new naming conventions

Author: oesteban

CHANGES

@@ -1,8 +1,11 @@
 Next Release
 ============
 
-* ENH: New miscelaneous interfaces: SplitROIs, MergeROIs to enable parallel processing of very large images.
-* ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still available with the prefix `Old`.
+* ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer) 
+       to enable parallel processing of very large images.
+* ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
+       available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu 
+       versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
 * ENH: New FSL interface: EpiReg
 * ENH: New Freesurfer interface: Tkregister2 (for conversion of fsl style matrices to freesurfer format)
 * ENH: New FSL interfaces: WarpPoints, WarpPointsToStd.

doc/conf.py

@@ -39,8 +39,8 @@
               'numpy_ext.numpydoc',
               'matplotlib.sphinxext.plot_directive',
               'matplotlib.sphinxext.only_directives',
-              'matplotlib.sphinxext.ipython_directive',
-              'ipython_console_highlighting'
+              'IPython.sphinxext.ipython_directive',
+              'IPython.sphinxext.ipython_console_highlighting'
               ]
 
 # Add any paths that contain templates here, relative to this directory.

nipype/algorithms/tests/test_auto_MergeROIs.py

@@ -0,0 +1,24 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import MergeROIs
+
+def test_MergeROIs_inputs():
+    input_map = dict(in_files=dict(),
+    in_index=dict(),
+    in_reference=dict(),
+    )
+    inputs = MergeROIs.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_MergeROIs_outputs():
+    output_map = dict(merged_file=dict(),
+    )
+    outputs = MergeROIs.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/algorithms/tests/test_auto_SplitROIs.py

@@ -0,0 +1,27 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.misc import SplitROIs
+
+def test_SplitROIs_inputs():
+    input_map = dict(in_file=dict(mandatory=True,
+    ),
+    in_mask=dict(),
+    roi_size=dict(),
+    )
+    inputs = SplitROIs.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_SplitROIs_outputs():
+    output_map = dict(out_files=dict(),
+    out_index=dict(),
+    out_masks=dict(),
+    )
+    outputs = SplitROIs.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+

nipype/interfaces/dcmstack.py

@@ -84,7 +84,7 @@ class DcmStackInputSpec(NiftiGeneratorBaseInputSpec):
                                   "any default exclude filters")
     include_regexes = traits.List(desc="Meta data to include, overriding any "
                                   "exclude filters")
-    force_read = traits.Bool(True, usedefault=True, 
+    force_read = traits.Bool(True, usedefault=True,
                              desc=('Force reading files without DICM marker'))
 
 

nipype/interfaces/freesurfer/utils.py

@@ -1208,7 +1208,7 @@ class Tkregister2OutputSpec(TraitedSpec):
 
 
 class Tkregister2(FSCommand):
-    """Use tkregister2 without the manual editing stage to convert 
+    """Use tkregister2 without the manual editing stage to convert
     FSL-style registration matrix (.mat) to FreeSurfer-style registration matrix (.dat)
 
     Examples
@@ -1224,6 +1224,6 @@ class Tkregister2(FSCommand):
     _cmd = "tkregister2"
     input_spec = Tkregister2InputSpec
     output_spec = Tkregister2OutputSpec
-    
 
-    
+
+

nipype/interfaces/fsl/__init__.py

@@ -21,9 +21,11 @@
 from .epi import (PrepareFieldmap, TOPUP, ApplyTOPUP, Eddy, EPIDeWarp,
                   SigLoss, EddyCorrect, EpiReg)
 
