python-microscopy 25.6.5__cp39-cp39-win_amd64.whl

PYME/experimental/triangular_mesh.py

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+# -*- coding: utf8 -*-
+
+import numpy as np
+
+# Regular, boundary, and max vertex valences. These need tp be
+VALENCE = 6
+BOUNDARY_VALENCE = 4
+NEIGHBORSIZE = 20  # Note this must match NEIGHBORSIZE in triangle_mesh_utils.h
+
+USE_C = True
+
+if USE_C:
+    from PYME.experimental import triangle_mesh_utils
+
+# def pack_edges(arr, axis=1):
+#     """
+#     Stores edges as a single unique integer. 
+    
+#     NOTE: that this implictly caps the mesh at 2**32
+#     vertices.
+#     """
+#     arr = np.sort(arr, axis=axis)
+#     res = ((arr[:,0].astype(np.uint64)) << 32)
+#     res += arr[:,1].astype(np.uint64)
+    
+#     return res
+
+MAX_VERTEX_COUNT = 2**64
+
+def fast_3x3_cross(a,b):
+    # Index only once
+    a0 = a[0]
+    a1 = a[1]
+    a2 = a[2]
+    b0 = b[0]
+    b1 = b[1]
+    b2 = b[2]
+
+    x = a1*b2 - a2*b1
+    y = a2*b0 - a0*b2
+    z = a0*b1 - a1*b0
+
+    vec = np.array([x,y,z])
+    return vec
+
+HALFEDGE_DTYPE = np.dtype([('vertex', 'i4'), ('face', 'i4'), ('twin', 'i4'), ('next', 'i4'), ('prev', 'i4'), ('length', 'f4'), ('component', 'i4')])
+FACE_DTYPE = np.dtype([('halfedge', 'i4'), ('normal', '3f4'), ('area', 'f4'), ('component', 'i4')])
+# Note that VERTEX_DTYPE neighbors size must match NEIGHBORSIZE
+VERTEX_DTYPE = np.dtype([('position', '3f4'), ('normal', '3f4'), ('halfedge', 'i4'), ('valence', 'i4'), ('neighbors', '20i4'), ('component', 'i4')])
+
+LOOP_ALPHA_FACTOR = (np.log(13)-np.log(3))/12
+
+class TriangleMesh(object):
+    def __init__(self, vertices=None, faces=None, mesh=None, **kwargs):
+        """
+        Base class for triangle meshes stored using halfedge data structure. 
+        Expects STL-like input.
+
+        Parameters
+        ----------
+            vertices : np.array
+                N x 3 array of Euclidean points.
+            faces : np .array
+                M x 3 array of vertex indices indicating triangle connectivity.
+                Expects STL redundancy.
+            debug : bool
+                Print debug statements (assumes manifold mesh).
+        """
+        if mesh is not None:
+            import copy
+            
+            self._vertices = np.copy(mesh._vertices)
+            self._vertex_vacancies = copy.copy(mesh._vertex_vacancies)
+
+            self._faces = np.copy(mesh._faces)
+            self._face_vacancies = copy.copy(mesh._face_vacancies)
+
+            self._halfedges = np.copy(mesh._halfedges)
+            self._halfedge_vacancies = copy.copy(mesh._halfedge_vacancies)
+        else:
+            self._vertices = np.zeros(vertices.shape[0], dtype=VERTEX_DTYPE)
+            self._vertices[:] = -1  # initialize everything to -1 to start with
+            self._vertices['position'] = vertices
+            self._vertex_vacancies = []
+
+            self._faces = None  # Contains a pointer to one halfedge associated with each face
+            self._face_vacancies = []
+
+            # Halfedges
+            self._halfedges = None
+            self._halfedge_vacancies = []
+            
+            print('initializing halfedges ...')
+            print('vertices.shape = %s, faces.shape = %s' % (vertices.shape, faces.shape))
+            if vertices.shape[0] >= MAX_VERTEX_COUNT:
+                raise RuntimeError('Maximum vertex count is %d, mesh has %d' % (MAX_VERTEX_COUNT, vertices.shape[0]))
+            self._initialize_halfedges(vertices, faces)
+            print('done initializing halfedges')
+
+        # Representation of faces by triplets of vertices
+        self._faces_by_vertex = None
+
+        # loop subdivision vars
+        self._loop_subdivision_flip_edges = []
+        self._loop_subdivision_new_vertices = []
+
+        # Singular edges
+        self._singular_edges = None
+        self._singular_vertices = None
+
+        # Populate the normals
+        self.face_normals
+        self.vertex_normals
+
+        # Properties we can visualize
+        self.vertex_properties = ['x', 'y', 'z', 'component', 'boundary', 'singular']
+
+        self.fix_boundary = True  # Hold boundary edges in place
+        self.debug = False  # Print debug statements
+
+        # Is the mesh manifold?
+        self._manifold = None
+
+        # Set debug, fix_boundary, etc.
+        for key, value in kwargs.items():
+            setattr(self, key, value)
+
+    def __getitem__(self, k):
+        # this defers evaluation of the properties until we actually access them, 
+        # as opposed to the mappings which stored the values on class creation.
+        try:
+            res = getattr(self, k)
+        except AttributeError:
+            raise KeyError('Key %s not defined' % k)
+        
+        return res
+
+    def __copy__(self):
+        return type(self)(mesh=self)
+
+    @classmethod
+    def from_stl(cls, filename, **kwargs):
+        """
+        Read from an STL file.
+        """
+        from PYME.IO.FileUtils import stl
+
+        # Load an STL from file
+        triangles_stl = stl.load_stl_binary(filename)
+
+        # Call from_np_stl on the file stream
+        return cls.from_np_stl(triangles_stl, **kwargs)
+
+    @classmethod
+    def from_ply(cls, filename, **kwargs):
+        """
+        Read from PLY file.
+        """
+        from PYME.IO.FileUtils import ply
+
+        # Load a PLY from file
+        vertices, faces, _ = ply.load_ply(filename)
+
+        return cls(vertices, faces, **kwargs)
+
+    @classmethod
+    def from_np_stl(cls, triangles_stl, **kwargs):
+        """
+        Read from an already-loaded STL stream.
+        """
+        vertices_raw = np.vstack((triangles_stl['vertex0'], 
+                                  triangles_stl['vertex1'], 
+                                  triangles_stl['vertex2']))
+        vertices, faces_raw = np.unique(vertices_raw, 
+                                        return_inverse=True, 
+                                        axis=0)
+        faces = faces_raw.reshape(faces_raw.shape[0] // 3, 3, order='F')
+
+        print('Data munged to vertices, faces')
+        return cls(vertices, faces, **kwargs)
+
+    @property
+    def x(self):
+        return self.vertices[:,0]
+        
+    @property
+    def y(self):
+        return self.vertices[:,1]
+        
+    @property
+    def z(self):
+        return self.vertices[:,2]
+
+    @property
+    def component(self):
+        # if np.all(self._vertices['component'] == -1):
+        self.find_connected_components()
+        return self._vertices['component']
+
+    @property
+    def vertices(self):
+        return self._vertices['position']
+
+    @property
+    def faces(self):
+        """
+        Returns faces by vertex for rendering and STL applications.
+        """
+        if self._faces_by_vertex is None:
+            faces = self._faces['halfedge'][self._faces['halfedge'] != -1]
+            v0 = self._halfedges['vertex'][self._halfedges['prev'][faces]]
+            v1 = self._halfedges['vertex'][faces]
+            v2 = self._halfedges['vertex'][self._halfedges['next'][faces]]
+            self._faces_by_vertex = np.vstack([v0, v1, v2]).T
+        return self._faces_by_vertex
+
+    @property
+    def boundary(self):
+        nn = self._vertices['neighbors']
+        nn_mask = (nn!=-1)
+        return np.any((self._halfedges['twin'][nn] == -1)*nn_mask, axis=1)
+
+    @property
+    def singular(self):
+        self._singular_edges = None
+        self._singular_vertices = None
+        singular_vertices = np.zeros_like(self._vertices['halfedge'])
+        if len(self.singular_vertices) > 0:
+            singular_vertices[np.array(self.singular_vertices)] = 1
+        return singular_vertices
+
+    @property
+    def singular_edges(self):
+        """
+        Get a list of singular edges. A singular edge is any edge shared by
+        more than two faces.
+        """
+        if self._singular_edges is None:
+            edges = np.vstack([self._halfedges['vertex'], self._halfedges[self._halfedges['prev']]['vertex']]).T
+            edges = edges[edges[:,0] != -1]  # Drop non-edges
+            # packed_edges = pack_edges(edges)
+            packed_edges = np.sort(edges, axis=1)
+            e, c = np.unique(packed_edges, return_counts=True, axis=0)
+            singular_packed_edges = e[c>2]
+            singular_edges = []
+            for singular_packed_edge in singular_packed_edges:
+                singular_edges.extend(list(np.where(packed_edges[:, None] == singular_packed_edge)[0]))
+
+            singular_edges.extend(self._halfedges['twin'][singular_edges])
+            self._singular_edges = list(set(singular_edges) - set([-1]))
+
+        return self._singular_edges
+
+    @property
+    def singular_vertices(self):
+        """
+        Get a list of singular vertices. This includes endpoints of singular 
+        edges, and isolated singular vertices. Isolated singular vertices
+        have more than one 1-neighbor ring.
+        """
+        if self._singular_vertices is None:
+            # Mark vertices that are endpoints of these edges
+            singular_vertices = list(set(list(np.hstack([self._halfedges['vertex'][self.singular_edges], self._halfedges['vertex'][self._halfedges['twin'][self.singular_edges]]]))))
+            
+            # Mark isolated singular vertices
+            for _vertex in np.arange(self._vertices.shape[0]):
+                if self._vertices['halfedge'][_vertex] == -1:
+                    continue
+
+                # If the number of elements in the 1-neighbor ring does not match 
+                # the number of halfedges pointing to a vertex, we have an isolated
+                # singular vertex (note this requires the C code version of
+                # update_vertex_neighbors, which reverses direction upon hitting
+                # an edge to ensure a more accurate neighborhood)
+                n_incident = np.flatnonzero(self._halfedges['vertex'] == _vertex).size
+                n_neighbors = np.flatnonzero(self._vertices['neighbors'][_vertex] != -1).size
+                if n_neighbors != n_incident:
+                    singular_vertices.append(_vertex)
+
+            # Remove duplicates
+            self._singular_vertices = list(set(singular_vertices) - set([-1]))
+
+        return self._singular_vertices
+
+    @property
+    def face_normals(self):
+        """
+        Return the normal of each triangular face.
+        """
+        if np.all(self._faces['normal'] == -1):
+            if USE_C:
+                triangle_mesh_utils.c_update_face_normals(list(np.arange(len(self._faces)).astype(np.int32)), self._halfedges, self._vertices, self._faces)
+            else:
+                v2 = self._vertices['position'][self._halfedges['vertex'][self._halfedges['prev'][self._faces['halfedge']]]]
+                v1 = self._vertices['position'][self._halfedges['vertex'][self._faces['halfedge']]]
+                v0 = self._vertices['position'][self._halfedges['vertex'][self._halfedges['next'][self._faces['halfedge']]]]
+                u = v2 - v1
+                v = v0 - v1
+                n = np.cross(u, v, axis=1)
+                nn = np.linalg.norm(n, axis=1)
+                self._faces['area'] = 0.5*nn
+                self._faces['normal'] = n/nn[:, None]
+                self._faces['normal'][np.isnan(self._faces['normal'])] = 0
+                self._faces['normal'][self._faces['halfedge'] == -1] = -1
+        return self._faces['normal'][self._faces['halfedge'] != -1]
+
+    @property
+    def face_areas(self):
+        """
+        Return the area of each triangular face.
