Uses of Class
mgui.geometry.Mesh3D

Packages that use Mesh3D

Package	Description
mgui.geometry	Provides 2D and 3D geometry representations and utilities for all shapes used in ModelGUI.
mgui.geometry.mesh	Provides classes representing and operating on 3D mesh shapes.
mgui.geometry.neuro.connectivity
mgui.geometry.neuro.mesh
mgui.geometry.util	Uility classes for geometric operations.
mgui.interfaces.graphs.util
mgui.interfaces.shapes	This package provides interfaces for user interaction with shapes and shape models.
mgui.interfaces.shapes.util
mgui.io.standard.gifti

Uses of Mesh3D in mgui.geometry

Methods in mgui.geometry with parameters of type Mesh3D

Modifier and Type	Method	Description
void	Mesh3D.setFromMesh(Mesh3D mesh)	Set this mesh from another mesh.

Constructors in mgui.geometry with parameters of type Mesh3D

Constructor	Description
Mesh3D(Mesh3D mesh_to_copy)

Uses of Mesh3D in mgui.geometry.mesh

Fields in mgui.geometry.mesh declared as Mesh3D

Modifier and Type	Field	Description
Mesh3D	EnergySphere.mesh
Mesh3D	MeshEdgeSet.mesh
Mesh3D	NeighbourhoodMesh.mesh

Methods in mgui.geometry.mesh that return Mesh3D

Modifier and Type	Method	Description
static Mesh3D	MeshFunctions.combine(Mesh3D mesh1, Mesh3D mesh2)	Combines mesh1 and mesh2 and returns the result.
static Mesh3D	MeshFunctions.condenseMesh(Mesh3D mesh)	Condenses a mesh by removing all coincident nodes.
static Mesh3D	MeshFunctions.getConvexHull(Mesh3D mesh)	Returns a new mesh which is the convex hull of the given mesh.
static Mesh3D	MeshFunctions.getConvexHull(Mesh3D mesh, java.lang.String method)
static Mesh3D	MeshFunctions.getConvexHull(Mesh3D mesh, java.lang.String method, ProgressUpdater progress)	Returns a new mesh which is the convex hull of the given mesh.
static Mesh3D	MeshFunctions.getConvexHull(Mesh3D mesh, ProgressUpdater progress)
static Mesh3D	MeshFunctions.getFractalSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int min_nodes)
static Mesh3D	MeshFunctions.getGlobeSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int n_nodes)
static Mesh3D	MeshFunctions.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 Mesh3D	MeshFunctions.getMeanSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int n_nodes, float stop_delta, long max_itrs)
static Mesh3D	MeshFunctions.getMeshExpandedAlongNormals(Mesh3D mesh, float expansion)	Expands mesh along its vertex normals by a distance of expansion.
static Mesh3D	MeshFunctions.getNeighbourhoodSubmesh(Mesh3D mesh, int i)	Gets a submesh from mesh consisting of the neighbourhood of vertex i.
static Mesh3D	MeshFunctions.getOptimalSubmesh(Mesh3D mesh, java.util.ArrayList<MguiInteger> ring)	Returns the optimal submesh defined by the connect ring ring.
static Mesh3D	MeshFunctions.getOptimizedSphereMesh(org.jogamp.vecmath.Point3f center, float radius, int n_nodes, double stop_value, long max_iter, float entropy)
static Mesh3D	MeshFunctions.getRoiSubmesh(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int roi)	Returns a submesh of mesh including all vertices corresponding to rois == roi.
static Mesh3D	MeshFunctions.getSubMesh(Mesh3D mesh, java.util.ArrayList<java.lang.Integer> ring)	Returns a submesh defined by the connect ring ring.
static Mesh3D	MeshFunctions.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	MeshFunctions.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	MeshFunctions.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	MeshFunctions.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	MeshFunctions.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	MeshFunctions.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 Mesh3D	MeshFunctions.getTriangulation(org.jogamp.vecmath.Point3f[] nodes)	Triangulates a set of nodes that form a ring.
static Mesh3D	MeshFunctions.inflateMeshTRP(Mesh3DInt mesh3D, double lambda, double beta, long max_itr, ProgressUpdater progress)	Inflate this mesh using the TRP method.
static Mesh3D	MeshInflation.inflateMeshTRP(Mesh3DInt mesh3D, double lambda, double beta, long max_itr, ProgressUpdater progress)	Inflates a given mesh, by relaxing its vertices towards the mean of its neighbours, as described by:
static Mesh3D	MeshFunctions.mergeMeshes(java.util.ArrayList<Mesh3D> mesh_list)	Merges the mesh shapes in list and returns the resulting single mesh.
static Mesh3D	MeshFunctions.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.
static Mesh3D	MeshFunctions.transformWithMatrix(Mesh3D mesh_in, org.jogamp.vecmath.Matrix4d matrix, InterfaceProgressBar progress_bar)

