Merge upstream/master [skip ci]

Author: effigies

.gitignore

@@ -19,6 +19,7 @@
 .DS_Store
 nipype/testing/data/von-ray_errmap.nii.gz
 nipype/testing/data/von_errmap.nii.gz
+nipype/testing/data/.proc*
 crash*.pklz
 .coverage
 htmlcov/

CHANGES

@@ -2,6 +2,9 @@ Upcoming release (0.14.1)
 =========================
 
 * FIX: Errors parsing ``$DISPLAY`` (https://github.com/nipy/nipype/pull/2363)
+* FIX: MultiProc starting workers at dubious wd (https://github.com/nipy/nipype/pull/2368)
+* REF+FIX: Move BIDSDataGrabber to `interfaces.io` + fix correct default behavior (https://github.com/nipy/nipype/pull/2336)
+* ENH: Add AFNI interface for 3dConvertDset (https://github.com/nipy/nipype/pull/2337)
 * MAINT: Cleanup EngineBase (https://github.com/nipy/nipype/pull/2376)
 * FIX: Robustly handled outputs of 3dFWHMx across different versions of AFNI (https://github.com/nipy/nipype/pull/2373)
 * FIX: Cluster threshold in randomise + change default prefix (https://github.com/nipy/nipype/pull/2369)

doc/quickstart.rst

@@ -43,6 +43,12 @@ __ http://nipy.org/workshops/2017-03-boston/index.html
 
 `All notebooks visualized <http://nbviewer.jupyter.org/github/nipy/workshops/tree/master/170327-nipype/notebooks/>`_
 
+Learning Resources
+==================
+
+`Porcupine <https://timvanmourik.github.io/Porcupine/getting-started/>`_ : create Nipype pipelines using a graphical interface
+View the `examples gallery here <https://timvanmourik.github.io/Porcupine/examples/>`_
+
 Developer guides
 ================
 
@@ -52,4 +58,3 @@ Developer guides
    devel/writing_custom_interfaces
 
 .. include:: links_names.txt
-

nipype/interfaces/__init__.py

@@ -10,5 +10,5 @@
                         absolute_import)
 __docformat__ = 'restructuredtext'
 
-from .io import DataGrabber, DataSink, SelectFiles
+from .io import DataGrabber, DataSink, SelectFiles, BIDSDataGrabber
 from .utility import IdentityInterface, Rename, Function, Select, Merge

nipype/interfaces/afni/__init__.py

@@ -15,9 +15,10 @@
     ROIStats, Retroicor, Seg, SkullStrip, TCorr1D, TCorrMap, TCorrelate, TNorm,
     TShift, Volreg, Warp, QwarpPlusMinus, Qwarp)
 from .svm import (SVMTest, SVMTrain)
-from .utils import (ABoverlap, AFNItoNIFTI, Autobox, Axialize, BrickStat,
-                    Bucket, Calc, Cat, CatMatvec, CenterMass, Copy, Dot, Edge3,
-                    Eval, FWHMx, MaskTool, Merge, Notes, NwarpApply, NwarpCat,
-                    OneDToolPy, Refit, Resample, TCat, TCatSubBrick, TStat,
-                    To3D, Unifize, Undump, ZCutUp, GCOR, Zcat, Zeropad)
+from .utils import (
+    ABoverlap, AFNItoNIFTI, Autobox, Axialize, BrickStat, Bucket, Calc, Cat,
+    CatMatvec, CenterMass, ConvertDset, Copy, Dot, Edge3, Eval, FWHMx,
+    MaskTool, Merge, Notes, NwarpApply, NwarpCat, OneDToolPy, Refit, Resample,
+    TCat, TCatSubBrick, TStat, To3D, Unifize, Undump, ZCutUp, GCOR, Zcat,
+    Zeropad)
 from .model import (Deconvolve, Remlfit, Synthesize)

nipype/interfaces/afni/tests/test_auto_ConvertDset.py

@@ -0,0 +1,45 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import ConvertDset
+
+
+def test_ConvertDset_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(deprecated='1.0.0',
+    nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-input %s',
+    mandatory=True,
+    position=-2,
+    ),
+    out_file=dict(argstr='-prefix %s',
+    position=-1,
+    ),
+    out_type=dict(argstr='-o_%s',
+    mandatory=True,
+    position=0,
+    ),
+    terminal_output=dict(deprecated='1.0.0',
+    nohash=True,
+    ),
+    )
+    inputs = ConvertDset.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_ConvertDset_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = ConvertDset.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/afni/utils.py

@@ -712,6 +712,59 @@ def _list_outputs(self):
         return outputs
 
 
+class ConvertDsetInputSpec(AFNICommandInputSpec):
+    in_file = File(
+        desc='input file to ConvertDset',
+        argstr='-input %s',
+        position=-2,
+        mandatory=True,
+        exists=True)
+
+    out_file = File(
+        desc='output file for ConvertDset',
+        argstr='-prefix %s',
+        position=-1,
+        mandatory=True)
+
+    out_type = traits.Enum(
+        ('niml', 'niml_asc', 'niml_bi',
+         '1D', '1Dp', '1Dpt',
+         'gii', 'gii_asc', 'gii_b64', 'gii_b64gz'),
+        desc='output type',
+        argstr='-o_%s',
+        mandatory=True,
+        position=0)
+
+
+class ConvertDset(AFNICommandBase):
+    """Converts a surface dataset from one format to another.
+
+    For complete details, see the `ConvertDset Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/ConvertDset.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> convertdset = afni.ConvertDset()
+    >>> convertdset.inputs.in_file = 'lh.pial_converted.gii'
+    >>> convertdset.inputs.out_type = 'niml_asc'
+    >>> convertdset.inputs.out_file = 'lh.pial_converted.niml.dset'
+    >>> convertdset.cmdline
+    'ConvertDset -o_niml_asc -input lh.pial_converted.gii -prefix lh.pial_converted.niml.dset'
+    >>> res = convertdset.run()  # doctest: +SKIP
+    """
+
+    _cmd = 'ConvertDset'
+    input_spec = ConvertDsetInputSpec
+    output_spec = AFNICommandOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        return outputs
+
+
 class CopyInputSpec(AFNICommandInputSpec):
     in_file = File(
         desc='input file to 3dcopy',