-from .dti import (BEDPOSTX, XFibres, DTIFit, ProbTrackX, ProbTrackX2,
+from .dti import (BEDPOSTX, BEDPOSTXGPU, XFibres, DTIFit,
+                  ProbTrackX, ProbTrackX2,
                   VecReg, ProjThresh, FindTheBiggest, DistanceMap,
-                  TractSkeleton, MakeDyadicVectors, OldBEDPOSTX, OldXFibres)
+                  TractSkeleton, MakeDyadicVectors, BEDPOSTX5, XFibres5,
+                  BEDPOSTX4, XFibres4, BEDPOSTX5GPU, BEDPOSTX4GPU)
 from .maths import (ChangeDataType, Threshold, MeanImage, ApplyMask,
                     IsotropicSmooth, TemporalFilter, DilateImage, ErodeImage,
                     SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths)

nipype/interfaces/fsl/dti.py

@@ -16,6 +16,7 @@
 import shutil
 import warnings
 
+from ... import LooseVersion
 from nipype.interfaces.fsl.base import (FSLCommand, FSLCommandInputSpec, Info,
                                         FSLXCommand, FSLXCommandInputSpec,
                                         FSLXCommandOutputSpec)
@@ -100,14 +101,14 @@ def _list_outputs(self):
         return outputs
 
 
-class BEDPOSTXInputSpec(FSLXCommandInputSpec):
+class BEDPOSTX5InputSpec(FSLXCommandInputSpec):
     out_dir = Directory('.', mandatory=True, desc='output directory',
                         usedefault=True, position=1, argstr='%s')
     gradnonlin = traits.Bool(False, argstr='-g', desc=('consider gradient '
                              'nonlinearities, default off'))
 
 
-class BEDPOSTXOutputSpec(FSLXCommandOutputSpec):
+class BEDPOSTX5OutputSpec(FSLXCommandOutputSpec):
     mean_thsamples = OutputMultiPath(File(), desc=('Mean of '
                                      'distribution on theta'))
     mean_phsamples = OutputMultiPath(File(), desc=('Mean of '
@@ -124,7 +125,7 @@ class BEDPOSTXOutputSpec(FSLXCommandOutputSpec):
                                  ' estimated fiber orientation'))
 
 
-class BEDPOSTX(FSLXCommand):
+class BEDPOSTX5(FSLXCommand):
     """
     BEDPOSTX stands for Bayesian Estimation of Diffusion Parameters Obtained
     using Sampling Techniques. The X stands for modelling Crossing Fibres.
@@ -143,7 +144,7 @@ class BEDPOSTX(FSLXCommand):
     -------
 
     >>> from nipype.interfaces import fsl
-    >>> bedp = fsl.BEDPOSTX(bvecs='bvecs', bvals='bvals', dwi='diffusion.nii',
+    >>> bedp = fsl.BEDPOSTX5(bvecs='bvecs', bvals='bvals', dwi='diffusion.nii',
     ...                     mask='mask.nii', n_fibres=1)
     >>> bedp.cmdline
     'bedpostx . --bvals=bvals --bvecs=bvecs --data=diffusion.nii \
@@ -152,8 +153,8 @@ class BEDPOSTX(FSLXCommand):
     """
 
     _cmd = 'bedpostx'
-    input_spec = BEDPOSTXInputSpec
-    output_spec = BEDPOSTXOutputSpec
+    input_spec = BEDPOSTX5InputSpec
+    output_spec = BEDPOSTX5OutputSpec
     _can_resume = True
 
     def _run_interface(self, runtime):
@@ -179,7 +180,7 @@ def _run_interface(self, runtime):
         copyfile(self.inputs.bvecs,
                  os.path.join(subjectdir, 'bvecs'))
 
-        return super(BEDPOSTX, self)._run_interface(runtime)
+        return super(BEDPOSTX5, self)._run_interface(runtime)
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
@@ -209,26 +210,30 @@ def _list_outputs(self):
             outputs['dyads_disp'].append(self._gen_fname(('dyads%d'
                                          '_dispersion') % i, cwd=out_dir))
 
-        super_out = super(BEDPOSTX, self)._list_outputs()
+        super_out = super(BEDPOSTX5, self)._list_outputs()
 
         for k, v in super_out.iteritems():
             outputs[k] = v
 
         return outputs
 
 
-class XFibresInputSpec(FSLXCommandInputSpec):
+class BEDPOSTX5GPU(BEDPOSTX5):
+    _cmd = 'bedpostx_gpu'
+
+
+class XFibres5InputSpec(FSLXCommandInputSpec):
     gradnonlin = File(exists=True, argstr='--gradnonlin=%s',
                       desc='gradient file corresponding to slice')
 
