java.lang.Object

mgui.geometry.mesh.MeshFunctions

public class MeshFunctions
extends Utility

Utility class containing static methods that perform some operation upon Mesh3D shape objects. This class should contain all methods for mesh functions, which may or may not reference more specialized mesh algorithm classes. I.e., it is intended as the standard interface for mesh operations within mgui.

Policy: See ProgressUpdater for details on how to incorporate progress updaters into your methods. In general, if progress updating is desired, functions must be able to handle null updater arguments, and preferably provide a second method with no updater which calls the first with a null updater (thus allowing stand-alone calls to blocking methods). TODO: Remove all calls to Worker in this class. All functions should block.

Since:: 1.0
Version:: 1.0
Author:: Andrew Reid
See Also:: ProgressUpdater, InterfaceProgressBar

Nested Class Summary

Nested Classes

Modifier and Type Class Description

protected static class MeshFunctions.IndexedPoint3f
Field Summary

Fields

Modifier and Type Field Description

static javax.swing.JProgressBar progressBar

static double tolerance
Constructor Summary

Constructors

Constructor Description

MeshFunctions()

Method Summary

Modifier and Type	Method	Description
`static void`	`addIndexedTriangleArray(Mesh3D mesh, org.jogamp.java3d.IndexedTriangleArray tris)`	Adds an IndexedTriangleArray to the current mesh.
`static void`	`cleanMesh(Mesh3D mesh)`
`static Mesh3D`	`combine(Mesh3D mesh1, Mesh3D mesh2)`	Combines `mesh1` and `mesh2` and returns the result.
`static boolean`	`computeVertexWiseCurvature(Mesh3DInt mesh3D, java.lang.String target_column, ProgressUpdater progress)`	Computes the curvature of a mesh at each of its nodes, as the magnitude of the sum of surface normals of the triangles of which it is a node.
`static Mesh3D`	`condenseMesh(Mesh3D mesh)`	Condenses a mesh by removing all coincident nodes.
`static void`	`correctOrientation(Mesh3D mesh)`	Orients all faces with each other, starting with the first face
`static void`	`correctOrientation(Mesh3D mesh, boolean reverse)`	Orients all faces with each other (starting with face 0)
`static java.util.ArrayList<Mesh3D>`	`cutMeshWithPlane(Mesh3D mesh, Plane3D plane, InterfaceProgressBar progress_bar)`	Cuts `mesh` with `plane`, creating new faces along the cut seam.
`static java.util.ArrayList<Mesh3D>`	`cutMeshWithPlane3(Mesh3D mesh, Plane3D plane)`	Cuts `mesh` with `plane`, creating new faces along the cut seam.
`static void`	`decimateByDistance(Mesh3D mesh, Mesh3D newmesh, double threshold)`	Decimates this mesh by merging multiple nodes into a single node if they are separated by less than .
`static org.jogamp.vecmath.Vector3f[]`	`flipNormals(org.jogamp.vecmath.Vector3f[] normals)`
`protected static java.util.ArrayList<MguiInteger>`	`getAllNeighbours(int n, NeighbourhoodMesh nmesh, boolean[] removed, int[] added, boolean[] processed)`	Searches for all neighbours of `n` in `nmesh`.
`static double`	`getArea(Mesh3D mesh)`	Returns the surface area of the given mesh
`static double`	`getAverageEdgeLength(Mesh3D mesh)`	Returns the average edge length keyin a mesh.
`static java.util.ArrayList<java.lang.Integer>`	`getBoundaryNodeIndices(Mesh3D mesh)`
`static boolean[]`	`getBoundaryNodes(Mesh3D mesh)`	Determine which nodes are boundary nodes, return an array of booleans.
`static int`	`getClosestVertex(Mesh3D mesh, int idx, java.util.ArrayList<java.lang.Integer> search_vertices, MguiDouble distance)`	Returns the closest vertex in a list of vertices, or from all vertices if the list is empty.
`static java.util.ArrayList<java.lang.Integer>`	`getClosestVertices(Mesh3D mesh)`	Returns a list of size `mesh.n` integers, such that list(i) = the index of the closest vertex j from vertex i.
`static java.util.ArrayList<java.lang.Integer>`	`getClosestVertices(Mesh3D mesh, java.util.ArrayList<java.lang.Double> distances)`	Returns a list of size `mesh.n` integers, such that list(i) = the index of the closest vertex j from vertex i.
`static Mesh3D`	`getConvexHull(Mesh3D mesh)`	Returns a new mesh which is the convex hull of the given mesh.
`static Mesh3D`	`getConvexHull(Mesh3D mesh, java.lang.String method)`
`static Mesh3D`	`getConvexHull(Mesh3D mesh, java.lang.String method, ProgressUpdater progress)`	Returns a new mesh which is the convex hull of the given mesh.
`static Mesh3D`	`getConvexHull(Mesh3D mesh, ProgressUpdater progress)`
`static java.util.ArrayList<java.lang.Boolean>`	`getDuplicateFaces(Mesh3D mesh)`	Returns an array of booleans where true indicates a duplicate face
`static java.util.List<java.lang.Integer>`	`getDuplicateNodes(Mesh3D mesh)`	Returns an array of booleans where true indicates a duplicate node
`static java.util.ArrayList<MguiDouble>`	`getEdgeLengths(Mesh3D mesh, java.util.ArrayList<MeshEdge> edges)`	Returns a list of edge lengths for the given set of edges
`static java.util.ArrayList<java.lang.Integer>`	`getFarthestVertices(Mesh3D mesh)`	Returns a list of size `mesh.n` integers, such that list(i) = the index of the farthest vertex j from vertex i.
`static java.util.ArrayList<java.lang.Integer>`	`getFarthestVertices(Mesh3D mesh, java.util.ArrayList<java.lang.Double> distances)`	Returns a list of size `mesh.n` integers, such that list(i) = the index of the farthest vertex j from vertex i.
`static java.util.ArrayList<java.lang.Integer>`	`getFarthestVertices(Mesh3D mesh, java.util.ArrayList<java.lang.Double> distances, java.util.ArrayList<java.lang.Integer> vertices)`	Returns a list of size `mesh.n` integers, such that list(i) = the index of the farthest vertex j from vertex i.
`static Mesh3D`	`getFractalSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int min_nodes)`
`static Mesh3D`	`getGlobeSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int n_nodes)`
`static java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>`	`getIntersectingFaces(Mesh3D mesh1, Mesh3D mesh2, float search_max)`	Returns a list of face indices indicating which faces intersect between `mesh1` and `mesh2`.
`static java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>`	`getIntersectingFaces(Mesh3D mesh_1, Mesh3D mesh_2, float search_max, ProgressUpdater progress)`	Returns two lists of face indices indicating which faces intersect between `mesh1` and `mesh2`.
`static java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>`	`getIntersectingFacesBlocking(Mesh3D mesh_1, Mesh3D mesh_2, float search_max, ProgressUpdater progress)`	Returns two lists of face indices indicating which faces intersect between `mesh1` and `mesh2`.
`static org.jogamp.vecmath.Point3f`	`getIntersectionPoint(Mesh3D mesh, org.jogamp.vecmath.Point3f p, org.jogamp.vecmath.Vector3f v)`	Finds the point from the first face in the nodes list which intersects the line segment defined by `p` and v.
`static java.util.ArrayList<Polygon3D>`	`getIntersectionSegments(Mesh3D mesh1, Mesh3D mesh2, InterfaceProgressBar progress_bar)`	Return a set of line segments which represent the intersection of one mesh with another.