+        """
+        if np.all(self._faces['area'] == -1):
+            self._faces['normal'][:] = -1
+            self.face_normals
+        return self._faces['area']
+    
+    @property
+    def vertex_neighbors(self):
+        """
+        Return the up to NEIGHBORSIZE neighbors of each vertex.
+        """
+        if np.all(self._vertices['neighbors'] == -1):
+            if USE_C:
+                triangle_mesh_utils.c_update_vertex_neighbors(list(np.arange(len(self._vertices)).astype(np.int32)), self._halfedges, self._vertices, self._faces)
+            else:
+                for v_idx in np.arange(len(self._vertices)):
+                    _orig = self._vertices['halfedge'][v_idx]
+                    _curr = _orig
+
+                    curr_edge = self._halfedges[_curr]
+                    _twin = curr_edge['twin']
+                    twin_edge = self._halfedges[_twin]
+
+                    self._vertices['normal'][v_idx] = 0
+
+                    i = 0
+                    self._vertices['valence'][v_idx] = 0
+                    while True:
+                        if _curr == -1:
+                            break
+                        _vertex = curr_edge['vertex']
+                        _face = curr_edge['face']
+                        if (i < NEIGHBORSIZE):
+                            self._vertices['neighbors'][v_idx, i] = _curr
+                            n = self._faces['normal'][_face]
+                            a = self._faces['area'][_face]
+                            self._vertices['normal'][v_idx] += n*a
+                        
+                        l = self._vertices['position'][_vertex] - self._vertices['position'][self._halfedges['vertex'][curr_edge['prev']]]
+                        curr_edge['length'] = np.sqrt((l*l).sum())
+
+                        _curr = twin_edge['next']
+                        curr_edge = self._halfedges[_curr]
+                        if _twin == -1:
+                            break
+                        _twin = curr_edge['twin']
+                        twin_edge = self._halfedges[_twin]
+
+                        i += 1
+                        if (_curr == _orig):
+                            break
+                    self._vertices['valence'][v_idx] = i
+                nn = np.linalg.norm(self._vertices['normal'], axis=1)
+                self._vertices['normal'] /= nn[:, None]
+                self._vertices['normal'][np.isnan(self._vertices['normal'])] = 0
+                self._vertices['normal'][self._vertices['halfedge'] == -1] = -1
+
+        return self._vertices['neighbors']
+
+    @property
+    def vertex_normals(self):
+        """
+        Return the normal of each vertex.
+        """
+        if np.all(self._vertices['normal'] == -1):
+            self._vertices['neighbors'][:] = -1
+            self.vertex_neighbors
+        return self._vertices['normal']
+
+    @property
+    def valences(self):
+        """
+        Return the valence of each vertex.
+        """
+        if np.all(self._vertices['valence'] == -1):
+            self._vertices['neighbors'][:] = -1
+            self.vertex_neighbors
+        return self._vertices['valence']
+
+    @property
+    def manifold(self):
+        """
+        Checks if the mesh is manifold: Is every edge is shared by exactly two 
+        triangles?
+
+        TODO: Check that we don't have any isolated singular vertices, which 
+        also make the mesh non-manifold.
+        """
+        # edges = np.vstack([self._halfedges['vertex'], self._halfedges[self._halfedges['prev']]['vertex']]).T
+        # edges[edges[:, 0] != -1]
+        # edges = np.vstack([self.faces[:,[0,1]], self.faces[:,[1,2]], self.faces[:,[2,0]]])
+        # packed_edges = pack_edges(edges)
+        # _, c = np.unique(packed_edges, return_counts=True)
+        
+        # return np.all(c==2)
+
+        if self._manifold is None:
+            self._singular_edges = None
+            self._singular_vertices = None
+            vertex_mask = (self._halfedges['vertex'] != -1)
+            twin_mask = (self._halfedges['twin'] == -1)
+            boundary_check = ((np.flatnonzero(vertex_mask & twin_mask).size) == 0)
+            self._manifold = (len(self.singular_vertices) == 0) & boundary_check
+
+        return self._manifold
+
+    def keys(self):
+        return list(self.vertex_properties)
+
+    def _initialize_halfedges(self, vertices, faces):
+        """
+        Accepts unordered vertices, indices parameterization of a triangular 
+        mesh from an STL file and converts to topologically-connected halfedge
+        representation.
+
+        Parameters
+        ----------
+            vertices : np.array
+                N x 3 array of Euclidean points.
+            faces : np .array
+                M x 3 array of vertex indices indicating triangle connectivity. 
+                Expects STL redundancy.
+        """
+        if vertices is not None and faces is not None:
+            # Unordered halfedges
+            edges = np.vstack([faces[:,[0,1]], faces[:,[1,2]], faces[:,[2,0]]])
+
+            # Now order them...
+            n_faces = len(faces)
+            n_edges = len(edges)
+            j = np.arange(n_faces)
+            
+            self._halfedges = np.zeros(n_edges, dtype=HALFEDGE_DTYPE)
+            self._halfedges[:] = -1  # initialize everything to -1 to start with
+
+            self._halfedges['vertex'] = edges[:, 1]
+            
+            self._faces = np.zeros(n_faces, dtype=FACE_DTYPE)
+            self._faces[:] = -1  # initialize everything to -1 to start with
+
+            # Create a unique handle for each edge
+            # edges_packed = pack_edges(edges)
+
+            # Sort the edges lo->hi so we can arrange them uniquely
+            # Convert to list of tuples for use with dictionary
+            edges_packed = [tuple(e) for e in np.sort(edges, axis=1)]
+
+            # Account for multivalent edges
+            # edges_unique, edges_counts = np.unique(edges, return_counts=True, axis=0)
+
+            # print('iterating edges')
+            # # Use a dictionary to keep track of which edges are already assigned twins
+            # d = {}
+            # multivalent_edge = False
+            # multivalent_dict = {}
+            # for i, e in enumerate(edges_packed):
+            #     if e in d:
+            #         idx = d.pop(e)
+            #         if self._halfedges['vertex'][idx] == self._halfedges['vertex'][i]:
+            #             # Push it back in the queue and let's see if the next time we
+            #             # pull it out we get the right matching edge.
+            #             d[e] = idx
+            #             # Trip the flag
+            #             multivalent_edge = True
+            #             multivalent_dict[e] = i
+            #             continue
+                        
+            #         self._halfedges['twin'][idx] = i
+            #         self._halfedges['twin'][i] = idx
+            #     else:
+            #         d[e] = i
+
+            print('iterating edges')
+            # Use a dictionary to keep track of which edges are already assigned twins
+            d = {}
+            for i, e in enumerate(edges_packed):
+                if e in d:
+                    idx = d.pop(e)
+                    if self._halfedges['vertex'][idx] == self._halfedges['vertex'][i]:
+                        # Don't assign a halfedge to multivalent edges
+                        continue
+                        
+                    self._halfedges['twin'][idx] = i
+                    self._halfedges['twin'][i] = idx
+                else:
+                    d[e] = i
+
+            # print('multivalent')
+            # # Go back and grab the remaining multivalent edges
+            # if multivalent_edge:
+            #     n_multivalent = len(list(multivalent_dict.keys()))
+            #     print('%d multivalent edges' % n_multivalent)
+            #     for j_, k in enumerate(list(multivalent_dict.keys())):
+            #         if (not (j_ % 10)):
+            #             print('mv edge %d of %d' % (j_, n_multivalent))
+            #
+            #         idx = multivalent_dict.pop(k)
+            #         for i, e in enumerate(edges_packed):
+            #             if e != idx:
+            #                 continue
+            #
+            #             if self._halfedges['vertex'][idx] == self._halfedges['vertex'][i]:
+            #                 continue
+            #
+            #             self._halfedges['twin'][idx] = i
+            #             self._halfedges['twin'][i] = idx
+            #             break
+            #
+            # print('multivalent done')
+            
+            self._halfedges['face'] = np.hstack([j, j, j])
+            self._halfedges['next'] = np.hstack([j+n_faces, j+2*n_faces, j])
+            self._halfedges['prev'] = np.hstack([j+2*n_faces, j, j+n_faces])
+            self._halfedges['length'] = np.linalg.norm(self._vertices['position'][self._halfedges['vertex']] - self._vertices['position'][self._halfedges['vertex'][self._halfedges['prev']]], axis=1)
+            
+            # Set the vertex halfedges (multiassignment, but should be fine)
+            self._vertices['halfedge'][self._halfedges['vertex']] = self._halfedges['next']
+
+            self._faces['halfedge'] = j  # Faces are defined by associated halfedges
+        else:
+            raise ValueError('Mesh does not contain vertices and faces.')
+
+    def _update_face_normals(self, f_idxs):
+        """
+        Recompute len(f_idxs) face normals.
+
+        Parameters
+        ----------
+        f_idxs : list or np.array
+            List of face indices to recompute.
+        """
+
+        if USE_C:
+            if isinstance(f_idxs, list):
+                f_idxs = np.int32(f_idxs)
+            triangle_mesh_utils.c_update_face_normals(f_idxs, self._halfedges, self._vertices, self._faces)
+        else:
+            for f_idx in f_idxs:
+                v2 = self._vertices['position'][self._halfedges['vertex'][self._halfedges['prev'][self._faces['halfedge'][f_idx]]]]
+                v1 = self._vertices['position'][self._halfedges['vertex'][self._faces['halfedge'][f_idx]]]
+                v0 = self._vertices['position'][self._halfedges['vertex'][self._halfedges['next'][self._faces['halfedge'][f_idx]]]]
+                u = v2 - v1
+                v = v0 - v1
+                n = fast_3x3_cross(u.squeeze(), v.squeeze())
+                nn = np.sqrt((n*n).sum())
+                self._faces['area'][f_idx] = 0.5*nn
+                if (self._faces['halfedge'][f_idx] == -1):
+                    self._faces['normal'][f_idx] = -1
+                if (nn > 0):
+                    self._faces['normal'][f_idx] = n/nn
+                else:
+                    self._faces['normal'][f_idx] = 0
+
+    def _update_vertex_neighbors(self, v_idxs):
+        """
+        Recalculate len(v_idxs) vertex neighbors/normals.
+
+        Parameters
+        ----------
+            v_idxs : list or np.array
+                List of vertex indicies indicating which vertices to update.
+        """
+
+        if USE_C:
+            if isinstance(v_idxs, list):
+                v_idxs = np.int32(v_idxs)
+            triangle_mesh_utils.c_update_vertex_neighbors(v_idxs, self._halfedges, self._vertices, self._faces)
+        else:
+            for v_idx in v_idxs:
+                _orig = self._vertices['halfedge'][v_idx]
+                _curr = _orig
+                
+                curr_edge = self._halfedges[_curr]
+                _twin = curr_edge['twin']
+                twin_edge = self._halfedges[_twin]
+                
+                if self.debug and (twin_edge['vertex'] != v_idx):
+                    print(_curr, curr_edge, _twin,twin_edge)
+                    raise RuntimeError('Twin (%d) should point back to starting vertex (%d) but points to %d' % (_twin, v_idx, twin_edge['vertex']))
+                
+                i = 0
+                self._vertices['valence'][v_idx] = 0
+                self._vertices['neighbors'][v_idx] = -1
+                self._vertices['normal'][v_idx] = 0
+                
+                _normal = 0*self._vertices['normal'][v_idx]  # avoid a few lookups by using a local variable
+
+                while True:
+                    if (_curr == -1):
+                        break
+
+                    if (i < NEIGHBORSIZE):
+                        self._vertices['neighbors'][v_idx, i] = _curr
+                        
+                        #TODO - should these be in if clause?