 
-class XFibres(FSLXCommand):
+class XFibres5(FSLXCommand):
     """
     Perform model parameters estimation for local (voxelwise) diffusion
     parameters
     """
     _cmd = 'xfibres'
-    input_spec = XFibresInputSpec
+    input_spec = XFibres5InputSpec
     output_spec = FSLXCommandOutputSpec
 
 
@@ -902,7 +907,7 @@ def _list_outputs(self):
         return outputs
 
 
-class OldXFibresInputSpec(FSLCommandInputSpec):
+class XFibres4InputSpec(FSLCommandInputSpec):
     dwi = File(exists=True, argstr="--data=%s", mandatory=True)
     mask = File(exists=True, argstr="--mask=%s", mandatory=True)
     gradnonlin = File(exists=True, argstr="--gradnonlin=%s")
@@ -941,7 +946,7 @@ class OldXFibresInputSpec(FSLCommandInputSpec):
                                argstr='--forcedir', usedefault=True)
 
 
-class OldXFibresOutputSpec(TraitedSpec):
+class XFibres4OutputSpec(TraitedSpec):
     dyads = OutputMultiPath(File(exists=True), desc="Mean of PDD distribution in vector form.")
     fsamples = OutputMultiPath(File(exists=True), desc="Samples from the distribution on anisotropic volume fraction")
     mean_dsamples = File(exists=True, desc="Mean of distribution on diffusivity d")
@@ -951,22 +956,22 @@ class OldXFibresOutputSpec(TraitedSpec):
     thsamples = OutputMultiPath(File(exists=True), desc="Samples from the distribution on theta")
 
 
-class OldXFibres(FSLCommand):
+class XFibres4(FSLCommand):
     """
     Perform model parameters estimation for local (voxelwise) diffusion
     parameters
 
     .. deprecated:: 0.9.2
-      Use :class:`.XFibres` instead.
+      Use :class:`.XFibres5` instead.
 
 
     """
     _cmd = "xfibres"
-    input_spec = OldXFibresInputSpec
-    output_spec = OldXFibresOutputSpec
+    input_spec = XFibres4InputSpec
+    output_spec = XFibres4OutputSpec
 
     def _run_interface(self, runtime):
-        runtime = super(OldXFibres, self)._run_interface(runtime)
+        runtime = super(XFibres4, self)._run_interface(runtime)
         if runtime.stderr:
             self.raise_exception(runtime)
         return runtime
@@ -992,7 +997,7 @@ def _list_outputs(self):
         return outputs
 
 
-class OldBEDPOSTXInputSpec(FSLCommandInputSpec):
+class BEDPOSTX4InputSpec(FSLCommandInputSpec):
     dwi = File(exists=True, desc='diffusion weighted image data file',
                mandatory=True)
     mask = File(exists=True, desc='bet binary mask file', mandatory=True)
@@ -1017,7 +1022,7 @@ class OldBEDPOSTXInputSpec(FSLCommandInputSpec):
                           'hardware/queue (if found)'))
 
 
-class OldBEDPOSTXOutputSpec(TraitedSpec):
+class BEDPOSTX4OutputSpec(TraitedSpec):
     bpx_out_directory = Directory(exists=True,
                                   desc='path/name of directory with all ' +
                                        'bedpostx output files for this subject')
@@ -1044,7 +1049,7 @@ class OldBEDPOSTXOutputSpec(TraitedSpec):
     dyads = traits.List(File(exists=True),  desc='a list of path/name of mean of PDD distribution in vector form')
 
 
-class OldBEDPOSTX(FSLCommand):
+class BEDPOSTX4(FSLCommand):
     """
     bedpostx has an old interface, implemented here
 
@@ -1061,21 +1066,22 @@ class OldBEDPOSTX(FSLCommand):
     -------
 
     >>> from nipype.interfaces import fsl
-    >>> bedp = fsl.OldBEDPOSTX(bpx_directory='subjdir', bvecs='bvecs', \
+    >>> bedp = fsl.BEDPOSTX4(bpx_directory='subjdir', bvecs='bvecs', \
 bvals='bvals', dwi='diffusion.nii', mask='mask.nii', fibres=1)
     >>> bedp.cmdline
     'bedpostx subjdir -n 1'
 
