Merge remote-tracking branch 'oesteban/fix/AreaWeighedP2PDistance'

Conflicts:
	CHANGES

Author: chrisgorgo

CHANGES

@@ -1,6 +1,11 @@
 Next release
 ============
 
+* ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
+       (https://github.com/nipy/nipype/pull/1016)
+* FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
+       fix bug in area weighted distance, and added optimizations
+       (https://github.com/nipy/nipype/pull/1016)
 * ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (https://github.com/nipy/nipype/pull/1002)
 * FIX: FUGUE is now properly listing outputs. (https://github.com/nipy/nipype/pull/978)
 * ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.

nipype/algorithms/mesh.py

@@ -13,55 +13,78 @@
 
 
 import numpy as np
-from scipy.spatial.distance import euclidean
+from numpy import linalg as nla
+import os.path as op
+from nipype.external import six
 
 from .. import logging
 
 from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
                                BaseInterfaceInputSpec)
+from warnings import warn
 iflogger = logging.getLogger('interface')
 
 
-class P2PDistanceInputSpec(BaseInterfaceInputSpec):
+class ComputeMeshWarpInputSpec(BaseInterfaceInputSpec):
     surface1 = File(exists=True, mandatory=True,
-                    desc=("Reference surface (vtk format) to which compute "
-                          "distance."))
+                    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", usedefault=True,
-                            desc=('"none": no weighting is performed, '
-                                  '"surface": edge distance is weighted by the '
-                                  'corresponding surface area'))
+                    desc=('Test surface (vtk format) from which compute '
+                          'distance.'))
+    metric = traits.Enum('euclidean', 'sqeuclidean', usedefault=True,
+                         desc=('norm used to report distance'))
+    weighting = traits.Enum(
+        'none', 'area', usedefault=True,
+        desc=('"none": no weighting is performed, surface": edge distance is '
+              'weighted by the corresponding surface area'))
+    out_warp = File('surfwarp.vtk', usedefault=True,
+                    desc='vtk file based on surface1 and warpings mapping it '
+                    'to surface2')
+    out_file = File('distance.npy', usedefault=True,
+                    desc='numpy file keeping computed distances and weights')
 
 
-class P2PDistanceOutputSpec(TraitedSpec):
+class ComputeMeshWarpOutputSpec(TraitedSpec):
     distance = traits.Float(desc="computed distance")
+    out_warp = File(exists=True, desc=('vtk file with the vertex-wise '
+                                       'mapping of surface1 to surface2'))
+    out_file = File(exists=True,
+                    desc='numpy file keeping computed distances and weights')
 
 
-class P2PDistance(BaseInterface):
+class ComputeMeshWarp(BaseInterface):
 
-    """Calculates a point-to-point (p2p) distance between two corresponding
-    VTK-readable meshes or contours.
+    """
+    Calculates a the vertex-wise warping to get surface2 from surface1.
+    It also reports the average distance of vertices, using the norm specified
+    as input.
+
+    .. warning:
+
+      A point-to-point correspondence between surfaces is required
 
-    A point-to-point correspondence between nodes is required
 
     Example
     -------
 
-    >>> import nipype.algorithms.mesh as mesh
-    >>> dist = mesh.P2PDistance()
+    >>> import nipype.algorithms.mesh as m
+    >>> dist = m.ComputeMeshWarp()
     >>> dist.inputs.surface1 = 'surf1.vtk'
     >>> dist.inputs.surface2 = 'surf2.vtk'
     >>> res = dist.run() # doctest: +SKIP
+
     """
 
-    input_spec = P2PDistanceInputSpec
-    output_spec = P2PDistanceOutputSpec
+    input_spec = ComputeMeshWarpInputSpec
+    output_spec = ComputeMeshWarpOutputSpec
 
     def _triangle_area(self, A, B, C):
-        ABxAC = euclidean(A, B) * euclidean(A, C)
-        prod = np.dot(np.array(B) - np.array(A), np.array(C) - np.array(A))
+        A = np.array(A)
+        B = np.array(B)
+        C = np.array(C)
+        ABxAC = nla.norm(A - B) * nla.norm(A - C)
+        prod = np.dot(B - A, C - A)
         angle = np.arccos(prod / ABxAC)
         area = 0.5 * ABxAC * np.sin(angle)
         return area
@@ -70,14 +93,17 @@ def _run_interface(self, runtime):
         try:
             from tvtk.api import tvtk
         except ImportError:
-            raise ImportError('Interface P2PDistance requires tvtk')
+            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'))
             pass
+        except ValueError:
+            iflogger.warn(('ETS toolkit is already set'))
+            pass
 
         r1 = tvtk.PolyDataReader(file_name=self.inputs.surface1)
         r2 = tvtk.PolyDataReader(file_name=self.inputs.surface2)
@@ -86,32 +112,213 @@ def _run_interface(self, runtime):
         r1.update()
         r2.update()
         assert(len(vtk1.points) == len(vtk2.points))
-        d = 0.0
-        totalWeight = 0.0
 
