Merge remote-tracking branch 'origin/pr/831'

Conflicts:
	CHANGES

Author: chrisgorgo

CHANGES

@@ -1,9 +1,10 @@
 Next Release
 ============
 
-* API: Interfaces to external packages are no longer available in the top-level ``nipype`` namespace, and must be imported directly (e.g. ``from nipype.interfaces import fsl``).
-* ENH: nipy.utils.Similarity has been deprecated by algorithms.metrics.Similarity
-       which is an extension of the former to allow 4D images.
+* API: Interfaces to external packages are no longer available in the top-level
+       ``nipype`` namespace, and must be imported directly (e.g.
+       ``from nipype.interfaces import fsl``).
+* ENH: New FSL interface: ProbTrackX2
 * ENH: New ANTs interface: ApplyTransformsToPoints
 * ENH: New metrics group in algorithms. Now Distance, Overlap, and FuzzyOverlap
        are found in nipype.algorithms.metrics instead of misc
@@ -33,7 +34,8 @@ Release 0.9.0 (December 20, 2013)
 * ENH: new tools for defining workflows: JoinNode, synchronize and itersource
 * ENH: W3C PROV support with optional RDF export built into Nipype
 * ENH: Added support for Simple Linux Utility Resource Management (SLURM)
-* ENH: AFNI interfaces refactor, prefix, suffix are replaced by "flexible_%s_templates"
+* ENH: AFNI interfaces refactor, prefix, suffix are replaced by
+       "flexible_%s_templates"
 * ENH: New SPM interfaces:
 		- spm.ResliceToReference,
 		- spm.DicomImport

nipype/interfaces/fsl/__init__.py

@@ -21,9 +21,9 @@
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
                   SigLoss, EddyCorrect)
 
-from .dti import (BEDPOSTX, DTIFit, ProbTrackX, VecReg, ProjThresh,
-                  FindTheBiggest, DistanceMap, TractSkeleton, XFibres,
-                  MakeDyadicVectors)
+from .dti import (BEDPOSTX, DTIFit, ProbTrackX, ProbTrackX2,
+                  VecReg, ProjThresh, FindTheBiggest, DistanceMap,
+                  TractSkeleton, XFibres, MakeDyadicVectors)
 from .maths import (ChangeDataType, Threshold, MeanImage, ApplyMask,
                     IsotropicSmooth, TemporalFilter, DilateImage, ErodeImage,
                     SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths)

nipype/interfaces/fsl/dti.py

@@ -230,7 +230,7 @@ def _list_outputs(self):
         return outputs
 
 
-class ProbTrackXInputSpec(FSLCommandInputSpec):
+class ProbTrackXBaseInputSpec(FSLCommandInputSpec):
     thsamples = InputMultiPath(File(exists=True), mandatory=True)
     phsamples = InputMultiPath(File(exists=True), mandatory=True)
     fsamples = InputMultiPath(File(exists=True), mandatory=True)
@@ -243,21 +243,13 @@ class ProbTrackXInputSpec(FSLCommandInputSpec):
                          desc='seed volume(s), or voxel(s)' +
                          'or freesurfer label file',
                          argstr='--seed=%s', mandatory=True)
-    mode = traits.Enum("simple", "two_mask_symm", "seedmask",
-                       desc='options: simple (single seed voxel), seedmask (mask of seed voxels), '
-                            + 'twomask_symm (two bet binary masks) ',
-                       argstr='--mode=%s', genfile=True)
     target_masks = InputMultiPath(File(exits=True), desc='list of target masks - ' +
                        'required for seeds_to_targets classification', argstr='--targetmasks=%s')
-    mask2 = File(exists=True, desc='second bet binary mask (in diffusion space) in twomask_symm mode',
-                 argstr='--mask2=%s')
     waypoints = File(exists=True, desc='waypoint mask or ascii list of waypoint masks - ' +
                      'only keep paths going through ALL the masks', argstr='--waypoints=%s')
     network = traits.Bool(desc='activate network mode - only keep paths going through ' +
                           'at least one seed mask (required if multiple seed masks)',
                           argstr='--network')
-    mesh = File(exists=True, desc='Freesurfer-type surface descriptor (in ascii format)',
-                argstr='--mesh=%s')
     seed_ref = File(exists=True, desc='reference vol to define seed space in ' +
                    'simple mode - diffusion space assumed if absent',
                    argstr='--seedref=%s')
@@ -307,6 +299,15 @@ class ProbTrackXInputSpec(FSLCommandInputSpec):
                           "Level 2 is required to output particle files.",
                           argstr="--verbose=%d")
 
