Merge branch 'master' of git://github.com/nipy/nipype into fix_afni_allineate

Author: rmarkello

.zenodo.json

@@ -518,6 +518,11 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "University of Amsterdam",
+      "name": "Lukas Snoek",
+      "orcid": "0000-0001-8972-204X"
     }
   ],
   "keywords": [

nipype/algorithms/confounds.py

@@ -489,10 +489,11 @@ def _run_interface(self, runtime):
             header = ['{}{:02d}'.format(ftype, i) for i in range(ncols)]
             if skip_vols:
                 old_basis = filter_basis
-                nrows = filter_basis.shape[0] if filter_basis.size > 0 else 0
-                filter_basis = np.zeros((nrows + skip_vols, ncols + skip_vols),
+                # nrows defined above
+                filter_basis = np.zeros((nrows, ncols + skip_vols),
                                         dtype=filter_basis.dtype)
-                filter_basis[skip_vols:, :ncols] = old_basis
+                if old_basis.size > 0:
+                    filter_basis[skip_vols:, :ncols] = old_basis
                 filter_basis[:skip_vols, -skip_vols:] = np.eye(skip_vols)
                 header.extend(['NonSteadyStateOutlier{:02d}'.format(i)
                                for i in range(skip_vols)])

nipype/interfaces/afni/__init__.py

@@ -8,17 +8,21 @@
 """
 
 from .base import Info
-from .preprocess import (Allineate, Automask, AutoTcorrelate,
+from .preprocess import (AlignEpiAnatPy, Allineate, Automask,
+                         AutoTcorrelate, AutoTLRC,
                          Bandpass, BlurInMask, BlurToFWHM,
                          ClipLevel, DegreeCentrality, Despike,
                          Detrend, ECM, Fim, Fourier, Hist, LFCD,
                          Maskave, Means, OutlierCount,
                          QualityIndex, ROIStats, Retroicor,
                          Seg, SkullStrip, TCorr1D, TCorrMap, TCorrelate,
+                         TNorm,
                          TShift, Volreg, Warp, QwarpPlusMinus, Qwarp)
 from .svm import (SVMTest, SVMTrain)
-from .utils import (AFNItoNIFTI, Autobox, Axialize, BrickStat, Calc, Cat, Copy,
+from .utils import (ABoverlap, AFNItoNIFTI, Autobox, Axialize, BrickStat,
+                    Bucket, Calc, Cat, CatMatvec, Copy, Dot,
                     Edge3, Eval, FWHMx, MaskTool, Merge, Notes, NwarpApply,
-                    Refit, Resample, TCat, TStat, To3D, Unifize, ZCutUp, GCOR,
+                    OneDToolPy,
+                    Refit, Resample, TCat, TCatSubBrick, TStat, To3D, Unifize, ZCutUp, GCOR,
                     Zcat, Zeropad)
 from .model import (Deconvolve, Remlfit)

nipype/interfaces/afni/base.py

@@ -8,6 +8,7 @@
 
 import os
 from sys import platform
+from distutils import spawn
 
 from ... import logging
 from ...utils.filemanip import split_filename, fname_presuffix
@@ -144,7 +145,6 @@ class AFNICommandOutputSpec(TraitedSpec):
     out_file = File(desc='output file',
                     exists=True)
 
-
 class AFNICommand(AFNICommandBase):
     """Shared options for several AFNI commands """
     input_spec = AFNICommandInputSpec
@@ -283,3 +283,23 @@ def no_afni():
     if Info.version() is None:
         return True
     return False
+
+
+class AFNIPythonCommandInputSpec(CommandLineInputSpec):
+    outputtype = traits.Enum('AFNI', list(Info.ftypes.keys()),
+                             desc='AFNI output filetype')
+    py27_path = traits.Either('python2', File(exists=True),
+        usedefault=True,
+        default='python2')
+
+class AFNIPythonCommand(AFNICommand):
+    @property
+    def cmd(self):
+        if spawn.find_executable(super(AFNIPythonCommand, self).cmd) is not None:
+            return spawn.find_executable(super(AFNIPythonCommand, self).cmd)
+        else:
+            return super(AFNIPythonCommand, self).cmd
+
+    @property
+    def cmdline(self):
+        return "{} {}".format(self.inputs.py27_path, super(AFNIPythonCommand, self).cmdline)