Methods in mgui.geometry.mesh that return types with arguments of type Mesh3D

Modifier and Type	Method	Description
static java.util.ArrayList<Mesh3D>	MeshFunctions.cutMeshWithPlane(Mesh3D mesh, Plane3D plane, InterfaceProgressBar progress_bar)	Cuts mesh with plane, creating new faces along the cut seam.
static java.util.ArrayList<Mesh3D>	MeshFunctions.cutMeshWithPlane3(Mesh3D mesh, Plane3D plane)	Cuts mesh with plane, creating new faces along the cut seam.
static java.util.ArrayList<Mesh3D>	MeshFunctions.getMeshParts(Mesh3D mesh)
static java.util.ArrayList<Mesh3D>	MeshFunctions.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>	MeshFunctions.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.

Methods in mgui.geometry.mesh with parameters of type Mesh3D

Modifier and Type	Method	Description
static void	MeshFunctions.addIndexedTriangleArray(Mesh3D mesh, org.jogamp.java3d.IndexedTriangleArray tris)	Adds an IndexedTriangleArray to the current mesh.
static void	MeshFunctions.cleanMesh(Mesh3D mesh)
static Mesh3D	MeshFunctions.combine(Mesh3D mesh1, Mesh3D mesh2)	Combines mesh1 and mesh2 and returns the result.
static Mesh3D	MeshFunctions.condenseMesh(Mesh3D mesh)	Condenses a mesh by removing all coincident nodes.
static void	MeshFunctions.correctOrientation(Mesh3D mesh)	Orients all faces with each other, starting with the first face
static void	MeshFunctions.correctOrientation(Mesh3D mesh, boolean reverse)	Orients all faces with each other (starting with face 0)
static java.util.ArrayList<Mesh3D>	MeshFunctions.cutMeshWithPlane(Mesh3D mesh, Plane3D plane, InterfaceProgressBar progress_bar)	Cuts mesh with plane, creating new faces along the cut seam.
static java.util.ArrayList<Mesh3D>	MeshFunctions.cutMeshWithPlane3(Mesh3D mesh, Plane3D plane)	Cuts mesh with plane, creating new faces along the cut seam.
void	MeshEngine.decimate(Mesh3D mesh, java.lang.String method)
static void	MeshFunctions.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 .
void	MeshEngine.DecimateByDistance(Mesh3D mesh, Mesh3D newmesh)	Calls the function DecimateByDistance in the MeshFunctions function class, using parameters specified in the AttributeList "Decimate By Distance"
static void	MeshDecimation.decimateNeighbours(Mesh3D mesh)	Decimates by removing nodes one-by-one, skipping boundary nodes: 1.
void	MeshEngine.decimateSchroeder(Mesh3D mesh)
static void	MeshDecimation.decimateVTK(Mesh3D mesh, double featureAngle, double errorThreshold, int targetSize, boolean ensureTarget)	Decimates a mesh as decribed in:
static double	MeshFunctions.getArea(Mesh3D mesh)	Returns the surface area of the given mesh
static double	MeshFunctions.getAverageEdgeLength(Mesh3D mesh)	Returns the average edge length keyin a mesh.
static java.util.ArrayList<java.lang.Integer>	MeshFunctions.getBoundaryNodeIndices(Mesh3D mesh)
static boolean[]	MeshFunctions.getBoundaryNodes(Mesh3D mesh)	Determine which nodes are boundary nodes, return an array of booleans.
static int	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.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	MeshFunctions.getConvexHull(Mesh3D mesh)	Returns a new mesh which is the convex hull of the given mesh.
static Mesh3D	MeshFunctions.getConvexHull(Mesh3D mesh, java.lang.String method)
static Mesh3D	MeshFunctions.getConvexHull(Mesh3D mesh, java.lang.String method, ProgressUpdater progress)	Returns a new mesh which is the convex hull of the given mesh.
static Mesh3D	MeshFunctions.getConvexHull(Mesh3D mesh, ProgressUpdater progress)
static java.util.ArrayList<java.lang.Boolean>	MeshFunctions.getDuplicateFaces(Mesh3D mesh)	Returns an array of booleans where true indicates a duplicate face
static java.util.List<java.lang.Integer>	MeshFunctions.getDuplicateNodes(Mesh3D mesh)	Returns an array of booleans where true indicates a duplicate node
static java.util.ArrayList<MguiDouble>	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.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 java.util.ArrayList<java.util.ArrayList<java.lang.Integer>>	MeshFunctions.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>>	MeshFunctions.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>>	MeshFunctions.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	MeshFunctions.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>	MeshFunctions.getIntersectionSegments(Mesh3D mesh1, Mesh3D mesh2, InterfaceProgressBar progress_bar)	Return a set of line segments which represent the intersection of one mesh with another.