+class ProbTrackXInputSpec(ProbTrackXBaseInputSpec):
+    mode = traits.Enum("simple", "two_mask_symm", "seedmask",
+                       desc='options: simple (single seed voxel), seedmask (mask of seed voxels), '
+                            + 'twomask_symm (two bet binary masks) ',
+                       argstr='--mode=%s', genfile=True)
+    mask2 = File(exists=True, desc='second bet binary mask (in diffusion space) in twomask_symm mode',
+                 argstr='--mask2=%s')
+    mesh = File(exists=True, desc='Freesurfer-type surface descriptor (in ascii format)',
+                argstr='--mesh=%s')
 
 class ProbTrackXOutputSpec(TraitedSpec):
     log = File(exists=True, desc='path/name of a text record of the command that was run')
@@ -320,7 +321,6 @@ class ProbTrackXOutputSpec(TraitedSpec):
                                  'all of the tract samples. Generated only if ' +
                                  'verbose is set to 2')
 
-
 class ProbTrackX(FSLCommand):
     """ Use FSL  probtrackx for tractography on bedpostx results
 
@@ -435,6 +435,96 @@ def _gen_filename(self, name):
             else:
                 return "seedmask"
 
+class ProbTrackX2InputSpec(ProbTrackXBaseInputSpec):
+    simple = traits.Bool(desc='rack from a list of voxels (seed must be a ASCII list of coordinates)',
+                         usedefault=False, argstr='--simple')
+    fopd = File(exists=True, desc='Other mask for binning tract distribution',
+                argstr='--fopd=%s')
+    waycond = traits.Enum("OR", "AND", argstr='--waycond=%s',
+                          desc='Waypoint condition. Either "AND" (default) or "OR"')
+    wayorder = traits.Bool(desc='Reject streamlines that do not hit waypoints in given order. ' +
+                            'Only valid if waycond=AND', argstr='--wayorder')
+    onewaycondition = traits.Bool(desc='Apply waypoint conditions to each half tract separately',
+                                  argstr='--onewaycondition')
+    omatrix1 = traits.Bool(desc='Output matrix1 - SeedToSeed Connectivity',
+                           argstr='--omatrix1')
+    distthresh1 = traits.Float(argstr='--distthresh1=%.3f',
+                               desc='Discards samples (in matrix1) shorter than this threshold ' +
+                                '(in mm - default=0)')
+    omatrix2 = traits.Bool(desc='Output matrix2 - SeedToLowResMask', argstr='--omatrix2', requires=['target2'])
+    target2 = File(exists=True, desc='Low resolution binary brain mask for storing ' +
+                    'connectivity distribution in matrix2 mode', argstr='--target2=%s')
+    omatrix3 = traits.Bool(desc='Output matrix3 (NxN connectivity matrix)', argstr='--omatrix3',
+                           requires=['target3', 'lrtarget3'])
+    target3 = File(exists=True, desc='Mask used for NxN connectivity matrix ' +
+                    '(or Nxn if lrtarget3 is set)', argstr='--target3=%s')
+    lrtarget3 = File(exists=True, desc='Column-space mask used for Nxn connectivity matrix',
+                     argstr='--lrtarget3=%s')
+    distthresh3 = traits.Float(argstr='--distthresh3=%.3f',
