add an example

Author: bpinsard

CHANGES

@@ -1,6 +1,6 @@
 Next release
 ============
-* ENH: New interfaces: nipy.Trim
+* ENH: New interfaces: nipy.Trim, fsl.GLM, fsl.SigLoss
 
 * ENH: Allow control over terminal output for commandline interfaces
 * ENH: New workflows for dMRI and fMRI pre-processing: added motion artifact correction

nipype/interfaces/afni/preprocess.py

@@ -320,7 +320,13 @@ class AutoTcorrelateInputSpec(AFNICommandInputSpec):
     mask = File(exists=True, desc="mask of voxels",
                 argstr="-mask %s")
     mask_only_targets = traits.Bool(desc="use mask only on targets voxels",
-                                    argstr="-mask_only_targets")
+                                    argstr="-mask_only_targets",
+                                    xor=['mask_source'])
+                                    
+    mask_source = File(exists=True, 
+                        desc="mask for source voxels", 
+                        argstr="-mask_source %s",
+                        xor=['mask_only_targets'])
 
     out_file = File("%s_similarity_matrix.1D", desc='output image file name',
                     argstr='-prefix %s', name_source="in_file", usedefault=True)

nipype/interfaces/afni/tests/test_preprocess.py

@@ -18,7 +18,7 @@ def test_allineate():
                      environ = dict(usedefault=True,),
                      ignore_exception = dict(usedefault=True,),
                      in_file = dict(argstr='-source %s',mandatory=True,),
-                     matrix = dict(argstr='-1dmatrix_apply %s',),
+                     in_matrix = dict(argstr='-1Dmatrix_apply %s',),
                      out_file = dict(argstr='-prefix %s'),
                      outputtype = dict(),
                      )

nipype/interfaces/fsl/__init__.py

@@ -11,11 +11,12 @@
                          SliceTimer, SUSAN, PRELUDE, FUGUE, FIRST)
 from .model import (Level1Design, FEAT, FEATModel, FILMGLS, FEATRegister,
                     FLAMEO, ContrastMgr, MultipleRegressDesign, L2Model, SMM,
-                    MELODIC, SmoothEstimate, Cluster, Randomise)
+                    MELODIC, SmoothEstimate, Cluster, Randomise, GLM)
 from .utils import (Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
                     ImageStats, FilterRegressor, Overlay, Slicer,
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,
-                    SwapDimensions, PowerSpectrum, Reorient2Std)
+                    SwapDimensions, PowerSpectrum, SigLoss, Reorient2Std,
+                    Complex)
 from .dti import (EddyCorrect, BEDPOSTX, DTIFit, ProbTrackX, VecReg, ProjThresh,
                   FindTheBiggest, DistanceMap, TractSkeleton, XFibres,
                   MakeDyadicVectors)

nipype/interfaces/fsl/model.py

@@ -18,12 +18,12 @@
 
 import numpy as np
 
-from nipype.interfaces.fsl.base import (FSLCommand, FSLCommandInputSpec)
+from nipype.interfaces.fsl.base import (FSLCommand, FSLCommandInputSpec, Info)
 from nipype.interfaces.base import (load_template, File, traits, isdefined,
                                     TraitedSpec, BaseInterface, Directory,
                                     InputMultiPath, OutputMultiPath,
                                     BaseInterfaceInputSpec)
-from nipype.utils.filemanip import (list_to_filename, filename_to_list)
+from nipype.utils.filemanip import (list_to_filename, filename_to_list, split_filename)
 from nibabel import load
 
