <thresh>
+    classify = traits.Bool(desc='Classify ICA components using a specific training dataset (<thresh> is in the range 0-100, typically 5-20)',
+                                   argstr='-c', xor=_xor_inputs, requires='mel_ica')
+
+    # /usr/local/fix/fix -a <mel.ica/fix4melview_TRAIN_thr.txt>  [-m [-h <highpass>]]  [-A]  [-x <confound>] [-x <confound2>] etc.
+    apply_cleanup = traits.Bool(desc='Apply cleanup, using artefacts listed in the .txt file',
+                                   argstr='-a', xor=_xor_inputs, requires='artifacts_list_file') # todo, optional args, required inputs
+
+    train = traits.Bool(desc='Train the classifier based on your own FEAT/MELODIC output directory',
+                                   argstr='-t %s', value="training", xor=_xor_inputs) # todo, optional args
+
+    test_accuracy = traits.Bool(desc='Test the accuracy of an existing training dataset on a set of hand-labelled subjects',
+                                   argstr='-C', xor=_xor_inputs)
+
+
+    # shared args for different modes
+    artifacts_list_file = File(desc='Text file listing which ICs are artifacts; can be the output from classification or can be created manually', argstr='%s')  
+
+    trained_wts_file = File(desc='trained-weights file', argstr='%s')  
+
+
+
+
+    # leave-one-out cross validation
+    loo = traits.Bool(argstr='-l', requires=['train'],
+                            desc='full leave-one-out test with classifier training')
+    
+    # args for classify
+
+    highpass = traits.Float(argstr='-m -h %f', requires=['apply_cleanup'],
+                            desc='cleanup motion confounds', value=100, xor=_xor_cleanup)
+
+
+    # for apply_cleanup
+
+    _xor_cleanup = ('cleanup_motion', 'highpass_filter')
+
+    cleanup_motion = traits.Bool(argstr='-m', requires=['apply_cleanup'],
+                                 desc='cleanup motion confounds, looks for design.fsf for highpass filter cut-off', xor=_xor_cleanup)
+
+    highpass = traits.Float(argstr='-m -h %f', requires=['apply_cleanup'],
+                            desc='cleanup motion confounds', value=100, xor=_xor_cleanup)
+
+    aggressive = traits.Bool(argstr='-A', requires=['apply_cleanup'],
+                             desc='Apply aggressive (full variance) cleanup, instead of the default less-aggressive (unique variance) cleanup.')
+
+    confound_file = traits.File(argstr='-x %s', requires=['apply_cleanup'],
+                             desc='Include additional confound file.')
+
+    confound_file_1 = traits.File(argstr='-x %s', requires=['apply_cleanup'],
+                             desc='Include additional confound file.')
+
+    confound_file_2 = traits.File(argstr='-x %s', requires=['apply_cleanup'],
+                             desc='Include additional confound file.')
+
+    
+
+class FIXOutputSpec(TraitedSpec):
+    output_file = File(desc = "Zip file", exists = True)
+
+class FIX(CommandLine):
+    input_spec = FIXInputSpec
+    output_spec = FIXOutputSpec
+    cmd = 'fix'
+
+    def _list_outputs(self):
+            outputs = self.output_spec().get()
+            return outputs
+
+if __name__ == '__main__':
+
+    fix = FIX()
+    print fix.cmdline
+    fix.run()