+                        _face = curr_edge['face']
+                        n = self._faces['normal'][_face]
+                        a = self._faces['area'][_face]
+                        _normal += n*a
+                    else:
+                        pass
+                        if self.debug and (i > 2*NEIGHBORSIZE):
+                            print('Abnormal vertex valance detected on vertex %d' % v_idx)
+                            # raise RuntimeError('Abnormal vertex valance detected on vertex %d' % v_idx)
+                    
+                    vertex = self._vertices['position'][v_idx]
+                    l = vertex - self._vertices['position'][curr_edge['vertex']]
+                    l = np.sqrt((l*l).sum())
+                    self._halfedges['length'][_curr] = l
+                    if (_twin == -1):
+                        break
+                    self._halfedges['length'][_twin] = l
+                    # curr_edge['length'] = l
+                    # twin_edge['length'] = l
+                    
+                    _curr = twin_edge['next']
+                    curr_edge = self._halfedges[_curr]
+                    _twin = curr_edge['twin']
+                    twin_edge = self._halfedges[_twin]
+                    
+                    i += 1
+                    
+                    if (_curr == _orig):
+                        break
+
+                self._vertices['valence'][v_idx] = i
+
+                if self.debug and (self._vertices['valence'][v_idx] < 3):
+                    raise RuntimeError('Detected valence <3 on vertex %d' % v_idx)
+
+                nn = np.sqrt((_normal*_normal).sum())
+                if nn > 0:
+                    self._vertices['normal'][v_idx] = _normal/nn
+                else:
+                    self._vertices['normal'][v_idx] = 0
+
+    def _resize(self, vec, axis=0, skip_entries=False, return_orig=False, key=None):
+        """
+        Increase the size of an input vector 1.5x, keeping all active data.
+
+        Parameters
+        ---------
+            vec : np.array
+                Vector to expand, -1 stored in unused entries.
+            axis : int
+                Axis (0 or 1) along which to resize vector (only works for 2D 
+                arrays).
+            skip_entries : bool
+                Don't copy -1 entries to the new array.
+            return_orig : bool
+                Return indices of non-negative-one entries in the array prior 
+                to resize.
+            key : string
+                Optional array key on which to check for -1 value.
+        """
+
+        if (axis > 1) or (len(vec.shape) > 2):
+            raise NotImplementedError('This function only works for 2D arrays along axes 0 and 1.')
+
+        # Increase the size 1.5x along the axis.
+        dt = vec.dtype
+        new_size = np.array(vec.shape)
+        new_size[axis] = int(1.5*new_size[axis] + 0.5)
+        new_size = tuple(new_size)
+        
+        # Allocate memory for new array
+        new_vec = np.empty(new_size, dtype=dt)
+        new_vec[:] = -1
+
+        if skip_entries:
+            # Check for invalid entries
+            if key:
+                copy_mask = (vec[key] != 1)
+            else:
+                copy_mask = (vec != -1)
+            
+            if len(copy_mask.shape) > 1:
+                copy_mask = np.any(copy_mask, axis=(1-axis))
+                copy_size = np.flatnonzero(copy_mask).size
+            else:
+                copy_size = np.flatnonzero(copy_mask).size
+
+            if axis:
+                new_vec[:,:copy_size] = vec[:, copy_mask]
+            else:
+                new_vec[:copy_size] = vec[copy_mask]
+
+            # Return positions of non-negative-1 entries prior to re-ordering
+            if return_orig:
+                _orig = np.where(copy_mask)[0]
+                # Return empty list if original values are all at the same place
+                if np.all(_orig == np.arange(len(_orig))):
+                    _orig = []
+                return new_vec, _orig
+
+            return new_vec
+        else:
+            # We're not skipping entries
+            if axis:
+                copy_size = vec.shape[1]
+                new_vec[:,:copy_size] = vec
+            else:
+                copy_size = vec.shape[0]
+                new_vec[:copy_size] = vec
+                
+            if return_orig:
+                return new_vec, []
+    
+            # Update array
+            return new_vec
+
+    def edge_collapse(self, _curr, live_update=True):
+        """
+        A.k.a. delete two triangles. Remove an edge, defined by halfedge _curr,
+        and its associated triangles, while keeping mesh connectivity.
+
+        Parameters
+        ----------
+            _curr: int
+                Pointer to halfedge defining edge to collapse.
+            live_update : bool
+                Update associated faces and vertices after collapse. Set to 
+                False to handle this externally (useful if operating on 
+                multiple, disjoint edges).
+        """
+
+        if _curr == -1:
+            return
+
+        # Create the pointers we need
+        curr_halfedge = self._halfedges[_curr]
+        _prev = curr_halfedge['prev']
+        _next = curr_halfedge['next']
+        _twin = curr_halfedge['twin']
+
+        if (self._halfedges['twin'][_next] == -1) or (self._halfedges['twin'][_prev] == -1):
+            # Collapsing this edge will create another free edge
+            return
+
+        interior = (_twin != -1)  # Are we on a boundary?
+
+        if interior:
+            nn = self._vertices['neighbors'][curr_halfedge['vertex']]
+            nn_mask = (nn != -1)
+            if (-1 in self._halfedges['twin'][nn]*nn_mask):
+                return
+
+            nn = self._vertices['neighbors'][self._halfedges['vertex'][_twin]]
+            nn_mask = (nn != -1)
+            if (-1 in self._halfedges['twin'][nn]*nn_mask):
+                return
+
+            twin_halfedge = self._halfedges[_twin]
+            _twin_prev = twin_halfedge['prev']
+            _twin_next = twin_halfedge['next']
+
+            if self.debug:
+                assert(_twin_prev != -1)
+                assert(_twin_next != -1)
+
+            if (self._halfedges['twin'][_twin_prev] == -1) or (self._halfedges['twin'][_twin_next] == -1):
+                # Collapsing this edge will create another free edge
+                return 
+
+        _dead_vertex = self._halfedges['vertex'][_prev]
+        _live_vertex = curr_halfedge['vertex']
+
+        # Grab the valences of the 4 points near the edge
+        if interior:
+            vn, vtn = self._vertices['valence'][self._halfedges['vertex'][_next]], self._vertices['valence'][self._halfedges['vertex'][_twin_next]]
+
+            # Make sure we create no vertices of valence <3 (manifoldness)
+            # ((vl + vd - 3) < 4) or 
+            if (vn < 4) or (vtn < 4):
+                return
+
+        vl, vd = self._vertices['valence'][_live_vertex], self._vertices['valence'][_dead_vertex]
+        
+        if ((vl + vd - 3) < 4):
+            return
+
+        # Check for creation of multivalent edges and prevent this (manifoldness)
+        fast_collapse_bool = (self.manifold and (vl < NEIGHBORSIZE) and (vd < NEIGHBORSIZE))
+        if fast_collapse_bool:
+            # Do it the fast way if we can
+            live_nn = self._vertices['neighbors'][_live_vertex]
+            dead_nn =  self._vertices['neighbors'][_dead_vertex]
+            live_mask = (live_nn != -1)
+            dead_mask = (dead_nn != -1)
+            live_list = self._halfedges['vertex'][live_nn[live_mask]]
+            dead_list = self._halfedges['vertex'][dead_nn[dead_mask]]
+        else:
+            twin_mask = (self._halfedges['twin'] != -1)
+            dead_mask = (self._halfedges['vertex'] == _dead_vertex)
+            dead_list = self._halfedges['vertex'][self._halfedges['twin'][dead_mask & twin_mask]]
+            live_list = self._halfedges['vertex'][self._halfedges['twin'][(self._halfedges['vertex'] == _live_vertex) & twin_mask]]
+        twin_list = list((set(dead_list) & set(live_list)) - set([-1]))
+        if len(twin_list) != 2:
+            return
+        
+        if self.debug and (_live_vertex == _dead_vertex):
+            print(_curr, curr_halfedge, _twin, twin_halfedge)
+            raise RuntimeError('Live vertex equals dead vertex (both halves of edge point to same place)')
+
+        # Collapse to the midpoint of the original edge vertices
+        if fast_collapse_bool:
+            self._halfedges['vertex'][self._halfedges['twin'][dead_nn[dead_mask]]] = _live_vertex
+        else:
+            self._halfedges['vertex'][dead_mask] = _live_vertex
+        _live_pos = self._vertices['position'][_live_vertex]
+        _dead_pos = self._vertices['position'][_dead_vertex]
+        self._vertices['position'][_live_vertex] = 0.5*(_live_pos + _dead_pos)
+        
+        # update valence of vertex we keep
+        self._vertices['valence'][_live_vertex] = vl + vd - 3
+        
+        if self.debug:
+            print(self._vertices['valence'][_live_vertex], self._vertices['valence'][_dead_vertex])
+            assert(self._vertices['valence'][_live_vertex] >=3)
+        
+        # delete dead vertex
+        self._vertices[_dead_vertex] = -1
+
+        # Zipper the remaining triangles
+        def _zipper(edge1, edge2):
+            # DB optimization notes:
+            # 1) there is a (very?) small performance penalty for nested functions - move this up to class level?
+            # 2) This would be a good candidate for a c/cython implementation (but possibly applies to whole edge collapse function)
+            # 3) function can be simplified (see _zipper1 implementation below). Probably minimal performance impact in
+            #    python version, but logic flow likely necessary in c/cython (avoids indexing with -1)
+            t1 = self._halfedges['twin'][edge1]
+            t2 = self._halfedges['twin'][edge2]
+
+            if edge1 == -1:
+                t1 = -1
+            if edge2 == -1:
+                t2 = -1
+            
+            if (t1 != -1) and (t2 != -1):
+                self._halfedges['twin'][t2] = t1
+                self._halfedges['twin'][t1] = t2
+            else:
+                if (t1 != -1):
+                    self._halfedges['twin'][t1] = -1
+                if (t2 != -1):
+                    self._halfedges['twin'][t2] = -1
+
+        def _zipper1(edge1, edge2):
+            t1 = -1 if edge1 == -1 else self._halfedges['twin'][edge1]
+            t2 = -1 if edge2 == -1 else self._halfedges['twin'][edge2]
+    
+            if (t1 != -1):
+                self._halfedges['twin'][t1] = t2
+                
+            if (t2 != -1):
+                self._halfedges['twin'][t2] = t1
+            
+
+        _zipper1(_next, _prev)
+        if interior:
+            _zipper1(_twin_next, _twin_prev)
+
+        # We need some more pointers
+        # TODO: make these safer
+        _prev_twin = self._halfedges['twin'][_prev]
+        _prev_twin_vertex = self._halfedges['vertex'][_prev_twin]
+        _next_prev_twin = self._halfedges['next'][_prev_twin]
+        _next_prev_twin_vertex = self._halfedges['vertex'][_next_prev_twin]
+        if interior:
+            _twin_next_vertex = self._halfedges['vertex'][_twin_next]
+            _next_twin_twin_next = self._halfedges['next'][self._halfedges['twin'][_twin_next]]
+            _next_twin_twin_next_vertex = self._halfedges['vertex'][_next_twin_twin_next]
+            
+        # Make sure we have good _vertex_halfedges references
+        self._vertices['halfedge'][_live_vertex] = _prev_twin
+        self._vertices['halfedge'][_prev_twin_vertex] = _next_prev_twin
+        if interior:
+            self._vertices['halfedge'][_twin_next_vertex] = self._halfedges['twin'][_twin_next]
+            self._vertices['halfedge'][_next_twin_twin_next_vertex] = self._halfedges['next'][_next_twin_twin_next]
+
+        # Grab faces to update
+        face0 = self._halfedges['face'][self._halfedges['twin'][_next]]
+        face1 = self._halfedges['face'][self._halfedges['twin'][_prev]]
+        if interior:
+            face2 = self._halfedges['face'][self._halfedges['twin'][_twin_next]]
+            face3 = self._halfedges['face'][self._halfedges['twin'][_twin_prev]]
+
+        # Delete the inner triangles
+        self._face_delete(_curr)
+        if interior:
+            self._face_delete(_twin)
+
+        if self.debug and interior:
+            print(curr_halfedge, twin_halfedge)
+
+        try:
+            if live_update:
+                if interior:
+                    # Update faces
+                    self._update_face_normals([face0, face1, face2, face3])
+                    self._update_vertex_neighbors([_live_vertex, _prev_twin_vertex, _next_prev_twin_vertex, _twin_next_vertex])
+                else:
+                    self._update_face_normals([face0, face1])
+                    self._update_vertex_neighbors([_live_vertex, _prev_twin_vertex, _next_prev_twin_vertex])
+                self._faces_by_vertex = None
+        
+        except RuntimeError as e:
+            print(_curr, _twin, _next, _prev, _twin_next, _twin_prev, _next_prev_twin, _next_twin_twin_next, _prev_twin)
+            print([_live_vertex, _prev_twin_vertex, _next_prev_twin_vertex, _twin_next_vertex])
+            raise e
+
+    def _face_delete(self, _edge):
+        """
+        Delete a face defined by the halfedge _edge.