 warn = warnings.warn
@@ -1511,3 +1511,66 @@ def _list_outputs(self):
             outputs['f_corrected_p_files'] = glob(self._gen_fname(\
                 '%s_%s_corrp_fstat*.nii' % (self.inputs.base_name, prefix)))
         return outputs
+
+
+class GLMInputSpec(FSLCommandInputSpec):
+    in_file = File(
+        exists=True,mandatory=True,
+        argstr='-i %s',
+        desc='input 3d+t file',)
+    design = File(
+        exists=True, mandatory=True,
+        argstr='-d %s',
+        desc='design file or image file')
+    out_file = File(
+        genfile=True, argstr="-o %s",
+        desc="file or image output")
+    mask = File(
+        exists=True,
+        argstr='-m %s',
+        desc='mask file')
+    contrasts = File(
+        exists=True,
+        argstr='-c %s',
+        desc='t-contrasts file')
+    options = traits.String(
+        argstr='%s',
+        desc = 'fsl_glm options')
+class GLMOutputSpec(TraitedSpec):
+    out_file = File(
+        exists=True,
+        desc = 'file or image output')
+
+class GLM(FSLCommand):
+    """
+    FSL GLM: 
+
+    Example
+    -------
+    >>> import nipype.interfaces.fsl as fsl
+    >>> glm = fsl.GLM(in_file='functional.nii', design = 'maps.nii')
+    >>> glm.cmdline
+    """
+    _cmd = 'fsl_glm'
+    input_spec = GLMInputSpec
+    output_spec = GLMOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = self.inputs.out_file
+        # Generate an out_file if one is not provided
+        if not isdefined(outputs['out_file']) and isdefined(self.inputs.in_file):
+            ext = Info.output_type_to_ext(self.inputs.output_type)
+            if split_filename(self.inputs.in_file)[-1] in Info.ftypes.values():
+                ext = '.txt'
+            outputs['out_file'] = self._gen_fname(self.inputs.in_file,
+                                                  suffix='_glm',
+                                                  ext=ext)
+
+        return outputs
+
+    def _gen_filename(self, name):
+        if name in ('out_file'):
+            return self._list_outputs()[name]
+        else:
+            return None

nipype/interfaces/fsl/preprocess.py

@@ -1188,14 +1188,15 @@ def _gen_filename(self, name):
 class FUGUEInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr='--in=%s',
                    desc='filename of input volume')
-    unwarped_file = File(argstr='--unwarp=%s', genfile=True,
-                         desc='apply unwarping and save as filename', hash_files=False)
-
-    save_warped = traits.Bool(desc='apply forward warp and save')
-
-    warped_file = File(argstr='--warp=%s', genfile=True,
-                         desc='apply forward warp and save as filename', hash_files=False)
-
+    unwarped_file = File(
+        argstr='--unwarp=%s', genfile=True,
+        desc='apply unwarping and save as filename', hash_files=False)
+    forward_warping = traits.Bool(
+        False, usedefault=True,
+        desc='apply forward warping instead of unwarping')
+    warped_file = File(argstr='--warp=%s', 
+                       desc='apply forward warping and save as filename',
+                       hash_files=False)
     phasemap_file = File(exists=True, argstr='--phasemap=%s',
                          desc='filename for input phase image')
     dwell_to_asym_ratio = traits.Float(argstr='--dwelltoasym=%.10f',
@@ -1211,7 +1212,7 @@ class FUGUEInputSpec(FSLCommandInputSpec):
 
     save_shift = traits.Bool(desc='output pixel shift volume')
 
-    shift_out_file = traits.File(argstr='--saveshift=%s', genfile=True,
+    shift_out_file = traits.File(argstr='--saveshift=%s', 
                            desc='filename for saving pixel shift volume', hash_files=False)
 
     shift_in_file = File(exists=True, argstr='--loadshift=%s',
@@ -1247,25 +1248,20 @@ class FUGUEInputSpec(FSLCommandInputSpec):
                              desc='apply intensity correction only')
     mask_file = File(exists=True, argstr='--mask=%s',
                      desc='filename for loading valid mask')
-    save_unmasked_fmap = traits.Either(traits.Bool,
-                                       traits.File,
-                                       argstr='--unmaskfmap=%s',
-                                       requires=['fmap_out_file'],
-                                       desc='saves the unmasked fieldmap when using --savefmap', hash_files=False)
-    save_unmasked_shift = traits.Either(traits.Bool,
-                                       traits.File,
-                                       argstr='--unmaskshift=%s',
-                                       requires=['shift_out_file'],
-                                       desc='saves the unmasked shiftmap when using --saveshift', hash_files=False)
-    nokspace = traits.Bool(
-        argstr='--nokspace', desc='do not use k-space forward warping')
+    save_unmasked_fmap = traits.Bool(argstr='--unmaskfmap',
+                                     requires=['fmap_out_file'],
+                                     desc='saves the unmasked fieldmap when using --savefmap')
+    save_unmasked_shift = traits.Bool(argstr='--unmaskshift',
+                                      requires=['shift_out_file'],
+                                      desc='saves the unmasked shiftmap when using --saveshift')
+    nokspace = traits.Bool(argstr='--nokspace', desc='do not use k-space forward warping')
 
