Merge http://github.com/nipy/nipype into debugging

Author: Shoshana Berleant

CHANGES

@@ -1,6 +1,7 @@
 Upcoming release 0.13
 =====================
 
+* FIX: Semaphore capture using MultiProc plugin (https://github.com/nipy/nipype/pull/1689)
 * REF: Refactor AFNI interfaces (https://github.com/nipy/nipype/pull/1678, https://github.com/nipy/nipype/pull/1680)
 * ENH: Move nipype commands to group command using click (https://github.com/nipy/nipype/pull/1608)
 * FIX: AFNI Retroicor interface fixes (https://github.com/nipy/nipype/pull/1669)
@@ -26,7 +27,8 @@ Upcoming release 0.13
 * ENH: Implement missing inputs/outputs in FSL AvScale (https://github.com/nipy/nipype/pull/1563)
 * FIX: Fix symlink test in copyfile (https://github.com/nipy/nipype/pull/1570, https://github.com/nipy/nipype/pull/1586)
 * ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
-
+* ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
+       (https://github.com/nipy/nipype/pull/1654)
 
 Release 0.12.1 (August 3, 2016)
 ===============================

nipype/interfaces/ants/__init__.py

@@ -19,4 +19,4 @@
 from .visualization import ConvertScalarImageToRGB, CreateTiledMosaic
 
 # Utility Programs
-from .utils import AverageAffineTransform, AverageImages, MultiplyImages, JacobianDeterminant
+from .utils import AverageAffineTransform, AverageImages, MultiplyImages, CreateJacobianDeterminantImage

nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py renamed to nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py

@@ -1,61 +1,55 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
 from ....testing import assert_equal
-from ..utils import JacobianDeterminant
+from ..utils import CreateJacobianDeterminantImage
 
 
-def test_JacobianDeterminant_inputs():
+def test_CreateJacobianDeterminantImage_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
-    dimension=dict(argstr='%d',
+    deformationField=dict(argstr='%s',
     mandatory=True,
-    position=0,
-    usedefault=False,
+    position=1,
+    ),
+    doLogJacobian=dict(argstr='%d',
+    mandatory=False,
+    position=3,
     ),
     environ=dict(nohash=True,
     usedefault=True,
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    norm_by_total=dict(argstr='%d',
-    position=5,
+    imageDimension=dict(argstr='%d',
+    mandatory=True,
+    position=0,
+    usedefault=False,
     ),
     num_threads=dict(nohash=True,
     usedefault=True,
     ),
-    output_prefix=dict(argstr='%s',
-    genfile=True,
-    hash_files=False,
+    outputImage=dict(argstr='%s',
+    mandatory=True,
     position=2,
     ),
-    projection_vector=dict(argstr='%s',
-    position=6,
-    sep='x',
-    ),
-    template_mask=dict(argstr='%s',
-    position=4,
-    ),
     terminal_output=dict(nohash=True,
     ),
-    use_log=dict(argstr='%d',
-    position=3,
-    ),
-    warp_file=dict(argstr='%s',
-    mandatory=True,
-    position=1,
+    useGeometric=dict(argstr='%d',
+    mandatory=False,
+    position=4,
     ),
     )
-    inputs = JacobianDeterminant.input_spec()
+    inputs = CreateJacobianDeterminantImage.input_spec()
 
     for key, metadata in list(input_map.items()):
         for metakey, value in list(metadata.items()):
             yield assert_equal, getattr(inputs.traits()[key], metakey), value
 
 
-def test_JacobianDeterminant_outputs():
+def test_CreateJacobianDeterminantImage_outputs():
     output_map = dict(jacobian_image=dict(),
     )
-    outputs = JacobianDeterminant.output_spec()
+    outputs = CreateJacobianDeterminantImage.output_spec()
 
     for key, metadata in list(output_map.items()):
         for metakey, value in list(metadata.items()):

nipype/interfaces/ants/utils.py

@@ -137,65 +137,44 @@ def _list_outputs(self):
             self.inputs.output_product_image)
         return outputs
 
-
-class JacobianDeterminantInputSpec(ANTSCommandInputSpec):
-    dimension = traits.Enum(3, 2, argstr='%d', usedefault=False, mandatory=True,
+class CreateJacobianDeterminantImageInputSpec(ANTSCommandInputSpec):
+    imageDimension = traits.Enum(3, 2, argstr='%d', usedefault=False, mandatory=True,
                             position=0, desc='image dimension (2 or 3)')
-    warp_file = File(argstr='%s', exists=True, mandatory=True,
-                     position=1, desc='input warp file')
-    output_prefix = File(argstr='%s', genfile=True, hash_files=False,
+    deformationField = File(argstr='%s', exists=True, mandatory=True,
+                     position=1, desc='deformation transformation file')
+    outputImage = File(argstr='%s', mandatory=True,
                          position=2,
-                         desc=('prefix of the output image filename: '
-                               'PREFIX(log)jacobian.nii.gz'))
-    use_log = traits.Enum(0, 1, argstr='%d', position=3,
-                          desc='log transform the jacobian determinant')
-    template_mask = File(argstr='%s', exists=True, position=4,
-                         desc='template mask to adjust for head size')
-    norm_by_total = traits.Enum(0, 1, argstr='%d', position=5,
-                                desc=('normalize jacobian by total in mask to '
-                                      'adjust for head size'))
-    projection_vector = traits.List(traits.Float(), argstr='%s', sep='x',
-                                    position=6,
-                                    desc='vector to project warp against')
-
+                         desc='output filename')
+    doLogJacobian = traits.Enum(0, 1, argstr='%d', mandatory=False, position=3,
+                          desc='return the log jacobian')
+    useGeometric = traits.Enum(0, 1, argstr='%d', mandatory=False, position=4,
+                          desc='return the geometric jacobian')
 