`static Mesh3D`	`getIsosurfaceFromVolume(Volume3DInt volume, java.lang.String column, double iso_level)`	Constructs an isosurface from `volume`; i.e., computes a mesh which represents the location where values in the 3D scalar field in `volume` are equal to `iso_level`.
`static java.util.HashMap<java.lang.Integer,java.lang.Integer>`	`getJaggedEdgeNodes(Mesh3D mesh, java.util.ArrayList<MguiNumber> values, int min_nbrs, int max_nbrs, boolean islands)`	Detects nodes corresponding to "jagged" edges; a jagged edge node is defined as one which has only `max_nbrs` neighbours with the same value as itself, and at least `min_nbrs` neighbours which are the same value.
`static java.util.ArrayList<java.lang.Double>`	`getLaplacian(Mesh3D mesh)`	Computes the discrete Laplacian for each vertex in `mesh.`
`static java.util.ArrayList<MguiNumber>`	`getLargestContiguousRois(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int out_value)`	Retains only the largest contiguous ROIs in the given set of values; all others are set to `out_value`.
`static float`	`getMaximumEdgeLength(Mesh3D mesh)`	Searches all edges and returns the maximum length
`static float`	`getMeanCurvature(Mesh3D mesh)`
`static Mesh3D`	`getMeanSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int n_nodes, float stop_delta, long max_itrs)`
`static Mesh3D`	`getMeshExpandedAlongNormals(Mesh3D mesh, float expansion)`	Expands `mesh` along its vertex normals by a distance of `expansion`.
`static java.util.ArrayList<Mesh3D>`	`getMeshParts(Mesh3D mesh)`
`static java.util.ArrayList<Mesh3D>`	`getMeshParts(Mesh3D mesh, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> old_data, java.util.ArrayList<java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>>> parts_data)`
`static java.util.ArrayList<Mesh3D>`	`getMeshParts(Mesh3D mesh, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> old_data, java.util.ArrayList<java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>>> parts_data, ProgressUpdater updater)`	Returns a set of non-contiguous meshes from `mesh`.
`static float`	`getMinimumEdgeLength(Mesh3D mesh)`	Searches all edges and returns the minimum length
`protected static void`	`getNeighbourhoodPoints(java.util.TreeSet<org.jogamp.vecmath.Point3f> points, Mesh3D mesh, NeighbourhoodMesh neighbourhoods, int node, int levels)`
`static java.util.ArrayList<org.jogamp.vecmath.Point3f>`	`getNeighbourhoodPoints(Mesh3D mesh, NeighbourhoodMesh neighbourhoods, int node)`	Returns a list of points corresponding to the immediate (1st level) neighbourhood of node `node`.
`static java.util.ArrayList<org.jogamp.vecmath.Point3f>`	`getNeighbourhoodPoints(Mesh3D mesh, NeighbourhoodMesh neighbourhoods, int node, int levels)`	Returns a list of points corresponding to the n-th level neighbourhood of node `node`, where n is specified by the parameter `levels`
`static Mesh3D`	`getNeighbourhoodSubmesh(Mesh3D mesh, int i)`	Gets a submesh from `mesh` consisting of the neighbourhood of vertex `i`.
`static Mesh3D`	`getOptimalSubmesh(Mesh3D mesh, java.util.ArrayList<MguiInteger> ring)`	Returns the optimal submesh defined by the connect ring `ring`.
`static Mesh3D`	`getOptimizedSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int n_nodes, double stop_value, long max_iter, float entropy)`
`static java.util.ArrayList<java.lang.Integer>`	`getRegionBoundaryNodeIndices(Mesh3D mesh, java.util.ArrayList<MguiNumber> values, int value)`	Returns a list of nodes which form the boundary of all regions defined by `value`, specified by the vertex-wise list `values`.
`static java.util.ArrayList<java.lang.Integer>`	`getRoiIndices(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int roi)`	Returns a list of indices corresponding to `rois == roi`.
`static VertexSelection`	`getRoiSelection(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int roi)`	Returns a vertex selection corresponding to `rois == roi`.
`static Mesh3D`	`getRoiSubmesh(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int roi)`	Returns a submesh of `mesh` including all vertices corresponding to `rois == roi`.
`static java.util.ArrayList<java.lang.Integer>`	`getSelfIntersections(Mesh3D mesh, float search_max)`	Returns a list of face indices indicating which faces intersect within `mesh`.
`static java.util.ArrayList<java.lang.Integer>`	`getSelfIntersections(Mesh3D mesh, float search_max, ProgressUpdater progress)`
`protected static java.util.ArrayList<java.lang.Integer>`	`getSelfIntersectionsBlocking(Mesh3D mesh, float search_max, ProgressUpdater progress)`	Returns a list of face indices indicating which faces intersect within `mesh`.
`static Mesh3D`	`getSubMesh(Mesh3D mesh, java.util.ArrayList<java.lang.Integer> ring)`	Returns a submesh defined by the connect ring `ring`.
`static Mesh3D`	`getSubMesh(Mesh3D mesh_old, java.util.ArrayList<MguiNumber> mask, int value, boolean retain)`	Returns a submesh comprised of all unmasked (mask != 0) vertices and all faces whose vertices are retained.
`static Mesh3D`	`getSubMesh(Mesh3D mesh_old, java.util.ArrayList<MguiNumber> mask, int value, boolean retain, boolean any_in_face, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_old, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_new)`	Returns a submesh based upon a mask.
`static Mesh3D`	`getSubMesh(Mesh3D mesh_old, java.util.ArrayList<MguiNumber> mask, int value, boolean retain, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_old, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_new)`
`static Mesh3D`	`getSubMesh(Mesh3D mesh_old, java.util.ArrayList<MguiNumber> mask, int value_from, int value_to, boolean retain, boolean any_in_face, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_old, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_new)`	Returns a submesh comprised of all unmasked (mask != 0) vertices and all faces whose vertices are retained.
`static Mesh3D`	`getSubMesh(Mesh3D mesh_old, VertexSelection selection, boolean retain)`	Returns a sub-mesh of `mesh_old` containing all vertices and associated faces in `selection`.
`static Mesh3D`	`getSubMesh(Mesh3D mesh_old, VertexSelection selection, boolean retain, boolean any_in_face, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_old, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_new)`	Returns a sub-mesh of `mesh_old` containing all vertices and associated faces in `selection`.
`static java.util.ArrayList<org.jogamp.vecmath.Vector3f>`	`getSurfaceNormals(Mesh3D mesh)`	Returns surface normals for all vertices of `mesh`, determined as the average vector of all triangular face normals.
`static Mesh3D`	`getTriangulation(org.jogamp.vecmath.Point3f[] nodes)`	Triangulates a set of nodes that form a ring.
`static java.util.ArrayList<MguiNumber>`	`getVertexWiseCurvature(Mesh3D mesh, ProgressUpdater progress)`	Computes the mean curvature at each node in the mesh.
`static java.util.ArrayList<MguiNumber>`	`getVertexWiseCurvature_bak(Mesh3D mesh, ProgressUpdater progress)`	Computes the mean curvature at each node in the mesh.