 
 class FUGUEOutputSpec(TraitedSpec):
-    unwarped_file = File(exists=True, desc='unwarped file')
+    unwarped_file = File(desc='unwarped file')
+    warped_file = File(desc='forward warped file')
     shift_out_file = File(desc='voxel shift map file')
-    warped_file = File(desc='warped file')
-
+    fmap_out_file = File(desc='fieldmap file')
 
 class FUGUE(FSLCommand):
     """Use FSL FUGUE to unwarp epi's with fieldmaps
@@ -1299,43 +1295,40 @@ def _parse_inputs(self, skip=None):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        out_file = self.inputs.unwarped_file
-        if not isdefined(out_file):
-            out_file = self._gen_fname(self.inputs.in_file,
-                                      suffix='_unwarped')
-        outputs['unwarped_file'] = os.path.abspath(out_file)
-
-        if isdefined(self.inputs.save_shift) and self.inputs.save_shift:
-            shift_out = self.inputs.shift_out_file
-            if not isdefined(shift_out):
-                shift_out = self._gen_fname(
-                    self.inputs.in_file, suffix='_shift')
+        if self.inputs.forward_warping:
+            out_field = 'warped_file'
+        else: 
+            out_field = 'unwarped_file'
 
-            outputs['shift_out_file'] = os.path.abspath(shift_out)
-
-        if isdefined(self.inputs.save_warped) and self.inputs.save_warped:
-            warped_out = self.inputs.warped_file
-            if not isdefined(warped_out):
-                warped_out = self._gen_fname(
-                    self.inputs.in_file, suffix='_fwdwarp')
-
-            outputs['warped_file'] = os.path.abspath(warped_out)
-            del outputs['unwarped_file']
+        out_file = getattr(self.inputs,out_field)
+        if not isdefined(out_file):
+            if isdefined(self.inputs.in_file):
+                out_file = self._gen_fname(self.inputs.in_file,
+                                           suffix='_'+out_field[:-5])
+        if isdefined(out_file):
+            outputs[out_field] = os.path.abspath(out_file)
+        if isdefined(self.inputs.fmap_out_file):
+            outputs['fmap_out_file'] = os.path.abspath(self.inputs.fmap_out_file)
+        if isdefined(self.inputs.shift_out_file):
+            outputs['shift_out_file'] = os.path.abspath(self.inputs.shift_out_file)
 
         return outputs
 
     def _gen_filename(self, name):
-        if name == 'unwarped_file':
+        if name == 'unwarped_file' and not self.inputs.forward_warping:
             return self._list_outputs()['unwarped_file']
-
-        if name == 'warped_file':
+        if name == 'warped_file' and self.inputs.forward_warping:
             return self._list_outputs()['warped_file']
-
-        if name == 'shift_out_file':
-            return self._list_outputs()['shift_out_file']
-
         return None
 
+    def _parse_inputs(self,skip=None):
+        if skip==None:
+            skip=[]
+        if self.inputs.forward_warping or not isdefined(self.inputs.in_file):
+            skip+=['unwarped_file']
+        if not self.inputs.forward_warping or not isdefined(self.inputs.in_file):
+            skip+=['warped_file']
+        return super(FUGUE,self)._parse_inputs(skip=skip)
 
 class PRELUDEInputSpec(FSLCommandInputSpec):
     complex_phase_file = File(exists=True, argstr='--complex=%s',

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -503,8 +503,8 @@ def test_fugue():
                      phase_conjugate = dict(argstr='--phaseconj',),
                      phasemap_file = dict(argstr='--phasemap=%s',),
                      poly_order = dict(argstr='--poly=%d',),
-                     save_unmasked_fmap = dict(requires=['fmap_out_file'],argstr='--unmaskfmap=%s',),
-                     save_unmasked_shift = dict(requires=['shift_out_file'],argstr='--unmaskshift=%s',),
+                     save_unmasked_fmap = dict(requires=['fmap_out_file'],argstr='--unmaskfmap',),
+                     save_unmasked_shift = dict(requires=['shift_out_file'],argstr='--unmaskshift',),
                      shift_in_file = dict(argstr='--loadshift=%s',),
                      shift_out_file = dict(argstr='--saveshift=%s',),
                      smooth2d = dict(argstr='--smooth2=%.2f',),