+
+        Note that this does not account for adjusting halfedges, twins.
+
+        Parameters
+        ----------
+            edge : int
+                One self._halfedge index of the edge defining a face to delete.
+        """
+        if _edge == -1:
+            return
+        
+        curr_edge = self._halfedges[_edge]
+        if curr_edge['vertex'] == -1:
+            return
+        self._faces[curr_edge['face']] = -1
+
+        self._face_vacancies.append(curr_edge['face'])
+        
+        self._edge_delete(curr_edge['next'])
+        self._edge_delete(curr_edge['prev'])
+        self._edge_delete(_edge)
+
+    def _edge_delete(self, _edge):
+        """
+        Delete edge _edge in place from self._halfedges.
+
+        Note that this does not account for adjusting halfedges, twins.
+
+        Parameters
+        ----------
+            edge : int
+                One self._halfedge index of the edge to delete.
+        """
+        if (_edge == -1):
+            return
+        
+        self._halfedges[_edge] = -1
+        self._halfedge_vacancies.append(_edge)
+
+        self._faces_by_vertex = None
+
+    def _insert(self, el, el_arr, el_vacancies, key, compact=False, insert_key=None, **kwargs):
+        """
+        Insert an element into an array at the position of the smallest empty 
+        entry when searching the array by key.
+
+        Parameters
+        ----------
+            el 
+                Element to add to the array. Must be one of the dtypes in the 
+                structured dtype of el_arr.
+            el_arr : np.array
+                Array where we add the element
+            el_vacancies : list
+                External list where we keep empty positions of el_arr.
+            key : string
+                Key on which to search the array
+            insert_key : string
+                Key on which to insert element el. This is by default the 
+                search key.
+            compact : bool
+                Do we copy -1 values in the resize of el_arr?
+            kwargs 
+                List of dtype parameters to additionally define el.
+
+        Returns
+        -------
+            ed
+                Element added, includes el stored in full structured dtype of
+                el_arr.
+            idx : int
+                Index of el_arr where ed is stored.
+            el_arr : np.array
+                Modified array containing ed.
+            el_vacancies : list
+                Modified list of el_arr vacancies.
+        """
+        try:
+            idx = el_vacancies.pop(0)
+        except IndexError:
+            # no vacant slot, resize
+            el_arr = self._resize(el_arr, skip_entries=compact, key=key)
+            #TODO - invalidate neighbours, vertex_halfedges etc ???
+            
+            # NOTE: If we search by a different key next time, el_vacancies will
+            # still contain the vacant positions when searching on the previous key.
+            if len(el_arr[key].shape) > 1:
+                # NOTE: If we search on self._vertices['position'] and one position is [-1,-1,-1],
+                # which is not unreasonable, this will replace that vertex. Hence we provide the
+                # option to search and insert on different keys.
+                el_vacancies = [int(x) for x in np.argwhere(np.all(el_arr[key] == -1, axis=1))]
+            else:
+                # el_vacancies = [int(x) for x in np.flatnonzero(el_arr[key] == -1)]
+                el_vacancies = np.flatnonzero(el_arr[key] == -1).tolist()
+
+            idx = el_vacancies.pop(0)
+
+        if idx == -1:
+            raise ValueError('Index cannot be -1.')
+
+        if insert_key is None:
+            # Default to searching and inserting on the same key
+            insert_key = key
+
+        # Put el in el_arr
+        ed = el_arr[idx]
+        ed[insert_key] = el
+        # Define additional structured dtype values for el
+        for k, v in kwargs.items():
+            ed[k] = v
+            
+        return ed, idx, el_arr, el_vacancies
+ 
+    def _new_edge(self, vertex, compact=False, **kwargs):
+        """
+        Create a new edge.
+
+        Parameters
+        ----------
+            vertex : idx
+                self._vertices index which this halfedge points to
+            compact : bool
+                Do we copy -1 values in the resize of _halfedges?
+            kwargs 
+                List of _halfedge dtype parameters (e.g. prev=10, next=2) to 
+                define halfedge via more than just its vertex.
+
+        Returns
+        -------
+            ed : HALFEDGE_DTYPE
+                Halfedge created
+            idx : int
+                Index of the halfedge in self._halfedges.
+        """
+
+        ed, idx, self._halfedges, self._halfedge_vacancies = self._insert(vertex, self._halfedges, self._halfedge_vacancies, 'vertex', compact, None, **kwargs)
+        
+        return ed, idx
+
+    def _new_face(self, _edge, compact=False, **kwargs):
+        """
+        Create a new face based on edge _edge.
+
+        Parameters
+        ----------
+            _edge : idx
+                self._halfedges index of a single halfedge on this face
+            compact : bool
+                Do we copy -1 values in the resize of _faces?
+            kwargs 
+                List of _faces dtype parameters (e.g. area=13.556) to define 
+                face via more than just one of its halfedges.
+
+        Returns
+        -------
+            fa : FACE_DTYPE
+                Face created
+            idx : int
+                Index of the face in self._faces.
+        """
+
+        fa, idx, self._faces, self._face_vacancies = self._insert(_edge, self._faces, self._face_vacancies, 'halfedge', compact, None, **kwargs)
+
+        return fa, idx
+
+    def _new_vertex(self, _vertex, compact=False, **kwargs):
+        """
+        Insert a new vertex into the mesh.
+
+        Parameters
+        ----------
+            _vertex : np.array
+                1D array of x, y, z coordinates of the new vertex.
+            compact : bool
+                Do we copy -1 values in the resize of _vertices?
+            kwargs 
+                List of _vertices dtype parameters (e.g. valence=2) to define 
+                vertex via more than just its position.
+
+        Returns
+        -------
+            vx : VERTEX_DTYPE
+                Vertex created
+            idx : int
+                Index of the vertex in self._vertices.
+        """
+        vx, idx, self._vertices, self._vertex_vacancies = self._insert(_vertex, self._vertices, self._vertex_vacancies, 'halfedge', compact, 'position', **kwargs)
+
+        self._faces_by_vertex = None  # Reset
+
+        return vx, idx
+
+    def edge_split(self, _curr, live_update=True, upsample=False):
+        """
+        Split triangles evenly along an edge specified by halfedege index _curr.
+
+        Parameters
+        ----------
+            _curr : int
+                Pointer to halfedge defining edge to split.
+            live_update : bool
+                Update associated faces and vertices after split. Set to False
+                to handle this externally (useful if operating on multiple, 
+                disjoint edges).
+            upsample: bool
+                Are we doing loop subdivision? If so, keep track of all edges
+                incident on both a new vertex and an old verex that do not
+                split an existing edge.
+        """
+        if _curr == -1:
+            return
+        
+        curr_edge = self._halfedges[_curr]
+        _prev = curr_edge['prev']
+        _next = curr_edge['next']
+
+        # Grab the new vertex position
+        _vertex = 0.5*(self._vertices['position'][curr_edge['vertex'], :] + self._vertices['position'][self._halfedges['vertex'][_prev], :])
+        _, _vertex_idx = self._new_vertex(_vertex)
+
+        _twin = curr_edge['twin']
+        interior = (_twin != -1)  # Are we on a boundary?
+        
+        if interior:
+            twin_edge = self._halfedges[_twin]
+            _twin_prev = twin_edge['prev']
+            _twin_next = twin_edge['next']
+        
+        # Ensure the original faces have the correct pointers and add two new faces
+        self._faces['halfedge'][curr_edge['face']] = _curr
+        if interior:
+            self._faces['halfedge'][twin_edge['face']] = _twin
+            _, _face_1_idx = self._new_face(_twin_prev)
+            self._halfedges['face'][_twin_prev] = _face_1_idx
+        _, _face_2_idx = self._new_face(_next)
+        self._halfedges['face'][_next] = _face_2_idx
+
+        # Insert the new faces
+        _, _he_0_idx = self._new_edge(self._halfedges['vertex'][_next], prev=_curr, next=_prev, face=self._halfedges['face'][_curr])
+        if interior:
+            _, _he_1_idx = self._new_edge(_vertex_idx, prev=_twin_next, next=_twin, face=self._halfedges['face'][_twin])
+        
+            _, _he_2_idx = self._new_edge(self._halfedges['vertex'][_twin_next], next=_twin_prev, face=_face_1_idx)
+            _, _he_3_idx = self._new_edge(_vertex_idx, prev=_twin_prev, next=_he_2_idx, face=_face_1_idx)
+            self._halfedges['prev'][_he_2_idx] = _he_3_idx
+
+        _, _he_4_idx = self._new_edge(self._halfedges['vertex'][_curr], next=_next, face=_face_2_idx, twin=-1)
+        _, _he_5_idx = self._new_edge(_vertex_idx, prev=_next, next=_he_4_idx, face=_face_2_idx)
+        self._halfedges['prev'][_he_4_idx] = _he_5_idx
+
+        self._halfedges['twin'][_he_0_idx] = _he_5_idx
+        self._halfedges['twin'][_he_5_idx] = _he_0_idx
+
+        if interior:
+            self._halfedges['twin'][_he_1_idx] = _he_2_idx
+            self._halfedges['twin'][_he_2_idx] = _he_1_idx
+
+            self._halfedges['twin'][_he_3_idx] = _he_4_idx
+            self._halfedges['twin'][_he_4_idx] = _he_3_idx
+
+        # Update _prev, next
+        self._halfedges['prev'][_prev] = _he_0_idx
+        self._halfedges['prev'][_next] = _he_4_idx
+        self._halfedges['next'][_next] = _he_5_idx
+
+        if interior:
+            # Update _twin_next, _twin_prev
+            self._halfedges['next'][_twin_next] = _he_1_idx
+            self._halfedges['prev'][_twin_prev] = _he_2_idx
+            self._halfedges['next'][_twin_prev] = _he_3_idx
+
+            self._halfedges['prev'][_twin] = _he_1_idx
+        # Update _curr and _twin
+        self._halfedges['vertex'][_curr] = _vertex_idx
+        self._halfedges['next'][_curr] = _he_0_idx
+
+        # Update halfedges
+        if interior:
+            self._vertices['halfedge'][self._halfedges['vertex'][_he_2_idx]] = _he_1_idx
+        self._vertices['halfedge'][self._halfedges['vertex'][_prev]] = _curr
+        self._vertices['halfedge'][self._halfedges['vertex'][_he_4_idx]] = _next
+        self._vertices['halfedge'][_vertex_idx] = _he_4_idx
+        self._vertices['halfedge'][self._halfedges['vertex'][_he_0_idx]] = _he_5_idx
+
+        if upsample:
+            # Make sure these edges emanate from the new vertex stored at _vertex_idx
+            if interior:
+                self._loop_subdivision_flip_edges.extend([_he_2_idx])
+            
+            self._loop_subdivision_flip_edges.extend([_he_0_idx])
+            self._loop_subdivision_new_vertices.extend([_vertex_idx])
+
+        if live_update:
+            if interior:
+                self._update_face_normals([self._halfedges['face'][_he_0_idx], self._halfedges['face'][_he_1_idx], self._halfedges['face'][_he_2_idx], self._halfedges['face'][_he_4_idx]])
+                self._update_vertex_neighbors([self._halfedges['vertex'][_curr], self._halfedges['vertex'][_twin], self._halfedges['vertex'][_he_0_idx], self._halfedges['vertex'][_he_2_idx], self._halfedges['vertex'][_he_4_idx]])
+            else:
+                self._update_face_normals([self._halfedges['face'][_he_0_idx], self._halfedges['face'][_he_4_idx]])
+                self._update_vertex_neighbors([self._halfedges['vertex'][_curr], self._halfedges['vertex'][_prev], self._halfedges['vertex'][_he_0_idx], self._halfedges['vertex'][_he_4_idx]])
+            self._faces_by_vertex = None
+    
+    def edge_flip(self, _curr, live_update=True):
+        """
+        Flip an edge specified by halfedge index _curr.
