Merge branch 'enh/3dTCorr1D'

Conflicts:
	CHANGES

Author: chrisgorgo

CHANGES

@@ -3,7 +3,7 @@ Next release
 
 * ENH: SelectFiles: a streamlined version of DataGrabber
 * ENH: New interfaces: spm.ResliceToReference, FuzzyOverlap, afni.AFNItoNIFTI
-       spm.DicomImport, P2PDistance
+       afni.TCorr1D, spm.DicomImport, P2PDistance
 * 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"

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