Merge remote-tracking branch 'upstream/pr/1278' into fix/use_current_prov

* upstream/pr/1278:
  Removed verbose input (only available in current master of ANTs). Will wait for next release to add.
  Added old class names for backwards compatibility, included DeprecationWarning
  Standardized imports for ANTs
  Finished TODO items in ApplyTransforms and added option to Atropos Added interpolation_parameters, float and verbose to ApplyTransforms and added use_random_seed and verbose to Atropos
  Finished TODO items in resampling (ApplyTransforms)
  PEP8 and other style corrections. Including doctstrings using multi-line string formatting. Changed class names for antsBrainExtraction and antsCorticalThickness.
  Removed redundant _format_xarray from ANTSCommand and replaced other join functions with _format_xarray

Author: satra

nipype/interfaces/ants/__init__.py

@@ -7,11 +7,12 @@
 from .registration import ANTS, Registration
 
 # Resampling Programs
-from .resampling import ApplyTransforms, ApplyTransformsToPoints, WarpImageMultiTransform, WarpTimeSeriesImageMultiTransform
-
+from .resampling import (ApplyTransforms, ApplyTransformsToPoints, WarpImageMultiTransform,
+                         WarpTimeSeriesImageMultiTransform)
 
 # Segmentation Programs
-from .segmentation import Atropos, LaplacianThickness, N4BiasFieldCorrection, JointFusion, antsCorticalThickness, antsBrainExtraction
+from .segmentation import (Atropos, LaplacianThickness, N4BiasFieldCorrection, JointFusion, CorticalThickness,
+                           BrainExtraction)
 
 # Visualization Programs
 from .visualization import ConvertScalarImageToRGB, CreateTiledMosaic

nipype/interfaces/ants/base.py

@@ -84,8 +84,3 @@ def set_default_num_threads(cls, num_threads):
         <instance>.inputs.num_threads
         """
         cls._num_threads = num_threads
-
-    def _format_xarray(self, val):
-        """ Convienence method for converting [1,2,3] -> 1x2x3 """
-        val = 'x'.join([str(x) for x in val])
-        return val

nipype/interfaces/ants/legacy.py

@@ -18,8 +18,7 @@
 
 
 from .base import ANTSCommand, ANTSCommandInputSpec
-from ..base import (TraitedSpec, File, traits, InputMultiPath,
-                    isdefined, OutputMultiPath)
+from ..base import TraitedSpec, File, traits, isdefined, OutputMultiPath
 from ...utils.filemanip import split_filename
 
 

nipype/interfaces/ants/registration.py

@@ -11,8 +11,7 @@
 import os
 
 from .base import ANTSCommand, ANTSCommandInputSpec
-from ..base import (TraitedSpec, File, traits,
-                    isdefined, InputMultiPath)
+from ..base import TraitedSpec, File, traits, isdefined, InputMultiPath
 from ...utils.filemanip import split_filename
 
 
@@ -64,7 +63,8 @@ class WarpTimeSeriesImageMultiTransform(ANTSCommand):
     >>> wtsimt.inputs.reference_image = 'ants_deformed.nii.gz'
     >>> wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt']
     >>> wtsimt.cmdline
-    'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt'
+    'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz \
+ants_Affine.txt'
 
     """
 
@@ -99,7 +99,7 @@ def _list_outputs(self):
                                                         ext)))
         return outputs
 
-    def _run_interface(self, runtime):
+    def _run_interface(self, runtime, correct_return_codes=[0]):
         runtime = super(WarpTimeSeriesImageMultiTransform, self)._run_interface(runtime, correct_return_codes=[0, 1])
         if "100 % complete" not in runtime.stdout:
             self.raise_exception(runtime)
@@ -113,7 +113,7 @@ class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
                        desc=('image to apply transformation to (generally a '
                               'coregistered functional)'), position=2)
     output_image = File(genfile=True, hash_files=False, argstr='%s',
-                        desc=('name of the output warped image'), position=3, xor=['out_postfix'])
+                        desc='name of the output warped image', position=3, xor=['out_postfix'])
     out_postfix = File("_wimt", usedefault=True, hash_files=False,
                        desc=('Postfix that is prepended to all output '
                              'files (default = _wimt)'), xor=['output_image'])
@@ -159,15 +159,18 @@ class WarpImageMultiTransform(ANTSCommand):
     >>> wimt.inputs.reference_image = 'ants_deformed.nii.gz'
     >>> wimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt']
     >>> wimt.cmdline
-    'WarpImageMultiTransform 3 structural.nii structural_wimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz ants_Affine.txt'
+    'WarpImageMultiTransform 3 structural.nii structural_wimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz \
+ants_Affine.txt'
 