static java.util.HashMap<java.lang.Integer,java.lang.Integer>	MeshFunctions.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>	MeshFunctions.getLaplacian(Mesh3D mesh)	Computes the discrete Laplacian for each vertex in mesh.
static java.util.ArrayList<MguiNumber>	MeshFunctions.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	MeshFunctions.getMaximumEdgeLength(Mesh3D mesh)	Searches all edges and returns the maximum length
static float	MeshFunctions.getMeanCurvature(Mesh3D mesh)
static Mesh3D	MeshFunctions.getMeshExpandedAlongNormals(Mesh3D mesh, float expansion)	Expands mesh along its vertex normals by a distance of expansion.
static java.util.ArrayList<Mesh3D>	MeshFunctions.getMeshParts(Mesh3D mesh)
static java.util.ArrayList<Mesh3D>	MeshFunctions.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>	MeshFunctions.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	MeshFunctions.getMinimumEdgeLength(Mesh3D mesh)	Searches all edges and returns the minimum length
protected static void	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.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	MeshFunctions.getNeighbourhoodSubmesh(Mesh3D mesh, int i)	Gets a submesh from mesh consisting of the neighbourhood of vertex i.
static Mesh3D	MeshFunctions.getOptimalSubmesh(Mesh3D mesh, java.util.ArrayList<MguiInteger> ring)	Returns the optimal submesh defined by the connect ring ring.
protected static java.util.ArrayList<mgui.geometry.mesh.MeshSmoothing.Particle>	MeshSmoothing.getParticles(Mesh3D mesh, int k)
protected static java.util.ArrayList<mgui.geometry.mesh.MeshSmoothing.Particle>	MeshSmoothing.getParticles(Mesh3D mesh, int k, boolean[] boundaries)
protected static org.jogamp.vecmath.Vector3f	MeshSmoothing.getProjectedVector(Mesh3D mesh, mgui.geometry.mesh.MeshSmoothing.Particle p)	Get the projection of this particle's charge vector onto the mesh surface.
protected static org.jogamp.vecmath.Vector3f	MeshSmoothing.getProjectedVector(Mesh3D mesh, mgui.geometry.mesh.MeshSmoothing.Particle p, boolean holdbounds)	Get the projection of this particle's charge vector onto the mesh surface.
static java.util.ArrayList<java.lang.Integer>	MeshFunctions.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>	MeshFunctions.getRoiIndices(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int roi)	Returns a list of indices corresponding to rois == roi.
static VertexSelection	MeshFunctions.getRoiSelection(Mesh3D mesh, java.util.ArrayList<MguiNumber> rois, int roi)	Returns a vertex selection corresponding to rois == roi.
static Mesh3D	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.getSelfIntersections(Mesh3D mesh, float search_max, ProgressUpdater progress)
protected static java.util.ArrayList<java.lang.Integer>	MeshFunctions.getSelfIntersectionsBlocking(Mesh3D mesh, float search_max, ProgressUpdater progress)	Returns a list of face indices indicating which faces intersect within mesh.
static Mesh3D	MeshFunctions.getSubMesh(Mesh3D mesh, java.util.ArrayList<java.lang.Integer> ring)	Returns a submesh defined by the connect ring ring.
static Mesh3D	MeshFunctions.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	MeshFunctions.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	MeshFunctions.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	MeshFunctions.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	MeshFunctions.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	MeshFunctions.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>	MeshFunctions.getSurfaceNormals(Mesh3D mesh)	Returns surface normals for all vertices of mesh, determined as the average vector of all triangular face normals.
static java.util.ArrayList<MguiNumber>	MeshFunctions.getVertexWiseCurvature(Mesh3D mesh, ProgressUpdater progress)	Computes the mean curvature at each node in the mesh.
static java.util.ArrayList<MguiNumber>	MeshFunctions.getVertexWiseCurvature_bak(Mesh3D mesh, ProgressUpdater progress)	Computes the mean curvature at each node in the mesh.