-        points = vtk1.points
-        faces = vtk1.polys.to_array().reshape(-1, 4).astype(int)[:, 1:]
+        points1 = np.array(vtk1.points)
+        points2 = np.array(vtk2.points)
+
+        diff = points2 - points1
+        weights = np.ones(len(diff))
+
+        try:
+            errvector = nla.norm(diff, axis=1)
+        except TypeError:  # numpy < 1.9
+            errvector = np.apply_along_axis(nla.norm, 1, diff)
+            pass
+
+        if self.inputs.metric == 'sqeuclidean':
+            errvector = errvector ** 2
+
+        if (self.inputs.weighting == 'area'):
+            faces = vtk1.polys.to_array().reshape(-1, 4).astype(int)[:, 1:]
 
-        for p1, p2 in zip(points, vtk2.points):
-            weight = 1.0
-            if (self.inputs.weighting == 'surface'):
+            for i, p1 in enumerate(points2):
                 # compute surfaces, set in weight
-                weight = 0.0
-                point_faces = faces[(faces[:, :] == 0).any(axis=1)]
+                w = 0.0
+                point_faces = faces[(faces[:, :] == i).any(axis=1)]
 
                 for idset in point_faces:
-                    p1 = points[int(idset[0])]
-                    p2 = points[int(idset[1])]
-                    p3 = points[int(idset[2])]
-                    weight = weight + self._triangle_area(p1, p2, p3)
+                    fp1 = points1[int(idset[0])]
+                    fp2 = points1[int(idset[1])]
+                    fp3 = points1[int(idset[2])]
+                    w += self._triangle_area(fp1, fp2, fp3)
+                weights[i] = w
 
-            d += weight * euclidean(p1, p2)
-            totalWeight = totalWeight + weight
+        result = np.vstack([errvector, weights])
+        np.save(op.abspath(self.inputs.out_file), result.transpose())
 
-        self._distance = d / totalWeight
+        out_mesh = tvtk.PolyData()
+        out_mesh.points = vtk1.points
+        out_mesh.polys = vtk1.polys
+        out_mesh.point_data.vectors = diff
+        out_mesh.point_data.vectors.name = 'warpings'
+        writer = tvtk.PolyDataWriter(
+            file_name=op.abspath(self.inputs.out_warp))
+        writer.set_input_data(out_mesh)
+        writer.write()
+
+        self._distance = np.average(errvector, weights=weights)
         return runtime
 