     >>> wimt = WarpImageMultiTransform()
     >>> wimt.inputs.input_image = 'diffusion_weighted.nii'
     >>> wimt.inputs.reference_image = 'functional.nii'
-    >>> wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz','dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt']
+    >>> wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz', \
+    'dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt']
     >>> wimt.inputs.invert_affine = [1]
     >>> wimt.cmdline
-    'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii -i func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz dwi2anat_coreg_Affine.txt'
+    'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii \
+-i func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz dwi2anat_coreg_Affine.txt'
 
     """
 
@@ -221,9 +224,8 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
                        desc=('image to apply transformation to (generally a '
                               'coregistered functional)'),
                        exists=True)
-    output_image = traits.Str(argstr='--output %s',
-                              desc=('output file name'), genfile=True,
-                              hash_files=False)
+    output_image = traits.Str(argstr='--output %s', desc='output file name',
+                              genfile=True, hash_files=False)
     out_postfix = traits.Str("_trans", usedefault=True,
                              desc=('Postfix that is appended to all output '
                                    'files (default = _trans)'))
@@ -240,17 +242,17 @@ class ApplyTransformsInputSpec(ANTSCommandInputSpec):
                                 'Gaussian',
                                 'BSpline',
                                 argstr='%s', usedefault=True)
-    # TODO: Implement these options for multilabel, gaussian, and bspline
-    # interpolation_sigma = traits.Float(requires=['interpolation'])
-    # interpolation_alpha = traits.Float(requires=['interpolation_sigma'])
-    # bspline_order = traits.Int(3, requires=['interpolation'])
+    interpolation_parameters = traits.Either(traits.Tuple(traits.Int()),  # BSpline (order)
+                                             traits.Tuple(traits.Float(),  # Gaussian/MultiLabel (sigma, alpha)
+                                                          traits.Float())
+                                             )
     transforms = InputMultiPath(
-        File(exists=True), argstr='%s', mandatory=True, desc=(''))
+        File(exists=True), argstr='%s', mandatory=True, desc='transform files')
     invert_transform_flags = InputMultiPath(traits.Bool())
-    default_value = traits.Float(
-        0.0, argstr='--default-value %g', usedefault=True)
-    print_out_composite_warp_file = traits.Enum(
-        0, 1, requires=["output_image"], desc=(''))  # TODO: Change to boolean
+    default_value = traits.Float(0.0, argstr='--default-value %g', usedefault=True)
+    print_out_composite_warp_file = traits.Bool(False, requires=["output_image"],
+                                                desc='output a composite warp file instead of a transformed image')
+    float = traits.Bool(argstr='--float %d', default=False, desc='Use float instead of double for computations.')
 
 
 class ApplyTransformsOutputSpec(TraitedSpec):
@@ -275,7 +277,24 @@ class ApplyTransforms(ANTSCommand):
     >>> at.inputs.transforms = ['trans.mat', 'ants_Warp.nii.gz']
     >>> at.inputs.invert_transform_flags = [False, False]
     >>> at.cmdline
-    'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation Linear --output deformed_moving1.nii --reference-image fixed1.nii --transform [trans.mat,0] --transform [ants_Warp.nii.gz,0]'
+    'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation Linear \
+--output deformed_moving1.nii --reference-image fixed1.nii --transform [ trans.mat, 0 ] \
+--transform [ ants_Warp.nii.gz, 0 ]'
+
+    >>> at1 = ApplyTransforms()
+    >>> at1.inputs.dimension = 3
+    >>> at1.inputs.input_image = 'moving1.nii'
+    >>> at1.inputs.reference_image = 'fixed1.nii'
+    >>> at1.inputs.output_image = 'deformed_moving1.nii'
+    >>> at1.inputs.interpolation = 'BSpline'
+    >>> at1.inputs.interpolation_parameters = (5,)
+    >>> at1.inputs.default_value = 0
+    >>> at1.inputs.transforms = ['trans.mat', 'ants_Warp.nii.gz']
+    >>> at1.inputs.invert_transform_flags = [False, False]
+    >>> at1.cmdline
+    'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation BSpline[ 5 ] \
+--output deformed_moving1.nii --reference-image fixed1.nii --transform [ trans.mat, 0 ] \
+--transform [ ants_Warp.nii.gz, 0 ]'
 
 
     """
@@ -292,35 +311,42 @@ def _gen_filename(self, name):
             return output
         return None
 
-    def _getTransformFileNames(self):
+    def _get_transform_filenames(self):
         retval = []
         for ii in range(len(self.inputs.transforms)):
             if isdefined(self.inputs.invert_transform_flags):
                 if len(self.inputs.transforms) == len(self.inputs.invert_transform_flags):
                     invert_code = 1 if self.inputs.invert_transform_flags[
                         ii] else 0
-                    retval.append("--transform [%s,%d]" %
+                    retval.append("--transform [ %s, %d ]" %
                                   (self.inputs.transforms[ii], invert_code))
                 else:
-                    raise Exception("ERROR: The useInverse list must have the same number of entries as the transformsFileName list.")
+                    raise Exception(("ERROR: The useInverse list must have the same number "
+                                     "of entries as the transformsFileName list."))
             else:
                 retval.append("--transform %s" % self.inputs.transforms[ii])
         return " ".join(retval)
 
