Merge pull request #2514 from kesshijordan/satra_fix_specs

FIX: DTITK Interface

Author: satra

nipype/interfaces/afni/preprocess.py

@@ -2510,7 +2510,7 @@ class TProjectInputSpec(AFNICommandInputSpec):
                rather than the value stored in the dataset header.""",
         argstr='-TR %g')
     mask = File(
-        exist=True,
+        exists=True,
         desc="""Only operate on voxels nonzero in the mset dataset.
                 ++ Voxels outside the mask will be filled with zeros.
                 ++ If no masking option is given, then all voxels

nipype/interfaces/afni/tests/test_auto_TProject.py

@@ -32,10 +32,7 @@ def test_TProject_inputs():
             mandatory=True,
             position=1,
         ),
-        mask=dict(
-            argstr='-mask %s',
-            exist=True,
-        ),
+        mask=dict(argstr='-mask %s', ),
         noblock=dict(argstr='-noblock', ),
         norm=dict(argstr='-norm', ),
         num_threads=dict(

nipype/interfaces/dtitk/__init__.py

@@ -6,10 +6,8 @@
 """
 
 # from .base import ()
-from .registration import (RigidTask, AffineTask, DiffeoTask,
-                           ComposeXfmTask, diffeoSymTensor3DVolTask,
-                           affSymTensor3DVolTask, affScalarVolTask,
-                           diffeoScalarVolTask)
-from .utils import (TVAdjustOriginTask, TVAdjustVoxSpTask,
-                    SVAdjustVoxSpTask, TVResampleTask, SVResampleTask,
-                    TVtoolTask, BinThreshTask)
+from .registration import (Rigid, Affine, Diffeo,
+                           ComposeXfm, DiffeoSymTensor3DVol, AffSymTensor3DVol,
+                           AffScalarVol, DiffeoScalarVol)
+from .utils import (TVAdjustVoxSp, SVAdjustVoxSp, TVResample, SVResample,
+                    TVtool, BinThresh)

nipype/interfaces/dtitk/base.py

@@ -13,6 +13,12 @@
 * Rigid Tensor Registration
 * Affine Tensor Registration
 * Diffeomorphic Tensor Registration
+* Combine affiine and diffeomorphic transforms
+* Application of transform to tensor and scalar volumes
+* Threshold and Binarize
+* Adjusting the voxel space of tensor and scalar volumes
+* Resampling tensor and scalar volumes
+* Calculation of tensor metrics from tensor volume
 
 Examples
 --------
@@ -28,10 +34,26 @@
 from ...utils.filemanip import fname_presuffix
 from ..base import CommandLine
 from nipype.interfaces.fsl.base import Info
+import warnings
 
 LOGGER = logging.getLogger('interface')
 
 
+class DTITKRenameMixin(object):
+    def __init__(self, *args, **kwargs):
+        classes = [cls.__name__ for cls in self.__class__.mro()]
+        dep_name = classes[0]
+        rename_idx = classes.index('DTITKRenameMixin')
+        new_name = classes[rename_idx + 1]
+        warnings.warn('The {} interface has been renamed to {}\n'
+                      'Please see the documentation for DTI-TK '
+                      'interfaces, as some inputs have been '
+                      'added or renamed for clarity.'
+                      ''.format(dep_name, new_name),
+                      DeprecationWarning)
+        super(DTITKRenameMixin, self).__init__(*args, **kwargs)
+
+
 class CommandLineDtitk(CommandLine):
 
     def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,