+
+        Parameters
+        ----------
+            _curr : int
+                Pointer to halfedge defining edge to flip.
+            live_update : bool
+                Update associated faces and vertices after flip. Set to False
+                to handle this externally (useful if operating on multiple, 
+                disjoint edges).
+        """
+
+        if (_curr == -1):
+            return
+
+        curr_edge = self._halfedges[_curr]
+        _twin = curr_edge['twin']
+        if (_twin == -1):
+            # This is a boundary edge
+            return
+        _prev = curr_edge['prev']
+        _next = curr_edge['next']
+        
+        twin_edge = self._halfedges[_twin]
+        _twin_prev = twin_edge['prev']
+        _twin_next = twin_edge['next']
+
+        # Make sure both vertices have valence > 3 (preserve manifoldness)
+        vc, vt = self._vertices['valence'][curr_edge['vertex']], self._vertices['valence'][twin_edge['vertex']]
+        if (vc < 4) or (vt < 4):
+            return
+
+        # Calculate adjustments to the halfedges we're flipping
+        new_v0 = self._halfedges['vertex'][_next]
+        new_v1 = self._halfedges['vertex'][_twin_next]
+
+        # If there's already an edge between these two vertices, don't flip (preserve manifoldness)
+        # NOTE: This is potentially a problem if we start with a high-valence mesh. In that case, swap this
+        # check with the more expensive commented one below.
+
+        # Check for creation of multivalent edges and prevent this (manifoldness)
+        fast_collapse_bool = (self.manifold and (vc < NEIGHBORSIZE) and (vt < NEIGHBORSIZE))
+        if fast_collapse_bool:
+            if new_v1 in self._vertices['neighbors'][new_v0]:
+                return
+        else:
+            if new_v1 in self._halfedges['vertex'][self._halfedges['twin'][self._halfedges['vertex'] == new_v0]]:
+                return
+
+        # Convexity check: Let's see if the midpoint of the flipped edge will be above or below the plane of the 
+        # current edge
+        flip_midpoint = 0.5*(self._vertices['position'][new_v0] + self._vertices['position'][new_v1])
+        plane_midpoint = (1./3)*(self._vertices['position'][curr_edge['vertex']] + self._vertices['position'][self._halfedges['vertex'][curr_edge['next']]] + self._vertices['position'][self._halfedges['vertex'][curr_edge['prev']]])
+        flipped_dot = ((self._faces['normal'][curr_edge['face']])*(flip_midpoint - plane_midpoint)).sum()
+
+        if flipped_dot < 0:
+            # If flipping moves the midpoint of the edge below the original triangle's plane, this introduces
+            # concavity, so don't flip.
+            return
+
+        # _next's next and prev must be adjusted
+        self._halfedges['prev'][_next] = _twin_prev
+        self._halfedges['next'][_next] = _twin
+
+        # _twin_next's next and prev must be adjusted
+        self._halfedges['prev'][_twin_next] = _prev
+        self._halfedges['next'][_twin_next] = _curr
+
+        # _prev's next and prev must be updated
+        self._halfedges['prev'][_prev] = _curr
+        self._halfedges['next'][_prev] = _twin_next
+
+        # _twin_prev's next and prev must be updated
+        self._halfedges['prev'][_twin_prev] = _twin
+        self._halfedges['next'][_twin_prev] = _next
+
+        # Don't even bother with checking, just make sure to update the
+        # vertex_halfedges references to halfedges we know work
+        self._vertices['halfedge'][curr_edge['vertex']] = _next
+        self._vertices['halfedge'][twin_edge['vertex']] = _twin_next
+
+        # Apply adjustments to the the halfedges we're flipping
+        curr_edge['vertex'] = new_v0
+        twin_edge['vertex'] = new_v1
+        curr_edge['next'] = _prev
+        twin_edge['next'] = _twin_prev
+        curr_edge['prev'] = _twin_next
+        twin_edge['prev'] = _next
+
+        # Update pointers
+        _prev = curr_edge['prev']
+        _next = curr_edge['next']
+        _twin_prev = twin_edge['prev']
+        _twin_next = twin_edge['next']
+
+        # Set faces
+        self._halfedges['face'][_next] = curr_edge['face']
+        self._halfedges['face'][_prev] = curr_edge['face']
+        self._halfedges['face'][_twin_next] = twin_edge['face']
+        self._halfedges['face'][_twin_prev] = twin_edge['face']
+
+        # Finish updating vertex_halfedges references, update face references
+        self._vertices['halfedge'][curr_edge['vertex']] = _twin
+        self._vertices['halfedge'][twin_edge['vertex']] = _curr
+        self._faces['halfedge'][curr_edge['face']] = _curr
+        self._faces['halfedge'][twin_edge['face']] = _twin
+
+        if live_update:
+            # Update face and vertex normals
+            self._update_face_normals([curr_edge['face'], twin_edge['face']])
+            self._update_vertex_neighbors([curr_edge['vertex'], twin_edge['vertex'], self._halfedges['vertex'][_next], self._halfedges['vertex'][_twin_next]])
+
+            self._faces_by_vertex = None
+
+    def regularize(self):
+        """
+        Adjust vertices so they tend toward valence VALENCE 
+        (or BOUNDARY_VALENCE for boundaries).
+        """
+        flip_count = 0
+
+        # Do a single pass over all active edges and flip them if the flip minimizes the deviation of vertex valences
+        # for i in np.arange(len(self._halfedges['vertex'])):
+        #     if (self._halfedges['vertex'][i] < 0):
+        #         continue
+        for i in np.flatnonzero(self._halfedges['vertex'] != -1):
+
+            curr_edge = self._halfedges[i]
+            _twin = curr_edge['twin']
+            twin_edge = self._halfedges[_twin]
+
+            target_valence = VALENCE
+            if _twin == -1:
+                # boundary
+                target_valence = BOUNDARY_VALENCE
+
+            # Pre-flip vertices
+            v1 = self._vertices['valence'][curr_edge['vertex']] - target_valence
+            v2 = self._vertices['valence'][twin_edge['vertex']] - target_valence
+
+            # Post-flip vertices
+            v3 = self._vertices['valence'][self._halfedges['vertex'][curr_edge['next']]] - target_valence
+            v4 = self._vertices['valence'][self._halfedges['vertex'][twin_edge['next']]] - target_valence
+
+            # Check valence deviation from VALENCE (or
+            # BOUNDARY_VALENCE for boundaries) pre- and post-flip
+            score_pre = np.abs([v1,v2,v3,v4]).sum()
+            score_post = np.abs([v1-1,v2-1,v3+1,v4+1]).sum()
+
+            if score_post < score_pre:
+                # Flip minimizes deviation of vertex valences from VALENCE (or
+                # BOUNDARY_VALENCE for boundaries)
+                self.edge_flip(i)
+                flip_count += 1
+
+        print('Flip count: %d' % (flip_count))
+
+    def relax(self, l=1, n=1):
+        """
+        Perform n iterations of Lloyd relaxation on the mesh.
+
+        Parameters
+        ----------
+            l : float
+                Regularization (damping) term, used to avoid oscillations.
+            n : int
+                Number of iterations to apply.
+        """
+
+        for k in range(n):
+            # Get vertex neighbors
+            nn = self._vertices['neighbors']
+            nn_mask = (self._vertices['neighbors'] != -1)
+            vn = self._vertices['position'][self._halfedges['vertex'][nn]]
+
+            # Weight by distance to neighors
+            an = (1./self._halfedges['length'][nn])*nn_mask
+            an[self._halfedges['length'][nn] == 0] = 0
+
+            # Calculate gravity-weighted centroids
+            A = np.sum(an, axis=1)
+            c = 1./(A[...,None])*np.sum(an[...,None]*vn, axis=1)
+            # Don't get messed up by slivers. NOTE: This is a hack in case
+            # edge split/collapse don't do their jobs.
+            A_mask = (A == 0)
+            c[A_mask] = self._vertices['position'][A_mask]
+            if self.fix_boundary:
+                # Don't move vertices on a boundary
+                boundary = self._halfedges[(self._halfedges['twin'] == -1)]
+                tn = np.hstack([boundary['vertex'], self._halfedges['vertex'][boundary['prev']]])
+                c[tn] = self._vertices['position'][tn]
+
+            # Construct projection vector into tangent plane
+            pn = self._vertices['normal'][...,None]*self._vertices['normal'][:,None,:]
+            p = np.eye(3)[None,:] - pn
+
+            # Update vertex positions
+            self._vertices['position'] = self._vertices['position'] + l*np.sum(p*((c-self._vertices['position'])[...,None]),axis=1)
+
+        # Now we gotta recalculate the normals
+        self._faces['normal'][:] = -1
+        self._vertices['normal'][:] = -1
+        self.face_normals
+        self.vertex_normals
+
+    def remesh(self, n=5, target_edge_length=-1, l=0.5, n_relax=10):
+        """
+        Produce a higher-quality mesh.
+
+        Follows procedure in Botsch and Kobbelt, A Remeshing Approach to 
+        Multiresoluton Modeling, Eurographics Symposium on Geometry Processing,
+        2004.
+
+        Parameters
+        ----------
+            n : int
+                Number of remeshing iterations to apply.
+            target_edge_length : float
+                Target edge length for all edges in the mesh.
