Merge remote-tracking branch 'upstream/master' into enh/vagrant

* upstream/master:
  changelog cleanup
  added test file for TCorr1D
  added missing import
  added new interface info to the changelog
  added example to docstring, removed leftover genfile
  fixed workflow name
  Made revisions to the new 3dTCorr1D interface.
  Introduced a wrapper for 3dTcorr1D.

Author: satra

CHANGES

@@ -2,12 +2,16 @@ Next release
 ============
 
 * ENH: SelectFiles: a streamlined version of DataGrabber
-* ENH: New interfaces: spm.ResliceToReference, FuzzyOverlap, afni.AFNItoNIFTI
-       spm.DicomImport, P2PDistance
+* 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: DataGrabber and SelectFiles use human (or natural) sort now
+* ENH: New SPM interfaces:
+		- spm.ResliceToReference,
+		- spm.DicomImport
+* ENH: New AFNI interfaces:
+		- afni.AFNItoNIFTI
+		- afni.TCorr1D
 * ENH: Several new interfaces related to Camino were added:
         - camino.SFPICOCalibData
         - camino.Conmat
@@ -20,6 +24,25 @@ Next release
         - mrtrix.GenerateDirections
         - mrtrix.FindShPeaks
         - mrtrix.Directions2Amplitude
+* ENH: New FSL interfaces:
+		- fsl.PrepareFieldmap
+		- fsl.TOPUP
+		- fsl.ApplyTOPUP
+		- fsl.Eddy
+* ENH: New misc interfaces:
+		- FuzzyOverlap,
+		- P2PDistance
+* ENH: New workflows: nipype.workflows.dmri.fsl.epi.[fieldmap_correction&topup_correction]
+* ENH: Added simplified outputname generation for command line interfaces.
+* ENH: Allow ants use a single mask image
+* ENH: Create configuration option for parameterizing directories with hashes
+* ENH: arrange nodes by topological sort with disconnected subgraphs
+* ENH: uses the nidm iri namespace for uuids
+* ENH: remove old reporting webpage
+
+* API: 'name' is now a positional argument for Workflow, Node, and MapNode constructors
+* API: SPM now defaults to SPM8 or SPM12b job format
+* API: DataGrabber and SelectFiles use human (or natural) sort now
 
 * FIX: Several fixes related to Camino interfaces:
         - ProcStreamlines would ignore many arguments silently (target, waypoint, exclusion ROIS, etc.)
@@ -29,29 +52,12 @@ Next release
         - Track input model names were outdated (and would generate an error)
         - Track numpds parameter could not be set for deterministic tractography
         - FA created output files with erroneous extension
-
 * FIX: Deals properly with 3d files in SPM Realign
 * FIX: SPM with MCR fixed
-
-* API: 'name' is now a positional argument for Workflow, Node, and MapNode constructors
-* API: SPM now defaults to SPM8 or SPM12b job format
-
-* ENH: New FSL interfaces: fsl.PrepareFieldmap, fsl.TOPUP, fsl.ApplyTOPUP, fsl.Eddy
-* ENH: New workflows: nipype.workflows.dmri.fsl.epi.[fieldmap_correction&topup_correction]
-
-* ENH: Added simplified outputname generation for command line interfaces.
 * FIX: Cleaned up input and output spec metadata
-
-* ENH: Allow ants use a single mask image
-* ENH: Create configuration option for parameterizing directories with hashes
-* ENH: arrange nodes by topological sort with disconnected subgraphs
-* ENH: uses the nidm iri namespace for uuids
-* ENH: remove old reporting webpage (this is a WIP i hope to finish in a day or two)
-
 * FIX: example openfmri script now makes the contrast spec a hashed input
 * FIX: FILMGLS compatibility with FSL 5.0.5
 * FIX: Freesurfer recon-all resume now avoids setting inputs
-
 * FIX: File removal from node respects file associations img/hdr/mat, BRIK/HEAD
 
 Release 0.8.0 (May 8, 2013)

nipype/interfaces/afni/__init__.py

@@ -11,5 +11,5 @@
                          ZCutUp, Calc, TShift, Warp, Detrend, Despike, Copy,
                          Fourier, Allineate, Maskave, SkullStrip, TCat, Fim,
                          BlurInMask, Autobox, TCorrMap, Bandpass, Retroicor,
-                         TCorrelate, BrickStat, ROIStats, AutoTcorrelate,
+                         TCorrelate, TCorr1D, BrickStat, ROIStats, AutoTcorrelate,
                          AFNItoNIFTI)

nipype/interfaces/afni/preprocess.py

@@ -1308,6 +1308,70 @@ class TCorrelate(AFNICommand):
     output_spec = AFNICommandOutputSpec
 