-    def _getOutputWarpedFileName(self):
+    def _get_output_warped_filename(self):
         if isdefined(self.inputs.print_out_composite_warp_file):
-            return "--output [%s,%s]" % (self._gen_filename("output_image"), self.inputs.print_out_composite_warp_file)
+            return "--output [ %s, %d ]" % (self._gen_filename("output_image"),
+                                            int(self.inputs.print_out_composite_warp_file))
         else:
             return "--output %s" % (self._gen_filename("output_image"))
 
     def _format_arg(self, opt, spec, val):
         if opt == "output_image":
-            return self._getOutputWarpedFileName()
+            return self._get_output_warped_filename()
         elif opt == "transforms":
-            return self._getTransformFileNames()
+            return self._get_transform_filenames()
         elif opt == 'interpolation':
-            # TODO: handle multilabel, gaussian, and bspline options
-            return '--interpolation %s' % self.inputs.interpolation
+            if self.inputs.interpolation in ['BSpline', 'MultiLabel', 'Gaussian'] and \
+                    isdefined(self.inputs.interpolation_parameters):
+                return '--interpolation %s[ %s ]' % (self.inputs.interpolation,
+                                                     ', '.join([str(param)
+                                                                for param in self.inputs.interpolation_parameters]))
+            else:
+                return '--interpolation %s' % self.inputs.interpolation
         return super(ApplyTransforms, self)._format_arg(opt, spec, val)
 
     def _list_outputs(self):
@@ -348,12 +374,12 @@ class ApplyTransformsToPointsInputSpec(ANTSCommandInputSpec):
                             "expecting."),
                       exists=True)
     output_file = traits.Str(argstr='--output %s',
-                             desc=('Name of the output CSV file'), name_source=['input_file'],
+                             desc='Name of the output CSV file', name_source=['input_file'],
                              hash_files=False, name_template='%s_transformed.csv')
     transforms = traits.List(File(exists=True), argstr='%s', mandatory=True,
-                             desc=('transforms that will be applied to the points'))
+                             desc='transforms that will be applied to the points')
     invert_transform_flags = traits.List(traits.Bool(),
-                                         desc=('list indicating if a transform should be reversed'))
+                                         desc='list indicating if a transform should be reversed')
 
 
 class ApplyTransformsToPointsOutputSpec(TraitedSpec):
@@ -374,30 +400,32 @@ class ApplyTransformsToPoints(ANTSCommand):
     >>> at.inputs.transforms = ['trans.mat', 'ants_Warp.nii.gz']
     >>> at.inputs.invert_transform_flags = [False, False]
     >>> at.cmdline
-    'antsApplyTransformsToPoints --dimensionality 3 --input moving.csv --output moving_transformed.csv --transform [trans.mat,0] --transform [ants_Warp.nii.gz,0]'
+    'antsApplyTransformsToPoints --dimensionality 3 --input moving.csv --output moving_transformed.csv \
+--transform [ trans.mat, 0 ] --transform [ ants_Warp.nii.gz, 0 ]'
 
 
     """
     _cmd = 'antsApplyTransformsToPoints'
     input_spec = ApplyTransformsToPointsInputSpec
     output_spec = ApplyTransformsToPointsOutputSpec
 
-    def _getTransformFileNames(self):
+    def _get_transform_filenames(self):
         retval = []
         for ii in range(len(self.inputs.transforms)):
             if isdefined(self.inputs.invert_transform_flags):
                 if len(self.inputs.transforms) == len(self.inputs.invert_transform_flags):
                     invert_code = 1 if self.inputs.invert_transform_flags[
                         ii] else 0
-                    retval.append("--transform [%s,%d]" %
+                    retval.append("--transform [ %s, %d ]" %
                                   (self.inputs.transforms[ii], invert_code))
                 else:
-                    raise Exception("ERROR: The useInverse list must have the same number of entries as the transformsFileName list.")
+                    raise Exception(("ERROR: The useInverse list must have the same number "
+                                     "of entries as the transformsFileName list."))
             else:
                 retval.append("--transform %s" % self.inputs.transforms[ii])
         return " ".join(retval)
 
     def _format_arg(self, opt, spec, val):
         if opt == "transforms":
-            return self._getTransformFileNames()
+            return self._get_transform_filenames()
         return super(ApplyTransformsToPoints, self)._format_arg(opt, spec, val)