     def _list_outputs(self):
         outputs = self._outputs().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        outputs['out_warp'] = op.abspath(self.inputs.out_warp)
         outputs['distance'] = self._distance
         return outputs
+
+
+class MeshWarpMathsInputSpec(BaseInterfaceInputSpec):
+    in_surf = File(exists=True, mandatory=True,
+                   desc=('Input surface in vtk format, with associated warp '
+                         'field as point data (ie. from ComputeMeshWarp'))
+    float_trait = traits.Either(traits.Float(1.0), traits.Tuple(
+        traits.Float(1.0), traits.Float(1.0), traits.Float(1.0)))
+
+    operator = traits.Either(
+        float_trait, File(exists=True), default=1.0, mandatory=True,
+        desc=('image, float or tuple of floats to act as operator'))
+
+    operation = traits.Enum('sum', 'sub', 'mul', 'div', usedefault=True,
+                            desc=('operation to be performed'))
+
+    out_warp = File('warp_maths.vtk', usedefault=True,
+                    desc='vtk file based on in_surf and warpings mapping it '
+                    'to out_file')
+    out_file = File('warped_surf.vtk', usedefault=True,
+                    desc='vtk with surface warped')
+
+
+class MeshWarpMathsOutputSpec(TraitedSpec):
+    out_warp = File(exists=True, desc=('vtk file with the vertex-wise '
+                                       'mapping of surface1 to surface2'))
+    out_file = File(exists=True,
+                    desc='vtk with surface warped')
+
+
+class MeshWarpMaths(BaseInterface):
+
+    """
+    Performs the most basic mathematical operations on the warping field
+    defined at each vertex of the input surface. A surface with scalar
+    or vector data can be used as operator for non-uniform operations.
+
+    .. warning:
+
+      A point-to-point correspondence between surfaces is required
+
+
+    Example
+    -------
+
+    >>> import nipype.algorithms.mesh as m
+    >>> mmath = m.MeshWarpMaths()
+    >>> mmath.inputs.in_surf = 'surf1.vtk'
+    >>> mmath.inputs.operator = 'surf2.vtk'
+    >>> mmath.inputs.operation = 'mul'
+    >>> res = mmath.run() # doctest: +SKIP
+
+    """
+
+    input_spec = MeshWarpMathsInputSpec
+    output_spec = MeshWarpMathsOutputSpec
+
+    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'))
+            pass
+        except ValueError:
+            iflogger.warn(('ETS toolkit is already set'))
+            pass
+
+        r1 = tvtk.PolyDataReader(file_name=self.inputs.in_surf)
+        vtk1 = r1.output
+        r1.update()
+        points1 = np.array(vtk1.points)
+
+        if vtk1.point_data.vectors is None:
+            raise RuntimeError(('No warping field was found in in_surf'))
+
+        operator = self.inputs.operator
+        opfield = np.ones_like(points1)
+
+        if isinstance(operator, six.string_types):
+            r2 = tvtk.PolyDataReader(file_name=self.inputs.surface2)
+            vtk2 = r2.output
+            r2.update()
+            assert(len(points1) == len(vtk2.points))
+
+            opfield = vtk2.point_data.vectors
+
+            if opfield is None:
+                opfield = vtk2.point_data.scalars
+
+            if opfield is None:
+                raise RuntimeError(
+                    ('No operator values found in operator file'))
+
+            opfield = np.array(opfield)
+
+            if opfield.shape[1] < points1.shape[1]:
+                opfield = np.array([opfield.tolist()] * points1.shape[1]).T
+        else:
+            operator = np.atleast_1d(operator)
+            opfield *= operator
+
+        warping = np.array(vtk1.point_data.vectors)
+
+        if self.inputs.operation == 'sum':
+            warping += opfield
+        elif self.inputs.operation == 'sub':
+            warping -= opfield
+        elif self.inputs.operation == 'mul':
+            warping *= opfield
+        elif self.inputs.operation == 'div':
+            warping /= opfield
+
+        vtk1.point_data.vectors = warping
+        writer = tvtk.PolyDataWriter(
+            file_name=op.abspath(self.inputs.out_warp))
+        writer.set_input_data(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)
+        writer.write()
+
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['out_file'] = op.abspath(self.inputs.out_file)
+        outputs['out_warp'] = op.abspath(self.inputs.out_warp)
+        return outputs
+
+
+class P2PDistance(ComputeMeshWarp):
+
+    """
+    Calculates a point-to-point (p2p) distance between two corresponding
+    VTK-readable meshes or contours.
+
+    A point-to-point correspondence between nodes is required
+
+    .. deprecated:: 1.0-dev
+       Use :py:class:`ComputeMeshWarp` instead.
+    """
+
+    def __init__(self, **inputs):
+        super(P2PDistance, self).__init__(**inputs)
+        warn(('This interface has been deprecated since 1.0, please use '
+              'ComputeMeshWarp'),
+             DeprecationWarning)

nipype/algorithms/tests/test_auto_ComputeMeshWarp.py

@@ -0,0 +1,38 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.algorithms.mesh import ComputeMeshWarp
+
+def test_ComputeMeshWarp_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    metric=dict(usedefault=True,
+    ),
+    out_file=dict(usedefault=True,
+    ),
+    out_warp=dict(usedefault=True,
+    ),
+    surface1=dict(mandatory=True,
+    ),
+    surface2=dict(mandatory=True,
+    ),
+    weighting=dict(usedefault=True,
+    ),
+    )
+    inputs = ComputeMeshWarp.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_ComputeMeshWarp_outputs():
+    output_map = dict(distance=dict(),
+    out_file=dict(),
+    out_warp=dict(),
+    )
+    outputs = ComputeMeshWarp.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value
+