     """
 
     _cmd = 'bedpostx'
-    input_spec = OldBEDPOSTXInputSpec
-    output_spec = OldBEDPOSTXOutputSpec
+    input_spec = BEDPOSTX4InputSpec
+    output_spec = BEDPOSTX4OutputSpec
     _can_resume = True
 
     def __init__(self, **inputs):
-        warnings.warn("Deprecated: Please use create_bedpostx_pipeline instead", DeprecationWarning)
-        return super(OldBEDPOSTX, self).__init__(**inputs)
+        warnings.warn(('Deprecated: Please use BEDPOSTX5 or '
+                      'create_bedpostx_pipeline instead'), DeprecationWarning)
+        return super(BEDPOSTX4, self).__init__(**inputs)
 
     def _run_interface(self, runtime):
 
@@ -1097,7 +1103,7 @@ def _run_interface(self, runtime):
             shutil.copyfile(self.inputs.bvecs,
                             os.path.join(self.inputs.bpx_directory, 'bvecs'))
 
-        runtime = super(BEDPOSTX, self)._run_interface(runtime)
+        runtime = super(BEDPOSTX4, self)._run_interface(runtime)
         if runtime.stderr:
             self.raise_exception(runtime)
         return runtime
@@ -1138,3 +1144,33 @@ def _list_outputs(self):
                                                             suffix='',
                                                             cwd=outputs['bpx_out_directory']))
         return outputs
+
+
+class BEDPOSTX4GPU(BEDPOSTX4):
+    _cmd = 'bedpostx_gpu'
+
+
+if (Info.version() and
+   LooseVersion(Info.version()) >= LooseVersion('5.0.0')):
+    CurrentXFibres = XFibres5
+    CurrentBEDPOST = BEDPOSTX5
+    CurrentBEDPOSTgpu = BEDPOSTX5GPU
+else:
+    CurrentXFibres = XFibres4
+    CurrentBEDPOST = BEDPOSTX4
+    CurrentBEDPOSTgpu = BEDPOSTX4GPU
+
+
+class XFibres(CurrentXFibres):
+    def __init__(self, **inputs):
+        return super(XFibres, self).__init__(**inputs)
+
+
+class BEDPOSTX(CurrentBEDPOST):
+    def __init__(self, **inputs):
+        return super(BEDPOSTX, self).__init__(**inputs)
+
+
+class BEDPOSTXGPU(CurrentBEDPOSTgpu):
+    def __init__(self, **inputs):
+        return super(BEDPOSTXGPU, self).__init__(**inputs)

nipype/interfaces/fsl/epi.py

@@ -566,11 +566,11 @@ class EpiRegInputSpec(FSLCommandInputSpec):
                         (use if fmap already registered)')
     no_clean = traits.Bool(False, argstr='--noclean',
                         desc='do not clean up intermediate files')
-    
+
 
 class EpiRegOutputSpec(TraitedSpec):
     out_file = File(exists=True,
-                    desc='unwarped and coregistered epi input')     
+                    desc='unwarped and coregistered epi input')
     out_1vol = File(exists=True,
                           desc='unwarped and coregistered single volume')
     fmap2str_mat = File(exists=True,
@@ -596,7 +596,7 @@ class EpiRegOutputSpec(TraitedSpec):
 class EpiReg(FSLCommand):
     """
 
-    Runs FSL epi_reg script for simultaneous coregistration and fieldmap 
+    Runs FSL epi_reg script for simultaneous coregistration and fieldmap
     unwarping.
 
     Examples
@@ -618,7 +618,7 @@ class EpiReg(FSLCommand):
 --fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_brain.nii --pedir=y \
 --epi=epi.nii --t1=T1.nii --t1brain=T1_brain.nii --out=epi2struct'
     >>> epireg.run() # doctest: +SKIP
-    
+
     """
     _cmd = 'epi_reg'
     input_spec = EpiRegInputSpec