`static java.util.ArrayList<MguiFloat>`	`getVertexWiseCurvatureBak(Mesh3D mesh)`
`static double[]`	`getVolumeAndArea(Mesh3D mesh, java.util.ArrayList<MguiNumber> thickness, java.util.ArrayList<MguiNumber> filter, double cutoff)`	Given a mesh and a set of thickness values, returns an area and a volume calculation (in that order).
`static Mesh3D`	`inflateMeshTRP(Mesh3DInt mesh3D, double lambda, double beta, long max_itr, ProgressUpdater progress)`	Inflate this mesh using the TRP method.
`static boolean`	`intersects(Mesh3D mesh, org.jogamp.vecmath.Point3f p, org.jogamp.vecmath.Vector3f v)`	Determines whether a vector defined by `p` and `v` intersects `mesh`.
`static boolean`	`isBadFace(Mesh3D.MeshFace3D face)`
`static Volume3DInt`	`mapMeshToVolumeGaussian(Mesh3DInt mesh_int, Volume3DInt volume, java.lang.String mesh_column, java.lang.String grid_channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, boolean normalize, boolean is_discrete, ProgressUpdater progress)`	Projects vertex-wise data from a given `Mesh3DInt` data column to a `Grid3D` channel, normal and transverse (tangent) Gaussian functions.
`static java.util.ArrayList<MguiNumber>`	`mapVolumeToMeshEV(Mesh3D mesh, Volume3DInt volume, java.lang.String column, double no_value, float radius, int stat, ProgressUpdater progress)`	Maps the values in `channel` of `grid`, an instance of `Grid3D`, to the vertices of `mesh`, using a containing-voxel(s) approach.
`static java.util.ArrayList<MguiNumber>`	`mapVolumeToMeshEV(Mesh3D mesh, Volume3DInt volume, java.lang.String column, double no_value, ProgressUpdater progress)`	Maps the values in `channel` of `grid`, an instance of `Grid3D`, to the vertices of `mesh`, using a containing-voxel approach.
`protected static java.util.ArrayList<MguiNumber>`	`mapVolumeToMeshEVBlocking(Mesh3D mesh, Volume3DInt volume, java.lang.String column, double no_value, float radius, int stat, ProgressUpdater progress)`	Maps the values in `channel` of `grid`, an instance of `Grid3D`, to the vertices of `mesh`, using a containing-voxel(s) approach.
`static java.util.ArrayList<MguiNumber>`	`mapVolumeToMeshGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, java.lang.String setSigmaT, boolean normalize)`
`static java.util.ArrayList<MguiNumber>`	`mapVolumeToMeshGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, java.lang.String setSigmaT, boolean normalize, ProgressUpdater progress, boolean output_matrix, double normal_set_max_sigma, double tangent_set_max_sigma, java.lang.String matrix_file)`	Maps values from a `Grid3D` object to a mesh object by applying a Gaussian kernal to voxels in the vicinity of each mesh vertex.
`static java.util.ArrayList<MguiNumber>`	`maskMeshWithPlane(Mesh3D mesh, Plane3D plane, double above_val, double below_val)`
`static java.util.ArrayList<MguiNumber>`	`maskMeshWithPlane(Mesh3D mesh, Plane3D plane, double above_val, double below_val, double contained_val)`
`static java.util.ArrayList<MguiNumber>`	`maskMeshWithPlane(Mesh3D mesh, Plane3D plane, double above_val, double below_val, double contained_val, VertexSelection selection)`	Masks a mesh with a plane.
`static Mesh3D`	`mergeMeshes(java.util.ArrayList<Mesh3D> mesh_list)`	Merges the mesh shapes in `list` and returns the resulting single mesh.
`static Mesh3D`	`mergeMeshes(java.util.ArrayList<Mesh3D> mesh_list, java.util.ArrayList<java.util.HashMap<java.lang.Integer,java.lang.Integer>> index_map)`	Merges the mesh shapes in `list` and returns the resulting single mesh.
`protected void`	`orderNeighbours(java.util.ArrayList<MguiInteger> list, NeighbourhoodMesh nmesh)`
`protected static int`	`polygonizeCell(org.jogamp.vecmath.Point3f[] gridcell, double[] values, java.util.ArrayList<org.jogamp.vecmath.Point3f> triangles, double isolevel)`	Uses the marching cubes lookup tables to find triangular faces intersecting the given grid cell at the given isolevel
`static boolean`	`removeBadFaces(Mesh3D mesh)`
`static boolean`	`removeDuplicateFaces(Mesh3D mesh)`
`static boolean`	`removeDuplicateNodes(Mesh3D mesh)`	Removes all duplicate vertices from `mesh`, and changes `mesh` in place.
`static void`	`removeNodes(Mesh3D mesh, boolean[] removed)`	Removes all nodes specified in `nodes` from `mesh`, and retriangulates the remaining nodes.
`static void`	`removeNodes(Mesh3D mesh, boolean[] removed, NeighbourhoodMesh nmesh)`	Removes all nodes specified in `nodes` from `mesh`, and retriangulates the remaining nodes.
`static void`	`removeStrandedNodes(Mesh3D mesh)`	Removes all nodes from `mesh` which do not have a corresponding face.
`static void`	`selectFloodFill(Mesh3D mesh, VertexSelection selection, int seed_node, ProgressUpdater progress)`	Selects all nodes surrounding a seed node in a region enclosed by selected nodes; if seed node is not fully enclosed, this will select the entire mesh.
`static void`	`smoothEM(Mesh3DInt mesh)`
`static void`	`smoothLR(Mesh3D mesh)`
`static java.util.ArrayList<MguiNumber>`	`smoothVertexValuesIsotropicGaussian(Mesh3D mesh, java.util.ArrayList<MguiNumber> values, double sigma, double sigma_max, ProgressUpdater progress)`	Smooths `values` with an isotropic Gaussian kernel, along the surface of `mesh`.
`static java.util.ArrayList<MguiNumber>`	`splitRoiWithPlane(Mesh3D mesh, Plane3D plane, java.util.ArrayList<MguiNumber> rois, int roi, int new_roi, ProgressUpdater progress)`	Splits the ROI defined by `roi` into two parts, on either side of `plane`.
`static void`	`subdivideMesh(Mesh3D mesh, int iter)`
`static void`	`subdivideMesh(Mesh3DInt mesh, int iter)`	Subdivides iter times, for all triangle in mesh.
`static void`	`subdivideMesh(Mesh3DInt mesh, int iter, double edgeThreshold, double areaThreshold)`	Subdivides iter times, for triangles which meet the criteria specified by and .
`static java.util.ArrayList<MguiNumber>`	`subdivideRois(Mesh3D mesh, java.util.ArrayList<MguiNumber> old_rois, int min_size, int target_rois, int min_roi, int max_roi, ProgressUpdater progress)`	Subdivides a mesh into (roughly) equally sized ROIs, with the final number equal or close to `target_rois`.
`static java.util.ArrayList<MguiNumber>`	`subdivideRois(Mesh3D mesh, java.util.ArrayList<MguiNumber> old_rois, int min_size, int target_rois, ProgressUpdater progress)`	Subdivides a mesh into (roughly) equally sized ROIs, with the final number equal or close to `target_rois`.
`static java.util.ArrayList<MguiNumber>`	`subdivideRoisBlocking(Mesh3D mesh, java.util.ArrayList<MguiNumber> old_rois, int min_size, int target_rois, int min_roi, int max_roi, ProgressUpdater progress)`	Subdivides a mesh into (roughly) equally sized ROIs, with the final number equal or close to `target_rois`.
`static Mesh3D`	`transformWithMatrix(Mesh3D mesh_in, org.jogamp.vecmath.Matrix4d matrix, InterfaceProgressBar progress_bar)`
`static void`	`triangulate(Mesh3D mesh, java.util.ArrayList<MguiInteger> neighbours)`	Triangulates the given neighbourhood by adding faces using recursive loop splitting
`static boolean`	`validateSurface(Mesh3D mesh)`