+                               desc='Discards samples (in matrix3) shorter than this threshold ' +
+                                '(in mm - default=0)')
+    omatrix4 = traits.Bool(desc='Output matrix4 - DtiMaskToSeed (special Oxford Sparse Format)',
+                           argstr='--omatrix4')
+    colmask4 = File(exists=True, desc='Mask for columns of matrix4 (default=seed mask)',
+                     argstr='--colmask4=%s')
+    target4 = File(exists=True, desc='Brain mask in DTI space', argstr='--target4=%s')
+    meshspace = traits.Enum("caret", "freesurfer", "first", "vox", argstr='--meshspace=%s',
+                            desc='Mesh reference space - either "caret" (default) or ' +
+                             '"freesurfer" or "first" or "vox"')
+
+
+class ProbTrackX2OutputSpec(ProbTrackXOutputSpec):
+    network_matrix = File(exists=True, desc='the network matrix generated by --omatrix1 option')
+    matrix1_dot = File(exists=True, desc='Output matrix1.dot - SeedToSeed Connectivity')
+    lookup_tractspace = File(exists=True, desc='lookup_tractspace generated by --omatrix2 option')
+    matrix2_dot = File(exists=True, desc='Output matrix2.dot - SeedToLowResMask')
+    matrix3_dot = File(exists=True, desc='Output matrix3 - NxN connectivity matrix')
+
+
+class ProbTrackX2(ProbTrackX):
+    """ Use FSL  probtrackx2 for tractography on bedpostx results
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces import fsl
+    >>> pbx2 = fsl.ProbTrackX2()
+    >>> pbx2.inputs.seed = 'seed_source.nii.gz'
+    >>> pbx2.inputs.thsamples = 'merged_th1samples.nii.gz'
+    >>> pbx2.inputs.fsamples = 'merged_f1samples.nii.gz'
+    >>> pbx2.inputs.phsamples = 'merged_ph1samples.nii.gz'
+    >>> pbx2.inputs.mask = 'nodif_brain_mask.nii.gz'
+    >>> pbx2.inputs.out_dir = '.'
+    >>> pbx2.inputs.n_samples = 3
+    >>> pbx2.inputs.n_steps = 10
+    >>> pbx2.cmdline
+    'probtrackx2 --forcedir -m nodif_brain_mask.nii.gz --nsamples=3 --nsteps=10 --opd --dir=. --samples=merged --seed=seed_source.nii.gz'
+    """
+    _cmd = 'probtrackx2'
+    input_spec = ProbTrackX2InputSpec
+    output_spec = ProbTrackX2OutputSpec
+
+    def _list_outputs(self):
+        outputs = super(ProbTrackX2, self)._list_outputs()
+
+        if not isdefined(self.inputs.out_dir):
+            out_dir = os.getcwd()
+        else:
+            out_dir = self.inputs.out_dir
+
+        if isdefined(self.inputs.omatrix1):
+            outputs['network_matrix'] = os.path.abspath(os.path.join(out_dir, 'fdt_network_matrix'))
+            outputs['matrix1_dot'] = os.path.abspath(os.path.join(out_dir, 'fdt_matrix1.dot'))
+
+        if isdefined(self.inputs.omatrix2):
+            outputs['lookup_tractspace'] = \
+              os.path.abspath(os.path.join(out_dir, 'lookup_tractspace_fdt_matrix2.nii.gz'))
+            outputs['matrix2_dot'] = os.path.abspath(os.path.join(out_dir, 'fdt_matrix2.dot'))
+
+        if isdefined(self.inputs.omatrix3):
+            outputs['matrix3_dot'] = os.path.abspath(os.path.join(out_dir, 'fdt_matrix3.dot'))
+        return outputs
+
 
 class VecRegInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr='-i %s', desc='filename for input vector or tensor field',

nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py

@@ -0,0 +1,152 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.fsl.dti import ProbTrackX2
+
+def test_ProbTrackX2_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    avoid_mp=dict(argstr='--avoid=%s',
+    ),
+    c_thresh=dict(argstr='--cthr=%.3f',
+    ),
+    colmask4=dict(argstr='--colmask4=%s',
+    ),
+    correct_path_distribution=dict(argstr='--pd',
+    ),
+    dist_thresh=dict(argstr='--distthresh=%.3f',
+    ),
+    distthresh1=dict(argstr='--distthresh1=%.3f',
+    ),
+    distthresh3=dict(argstr='--distthresh3=%.3f',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    fibst=dict(argstr='--fibst=%d',
+    ),
+    fopd=dict(argstr='--fopd=%s',
+    ),
+    force_dir=dict(argstr='--forcedir',
+    usedefault=True,
+    ),
+    fsamples=dict(mandatory=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    inv_xfm=dict(argstr='--invxfm=%s',
+    ),
+    loop_check=dict(argstr='--loopcheck',
+    ),
+    lrtarget3=dict(argstr='--lrtarget3=%s',
+    ),
+    mask=dict(argstr='-m %s',
+    mandatory=True,
+    ),
+    meshspace=dict(argstr='--meshspace=%s',
+    ),
+    mod_euler=dict(argstr='--modeuler',
+    ),
+    n_samples=dict(argstr='--nsamples=%d',
+    usedefault=True,
+    ),
+    n_steps=dict(argstr='--nsteps=%d',
+    ),
+    network=dict(argstr='--network',
+    ),
+    omatrix1=dict(argstr='--omatrix1',
+    ),
+    omatrix2=dict(argstr='--omatrix2',
+    requires=['target2'],
+    ),
+    omatrix3=dict(argstr='--omatrix3',
+    requires=['target3', 'lrtarget3'],
+    ),
+    omatrix4=dict(argstr='--omatrix4',
+    ),
+    onewaycondition=dict(argstr='--onewaycondition',
+    ),
+    opd=dict(argstr='--opd',
+    usedefault=True,
+    ),
+    os2t=dict(argstr='--os2t',
+    ),
+    out_dir=dict(argstr='--dir=%s',
+    genfile=True,
+    ),
+    output_type=dict(),
+    phsamples=dict(mandatory=True,
+    ),
+    rand_fib=dict(argstr='--randfib=%d',
+    ),
+    random_seed=dict(argstr='--rseed',
+    ),
+    s2tastext=dict(argstr='--s2tastext',
+    ),
+    sample_random_points=dict(argstr='--sampvox',
+    ),
+    samples_base_name=dict(argstr='--samples=%s',
+    usedefault=True,
+    ),
+    seed=dict(argstr='--seed=%s',
+    mandatory=True,
+    ),
+    seed_ref=dict(argstr='--seedref=%s',
+    ),
+    simple=dict(argstr='--simple',
+    usedefault=False,
+    ),
+    step_length=dict(argstr='--steplength=%.3f',
+    ),
+    stop_mask=dict(argstr='--stop=%s',
+    ),
+    target2=dict(argstr='--target2=%s',
+    ),
+    target3=dict(argstr='--target3=%s',
+    ),
+    target4=dict(argstr='--target4=%s',
+    ),
+    target_masks=dict(argstr='--targetmasks=%s',
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    thsamples=dict(mandatory=True,
+    ),
+    use_anisotropy=dict(argstr='--usef',
+    ),
+    verbose=dict(argstr='--verbose=%d',
+    ),
+    waycond=dict(argstr='--waycond=%s',
+    ),
+    wayorder=dict(argstr='--wayorder',
+    ),
+    waypoints=dict(argstr='--waypoints=%s',
+    ),
+    xfm=dict(argstr='--xfm=%s',
+    ),
+    )
+    inputs = ProbTrackX2.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+
+def test_ProbTrackX2_outputs():
+    output_map = dict(fdt_paths=dict(),
+    log=dict(),
+    lookup_tractspace=dict(),
+    matrix1_dot=dict(),
+    matrix2_dot=dict(),
+    matrix3_dot=dict(),
+    network_matrix=dict(),
+    particle_files=dict(),
+    targets=dict(),
+    way_total=dict(),
+    )
+    outputs = ProbTrackX2.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+