static java.util.ArrayList<MguiFloat>	MeshFunctions.getVertexWiseCurvatureBak(Mesh3D mesh)
static double[]	MeshFunctions.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 boolean	MeshFunctions.intersects(Mesh3D mesh, org.jogamp.vecmath.Point3f p, org.jogamp.vecmath.Vector3f v)	Determines whether a vector defined by p and v intersects mesh.
java.util.ArrayList<MguiNumber>	MeshEngine.mapVolumeToMesh(Mesh3D mesh, Volume3DInt volume, java.lang.String method)
java.util.ArrayList<MguiNumber>	MeshEngine.mapVolumeToMesh(Mesh3D mesh, Volume3DInt volume, java.lang.String method, InterfaceProgressBar progress_bar)
static java.util.ArrayList<MguiNumber>	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.maskMeshWithPlane(Mesh3D mesh, Plane3D plane, double above_val, double below_val)
static java.util.ArrayList<MguiNumber>	MeshFunctions.maskMeshWithPlane(Mesh3D mesh, Plane3D plane, double above_val, double below_val, double contained_val)
static java.util.ArrayList<MguiNumber>	MeshFunctions.maskMeshWithPlane(Mesh3D mesh, Plane3D plane, double above_val, double below_val, double contained_val, VertexSelection selection)	Masks a mesh with a plane.
protected static void	MeshSmoothing.moveParticleByVariance(Mesh3D mesh, mgui.geometry.mesh.MeshSmoothing.Particle particle)
protected static void	MeshSmoothing.moveParticleByVariance(Mesh3D mesh, mgui.geometry.mesh.MeshSmoothing.Particle particle, boolean holdbounds)
static boolean	MeshFunctions.removeBadFaces(Mesh3D mesh)
static boolean	MeshFunctions.removeDuplicateFaces(Mesh3D mesh)
static boolean	MeshFunctions.removeDuplicateNodes(Mesh3D mesh)	Removes all duplicate vertices from mesh, and changes mesh in place.
static void	MeshFunctions.removeNodes(Mesh3D mesh, boolean[] removed)	Removes all nodes specified in nodes from mesh, and retriangulates the remaining nodes.
static void	MeshFunctions.removeNodes(Mesh3D mesh, boolean[] removed, NeighbourhoodMesh nmesh)	Removes all nodes specified in nodes from mesh, and retriangulates the remaining nodes.
static void	MeshFunctions.removeStrandedNodes(Mesh3D mesh)	Removes all nodes from mesh which do not have a corresponding face.
static void	MeshFunctions.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.
protected static void	MeshSmoothing.setCharge(Mesh3D mesh, mgui.geometry.mesh.MeshSmoothing.Particle particle, double force, double decay, int m)	Set the charge repulsion for this particle based upon its neighbour's edge distances.
protected static void	MeshSmoothing.setEdgeVariance(Mesh3D mesh, mgui.geometry.mesh.MeshSmoothing.Particle particle)
static void	MeshSmoothing.setEquilateralFacesLR(Mesh3D mesh, double timeStep, double decay, int nodeStep, double limit, boolean holdbounds)	Uses an energy model to obtain a representation of with triangular faces having maximal equilaterality.
void	MeshEdgeSet.setMesh(Mesh3D mesh3d)
static void	MeshFunctions.smoothLR(Mesh3D mesh)
void	MeshEngine.SmoothLR(Mesh3D mesh)
static java.util.ArrayList<MguiNumber>	MeshFunctions.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>	MeshFunctions.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 boolean[]	MeshSubdivision.subdivideButterflyScheme(Mesh3D mesh, double w, boolean[] constraints)	Subdivide mesh once, using the "Butterfly Scheme" discussed by Dyn et al (1990), which will interpolate between existing nodes without altering these nodes.
static void	MeshFunctions.subdivideMesh(Mesh3D mesh, int iter)
static java.util.ArrayList<MguiNumber>	MeshFunctions.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>	MeshFunctions.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>	MeshFunctions.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.
boolean	MeshEngine.transformMesh(Mesh3D mesh, java.lang.String method, InterfaceProgressBar progress_bar)
static Mesh3D	MeshFunctions.transformWithMatrix(Mesh3D mesh_in, org.jogamp.vecmath.Matrix4d matrix, InterfaceProgressBar progress_bar)
boolean	MeshEngine.translateMesh(Mesh3D mesh)
static void	MeshFunctions.triangulate(Mesh3D mesh, java.util.ArrayList<MguiInteger> neighbours)	Triangulates the given neighbourhood by adding faces using recursive loop splitting
static boolean	MeshFunctions.validateSurface(Mesh3D mesh)