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- tolerance
  
  public static double tolerance
- progressBar
  
  public static javax.swing.JProgressBar progressBar
Constructor Details
- MeshFunctions
  
  public MeshFunctions()
Method Details
- getConvexHull
  
  public static Mesh3D getConvexHull(Mesh3D mesh)
  
  Returns a new mesh which is the convex hull of the given mesh. Defaults to the "Giftwrap" algorithm, by Tim Lambert:
  http://www.cse.unsw.edu.au/~lambert/java/3d/implementation.html
  
  Parameters:
  
  mesh - Mesh for which to compute a convex hull.
  
  method - The method to use
- getConvexHull
  
  public static Mesh3D getConvexHull(Mesh3D mesh, ProgressUpdater progress)
- getConvexHull
  
  public static Mesh3D getConvexHull(Mesh3D mesh, java.lang.String method)
- combine
  
  public static Mesh3D combine(Mesh3D mesh1, Mesh3D mesh2)
  
  Combines mesh1 and mesh2 and returns the result.
  
  Parameters:
  
  mesh1 -
  
  mesh2 -
  
  Returns:
- getConvexHull
  
  public static Mesh3D getConvexHull(Mesh3D mesh, java.lang.String method, ProgressUpdater progress)
  
  Returns a new mesh which is the convex hull of the given mesh. Algorithms provided by Joseph O'Rourke et al:
  http://maven.smith.edu/~orourke/books/ftp.html
  and Tim Lambert:
  http://www.cse.unsw.edu.au/~lambert/java/3d/implementation.html
  
  Parameters:
  
  mesh - Mesh for which to compute a convex hull
  
  method - The method to use
  
  bar - Optional progress bar
  
  Returns:
  
  the convex hull, or null if method failed or was cancelled.
- getSubMesh
  
  public static Mesh3D getSubMesh(Mesh3D mesh_old, VertexSelection selection, boolean retain)
  
  Returns a sub-mesh of mesh_old containing all vertices and associated faces in selection.
  
  Parameters:
  
  mesh_old - Mesh from which to obtain sub-mesh
  
  selection - Selected vertices for sub-mesh
  
  retain - Whether to retain the selection (otherwise it is removed)
  
  Returns:
  
  Newly created sub-mesh
- getSubMesh
  
  public static Mesh3D getSubMesh(Mesh3D mesh_old, VertexSelection selection, boolean retain, boolean any_in_face, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_old, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_new)
  
  Returns a sub-mesh of mesh_old containing all vertices and associated faces in selection.
  
  Parameters:
  
  mesh_old - Mesh from which to obtain sub-mesh
  
  selection - Selected vertices for sub-mesh
  
  retain - Whether to retain the selection (otherwise it is removed)
  
  any_in_face - Include faces with any vertices in selection? Otherwise, requires all vertices to be in the selection.
  
  data_old - Data from mesh_old to transfer to mesh_new (can be null)
  
  data_new - New data for the sub-mesh; this should be a reference to an empty HashMap
  
  Returns:
  
  Newly created sub-mesh
- getLargestContiguousRois
  
  public static java.util.ArrayList<MguiNumber> getLargestContiguousRois(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int out_value)
  
  Retains only the largest contiguous ROIs in the given set of values; all others are set to out_value.
  
  Parameters:
  
  mesh -
  
  rois -
  
  out_value -
  
  Returns:
- splitRoiWithPlane
  
  public static java.util.ArrayList<MguiNumber> splitRoiWithPlane(Mesh3D mesh, Plane3D plane, java.util.ArrayList<MguiNumber> rois, int roi, int new_roi, ProgressUpdater progress)
  
  Splits the ROI defined by roi into two parts, on either side of plane.
  
  Parameters:
  
  mesh -
  
  plane -
  
  rois -
  
  roi -
  
  new_roi -
  
  progress -
  
  Returns:
  
  The new ROIs; or null if the plane does not intersect the ROI
- subdivideRois
  
  public static java.util.ArrayList<MguiNumber> subdivideRois(Mesh3D mesh, java.util.ArrayList<MguiNumber> old_rois, int min_size, int target_rois, ProgressUpdater progress) throws MeshFunctionException
  
  Subdivides a mesh into (roughly) equally sized ROIs, with the final number equal or close to target_rois. Generation is constrained by the min/max parameters.
  A starting parcellation can be specified using the old_rois parameter; this can also be null to start from a random seed.
  
  Parameters:
  
  mesh -
  
  old_rois -
  
  min_rois -
  
  max_rois -
  
  max_size -
  
  min_size -
  
  target_rois -
  
  Returns:
  
  Throws:
  
  MeshFunctionException
- subdivideRois
  
  public static java.util.ArrayList<MguiNumber> subdivideRois(Mesh3D mesh, java.util.ArrayList<MguiNumber> old_rois, int min_size, int target_rois, int min_roi, int max_roi, ProgressUpdater progress) throws MeshFunctionException
  
  Subdivides a mesh into (roughly) equally sized ROIs, with the final number equal or close to target_rois. Generation is constrained by the min/max parameters.
  A starting parcellation can be specified using the old_rois parameter; this can also be null to start from a random seed.
  
  Parameters:
  
  mesh -
  
  old_rois -
  
  min_rois -
  
  max_rois -
  
  max_size -
  
  min_size -
  
  target_rois -
  
  min_roi - Minimum roi value to include
  
  max_roi - Maximum roi value to include
  
  Returns:
  
  Throws:
  
  MeshFunctionException
- subdivideRoisBlocking
  
  public static java.util.ArrayList<MguiNumber> subdivideRoisBlocking(Mesh3D mesh, java.util.ArrayList<MguiNumber> old_rois, int min_size, int target_rois, int min_roi, int max_roi, ProgressUpdater progress) throws MeshFunctionException
  
  Subdivides a mesh into (roughly) equally sized ROIs, with the final number equal or close to target_rois. Generation is constrained by the min/max parameters.
  A starting parcellation can be specified using the old_rois parameter; this can also be null, in which case the mesh will first be split by the median x coordinate and then subdivided.
  
  Parameters:
  
  mesh -
  
  old_rois -
  
  min_rois -
  
  max_rois -
  
  max_size -
  
  min_size -
  
  target_rois -
  
  min_roi - Minimum roi value to include
  
  max_roi - Maximum roi value to include
  
  Returns:
  
  Throws:
  
  MeshFunctionException
- getFarthestVertices
  
  public static java.util.ArrayList<java.lang.Integer> getFarthestVertices(Mesh3D mesh)
  
  Returns a list of size mesh.n integers, such that list(i) = the index of the farthest vertex j from vertex i.
  
  Parameters:
  
  mesh -
  
  Returns:
- getFarthestVertices
  
  public static java.util.ArrayList<java.lang.Integer> getFarthestVertices(Mesh3D mesh, java.util.ArrayList<java.lang.Double> distances)
  
  Returns a list of size mesh.n integers, such that list(i) = the index of the farthest vertex j from vertex i.
  
  Parameters:
  
  mesh -
  
  distances - Stores the corresponding distances; can be null.
  
  Returns:
- getFarthestVertices
  
  public static java.util.ArrayList<java.lang.Integer> getFarthestVertices(Mesh3D mesh, java.util.ArrayList<java.lang.Double> distances, java.util.ArrayList<java.lang.Integer> vertices)
  
  Returns a list of size mesh.n integers, such that list(i) = the index of the farthest vertex j from vertex i.
  
  Parameters:
  
  mesh -
  
  distances - Stores the corresponding distances; can be null.
  
  n_vertex - Number of vertices to sample from mesh. n_vertex <= 0 samples from entire mesh (default). This should be specified for very large graphs to avoid resource issues.
  
  Returns:
- getClosestVertices
  
  public static java.util.ArrayList<java.lang.Integer> getClosestVertices(Mesh3D mesh)
  
  Returns a list of size mesh.n integers, such that list(i) = the index of the closest vertex j from vertex i.
  
  Parameters:
  
  mesh -
  
  Returns:
- getClosestVertices
  
  public static java.util.ArrayList<java.lang.Integer> getClosestVertices(Mesh3D mesh, java.util.ArrayList<java.lang.Double> distances)
  
  Returns a list of size mesh.n integers, such that list(i) = the index of the closest vertex j from vertex i.
  
  Parameters:
  
  mesh -
  
  distances - Stores the corresponding distances; can be null.
  
  Returns:
- getRoiSubmesh
  
  public static Mesh3D getRoiSubmesh(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int roi)
  
  Returns a submesh of mesh including all vertices corresponding to rois == roi.
  
  Parameters:
  
  mesh -
  
  rois -
  
  roi -
  
  Returns:
- getRoiSelection
  
  public static VertexSelection getRoiSelection(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int roi)
  
  Returns a vertex selection corresponding to rois == roi.
  
