Merge remote-tracking branch 'upstream/master' into fix/use_current_prov

* upstream/master:
  Correct versions and consistency in install.rst
  fix:import utils needed one more dot
  fix: absolute to relative imports
  add vtk version checking in fsl interfaces
  update CHANGES
  Fix #1218 only, not addressing #973
  force setting ETS_TOOLKIT before tvtk #972
  Created TVTKBaseInterface. Should fix #1218

Author: satra

CHANGES

@@ -1,11 +1,13 @@
-Next Release
+Next release
 ============
 
+* FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
 * ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
 * ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
 * API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
 * ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
 
+
 Release 0.11.0 (September 15, 2015)
 ============
 

doc/users/install.rst

@@ -160,10 +160,10 @@ matlab_
   2008a or later
 
 SPM_
-  SPM5/8
+  SPM5 or later
 
 FreeSurfer_
-  FreeSurfer version 4 and higher
+  FreeSurfer v4.0.0 or later
 
 AFNI_
   2009_12_31_1431 or later

nipype/algorithms/mesh.py

@@ -26,6 +26,20 @@
 iflogger = logging.getLogger('interface')
 
 
+class TVTKBaseInterface(BaseInterface):
+    _redirect_x = True
+    _vtk_major = 6
+
+    def __init__(self, **inputs):
+        try:
+            from tvtk.tvtk_classes.vtk_version import vtk_build_version
+            self._vtk_major = int(vtk_build_version[0])
+        except ImportError:
+            iflogger.warning('VTK version-major inspection using tvtk failed.')
+
+        super(TVTKBaseInterface, self).__init__(**inputs)
+
+
 class WarpPointsInputSpec(BaseInterfaceInputSpec):
     points = File(exists=True, mandatory=True,
                   desc=('file containing the point set'))
@@ -42,7 +56,7 @@ class WarpPointsOutputSpec(TraitedSpec):
     out_points = File(desc='the warped point set')
 
 
-class WarpPoints(BaseInterface):
+class WarpPoints(TVTKBaseInterface):
 
     """
     Applies a displacement field to a point set given in vtk format.
@@ -62,7 +76,6 @@ class WarpPoints(BaseInterface):
     """
     input_spec = WarpPointsInputSpec
     output_spec = WarpPointsOutputSpec
-    _redirect_x = True
 
     def _gen_fname(self, in_file, suffix='generated', ext=None):
         import os.path as op
@@ -81,30 +94,15 @@ def _gen_fname(self, in_file, suffix='generated', ext=None):
         return op.abspath('%s_%s.%s' % (fname, suffix, ext))
 
     def _run_interface(self, runtime):
-        vtk_major = 6
-        try:
-            import vtk
-            vtk_major = vtk.VTK_MAJOR_VERSION
-        except ImportError:
-            iflogger.warn(('python-vtk could not be imported'))
+        import nibabel as nb
+        import numpy as np
+        from scipy import ndimage
 
         try:
             from tvtk.api import tvtk
         except ImportError:
             raise ImportError('Interface requires tvtk')
 
-        try:
-            from enthought.etsconfig.api import ETSConfig
-            ETSConfig.toolkit = 'null'
-        except ImportError:
-            iflogger.warn(('ETS toolkit could not be imported'))
-        except ValueError:
-            iflogger.warn(('ETS toolkit could not be set to null'))
-
-        import nibabel as nb
-        import numpy as np
-        from scipy import ndimage
-
         r = tvtk.PolyDataReader(file_name=self.inputs.points)
         r.update()
         mesh = r.output
@@ -134,7 +132,7 @@ def _run_interface(self, runtime):
         newpoints = [p + d for p, d in zip(points, disps)]
         mesh.points = newpoints
         w = tvtk.PolyDataWriter()
-        if vtk_major <= 5:
+        if self._vtk_major <= 5:
             w.input = mesh
         else:
             w.set_input_data_object(mesh)
@@ -182,7 +180,7 @@ class ComputeMeshWarpOutputSpec(TraitedSpec):
                     desc='numpy file keeping computed distances and weights')
 