Method parameters in mgui.geometry.mesh with type arguments of type Mesh3D

Modifier and Type	Method	Description
static Mesh3D	MeshFunctions.mergeMeshes(java.util.ArrayList<Mesh3D> mesh_list)	Merges the mesh shapes in list and returns the resulting single mesh.
static Mesh3D	MeshFunctions.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.

Constructors in mgui.geometry.mesh with parameters of type Mesh3D

Constructor	Description
EnergySphere(Mesh3D mesh, NeighbourhoodMesh n_mesh, org.jogamp.vecmath.Point3f center, float radius)
FaceMesh(Mesh3D mesh)
MeshEdgeSet(Mesh3D mesh3d)
NeighbourhoodMesh(Mesh3D mesh)
SortedMesh(Mesh3D mesh)

Uses of Mesh3D in mgui.geometry.neuro.connectivity

Methods in mgui.geometry.neuro.connectivity with parameters of type Mesh3D

Modifier and Type	Method	Description
static Jama.Matrix	NeuroConnectivityFunctions.computeCorticalPatchCorrelations(Mesh3D mesh, java.util.ArrayList<MguiNumber> v_data, java.util.HashMap<java.lang.String,java.lang.Object> parameters)	Computes correlations between "patches" of cortex, defined by a set of vertices and a patch function.