  Parameters:
  
  mesh -
  
  rois -
  
  roi -
  
  Returns:
- getRoiIndices
  
  public static java.util.ArrayList<java.lang.Integer> getRoiIndices(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int roi)
  
  Returns a list of indices corresponding to rois == roi.
  
  Parameters:
  
  mesh -
  
  rois -
  
  roi -
  
  Returns:
- getClosestVertex
  
  public static int getClosestVertex(Mesh3D mesh, int idx, java.util.ArrayList<java.lang.Integer> search_vertices, MguiDouble distance)
  
  Returns the closest vertex in a list of vertices, or from all vertices if the list is empty. This searches links and accumulates distance along the links, rather than using Euclidean distance. If the vertex is unconnected to any of the target vertices, returns null. The distance parameter (if not null) stores the actual link-wise distance.
  
  Parameters:
  
  mesh -
  
  idx -
  
  search_vertices -
  
  distance -
  
  Returns:
- getRegionBoundaryNodeIndices
  
  public static java.util.ArrayList<java.lang.Integer> getRegionBoundaryNodeIndices(Mesh3D mesh, java.util.ArrayList<MguiNumber> values, int value)
  
  Returns a list of nodes which form the boundary of all regions defined by value, specified by the vertex-wise list values.
  
  Parameters:
  
  mesh -
  
  values -
  
  value -
  
  Returns:
- selectFloodFill
  
  public static void selectFloodFill(Mesh3D mesh, VertexSelection selection, int seed_node, ProgressUpdater progress)
  
  Selects all nodes surrounding a seed node in a region enclosed by selected nodes; if seed node is not fully enclosed, this will select the entire mesh.
  
  Parameters:
  
  mesh -
  
  selection -
  
  seed_node -
- getSubMesh
  
  public static Mesh3D getSubMesh(Mesh3D mesh_old, java.util.ArrayList<MguiNumber> mask, int value, boolean retain)
  
  Returns a submesh comprised of all unmasked (mask != 0) vertices and all faces whose vertices are retained.
  
  Parameters:
  
  mesh -
  
  mask -
  
  value -
  
  retain -
  
  Returns:
  
  submesh
- getSubMesh
  
  public static Mesh3D getSubMesh(Mesh3D mesh_old, java.util.ArrayList<MguiNumber> mask, int value, boolean retain, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_old, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_new)
- getSubMesh
  
  public static Mesh3D getSubMesh(Mesh3D mesh_old, java.util.ArrayList<MguiNumber> mask, int value, boolean retain, boolean any_in_face, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_old, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_new)
  
  Returns a submesh based upon a mask. If retain is true, retains all vertices where mask == value; otherwise retains the inverse. Removes all faces containing removed vertices. If data_old and data_new are non-null, populates data_new with the retained values from data_old.
  
  Parameters:
  
  mesh -
  
  mask -
  
  value -
  
  retain -
  
  any_in_face - retains a face if any of its vertices are retained
  
  data -
  
  Returns:
  
  submesh
- getSubMesh
  
  public static Mesh3D getSubMesh(Mesh3D mesh_old, java.util.ArrayList<MguiNumber> mask, int value_from, int value_to, boolean retain, boolean any_in_face, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_old, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> data_new)
  
  Returns a submesh comprised of all unmasked (mask != 0) vertices and all faces whose vertices are retained.
  
  Parameters:
  
  mesh -
  
  mask -
  
  value_from -
  
  value_to -
  
  retain -
  
  any_in_face - retains a face if any of its vertices are retained
  
  data -
  
  Returns:
  
  submesh
- removeStrandedNodes
  
  public static void removeStrandedNodes(Mesh3D mesh)
  
  Removes all nodes from mesh which do not have a corresponding face.
  
  Parameters:
  
  mesh -
- validateSurface
  
  public static boolean validateSurface(Mesh3D mesh)
- removeDuplicateFaces
  
  public static boolean removeDuplicateFaces(Mesh3D mesh)
- isBadFace
  
  public static boolean isBadFace(Mesh3D.MeshFace3D face)
- removeBadFaces
  
  public static boolean removeBadFaces(Mesh3D mesh)
- getDuplicateFaces
  
  public static java.util.ArrayList<java.lang.Boolean> getDuplicateFaces(Mesh3D mesh)
  
  Returns an array of booleans where true indicates a duplicate face
  
  Returns:
- removeDuplicateNodes
  
  public static boolean removeDuplicateNodes(Mesh3D mesh)
  
  Removes all duplicate vertices from mesh, and changes mesh in place.
  Duplicates are determined as pt1.distance(pt2) < MeshFunctions.tolerance.
  
  Parameters:
  
  mesh -
  
  Returns:
  
  true if successful
- getDuplicateNodes
  
  public static java.util.List<java.lang.Integer> getDuplicateNodes(Mesh3D mesh)
  
  Returns an array of booleans where true indicates a duplicate node
  
  Returns:
- transformWithMatrix
  
  public static Mesh3D transformWithMatrix(Mesh3D mesh_in, org.jogamp.vecmath.Matrix4d matrix, InterfaceProgressBar progress_bar)
- subdivideMesh
  
  public static void subdivideMesh(Mesh3D mesh, int iter)
- subdivideMesh
  
  public static void subdivideMesh(Mesh3DInt mesh, int iter)
  
  Subdivides iter times, for all triangle in mesh. Operates directly on mesh, so if user requires a retained original, he/she must make a copy before calling.
  
  Parameters:
  
  mesh - Mesh object to subdivide.
  
  iter - Number of times to subdivide this mesh. If <= 0, operation will do nothing.
- subdivideMesh
  
  public static void subdivideMesh(Mesh3DInt mesh, int iter, double edgeThreshold, double areaThreshold)
  
  Subdivides iter times, for triangles which meet the criteria specified by and . Operates directly on mesh, so if user requires a retained original, he/she must make a copy before calling.
  
  Parameters:
  
  mesh - Mesh object to subdivide
  
  edgeThreshold - Triangle will be subdivided if one edge is at least as long as . If edgeThreshold <= 0, edge length is not checked.
  
  areaThreshold - Triangle will be subdivided if its area is at least . If <= 0, area is not checked.
  
  iter - Number of times to subdivide this mesh. If <= 0, and either or > 0, operation will subdivide until no triangles satisfy criteria. Otherwise it will do nothing.
- maskMeshWithPlane
  
  public static java.util.ArrayList<MguiNumber> maskMeshWithPlane(Mesh3D mesh, Plane3D plane, double above_val, double below_val)
- maskMeshWithPlane
  
  public static java.util.ArrayList<MguiNumber> maskMeshWithPlane(Mesh3D mesh, Plane3D plane, double above_val, double below_val, double contained_val)
- maskMeshWithPlane
  
  public static java.util.ArrayList<MguiNumber> maskMeshWithPlane(Mesh3D mesh, Plane3D plane, double above_val, double below_val, double contained_val, VertexSelection selection)
  
  Masks a mesh with a plane.
- addIndexedTriangleArray
  
  public static void addIndexedTriangleArray(Mesh3D mesh, org.jogamp.java3d.IndexedTriangleArray tris)
  
  Adds an IndexedTriangleArray to the current mesh. Coincident nodes from either object will be represented as two seperate nodes, however. To merge these nodes into a single node, call decimateByLength with a minimal length threshold.
  
  Parameters:
  
  mesh - Mesh object to which nodes and faces will be added.
  
  tris - IndexedTriangleArray object from which nodes and face indices will be extracted.
- getTriangulation
  
  public static Mesh3D getTriangulation(org.jogamp.vecmath.Point3f[] nodes)
  
  Triangulates a set of nodes that form a ring.
  