-class JacobianDeterminantOutputSpec(TraitedSpec):
-    jacobian_image = File(exists=True, desc='(log transformed) jacobian image')
+class CreateJacobianDeterminantImageOutputSpec(TraitedSpec):
+    jacobian_image = File(exists=True, desc='jacobian image')
 
-
-class JacobianDeterminant(ANTSCommand):
+class CreateJacobianDeterminantImage(ANTSCommand):
     """
     Examples
     --------
-    >>> from nipype.interfaces.ants import JacobianDeterminant
-    >>> jacobian = JacobianDeterminant()
-    >>> jacobian.inputs.dimension = 3
-    >>> jacobian.inputs.warp_file = 'ants_Warp.nii.gz'
-    >>> jacobian.inputs.output_prefix = 'Sub001_'
-    >>> jacobian.inputs.use_log = 1
+    >>> from nipype.interfaces.ants import CreateJacobianDeterminantImage
+    >>> jacobian = CreateJacobianDeterminantImage()
+    >>> jacobian.inputs.imageDimension = 3
+    >>> jacobian.inputs.deformationField = 'ants_Warp.nii.gz'
+    >>> jacobian.inputs.outputImage = 'out_name.nii.gz'
     >>> jacobian.cmdline # doctest: +IGNORE_UNICODE
-    'ANTSJacobian 3 ants_Warp.nii.gz Sub001_ 1'
+    'CreateJacobianDeterminantImage 3 ants_Warp.nii.gz out_name.nii.gz'
     """
 
-    _cmd = 'ANTSJacobian'
-    input_spec = JacobianDeterminantInputSpec
-    output_spec = JacobianDeterminantOutputSpec
+    _cmd = 'CreateJacobianDeterminantImage'
+    input_spec = CreateJacobianDeterminantImageInputSpec
+    output_spec = CreateJacobianDeterminantImageOutputSpec
 
-    def _gen_filename(self, name):
-        if name == 'output_prefix':
-            output = self.inputs.output_prefix
-            if not isdefined(output):
-                _, name, ext = split_filename(self.inputs.warp_file)
-                output = name + '_'
-            return output
-        return None
+    def _format_arg(self, opt, spec, val):
+        return super(CreateJacobianDeterminantImage, self)._format_arg(opt, spec, val)
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        if self.inputs.use_log == 1:
-            outputs['jacobian_image'] = os.path.abspath(
-                self._gen_filename('output_prefix') + 'logjacobian.nii.gz')
-        else:
-            outputs['jacobian_image'] = os.path.abspath(
-                self._gen_filename('output_prefix') + 'jacobian.nii.gz')
+        outputs['jacobian_image'] = os.path.abspath(
+            self.inputs.outputImage)
         return outputs

nipype/pipeline/engine/utils.py

@@ -648,11 +648,13 @@ def _propagate_internal_output(graph, node, field, connections, portinputs):
         if field in portinputs:
             srcnode, srcport = portinputs[field]
             if isinstance(srcport, tuple) and isinstance(src, tuple):
-                raise ValueError(("Does not support two inline functions "
-                                  "in series (\'%s\'  and \'%s\'). "
-                                  "Please use a Function node") %
-                                 (srcport[1].split("\\n")[0][6:-1],
-                                  src[1].split("\\n")[0][6:-1]))
+                src_func = srcport[1].split("\\n")[0]
+                dst_func = src[1].split("\\n")[0]
+                raise ValueError("Does not support two inline functions "
+                                 "in series ('{}'  and '{}'), found when "
+                                 "connecting {} to {}. Please use a Function "
+                                 "node.".format(src_func, dst_func, srcnode, destnode))
+
             connect = graph.get_edge_data(srcnode, destnode,
                                           default={'connect': []})
             if isinstance(src, tuple):

nipype/pipeline/plugins/multiproc.py

@@ -160,7 +160,6 @@ def __init__(self, plugin_args=None):
     def _wait(self):
         if len(self.pending_tasks) > 0:
             semaphore_singleton.semaphore.acquire()
-        semaphore_singleton.semaphore.release()
 
     def _get_result(self, taskid):
         if taskid not in self._taskresult:

nipype/pipeline/plugins/semaphore_singleton.py

@@ -1,4 +1,4 @@
 # -*- coding: utf-8 -*-
 from __future__ import print_function, division, unicode_literals, absolute_import
 import threading
-semaphore = threading.Semaphore(1)
+semaphore = threading.Semaphore(0)

tools/build_interface_docs.py

@@ -40,7 +40,7 @@
                                        '\.testing',
                                        '\.scripts',
                                        ]
-    docwriter.class_skip_patterns += ['AFNI',
+    docwriter.class_skip_patterns += ['AFNICommand',
                                       'ANTS',
                                       'FSL',
                                       'FS',