 
+class TCorr1DInputSpec(AFNICommandInputSpec):
+    xset = File(desc = '3d+time dataset input',
+                  argstr = ' %s',
+                  position = -2,
+                  mandatory = True,
+                  exists = True)
+    y_1d = File(desc = '1D time series file input',
+                   argstr = ' %s',
+                   position = -1,
+                   mandatory = True,
+                   exists = True)
+    out_file = File(desc = 'output filename prefix',
+                   name_template='%s_correlation.nii.gz',
+                   argstr = '-prefix %s',
+                   name_source = 'xset',
+                   keep_extension = True)
+    pearson = traits.Bool(desc='Correlation is the normal' +
+                   ' Pearson correlation coefficient',
+                   argstr=' -pearson',
+                   xor=['spearman','quadrant','ktaub'],
+                   position=1)
+    spearman = traits.Bool(desc='Correlation is the' +
+                   ' Spearman (rank) correlation coefficient',
+                   argstr=' -spearman',
+                   xor=['pearson','quadrant','ktaub'],
+                   position=1)
+    quadrant = traits.Bool(desc='Correlation is the' +
+                   ' quadrant correlation coefficient',
+                   argstr=' -quadrant',
+                   xor=['pearson','spearman','ktaub'],
+                   position=1)
+    ktaub = traits.Bool(desc='Correlation is the' +
+                   ' Kendall\'s tau_b correlation coefficient',
+                   argstr=' -ktaub',
+                   xor=['pearson','spearman','quadrant'],
+                   position=1)
+
+
+
+class TCorr1DOutputSpec(TraitedSpec):
+    out_file = File(desc = 'output file containing correlations',
+                    exists = True)
+
+
+class TCorr1D(AFNICommand):
+    """Computes the correlation coefficient between each voxel time series
+    in the input 3D+time dataset.
+    For complete details, see the `3dTcorr1D Documentation.
+    <http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTcorr1D.html>`_
+
+    >>> from nipype.interfaces import afni as afni
+    >>> tcorr1D = afni.TCorr1D()
+    >>> tcorr1D.inputs.xset= 'u_rc1s1_Template.nii'
+    >>> tcorr1D.inputs.y_1d = 'seed.1D'
+    >>> tcorr1D.cmdline
+    '3dTcorr1D -prefix u_rc1s1_Template_correlation.nii.gz  u_rc1s1_Template.nii  seed.1D'
+    >>> res = tcorr1D.run() # doctest: +SKIP
+    """
+
+    _cmd = '3dTcorr1D'
+    input_spec = TCorr1DInputSpec
+    output_spec = TCorr1DOutputSpec
+
+
 class BrickStatInputSpec(AFNICommandInputSpec):
     in_file = File(desc='input file to 3dmaskave',
                    argstr='%s',
@@ -1861,3 +1925,4 @@ def _overload_extension(self, value):
     def _gen_filename(self, name):
         return os.path.abspath(super(AFNItoNIFTI, self)._gen_filename(name))
 
+

nipype/interfaces/afni/tests/test_auto_TCorr1D.py

@@ -0,0 +1,59 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.afni.preprocess import TCorr1D
+def test_TCorr1D_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    spearman=dict(position=1,
+    xor=['pearson', 'quadrant', 'ktaub'],
+    argstr=' -spearman',
+    ),
+    pearson=dict(position=1,
+    xor=['spearman', 'quadrant', 'ktaub'],
+    argstr=' -pearson',
+    ),
+    out_file=dict(name_source='xset',
+    argstr='-prefix %s',
+    name_template='%s_correlation.nii.gz',
+    keep_extension=True,
+    ),
+    y_1d=dict(position=-1,
+    mandatory=True,
+    argstr=' %s',
+    ),
+    ktaub=dict(position=1,
+    xor=['pearson', 'spearman', 'quadrant'],
+    argstr=' -ktaub',
+    ),
+    args=dict(argstr='%s',
+    ),
+    xset=dict(position=-2,
+    mandatory=True,
+    argstr=' %s',
+    ),
+    outputtype=dict(),
+    quadrant=dict(position=1,
+    xor=['pearson', 'spearman', 'ktaub'],
+    argstr=' -quadrant',
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    )
+    inputs = TCorr1D.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_TCorr1D_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = TCorr1D.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

tools/run_examples.py

@@ -22,7 +22,7 @@ def run_examples(example, pipelines, plugin):
 if __name__ == '__main__':
     path, file = os.path.split(__file__)
     sys.path.insert(0, os.path.realpath(os.path.join(path, '..', 'examples')))
-    examples = {'fmri_fsl_reuse':['l1pipeline'],
+    examples = {'fmri_fsl_reuse':['level1_workflow'],
                 'fmri_spm_nested':['level1','l2pipeline'],
                 'fmri_spm_dartel':['level1','l2pipeline'],
                 'fmri_fsl_feeds':['l1pipeline']}