  Parameters:
  
  mesh -
  
  nodes -
  
  Returns:
- mergeMeshes
  
  public static Mesh3D mergeMeshes(java.util.ArrayList<Mesh3D> mesh_list) throws MeshFunctionException
  
  Merges the mesh shapes in list and returns the resulting single mesh.
  
  Parameters:
  
  mesh_list -
  
  Throws:
  
  MeshFunctionException - If the merge failed
- mergeMeshes
  
  public static Mesh3D mergeMeshes(java.util.ArrayList<Mesh3D> mesh_list, java.util.ArrayList<java.util.HashMap<java.lang.Integer,java.lang.Integer>> index_map) throws MeshFunctionException
  
  Merges the mesh shapes in list and returns the resulting single mesh. If index_map is not null, also provides a mapping of the original indices to the merged mesh indices.
  
  Parameters:
  
  mesh_list -
  
  index_map -
  
  Throws:
  
  MeshFunctionException - If the merge failed
- decimateByDistance
  
  public static void decimateByDistance(Mesh3D mesh, Mesh3D newmesh, double threshold)
  
  Decimates this mesh by merging multiple nodes into a single node if they are separated by less than .
  
  Parameters:
  
  mesh - Mesh3D object to be decimated
  
  threshold - Threshold separation length at which to merge two nodes
- inflateMeshTRP
  
  public static Mesh3D inflateMeshTRP(Mesh3DInt mesh3D, double lambda, double beta, long max_itr, ProgressUpdater progress)
  
  Inflate this mesh using the TRP method. TODO: Remove worker here
  
  Parameters:
  
  mesh3D -
  
  lambda -
  
  beta -
  
  max_itr -
  
  progress -
  
  Returns:
- getMeshParts
  
  public static java.util.ArrayList<Mesh3D> getMeshParts(Mesh3D mesh)
- getMeshParts
  
  public static java.util.ArrayList<Mesh3D> getMeshParts(Mesh3D mesh, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> old_data, java.util.ArrayList<java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>>> parts_data)
- getMeshParts
  
  public static java.util.ArrayList<Mesh3D> getMeshParts(Mesh3D mesh, java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>> old_data, java.util.ArrayList<java.util.HashMap<java.lang.String,java.util.ArrayList<MguiNumber>>> parts_data, ProgressUpdater updater)
  
  Returns a set of non-contiguous meshes from mesh. If mesh is a single contiguous surface, this method will return only that surface.
  
  Parameters:
  
  mesh - Mesh from which to extract parts
  
  old_data - Vertex data to be transferred to the new meshes
  
  new_data - Vertex data transferred to the new meshes. Should be an empty object.
  
  Returns:
  
  List of created mesh parts
- getSubMesh
  
  public static Mesh3D getSubMesh(Mesh3D mesh, java.util.ArrayList<java.lang.Integer> ring)
  
  Returns a submesh defined by the connect ring ring. Triangulation is performed by connecting n to n + 2, to n - 1, to n + 3, etc.
  
  Returns:
  
  optimal submesh
- getOptimalSubmesh
  
  public static Mesh3D getOptimalSubmesh(Mesh3D mesh, java.util.ArrayList<MguiInteger> ring)
  
  Returns the optimal submesh defined by the connect ring ring. Triangulation is optimized by minimizing the sum of angles for each permutation of possible edge configurations.
  
  Returns:
  
  optimal submesh
- correctOrientation
  
  public static void correctOrientation(Mesh3D mesh)
  
  Orients all faces with each other, starting with the first face
  
  Parameters:
  
  mesh -
- correctOrientation
  
  public static void correctOrientation(Mesh3D mesh, boolean reverse)
  
  Orients all faces with each other (starting with face 0)
  
  Parameters:
  
  mesh -
  
  seed -
  
  reverse -
- flipNormals
  
  public static org.jogamp.vecmath.Vector3f[] flipNormals(org.jogamp.vecmath.Vector3f[] normals)
- condenseMesh
  
  public static Mesh3D condenseMesh(Mesh3D mesh)
  
  Condenses a mesh by removing all coincident nodes.
  
  Parameters:
  
  mesh - mesh to condense
  
  Returns:
  
  condensed mesh
- computeVertexWiseCurvature
  
  public static boolean computeVertexWiseCurvature(Mesh3DInt mesh3D, java.lang.String target_column, ProgressUpdater progress)
  
  Computes the curvature of a mesh at each of its nodes, as the magnitude of the sum of surface normals of the triangles of which it is a node. Adds this information to mesh3D as a variable named name.
  
  Parameters:
  
  mesh3D - Mesh for which to compute curvature
  
  name - Name of resulting variable
- getVertexWiseCurvature_bak
  
  public static java.util.ArrayList<MguiNumber> getVertexWiseCurvature_bak(Mesh3D mesh, ProgressUpdater progress)
  
  Computes the mean curvature at each node in the mesh. See:
  Tosun D, Rettman ME, Prince JL (2004). Mapping techniques for aligning sulci across multiple brains. Medical Image Analysis 8:295-309.
  Meyer M, Desbrun M, Schroeder P, Barr AH (2002). Discrete differential- geometry operators for triangulated 2-manifolds. http://citeseer.ist.psu.edu/meyer02discrete.html
  
  Parameters:
  
  mesh -
  
  Returns:
- getVertexWiseCurvature
  
  public static java.util.ArrayList<MguiNumber> getVertexWiseCurvature(Mesh3D mesh, ProgressUpdater progress)
  
  Computes the mean curvature at each node in the mesh. See:
  Tosun D, Rettman ME, Prince JL (2004). Mapping techniques for aligning sulci across multiple brains. Medical Image Analysis 8:295-309.
  Meyer M, Desbrun M, Schroeder P, Barr AH (2002). Discrete differential- geometry operators for triangulated 2-manifolds. http://citeseer.ist.psu.edu/meyer02discrete.html
  
  Parameters:
  
  mesh -
  
  Returns:
- getVertexWiseCurvatureBak
  
  public static java.util.ArrayList<MguiFloat> getVertexWiseCurvatureBak(Mesh3D mesh)
- getMeanCurvature
  
  public static float getMeanCurvature(Mesh3D mesh)
- smoothLR
  
  public static void smoothLR(Mesh3D mesh)
- smoothEM
  
  public static void smoothEM(Mesh3DInt mesh)
- smoothVertexValuesIsotropicGaussian
  
  public static java.util.ArrayList<MguiNumber> smoothVertexValuesIsotropicGaussian(Mesh3D mesh, java.util.ArrayList<MguiNumber> values, double sigma, double sigma_max, ProgressUpdater progress)
  
  Smooths values with an isotropic Gaussian kernel, along the surface of mesh.
  
  Parameters:
  
  mesh -
  
  values -
  
  sigma -
  
  sigma_max -
  
  progress -
  
  Returns:
- getEdgeLengths
  
  public static java.util.ArrayList<MguiDouble> getEdgeLengths(Mesh3D mesh, java.util.ArrayList<MeshEdge> edges)
  
  Returns a list of edge lengths for the given set of edges
  
  Parameters:
  
  mesh -
  
  Returns:
- getArea
  
  public static double getArea(Mesh3D mesh)
  
  Returns the surface area of the given mesh
  
  Parameters:
  
  mesh -
  
  Returns:
- getVolumeAndArea
  
  public static double[] getVolumeAndArea(Mesh3D mesh, java.util.ArrayList<MguiNumber> thickness, java.util.ArrayList<MguiNumber> filter, double cutoff)
  
  Given a mesh and a set of thickness values, returns an area and a volume calculation (in that order). Simply sums triangle areas for area, and multiplies area by the average thickness for volume.
  
  Parameters:
  
  mesh -
  
  thickness -
  
  cutoff - value below which the area and volume are not counted.
  
  Returns:
  
  double array with area and volume, in that order
- getNeighbourhoodPoints
  
  public static java.util.ArrayList<org.jogamp.vecmath.Point3f> getNeighbourhoodPoints(Mesh3D mesh, NeighbourhoodMesh neighbourhoods, int node)
  
  Returns a list of points corresponding to the immediate (1st level) neighbourhood of node node.
  
  Parameters:
  
  mesh -
  
  neighbourhoods -
  
  node -
  
  Returns:
- getNeighbourhoodPoints
  
  public static java.util.ArrayList<org.jogamp.vecmath.Point3f> getNeighbourhoodPoints(Mesh3D mesh, NeighbourhoodMesh neighbourhoods, int node, int levels)
  
  Returns a list of points corresponding to the n-th level neighbourhood of node node, where n is specified by the parameter levels
  
  Parameters:
  
  mesh -
  
  neighbourhoods -
  
  node -
  
  Returns:
- getNeighbourhoodPoints
  
  protected static void getNeighbourhoodPoints(java.util.TreeSet<org.jogamp.vecmath.Point3f> points, Mesh3D mesh, NeighbourhoodMesh neighbourhoods, int node, int levels)
- removeNodes
  
  public static void removeNodes(Mesh3D mesh, boolean[] removed)
  
  Removes all nodes specified in nodes from mesh, and retriangulates the remaining nodes.
  
  Parameters:
  
  mesh -
  
  vertices -
- removeNodes
  
  public static void removeNodes(Mesh3D mesh, boolean[] removed, NeighbourhoodMesh nmesh)
  
  Removes all nodes specified in nodes from mesh, and retriangulates the remaining nodes.
  
  Parameters:
  
  mesh -
  
  vertices -
  
  nmesh - Neighbourhood mesh (in case one is already made)
- getAllNeighbours
  
  protected static java.util.ArrayList<MguiInteger> getAllNeighbours(int n, NeighbourhoodMesh nmesh, boolean[] removed, int[] added, boolean[] processed)
  
  Searches for all neighbours of n in nmesh. If a neighbour is removed and not yet processed, its neighbours will also be added to this list recursively, and its index in the processed array will be set to true (to prevent its being reprocessed). This continues until all n's neighbours have been processed.
- orderNeighbours
  
  protected void orderNeighbours(java.util.ArrayList<MguiInteger> list, NeighbourhoodMesh nmesh)
- triangulate
  
  public static void triangulate(Mesh3D mesh, java.util.ArrayList<MguiInteger> neighbours)
  
  Triangulates the given neighbourhood by adding faces using recursive loop splitting
  
  Parameters:
  
  mesh -
  
  n -
- mapVolumeToMeshGaussian
  
  public static java.util.ArrayList<MguiNumber> mapVolumeToMeshGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, java.lang.String setSigmaT, boolean normalize)
- mapVolumeToMeshGaussian
  
  public static java.util.ArrayList<MguiNumber> mapVolumeToMeshGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, java.lang.String setSigmaT, boolean normalize, ProgressUpdater progress, boolean output_matrix, double normal_set_max_sigma, double tangent_set_max_sigma, java.lang.String matrix_file)
  Maps values from a Grid3D object to a mesh object by applying a Gaussian kernal to voxels in the vicinity of each mesh vertex. The Gaussian is defined in the direction normal to the vertex, by sigma_normal (one standard deviation) and sigma_max_normal (the distance, in standard deviations, at which to stop considering voxels). It is defined in the plane tangent to the normal depending on the value of setSigmaT:
  
  "Parameter": sigma_tangent is set to the passed parameter
  "From mean area": for each vertex, sigma_tangent is set to sqrt(A_tri_mean / Pi)
  "From mean length": for each vertex, sigma_tangent is set to the mean length of all edges connecting the vertex
  The values returned will be those obtained by the Grid3D.getDoubleValue method, but can alternatively be normalized by setting the normalized flag.
  Parameters:
  
  mesh - Mesh on which to project values
  
  grid - Input grid
  
  sigma_normal - Sigma defining the Gaussian in the normal direction
  
  sigma_tangent - Sigma defining the Gaussian in the tangent direction
  
  sigma_max_normal - Maximum sigma at which to obtain values in the normal direction
  
  sigma_max_tangent - Maximum sigma at which to obtain values in the tangent direction
  
  setSigmaT - How to determine the tangent sigma; one of "parameter", "area", or...
  
  normalize - Whether to normalize the resulting values
  
  normal_set_max_sigma - From all values within this proximity along the normal, set value to the maximum rather than the weighted average; set to 0 to avoid this behaviour (default)
  
  tangent_set_max_sigma - From all values within this proximity along the tangent, set value to the maximum rather than the weighted average; set to 0 to avoid this behaviour (default)
  
  Returns:
  
  Vertex-wise mapped values, or null if process fails or was cancelled.
- mapMeshToVolumeGaussian
  
  public static Volume3DInt mapMeshToVolumeGaussian(Mesh3DInt mesh_int, Volume3DInt volume, java.lang.String mesh_column, java.lang.String grid_channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, boolean normalize, boolean is_discrete, ProgressUpdater progress)
  
  Projects vertex-wise data from a given Mesh3DInt data column to a Grid3D channel, normal and transverse (tangent) Gaussian functions.
  
  Parameters:
  
  mesh_int - The mesh from which to project
  
  grid - The target 3D grid
  
  mesh_column - The column from which to obtain the projected data
  
  grid_channel - The target grid channel
  
  sigma_normal - The sigma defining a Gaussian normal to the vertex
  
  sigma_tangent - The sigma defining a Gaussian tangential to the vertex
  
  max_normal - The maximum distance to project data in the normal direction
  
  max_tangent - The maximum distance to project data in the tangential direction
  
  is_discrete - Indicates whether data are to be treated as discrete; if so, the mapped value will be the value of the neighbour with the highest Gaussian weight. Otherwise, value is the weighted real-valued mean.
  
  progress -
  
  Returns:
  
  A new Grid3D containing the projected values
- getAverageEdgeLength
  
  public static double getAverageEdgeLength(Mesh3D mesh)
  
  Returns the average edge length keyin a mesh.
  
  Parameters:
  
  mesh -
  
  Returns:
- getSurfaceNormals
  
  public static java.util.ArrayList<org.jogamp.vecmath.Vector3f> getSurfaceNormals(Mesh3D mesh)
  
  Returns surface normals for all vertices of mesh, determined as the average vector of all triangular face normals.
  
  Parameters:
  
  mesh -
  
  Returns:
- mapVolumeToMeshEV
  
  public static java.util.ArrayList<MguiNumber> mapVolumeToMeshEV(Mesh3D mesh, Volume3DInt volume, java.lang.String column, double no_value, ProgressUpdater progress)
  
  Maps the values in channel of grid, an instance of Grid3D, to the vertices of mesh, using a containing-voxel approach. This method essentially maps the value of the containing voxel to the vertex, ignoring all neighbours. Size is single voxel.
  
  Parameters:
  
  mesh - Mesh whose vertices are used to determine mapping
  
  volume - Volume to map
  
  column - Column to map
  
  no_value - Value to use when no mapping is made
  
  progress -
  
  Returns:
  
  A list of size n, where n = number of vertices in mesh
- mapVolumeToMeshEV
  
  public static java.util.ArrayList<MguiNumber> mapVolumeToMeshEV(Mesh3D mesh, Volume3DInt volume, java.lang.String column, double no_value, float radius, int stat, ProgressUpdater progress)
  
  Maps the values in channel of grid, an instance of Grid3D, to the vertices of mesh, using a containing-voxel(s) approach. This method essentially maps the value of the containing voxel to the vertex, ignoring all neighbours.
  