+            l : float
+                Relaxation regularization term, used to avoid oscillations.
+            n_relax : int 
+                Number of Lloyd relaxation (relax()) iterations to apply 
+                per remeshing iteration.
+        """
+
+        if (target_edge_length == -1):
+            # Guess edge_length
+            target_edge_length = np.mean(self._halfedges['length'][self._halfedges['length'] != -1])
+
+        for k in range(n):
+            # 1. Split all edges longer than (4/3)*target_edge_length at their midpoint.
+            split_count = 0
+            for i in np.arange(len(self._halfedges['length'])):
+                if (self._halfedges['vertex'][i] != -1) and (self._halfedges['length'][i] > 1.33*target_edge_length):
+                    self.edge_split(i)
+                    split_count += 1
+            print('Split count: %d' % (split_count))
+            
+            if self.debug:
+                # check for dud half edges
+                _valid = self._halfedges['vertex'] != -1
+                assert(not np.any(self._halfedges['twin'][_valid] == -1))
+                assert (not np.any(self._halfedges['next'][_valid] == -1))
+                assert (not np.any(self._halfedges['vertex'][self._halfedges['next'][_valid]] == -1))
+
+                assert (not np.any(self._halfedges['next'][self._halfedges['twin'][_valid]] == self._halfedges['twin'][self._halfedges['prev'][_valid]]))
+                
+                assert(self._vertices['valence'][self._vertices['valence']>0].min() >=3)
+        
+            # 2. Collapse all edges shorter than (4/5)*target_edge_length to their midpoint.
+            collapse_count = 0
+            for i in np.arange(len(self._halfedges['length'])):
+                if (self._halfedges['vertex'][i] != -1) and (self._halfedges['length'][i] < 0.8*target_edge_length):
+                    self.edge_collapse(i)
+                    collapse_count += 1
+            print('Collapse count: ' + str(collapse_count))
+
+            # 3. Flip edges in order to minimize deviation from VALENCE.
+            self.regularize()
+
+            # 4. Relocate vertices on the surface by tangential smoothing.
+            self.relax(l=l, n=n_relax)
+
+        # Let's double-check the mesh manifoldness
+        self._manifold = None
+        self.manifold
+
+    def upsample(self, n=1):
+        """
+        Upsample the mesh by a factor of 4 (factor of 2 along each axis in the
+        plane of the mesh) and smooth meshes by Loop's 5/8 and 3/8 rule.
+
+        References:
+            1. C. T. Loop, "Smooth Subdivision surfaces Based on Triangles," 
+               University of Utah, 1987
+            2. http://462cmu.github.io/asst2_meshedit/, task 4
+
+        Parameters
+        ----------
+            n : int
+                Number of upsampling operations to perform.
+        """
+
+        for k in range(n):
+            # Reset
+            split_edges = {}
+            self._loop_subdivision_new_vertices = []
+            self._loop_subdivision_flip_edges = []
+            new_vertex_idxs = []
+
+            # Mark the current edges as old
+            edges_to_split = np.where(self._halfedges['length'] != -1)[0]
+            split_halfedges = self._halfedges[edges_to_split]
+
+            # Compute new vertex positions for old vertices
+            old_vertex_idxs = split_halfedges['vertex']
+            old_vertices = self._vertices[old_vertex_idxs]
+            old_neighbors = old_vertices['neighbors']
+            neg_mask = (old_neighbors != -1)
+            # alpha is a function of vertex order N that satisifies constraints on equation 3.4 of Loop's thesis
+            alpha = np.tanh(LOOP_ALPHA_FACTOR*old_vertices['valence'])
+            old_vertex_positions = (alpha[:,None])*old_vertices['position'] + ((1-alpha)[:,None])*((1./old_vertices['valence'])[:,None])*np.sum(self._vertices['position'][self._halfedges['vertex'][old_neighbors]]*neg_mask[...,None],axis=1)
+            
+            # Compute new vertex positions for new vertices
+            p0 = 0.375*(old_vertices['position'] + self._vertices['position'][self._halfedges['vertex'][split_halfedges['twin']]])
+            p1 = 0.125*(self._vertices['position'][self._halfedges['vertex'][split_halfedges['next']]] + self._vertices['position'][self._halfedges['vertex'][self._halfedges['next'][split_halfedges['twin']]]])
+            new_vertex_positions = p0 + p1
+
+            # 1. Split every edge in the mesh
+            for j, i in enumerate(edges_to_split):
+                if i in split_edges:
+                    continue
+                
+                split_edges[self._halfedges['twin'][i]] = i
+                new_vertex_idxs.append(j)
+                self.edge_split(i, upsample=True)
+            
+            # 2. Flip any new edge that touches an old vertex and a new vertex
+            edges_to_flip = list(set(self._halfedges['vertex'][self._loop_subdivision_flip_edges]) - set(self._loop_subdivision_new_vertices))
+            for e in edges_to_flip:
+                self.edge_flip(e)
+
+            # Get any boundary vertices
+            boundary_vertex_idxs = self._halfedges['vertex'][(self._halfedges['twin'] == -1)]
+            boundary_vertex_positions = self._vertices['position'][boundary_vertex_idxs]
+
+            # Copy new position values into self._vertices['position']
+            self._vertices['position'][old_vertex_idxs] = old_vertex_positions
+            self._vertices['position'][self._loop_subdivision_new_vertices] = new_vertex_positions[new_vertex_idxs]
+
+            # Restore boundary vertex positions
+            self._vertices['position'][boundary_vertex_idxs] = boundary_vertex_positions
+
+        self._manifold = None
+
+    def downsample(self, n_triangles=None):
+        """
+        Mesh downsampling via quadratic error metrics.
+
+        Follows procedure in Garland and Heckbert, Surface Simplification Using
+        Quadtratic Error Metrics.
+
+        Parameters
+        ----------
+            n_triangles : int
+                Target number of triangles in the downsampled mesh.
+        """
+
+        import PYME.experimental._treap as treap
+
+        # 1. Compute quadratic matrices for all initial vertices
+        v = self._vertices['position']
+        n = self._vertices['normal']
+        d = (-n*v).sum(1)
+        p = np.vstack([n.T, d]).T  # plane
+        vn = self._vertices['neighbors']
+        vn_mask = (vn != -1)
+        pp = p[self._halfedges['vertex'][vn]]*vn_mask[...,None]  # neighbor planes
+        Q = (pp[...,None]*pp[:,:,None,:]).sum(1)  # per-vertex quadratic
+
+        # 2. Select all valid pairs
+        #   For now, operate on edges. In the future we can also operate on any
+        #   pair of vertex positions such that || v_1 - v_2 || < t, where v_1,
+        #   v_2 \in R^3, and t \in R is a threshold.
+
+        # 3. Compute optimal contraction target and cost of each contraction
+        # NOTE: we do this for all halfedges, empty or not. This saves us from having to search for
+        # unique halfedges later in step 5. Instead, we just ignore -1 values.
+        edges_mask = (self._halfedges['vertex'] != -1)
+        edges = np.vstack([self._halfedges['vertex'], self._halfedges['vertex'][self._halfedges['prev']]]).T
+        # Mask and shift to avoid a copy operation on Q
+        Q_mask = np.ones((4,4))
+        Q_mask[3,:] = 0
+        Q_shift = np.zeros((4,4))
+        Q_shift[3,3] = 1
+        # h is the solution vector for least squares
+        h = np.array([0,0,0,1])
+        # 3a. Compute the optimal contraction target for each valid pair
+        Q_edge = (Q[edges]).sum(1)  # Q paired
+        try:
+            vp = (np.linalg.inv(Q_edge*Q_mask[None,...] + Q_shift[None,...])*h).sum(2)
+        except(np.linalg.LinAlgError):
+            vp = 0.5*np.sum(self._vertices['position'][edges],axis=1)
+            vp = np.vstack([vp.T, np.ones(vp.shape[0])]).T
+
+        # 3b. Compute cost of contractions
+        err = ((vp[:,None,:]*Q_edge).sum(2)*vp).sum(1)
+
+        # 4. Place all the pairs in a heap keyed on cost with the minimum cost pair on top
+        cost_heap = treap.Treap()
+        for i in (np.arange(len(edges))[edges_mask]):
+            cost_heap.insert(np.float32(err[i]), np.int32(i))
+            
+        # 5. Iteratively remove the pair of least cost from the heap, 
+        #    contract this pair, and update the costs of all valid 
+        #    pairs involving the remaining live vertex.
+        n_faces = np.sum(self._faces['halfedge'] != -1)
+        if n_triangles is None:
+            # Assume we want to downsample by a factor of 4
+            n_triangles = int(0.25*n_faces)
+        collapse_tries = int(0.125*(n_faces - n_triangles))
+        while True:
+            if n_faces <= n_triangles:
+                # Sometimes edge_collapse does not collapse the edge
+                # because it would affect the manifoldness of the mesh,
+                # so we need to see how far off we are from the desired
+                # number of triangles n_triangles.
+                tmp = np.sum(self._faces['halfedge'] != -1)
+                if (n_faces == tmp) or (collapse_tries == 0):
+                    # We don't want to double check ourselves forever
+                    break
+                # Update our estimate and keep refining the mesh
+                n_faces = tmp
+                collapse_tries -= 1
+            
+            # Grab the edge with minimum cost
+            _, _edge = cost_heap.pop()
+
+            if _edge == -1:
+                print('Edge was -1???')
+                continue
+
+            # Compute the new quadratic
+            edge = self._halfedges[_edge]
+            # Grab the live and dead vertex
+            _live_vertex = edge['vertex']
+            _dead_vertex = self._halfedges['vertex'][edge['prev']]
+            Q_edge[_edge] = Q[_live_vertex] + Q[_dead_vertex]
+
+            if (_live_vertex == -1) or (_dead_vertex == -1):
+                print('Vertex was -1???')
+                continue
+
+            # Grab all neighboring halfedges
+            nn_live = self._vertices['neighbors'][_live_vertex]
+            nn_live_mask = (nn_live != -1)
+            nn_live_twin = self._halfedges['twin'][nn_live[nn_live_mask]]
+            nn_live_twin_mask = (nn_live_twin != -1)
+            nn_dead = self._vertices['neighbors'][_dead_vertex]
+            nn_dead_mask = (nn_dead != -1)
+            nn_dead_twin = self._halfedges['twin'][nn_dead[nn_dead_mask]]
+            nn_dead_twin_mask = (nn_dead_twin != -1)
+            neighbors = np.hstack([nn_live[nn_live_mask], nn_live_twin[nn_live_twin_mask], nn_dead[nn_dead_mask], nn_dead_twin[nn_dead_twin_mask]])
+
+            # Eliminate edges touching either vertex from the cost heap
+            for neighbor in neighbors:
+                cost_heap.delete(np.int32(neighbor))
+                            
+            # Collapse the edge
+            self.edge_collapse(_edge)
+            
+            # Decrement the estimate of the number of triangles in the 
+            # mesh accordingly
+            n_faces -= 2
+
+            # Set the quadratic of _live_vertex to the edge quadratic
+            Q[_live_vertex] = Q_edge[_edge] 
+            # self._vertices['position'][_live_vertex] = vp[_edge,:3]
+
+            # Grab the new neighbors
+            nn_live = self._vertices['neighbors'][_live_vertex]
+            nn_live_mask = (nn_live != -1)
+            nn_live_twin = self._halfedges['twin'][nn_live[nn_live_mask]]
+            nn_live_twin_mask = (nn_live_twin != -1)
+            neighbors = np.hstack([nn_live[nn_live_mask], nn_live_twin[nn_live_twin_mask]])
+
+            # Update the costs and positions of each of these neighbors and re-insert them into the queue
+            new_edges = np.vstack([self._halfedges['vertex'][neighbors], self._halfedges['vertex'][self._halfedges['prev'][neighbors]]]).T
+            Q_edge[neighbors] = (Q[new_edges]).sum(1)
+
+            try:
+                vp[neighbors] = (np.linalg.inv(Q_edge[neighbors]*Q_mask[None,...] + Q_shift[None,...])*h).sum(2)
+            except(np.linalg.LinAlgError):
+                vp_temp = 0.5*np.sum(self._vertices['position'][new_edges],axis=1)
+                vp[neighbors] = np.vstack([vp_temp.T, np.ones(vp_temp.shape[0])]).T
+
+            err[neighbors] = ((vp[neighbors,None,:]*Q_edge[neighbors]).sum(2)*vp[neighbors]).sum(1)
+
+            for n in neighbors:
+                cost_heap.insert(np.float32(err[n]), np.int32(n))
+
+        self._manifold = None
+
+    def find_connected_components(self):
+        """
+        Label connected components of the mesh.