 
-class ComputeMeshWarp(BaseInterface):
+class ComputeMeshWarp(TVTKBaseInterface):
 
     """
     Calculates a the vertex-wise warping to get surface2 from surface1.
@@ -207,7 +205,6 @@ class ComputeMeshWarp(BaseInterface):
 
     input_spec = ComputeMeshWarpInputSpec
     output_spec = ComputeMeshWarpOutputSpec
-    _redirect_x = True
 
     def _triangle_area(self, A, B, C):
         A = np.array(A)
@@ -223,15 +220,7 @@ def _run_interface(self, runtime):
         try:
             from tvtk.api import tvtk
         except ImportError:
-            raise ImportError('Interface ComputeMeshWarp requires tvtk')
-
-        try:
-            from enthought.etsconfig.api import ETSConfig
-            ETSConfig.toolkit = 'null'
-        except ImportError:
-            iflogger.warn(('ETS toolkit could not be imported'))
-        except ValueError:
-            iflogger.warn(('ETS toolkit is already set'))
+            raise ImportError('Interface requires tvtk')
 
         r1 = tvtk.PolyDataReader(file_name=self.inputs.surface1)
         r2 = tvtk.PolyDataReader(file_name=self.inputs.surface2)
@@ -280,7 +269,12 @@ def _run_interface(self, runtime):
         out_mesh.point_data.vectors.name = 'warpings'
         writer = tvtk.PolyDataWriter(
             file_name=op.abspath(self.inputs.out_warp))
-        writer.set_input_data(out_mesh)
+
+        if self._vtk_major <= 5:
+            writer.input = mesh
+        else:
+            writer.set_input_data_object(mesh)
+
         writer.write()
 
         self._distance = np.average(errvector, weights=weights)
@@ -322,7 +316,7 @@ class MeshWarpMathsOutputSpec(TraitedSpec):
                     desc='vtk with surface warped')
 
 
-class MeshWarpMaths(BaseInterface):
+class MeshWarpMaths(TVTKBaseInterface):
 
     """
     Performs the most basic mathematical operations on the warping field
@@ -348,21 +342,12 @@ class MeshWarpMaths(BaseInterface):
 
     input_spec = MeshWarpMathsInputSpec
     output_spec = MeshWarpMathsOutputSpec
-    _redirect_x = True
 
     def _run_interface(self, runtime):
         try:
             from tvtk.api import tvtk
         except ImportError:
-            raise ImportError('Interface ComputeMeshWarp requires tvtk')
-
-        try:
-            from enthought.etsconfig.api import ETSConfig
-            ETSConfig.toolkit = 'null'
-        except ImportError:
-            iflogger.warn(('ETS toolkit could not be imported'))
-        except ValueError:
-            iflogger.warn(('ETS toolkit is already set'))
+            raise ImportError('Interface requires tvtk')
 
         r1 = tvtk.PolyDataReader(file_name=self.inputs.in_surf)
         vtk1 = r1.output
@@ -412,14 +397,21 @@ def _run_interface(self, runtime):
         vtk1.point_data.vectors = warping
         writer = tvtk.PolyDataWriter(
             file_name=op.abspath(self.inputs.out_warp))
-        writer.set_input_data(vtk1)
+        if self._vtk_major <= 5:
+            writer.input = vtk1
+        else:
+            writer.set_input_data_object(vtk1)
         writer.write()
 
         vtk1.point_data.vectors = None
         vtk1.points = points1 + warping
         writer = tvtk.PolyDataWriter(
             file_name=op.abspath(self.inputs.out_file))
-        writer.set_input_data(vtk1)
+
+        if self._vtk_major <= 5:
+            writer.input = vtk1
+        else:
+            writer.set_input_data_object(vtk1)
         writer.write()
 
         return runtime

nipype/interfaces/fsl/utils.py

@@ -1870,9 +1870,18 @@ def _vtk_to_coords(self, in_file, out_file=None):
         except ImportError:
             raise ImportError('This interface requires tvtk to run.')
 
+        vtk_major = 5
+        try:
+            from tvtk.tvtk_classes.vtk_version import vtk_build_version
+            vtk_major = int(vtk_build_version[0])
+        except ImportError:
+            iflogger.warning('VTK version-major inspection using tvtk failed.')
+
         reader = tvtk.PolyDataReader(file_name=in_file + '.vtk')
         reader.update()
-        points = reader.output.points
+
+        mesh = reader.output if vtk_major < 6 else reader.get_output()
+        points = mesh.points
 
         if out_file is None:
             out_file, _ = op.splitext(in_file) + '.txt'
@@ -1887,12 +1896,24 @@ def _coords_to_vtk(self, points, out_file):
         except ImportError:
             raise ImportError('This interface requires tvtk to run.')
 
+        vtk_major = 5
+        try:
+            from tvtk.tvtk_classes.vtk_version import vtk_build_version
+            vtk_major = int(vtk_build_version[0])
+        except ImportError:
+            iflogger.warning('VTK version-major inspection using tvtk failed.')
+
         reader = tvtk.PolyDataReader(file_name=self.inputs.in_file)
         reader.update()
-        mesh = reader.output
+
+        mesh = reader.output if vtk_major < 6 else reader.get_output()
         mesh.points = points
 
-        writer = tvtk.PolyDataWriter(file_name=out_file, input=mesh)
+        writer = tvtk.PolyDataWriter(file_name=out_file)
+        if vtk_major < 6:
+            writer.input = mesh
+        else:
+            writer.set_input_data_object(mesh)
         writer.write()
 
     def _trk_to_coords(self, in_file, out_file=None):

nipype/interfaces/spm/preprocess.py

@@ -21,13 +21,13 @@
 import numpy as np
 
 # Local imports
-from nipype.interfaces.base import (OutputMultiPath, TraitedSpec, isdefined,
-                                    traits, InputMultiPath, File)
-from nipype.interfaces.spm.base import (SPMCommand, scans_for_fname,
-                                        func_is_3d, Info,
-                                        scans_for_fnames, SPMCommandInputSpec)
-from nipype.utils.filemanip import (fname_presuffix, filename_to_list,
-                                    list_to_filename, split_filename)
+from ..base import (OutputMultiPath, TraitedSpec, isdefined,
+                    traits, InputMultiPath, File)
+from .base import (SPMCommand, scans_for_fname,
+                   func_is_3d, Info,
+                   scans_for_fnames, SPMCommandInputSpec)
+from ...utils.filemanip import (fname_presuffix, filename_to_list,
+                                list_to_filename, split_filename)
 
 
 class SliceTimingInputSpec(SPMCommandInputSpec):

nipype/interfaces/spm/utils.py

@@ -1,15 +1,16 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-from nipype.interfaces.spm.base import SPMCommandInputSpec, SPMCommand, Info, scans_for_fnames, scans_for_fname
-from nipype.interfaces.matlab import MatlabCommand
-from nipype.interfaces.base import (TraitedSpec, BaseInterface,
-                                    BaseInterfaceInputSpec, isdefined,
-                                    OutputMultiPath, InputMultiPath)
-from nipype.interfaces.base import File, traits
-from nipype.utils.filemanip import split_filename, fname_presuffix, filename_to_list, list_to_filename
 import os
 import numpy as np
 
+from .base import SPMCommandInputSpec, SPMCommand, Info, scans_for_fnames, scans_for_fname
+from ..matlab import MatlabCommand
+from ..base import (TraitedSpec, BaseInterface,
+                    BaseInterfaceInputSpec, isdefined,
+                    OutputMultiPath, InputMultiPath)
+from ..base import File, traits
+from ...utils.filemanip import split_filename, fname_presuffix, filename_to_list, list_to_filename
+
 
 class Analyze2niiInputSpec(SPMCommandInputSpec):
     analyze_file = File(exists=True, mandatory=True)