  Parameters:
  
  mesh - Mesh whose vertices are used to determine mapping
  
  volume - Volume to map
  
  column - Column to map
  
  no_value - Value to use when no mapping is made
  
  size - Radius of the search sphere, in voxels; <=0 is single voxel (default)
  
  stat - Statistic to use for summarizing values in a search sphere; only used if radius > 0; one of: 1=max, 2=min, 3=abs max, 4=abs min, 0(or other)= mean
  
  progress -
  
  Returns:
  
  A list of size n, where n = number of vertices in mesh
- mapVolumeToMeshEVBlocking
  
  protected static java.util.ArrayList<MguiNumber> mapVolumeToMeshEVBlocking(Mesh3D mesh, Volume3DInt volume, java.lang.String column, double no_value, float radius, int stat, ProgressUpdater progress)
  
  Maps the values in channel of grid, an instance of Grid3D, to the vertices of mesh, using a containing-voxel(s) approach. This method essentially maps the value of the containing voxel to the vertex, ignoring all neighbours.
  
  Parameters:
  
  mesh - Mesh whose vertices are used to determine mapping
  
  volume - Volume to map
  
  column - Column to map
  
  no_value - Value to use when no mapping is made
  
  radius - Radius of the search sphere, in voxels; <=0 is single voxel (default)
  
  stat - Statistic to use for summarizing values in a search sphere; only used if radius > 0; one of: 1=max, 2=min, 3=abs max, 4=abs min, 5=mode, 6=median, 0(or other)= mean
  
  progress -
  
  Returns:
  
  A list of size n, where n = number of vertices in mesh
- getNeighbourhoodSubmesh
  
  public static Mesh3D getNeighbourhoodSubmesh(Mesh3D mesh, int i)
  
  Gets a submesh from mesh consisting of the neighbourhood of vertex i.
  
  Parameters:
  
  mesh -
  
  i -
  
  Returns:
- cleanMesh
  
  public static void cleanMesh(Mesh3D mesh)
- getMeanSphereMesh
  
  public static Mesh3D getMeanSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int n_nodes, float stop_delta, long max_itrs)
- getFractalSphereMesh
  
  public static Mesh3D getFractalSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int min_nodes)
- getOptimizedSphereMesh
  
  public static Mesh3D getOptimizedSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int n_nodes, double stop_value, long max_iter, float entropy)
- intersects
  
  public static boolean intersects(Mesh3D mesh, org.jogamp.vecmath.Point3f p, org.jogamp.vecmath.Vector3f v)
  
  Determines whether a vector defined by p and v intersects mesh.
  
  Parameters:
  
  mesh -
  
  p -
  
  v -
  
  Returns:
- getIntersectingFaces
  
  public static java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> getIntersectingFaces(Mesh3D mesh1, Mesh3D mesh2, float search_max)
  
  Returns a list of face indices indicating which faces intersect between mesh1 and mesh2. If there are no such faces, returns an empty list.
  
  Parameters:
  
  mesh1 -
  
  mesh2 -
  
  search_max - Maximum search radius; should be similar to largest face size; larger takes longer
  
  Returns:
- getIntersectingFaces
  
  public static java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> getIntersectingFaces(Mesh3D mesh_1, Mesh3D mesh_2, float search_max, ProgressUpdater progress)
  
  Returns two lists of face indices indicating which faces intersect between mesh1 and mesh2. If there are no such faces, returns an empty list.
  
  Parameters:
  
  mesh1 -
  
  mesh2 -
  
  search_max - Maximum search radius; should be similar to largest face size; larger takes longer
  
  progress -
  
  Returns:
- getIntersectingFacesBlocking
  
  public static java.util.ArrayList<java.util.ArrayList<java.lang.Integer>> getIntersectingFacesBlocking(Mesh3D mesh_1, Mesh3D mesh_2, float search_max, ProgressUpdater progress)
  
  Returns two lists of face indices indicating which faces intersect between mesh1 and mesh2. If there are no such faces, returns an empty list.
  
  Parameters:
  
  mesh1 -
  
  mesh2 -
  
  search_max - Maximum search radius; should be similar to largest face size; larger takes longer
  
  progress -
  
  Returns:
- getSelfIntersections
  
  public static java.util.ArrayList<java.lang.Integer> getSelfIntersections(Mesh3D mesh, float search_max)
  
  Returns a list of face indices indicating which faces intersect within mesh. If there are no such faces, returns an empty list.
  
  Parameters:
  
  mesh -
  
  search_max - Maximum search radius; should be similar to largest face size; larger takes longer
  
  Returns:
- getSelfIntersections
  
  public static java.util.ArrayList<java.lang.Integer> getSelfIntersections(Mesh3D mesh, float search_max, ProgressUpdater progress)
- getSelfIntersectionsBlocking
  
  protected static java.util.ArrayList<java.lang.Integer> getSelfIntersectionsBlocking(Mesh3D mesh, float search_max, ProgressUpdater progress)
  
  Returns a list of face indices indicating which faces intersect within mesh. If there are no such faces, returns an empty list.
  
  Parameters:
  
  mesh -
  
  search_max - Maximum search radius; should be similar to largest face size; larger takes longer
  
  progress -
  
  Returns:
- getMaximumEdgeLength
  
  public static float getMaximumEdgeLength(Mesh3D mesh)
  
  Searches all edges and returns the maximum length
  
  Returns:
- getMinimumEdgeLength
  
  public static float getMinimumEdgeLength(Mesh3D mesh)
  
  Searches all edges and returns the minimum length
  
  Returns:
- getIntersectionPoint
  
  public static org.jogamp.vecmath.Point3f getIntersectionPoint(Mesh3D mesh, org.jogamp.vecmath.Point3f p, org.jogamp.vecmath.Vector3f v)
  
  Finds the point from the first face in the nodes list which intersects the line segment defined by p and v. Returns null if no intersection exists.
  
  Parameters:
  
  mesh -
  
  p -
  
  v -
  
  Returns:
- getLaplacian
  
  public static java.util.ArrayList<java.lang.Double> getLaplacian(Mesh3D mesh)
  
  Computes the discrete Laplacian for each vertex in mesh. Adapted from matlab script; see Oostendorp, Oosterom & Huiskamp (1989), Interpolation on a triangulated 3D surface. Journal of Computational Physics, 80: 331-343
  Parameters: mesh - Returns: vertex-wise Laplacian values

Modifier and Type	Field	Description
`static javax.swing.JProgressBar`	`progressBar`
`static double`	`tolerance`

Class MeshFunctions

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

tolerance

progressBar

Constructor Details

MeshFunctions

Method Details

getConvexHull

getConvexHull

getConvexHull

combine

getConvexHull

getSubMesh

getSubMesh

getLargestContiguousRois

splitRoiWithPlane

subdivideRois

subdivideRois

subdivideRoisBlocking

getFarthestVertices

getFarthestVertices

getFarthestVertices

getClosestVertices

getClosestVertices

getRoiSubmesh

getRoiSelection

getRoiIndices

getClosestVertex

getRegionBoundaryNodeIndices

selectFloodFill

getSubMesh

getSubMesh

getSubMesh

getSubMesh

removeStrandedNodes

validateSurface

removeDuplicateFaces

isBadFace

removeBadFaces

getDuplicateFaces

removeDuplicateNodes

getDuplicateNodes

transformWithMatrix

subdivideMesh

subdivideMesh

subdivideMesh

maskMeshWithPlane

maskMeshWithPlane

maskMeshWithPlane

addIndexedTriangleArray

getTriangulation

mergeMeshes

mergeMeshes

decimateByDistance

inflateMeshTRP

getMeshParts

getMeshParts

getMeshParts

getSubMesh

getOptimalSubmesh

correctOrientation

correctOrientation

flipNormals

condenseMesh

computeVertexWiseCurvature

getVertexWiseCurvature_bak

getVertexWiseCurvature

getVertexWiseCurvatureBak

getMeanCurvature

smoothLR

smoothEM

smoothVertexValuesIsotropicGaussian

getEdgeLengths

getArea

getVolumeAndArea