+        """ 
+
+        # Set all components to -1 (background)
+        self._halfedges['component'] = -1
+        self._vertices['component'] = -1
+        self._faces['component'] = -1
+
+        # Connect component by vertex
+        component = 0
+        for _vertex in np.arange(self._vertices.shape[0]):
+            curr_vertex = self._vertices[_vertex]
+            if (curr_vertex['halfedge'] == -1) or (curr_vertex['component'] != -1):
+                # We only want to deal with valid, unassigned vertices
+                continue
+
+            # Search vertices contains vertices connected to this vertex.
+            # We want to see if there are other vertices connected to the
+            # search vertices.
+            search_vertices = []
+            self._vertices[_vertex]['component'] = component
+            search_vertices.append(_vertex)
+
+            # Find vertices connected to the search vertices
+            while search_vertices:
+                # Grab the latest search vertex neighbors
+                _v = search_vertices.pop()
+                nn = self._vertices['neighbors'][_v]
+                # Loop over the neighbors
+                for _edge in nn:
+                    if _edge == -1:
+                        continue
+                    # Assign the vertex component label to halfedges and faces
+                    # emanating from this vertex
+                    curr_edge = self._halfedges[_edge]
+                    self._halfedges['component'][_edge] = component
+                    self._halfedges['component'][curr_edge['prev']] = component
+                    self._halfedges['component'][curr_edge['next']] = component
+                    self._faces['component'][curr_edge['face']] = component
+                    
+                    # If the vertex is assigned, we've already visited it and
+                    # don't need to do so again.
+                    if self._vertices['component'][curr_edge['vertex']] != -1:
+                        continue
+                    self._vertices['component'][curr_edge['vertex']] = component
+                    search_vertices.append(curr_edge['vertex'])
+            
+            # Increment the label as any vertices not included in this
+            # iteration's search will be part of another component.
+            component += 1
+
+    def keep_largest_connected_component(self):
+        # Find the connected components
+        self.find_connected_components()
+
+        # Which connected component is largest? 
+        com, counts = np.unique(self._vertices['component'][self._vertices['component']!=-1], return_counts=True)
+        max_count = np.argmax(counts)
+        max_com = com[max_count]
+
+        # Remove the smaller components
+        _vertices = np.where((self._vertices['component'] != max_com))[0]
+        _edges = np.where((self._halfedges['component'] != max_com))[0]
+        _edges_with_twins = _edges[self._halfedges['twin'][_edges] != -1]
+        _faces = np.where((self._faces['component'] != max_com))[0]
+        self._vertices[_vertices] = -1
+        _kept_edges = self._halfedges['twin'][_edges_with_twins]
+        self._halfedges['twin'][_kept_edges] = -1
+        self._halfedges[_edges] = -1
+        self._faces[_faces] = -1
+
+        # Mark deleted faces as available
+        self._vertex_vacancies = list(set(self._vertex_vacancies).union(set(_vertices)))
+        self._halfedge_vacancies = list(set(self._halfedge_vacancies).union(set(_edges)))
+        self._face_vacancies = list(set(self._face_vacancies).union(set(_faces)))
+
+        # Update newly orphaned edges
+        self._update_face_normals(list(set(self._halfedges['face'][_kept_edges])))
+        self._update_vertex_neighbors(list(set(self._halfedges['vertex'][_kept_edges])))
+        
+        self._faces_by_vertex = None
+
+    def _find_boundary_polygons(self):
+        """
+        Return a list of closed polygons, each defined by a list of halfedges,
+        where each polygon defines a boundary in the mesh.
+        """
+        boundary_polygons = []
+
+        # 1. Construct an initial list of boundary edges
+        boundary_edges = list(np.where((self._halfedges['twin'] == -1) & (self._halfedges['vertex'] != -1))[0])
+
+        # 2. Get the boundary polygons
+        while len(boundary_edges) > 0:
+            _root = boundary_edges[-1]  # initial halfedge defining the polygon
+            curr_polygon = [_root]
+            # Step next-twin-next to move around the boundary
+            _next = self._halfedges['next'][_root]
+            _twin = self._halfedges['twin'][_next]
+            _curr = self._halfedges['next'][_twin]
+            if self._halfedges['twin'][_next] == -1:
+                _curr = _next
+            if self._halfedges['twin'][_twin] == -1:
+                _curr = _twin
+            
+            # We check open_chain instead of _curr != root since open_chain accounts for closed polygons
+            # ending at an isolated singular vertex (two boundaries emit from a single vertex)
+            open_chain = (self._halfedges['vertex'][self._halfedges['prev'][_root]] != self._halfedges['vertex'][curr_polygon[-1]])
+            
+            # Loop around the boundary until we return the initial halfedge
+            max_polygon_size = 100  # Put an upper limit on the polygon sizes so we don't look forever
+            while open_chain and (max_polygon_size > 0):
+                # We're not always guaranteed to hit the boundary again right 
+                # away doing next-twin-next, so wait until we do
+                twin_next_attemps = 2*BOUNDARY_VALENCE
+                while (twin_next_attemps > 0) and (self._halfedges['twin'][_curr] != -1):
+                    
+                    # Need to do twin next in between boundary edges
+                    _twin = self._halfedges['twin'][_curr]
+                    _curr = self._halfedges['next'][_twin]
+                    if _curr == -1:
+                        # We hit a isolated singular vertex
+                        break
+                    twin_next_attemps -= 1
+                
+                if _curr == -1:
+                    break
+                
+                curr_polygon.append(_curr)
+
+                _next = self._halfedges['next'][_curr]
+                _twin = self._halfedges['twin'][_next]
+                _curr = self._halfedges['next'][_twin]
+
+                if self._halfedges['twin'][_next] == -1:
+                    _curr = _next
+                if self._halfedges['twin'][_twin] == -1:
+                    _curr = _twin
+
+                open_chain = (self._halfedges['vertex'][self._halfedges['prev'][_root]] != self._halfedges['vertex'][curr_polygon[-1]])
+                max_polygon_size -= 1
+
+            if max_polygon_size == 0:
+                print('Polygon search took too long. Canceled.')
+
+            if ((_curr == -1) and (open_chain)) or (max_polygon_size == 0):
+                # We failed to find a boundary polygon
+                boundary_edges.pop()
+                continue
+            else:
+                # We found a boundary polygon!
+                boundary_polygons.append(curr_polygon)
+                # Delete the polygon from the potential polygon list
+                for edge in curr_polygon:
+                    if edge in boundary_edges:
+                        boundary_edges.remove(edge)
+
+        return boundary_polygons
+
+    def _fill_triangle(self, h0, h1, h2):
+        """
+        Create a triangle inside three halfedges.
+
+        Note that this does not update the vertices or faces.
+        """
+
+        _h0_twin_vertex = self._halfedges['vertex'][h2]
+        _, _h0_twin = self._new_edge(_h0_twin_vertex, twin=h0)
+        _, _face = self._new_face(_h0_twin)
+        _h1_twin_vertex = self._halfedges['vertex'][h0]
+        _, _h1_twin = self._new_edge(_h1_twin_vertex, twin=h1, face=_face, next=_h0_twin)
+        self._halfedges['face'][_h0_twin] = _face
+        self._halfedges['prev'][_h0_twin] = _h1_twin
+        _h2_twin_vertex = self._halfedges['vertex'][h1]
+        _, _h2_twin = self._new_edge(_h2_twin_vertex, twin=h2, face=_face, prev=_h0_twin, next=_h1_twin)
+        self._halfedges['next'][_h0_twin] = _h2_twin
+        self._halfedges['prev'][_h1_twin] = _h2_twin
+
+        if h0 != -1:
+            self._halfedges['twin'][h0] = _h0_twin
+        if h1 != -1:
+            self._halfedges['twin'][h1] = _h1_twin
+        if h2 != -1:
+            self._halfedges['twin'][h2] = _h2_twin
+
+    def _fan_triangulation(self, polygon):
+        """
+        Triangulate a polygon, defined by halfedges in the mesh,
+        by creating a fan emanating from a single vertex out to
+        the boundary halfedges.
+
+        Parameters
+        ----------
+            polygon : list
+                List of halfedges defining a closed polygon in the mesh.
+        """
+
+        if len(polygon) < 3:
+            raise ValueError('polygon must be of length >= 3')
+
+        # Reverse order
+        polygon = polygon[::-1]
+
+        while len(polygon) > 0:
+            h0 = polygon.pop()
+            h1 = polygon.pop()
+            if (len(polygon) == 1):
+                # Base case, make a triangle
+                # polygon = polygon[::-1]
+                h2 = polygon.pop()
+                self._fill_triangle(h0,h1,h2)
+                _h0_twin = self._halfedges['twin'][h0]
+            else:
+                # Create a new triangle with a boundary edge
+                self._fill_triangle(h0, h1, -1)
+                
+                # Due to the way fill_triangle works, we need to set h0's vertex after the fact
+                _h0_twin = self._halfedges['twin'][h0]
+                self._halfedges['vertex'][_h0_twin] = self._halfedges['vertex'][self._halfedges['prev'][h0]]
+                
+                # Adjust the boundary
+                polygon.append(self._halfedges['next'][_h0_twin])
+
+            # Update faces and vertices
+            self._update_face_normals([self._halfedges['face'][_h0_twin], self._halfedges['face'][h0], self._halfedges['face'][h1]])
+            self._update_vertex_neighbors([self._halfedges['vertex'][_h0_twin], self._halfedges['vertex'][h0], self._halfedges['vertex'][h1]])
+
+    def _zig_zag_triangulation(self, polygon):
+        """
+        Triangulate a polygon, defined by halfedges in the mesh,
+        by creating zig-zagging between edges of the boundary.
+
+        Parameters
+        ----------
+            polygon : list
+                List of halfedges defining a closed polygon in the mesh.
