Merge upstream/master [skip ci]

Author: effigies

.zenodo.json

@@ -568,6 +568,11 @@
       "affiliation": "University College London",
       "name": "Mancini, Matteo",
       "orcid": "0000-0001-7194-4568"
+    },
+    {
+      "affiliation": "Donders Institute for Brain, Cognition and Behavior, Center for Cognitive Neuroimaging",
+      "name": "Chetverikov, Andrey",
+      "orcid": "0000-0003-2767-6310"
     }
   ],
   "keywords": [

CHANGES

@@ -2,6 +2,7 @@ Upcoming release (0.14.1)
 =========================
 
 * 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)

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',

nipype/pipeline/plugins/base.py

@@ -528,15 +528,15 @@ def run(self, graph, config, updatehash=False):
         pyfiles = []
         dependencies = {}
         self._config = config
-        nodes = nx.topological_sort(graph)
+        nodes = list(nx.topological_sort(graph))
         logger.debug('Creating executable python files for each node')
         for idx, node in enumerate(nodes):
             pyfiles.append(
                 create_pyscript(
                     node, updatehash=updatehash, store_exception=False))
             dependencies[idx] = [
-                nodes.index(prevnode) for prevnode in graph.predecessors(node)
-            ]
+                nodes.index(prevnode)
+                for prevnode in list(graph.predecessors(node))]
         self._submit_graph(pyfiles, dependencies, nodes)
 
     def _get_args(self, node, keywords):

nipype/pipeline/plugins/multiproc.py

@@ -223,7 +223,9 @@ def _send_procs_to_workers(self, updatehash=False, graph=None):
 
         # Check to see if a job is available (jobs with all dependencies run)
         # See https://github.com/nipy/nipype/pull/2200#discussion_r141605722
-        jobids = np.nonzero(~self.proc_done & (self.depidx.sum(0) == 0))[1]
+        # See also https://github.com/nipy/nipype/issues/2372
+        jobids = np.flatnonzero(~self.proc_done &
+                                (self.depidx.sum(axis=0) == 0).__array__())
 
         # Check available resources by summing all threads and memory used
         free_memory_gb, free_processors = self._check_resources(

nipype/pipeline/plugins/pbs.py

@@ -49,18 +49,20 @@ def __init__(self, **kwargs):
         super(PBSPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
-        result = CommandLine(
-            'qstat {}'.format(taskid),
-            environ=dict(os.environ),
-            terminal_output='allatonce',
-            resource_monitor=False,
-            ignore_exception=True).run()
-        errmsg = 'Unknown Job Id'  # %s' % taskid
+        result = CommandLine('qstat -f {}'.format(taskid),
+                             environ=dict(os.environ),
+                             terminal_output='file_split',
+                             resource_monitor=False,
+                             ignore_exception=True).run()
+
+        stdout = result.runtime.stdout
+        stderr = result.runtime.stderr
+        errmsg = 'Unknown Job Id' 
         success = 'Job has finished'
-        if success in e:  # Fix for my PBS
+        if (success in stderr) or ('job_state = C' in stdout):  
             return False
         else:
-            return errmsg not in e
+            return errmsg not in stderr
 
     def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine(