Added new interface for mesh/contour handling

Added base code, just for computing node-to-node distanced.
Some other computations could be added here.

Author: oesteban

nipype/algorithms/mesh.py

@@ -0,0 +1,89 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+'''
+Miscellaneous algorithms for 2D contours and 3D triangularized meshes handling
+
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
+    >>> os.chdir(datadir)
+
+'''
+
+
+import os
+import os.path as op
+import warnings
+import nibabel as nb
+import numpy as np
+from scipy.spatial.distance import euclidean
+
+try:
+    from tvtk.api import tvtk
+except ImportError:
+    warnings.warn('tvtk or vtk not installed')
+    raise
+
+from .. import logging
+
+from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
+                               InputMultiPath, OutputMultiPath,
+                               BaseInterfaceInputSpec, isdefined)
+from ..utils.filemanip import fname_presuffix, split_filename
+iflogger = logging.getLogger('interface')
+
+
+class P2PDistanceInputSpec(BaseInterfaceInputSpec):
+    surface1 = File(exists=True, mandatory=True,
+                    desc="Reference surface (vtk format) to which compute distance.")
+    surface2 = File(exists=True, mandatory=True,
+                    desc="Test surface (vtk format) from which compute distance.")
+    weighting = traits.Enum("none", "surface", desc='""none": no weighting is performed\
+                            "surface": edge distance is weighted by the corresponding surface area',usedefault=True)
+
+class P2PDistanceOutputSpec(TraitedSpec):
+    distance = traits.Float(desc="computed distance")
+
+class P2PDistance(BaseInterface):
+    """
+    Calculates a point-to-point (p2p) distance between two corresponding meshes or contours.
+    Therefore, a point-to-point correspondence between nodes is required
+
+    Example
+    -------
+
+    >>> import nipype.algorithms.mesh as mesh
+    >>> dist = mesh.P2PDistance()
+    >>> dist.inputs.surface1 = 'surf1.vtk'
+    >>> dist.inputs.surface2 = 'surf2.vtk'
+    >>> res = dist.run() # doctest: +SKIP
+    """
+
+    def _run_interface(self, runtime):
+        r1 = tvtk.PolyDataReader( file_name=self.inputs.surface1 )
+        r2 = tvtk.PolyDataReader( file_name=self.inputs.surface2 )
+        vtk1 = r1.output
+        vtk2 = r2.output
+        r1.update()
+        r2.update()
+
+        d = 0.0
+        totalWeight = 0.0
+        for p1,p2 in zip( vtk1.points, vtk2.points ):
+            weight = 1.0
+            if (self.inputs.method == 'surface'):
+                #compute surfaces, set in weight
+                print "Error, not implemented"
+
+            d+= euclidean( p1, p2 )
+            totalWeight = totalWeight + weight
+
+        self._distance = d / weight
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['distance'] = self._distance
+        return outputs
+