+        """
+
+        if len(polygon) < 3:
+            raise ValueError('polygon must be of length >= 3')
+
+        # Reverse order
+        polygon = polygon[::-1]
+        odd = True
+
+        while len(polygon) > 0:
+            h0 = polygon.pop()
+            h1 = polygon.pop()
+            if (len(polygon) == 1):
+                # Base case, make a triangle
+                # polygon = polygon[::-1]
+                h2 = polygon.pop()
+                self._fill_triangle(h0,h1,h2)
+                _h0_twin = self._halfedges['twin'][h0]
+            else:
+                # Create a new triangle with a boundary edge
+                self._fill_triangle(h0, h1, -1)
+                
+                # Due to the way fill_triangle works, we need to set h0's vertex after the fact
+                _h0_twin = self._halfedges['twin'][h0]
+                self._halfedges['vertex'][_h0_twin] = self._halfedges['vertex'][self._halfedges['prev'][h0]]
+            
+                # Adjust the boundary
+                polygon = polygon[::-1]  # zig-zag
+                if odd:
+                    polygon.insert(-1,self._halfedges['next'][_h0_twin])
+                else:
+                    polygon.append(self._halfedges['next'][_h0_twin])
+                odd = (not odd)
+
+            # Update faces and vertices
+            self._update_face_normals([self._halfedges['face'][_h0_twin], self._halfedges['face'][h0], self._halfedges['face'][h1]])
+            self._update_vertex_neighbors([self._halfedges['vertex'][_h0_twin], self._halfedges['vertex'][h0], self._halfedges['vertex'][h1]])
+
+    def _fill_holes(self, method='zig-zag'):
+        """
+        Fill holes in the mesh.
+
+        Parameters
+        ----------
+            method : string
+                The method to use to patch boundary polygons. A string listed 
+                in options. 
+        """
+
+        options = ['fan', 'zig-zag']
+
+        if method not in options:
+            print('Unknown triangulation method. Using default.')
+            method = 'zig-zag'
+
+        boundary_polygons = self._find_boundary_polygons()
+        
+        # Find length 2 polygons and zipper them ("pinch")
+        to_remove = []
+        for polygon in boundary_polygons:
+            if len(polygon) == 2:
+                self._halfedges['twin'][polygon[0]] = polygon[1]
+                self._halfedges['twin'][polygon[1]] = polygon[0]
+                to_remove.append(polygon)
+        
+        # Eliminate the length 2 polygons before triangulation
+        for polygon in to_remove:
+            boundary_polygons.remove(polygon)
+
+        # Triangulate
+        if method == 'fan':
+            for polygon in boundary_polygons:
+                self._fan_triangulation(polygon)
+        
+        if method == 'zig-zag':
+            for polygon in boundary_polygons:
+                self._zig_zag_triangulation(polygon)
+
+        # Reset display
+        self._faces_by_vertex = None
+
+    def _connect_neighbors(self, _nn, starting_component=0):
+        """
+        Connect the neighbors in the list _nn starting from
+        starting_component.
+
+        Parameters
+        ----------
+            _nn : list
+                List of neighbors to connect.
+            starting_component : int
+                Component numbering to start at.
+
+        Returns
+        -------
+            component : int
+                Maxmimum component number used to group neighbors.
+        """
+        # Assign components via the 1-neighbors
+        component = starting_component
+        for _neighbor in _nn:
+            singular = (_neighbor in self.singular_edges)
+            if singular:
+                component += 1
+            if self._faces['component'][self._halfedges['face'][_neighbor]] != -1:
+                continue
+            self._faces['component'][self._halfedges['face'][_neighbor]] = component
+
+            # Extra check in case we're examining the edges out of order
+            if singular:
+                component += 1
+
+        # Loop through the neighbors again and group connected components
+        for _neighbor in _nn:
+            if (_neighbor in self.singular_edges):
+                continue
+    
+            _twin_neighbor = self._halfedges['twin'][_neighbor]
+            if _twin_neighbor != -1:
+                _face = self._halfedges['face'][_neighbor]
+                _twin_face = self._halfedges['face'][_twin_neighbor]
+                min_component = np.min([self._faces['component'][_face], self._faces['component'][_twin_face]])
+                self._faces['component'][_face] = min_component
+                self._faces['component'][_twin_face] = min_component
+
+        return component
+
+    def _group_neighbors(self, _vertex):
+        """
+        Group faces around the 1-neighbor ring of a vertex by reachability. 
+        Faces are not reachable if they are separated by a singular edge.
+
+        Parameters
+        ----------
+            _vertex : int
+                Index of vertex at the center of a 1-neighbor ring.
+        """
+
+        # Zero out connectivity
+        self._vertices['component'][:] = -1
+        self._faces['component'][:] = -1
+        self._halfedges['component'][:] = -1
+
+        # Grab the neighbors
+        _nn = self._vertices[_vertex]['neighbors']
+        _nn = _nn[_nn!=-1]
+
+        # Connect the neighbors
+        component = self._connect_neighbors(_nn, 0)
+
+        # Don't trust self._vertices['neighbors'] because we're dealing with 
+        # singular vertices
+        _twin_nn = list(np.where(self._halfedges['vertex'] == _vertex)[0])
+
+        # If there were any incident vertices not included in this list, group them, too
+        _remaining = list(set(_twin_nn) - set(self._halfedges['twin'][_nn]) - set([-1]))
+        
+        if _remaining:
+            component += 1  # We're off the original 1-neighbor ring, so disconnect
+            self._connect_neighbors(_remaining, component)
+
+    def _remove_singularities(self):
+        """
+        Excise singularities from the mesh. This essentially unzips multivalent
+        edges from the rest of the mesh, creating new, smaller connected 
+        components, each of which is free of singularities. This follows the
+        local method for cutting outlined in Gueziec et al.
+
+        References
+        ----------
+            Gueziec et al. Cutting and Stitching: Converting Sets of Polygons
+            to Manifold Surfaces, IEEE TRANSACTIONS ON VISUALIZATION AND 
+            COMPUTER GRAPHICS, 2001.
+        """
+
+        # Make sure we're working with the latest singular edges/vertices
+        self._singular_edges = None
+        self._singular_vertices = None
+
+        #  For each marked vertex, partition the faces of the 1-neighbor ring
+        #    into nc "is reachable" equivalence classes. Faces are reachable if
+        #    they share a non-singular edge incident on the marked vertex.
+        for _vertex in self.singular_vertices[::-1]:
+
+            _twin_nn = list(np.where(self._halfedges['vertex'] == _vertex)[0])
+            _update_vertices = np.hstack([_vertex, self._halfedges['vertex'][self._halfedges['twin'][_twin_nn]]])
+            # _update_faces = self._faces[self._halfedges['face'][_twin_nn]]
+
+            self._group_neighbors(_vertex)
+            
+            # Create nc-1 copies of the vertex and assign each equivalence class 
+            #    one of these vertices. (All but one component gets a new vertex).
+            components = np.unique(self._faces['component'][self._faces['component'] != -1])
+            for c in components[1:]:
+                _faces = self._faces[self._faces['component'] == c]
+                _edges = np.hstack([self._halfedges['prev'][_faces['halfedge']], _faces['halfedge'], self._halfedges['next'][_faces['halfedge']]])
+                _vertices = self._halfedges['vertex'][_edges]
+                
+                _modified_edges = _edges[_vertices == _vertex] 
+
+                _edge = self._halfedges['next'][_modified_edges[0]]
+
+                _, _new_vertex = self._new_vertex(self._vertices['position'][_vertex], halfedge=_edge)
+                # Assign edges in this component connected to _vertex to _new_vertex
+                self._halfedges['vertex'][_modified_edges] = _new_vertex
+
+                # Disconnect the boundaries of the components
+                # Any edge pointing to the new vertex with a twin in a 
+                # different component must be reassigned
+                _twin_face_component = self._faces['component'][self._halfedges['face'][self._halfedges['twin'][_modified_edges]]]
+                _boundary = (_twin_face_component != c)
+                _twin_edges = self._halfedges['twin'][_modified_edges[_boundary]]
+                _twin_edges_mask = (_twin_edges != -1)
+                _valid_edges = _modified_edges[_boundary][_twin_edges_mask]
+                self._halfedges['twin'][_twin_edges[_twin_edges_mask]] = -1
+                self._halfedges['twin'][_valid_edges] = -1
+                # Any edge emanating from the new vertex with a twin in a
+                # different component must be reassigned
+                _twin_next_face_component = self._faces['component'][self._halfedges['face'][self._halfedges['twin'][self._halfedges['next'][_modified_edges]]]]
+                _boundary = (_twin_next_face_component != c)                
+                _twin_next_edges = self._halfedges['twin'][self._halfedges['next'][_modified_edges[_boundary]]]
+                _twin_next_edges_mask = (_twin_next_edges != -1)
+                _valid_edges = self._halfedges['next'][_modified_edges[_boundary][_twin_next_edges_mask]]
+                self._halfedges['twin'][_twin_next_edges[_twin_next_edges_mask]] = -1
+                self._halfedges['twin'][_valid_edges] = -1
+
+                # Double check that the original vertex did not have a halfedge 
+                # in this component
+                _safe_faces_bool = (self._faces['component'][self._halfedges['face']] != c)
+                _safe_vertices = np.where((self._halfedges['vertex'] == _vertex) & (_safe_faces_bool))[0]
+                _safe_halfedge = self._halfedges['next'][_safe_vertices[0]]
+                self._vertices['halfedge'][_vertex] = _safe_halfedge
+
+                # self._update_face_normals(_update_faces)
+                self._update_vertex_neighbors(np.hstack([_update_vertices, _new_vertex]))
+
+        # Reset
+        self._singular_edges = None
+        self._singular_vertices = None
+
+    def repair(self):
+        """
+        Repair the mesh so it's topologically manifold.
+
+        References
+        ----------
+            M. Attene, A lightweight approach to repairing digitized polygon
+            meshes, The Visual Computer, 2010.
+        """
+        
+        # 1. Remove singularities (singular edges and isolated singular vertices)
+        self._remove_singularities()
+
+        # 2. Remove all connected components except the largest
+        self.keep_largest_connected_component()
+
+        # 3. Patch mesh holes with new triangles
+        self._fill_holes()
+
+        self._manifold = None
+
+    def to_stl(self, filename):
+        """
+        Save list of triangles to binary STL file.
+
+        Parameters
+        ----------
+            filename : string
+                File name to write
+
+        Returns
+        -------
+            None
+        """
+        from PYME.IO.FileUtils import stl
+
+        dt = np.dtype([('normal', '3f4'), ('vertex0', '3f4'), ('vertex1', '3f4'), 
+                       ('vertex2', '3f4'), ('attrib', 'u2')])
+
+        triangles_stl = np.zeros(self.face_normals.shape[0], dtype=dt)
+        triangles_stl['vertex0'] = self.vertices[self.faces[:, 0]]
+        triangles_stl['vertex1'] = self.vertices[self.faces[:, 1]]
+        triangles_stl['vertex2'] = self.vertices[self.faces[:, 2]]
+        triangles_stl['normal'] = self.face_normals
+
+        stl.save_stl_binary(filename, triangles_stl)
+
+    def to_ply(self, filename, colors=None):
+        """
+        Save a list of triangles and their vertex colors to a PLY file.
+        We assume colors are a Nx3 array where N is the number of vertices.
+        """
+        from PYME.IO.FileUtils import ply
+
+        # Construct a re-indexing for non-negative vertices
+        live_vertices = np.flatnonzero(self._vertices['halfedge'] != -1)
+        new_vertex_indices = np.arange(live_vertices.shape[0])
+        vertex_lookup = np.zeros(self._vertices.shape[0], dtype=int)
+        
+        vertex_lookup[live_vertices] = new_vertex_indices
+
+        # Grab the faces and vertices we want
+        faces = vertex_lookup[self.faces]
+        vertices = self._vertices['position'][live_vertices]
+
+        ply.save_ply(filename, vertices, faces, colors)