Uses of Mesh3D in mgui.geometry.neuro.mesh

Fields in mgui.geometry.neuro.mesh declared as Mesh3D

Modifier and Type	Field	Description
Mesh3D	ScalpAndSkullModelOptions.brain_surface

Methods in mgui.geometry.neuro.mesh that return Mesh3D

Modifier and Type	Method	Description
static Mesh3D[]	NeuroMeshFunctions.getAverageSkullAndScalpMeshes(Mesh3D hull_mesh, int[][] A, java.util.ArrayList<java.lang.Double> resample_scales, org.jogamp.vecmath.Point3f center_pt)	Returns average meshes for the control points in A.
static Mesh3D[]	NeuroMeshFunctions.getControlPointMeshes(int[][] A, java.util.ArrayList<SampleRay> rays, ScalpAndSkullModelOptions options)	Generates four meshes corresponding to the average control points.
static Mesh3D[]	NeuroMeshFunctions.getSkullAndScalpMeshes(int[][] A, java.util.ArrayList<SampleRay> scalp_rays, java.util.ArrayList<SampleRay> full_rays, ScalpAndSkullModelOptions options)	Generates meshes, given the control points; array is ordered as: inner skull outer skull scalp
static Mesh3D[]	NeuroMeshFunctions.getSkullAndScalpMeshes(int[][] A, java.util.ArrayList<SampleRay> scalp_rays, java.util.ArrayList<SampleRay> full_rays, ScalpAndSkullModelOptions options, ProgressUpdater updater)	Generates meshes, given the control points; array is ordered as: inner skull outer skull scalp control_point_A1 control_point_A2 control_point_A3 control_point_A4
static Mesh3D[]	NeuroMeshFunctions.getSkullAndScalpMeshesBlocking(int[][] A, java.util.ArrayList<SampleRay> scalp_rays, java.util.ArrayList<SampleRay> full_rays, ScalpAndSkullModelOptions options, ProgressUpdater updater)	Generates meshes, given the control points; array is ordered as: inner skull outer skull scalp control_point_A1 control_point_A2 control_point_A3 control_point_A4 ..and 4 additional meshes for subject control points
static Mesh3D	NeuroMeshFunctions.resampleMesh(Mesh3D source_mesh, Mesh3D resample_mesh)	Resamples the source mesh with the vertices of the resample mesh (typically a sphere).

Methods in mgui.geometry.neuro.mesh with parameters of type Mesh3D

Modifier and Type	Method	Description
static Mesh3D[]	NeuroMeshFunctions.getAverageSkullAndScalpMeshes(Mesh3D hull_mesh, int[][] A, java.util.ArrayList<java.lang.Double> resample_scales, org.jogamp.vecmath.Point3f center_pt)	Returns average meshes for the control points in A.
static java.util.ArrayList<java.util.ArrayList<java.lang.Double>>	NeuroMeshFunctions.getRayCurves(ScalpAndSkullModelOptions options, java.lang.String subject, java.lang.String output_file, java.util.ArrayList<java.util.ArrayList<java.lang.Double>> unnormalized, Mesh3D hull_mesh, java.util.ArrayList<java.lang.Double> scales)
static java.util.ArrayList<java.util.ArrayList<java.lang.Double>>	NeuroMeshFunctions.getRayCurvesBak(ScalpAndSkullModelOptions options, java.lang.String subject, java.lang.String output_file, java.util.ArrayList<java.util.ArrayList<java.lang.Double>> unnormalized, Mesh3D hull_mesh)
static int[][]	NeuroMeshFunctions.loadAverageRays(java.lang.String average_ray_file, boolean smooth, ScalpAndSkullModelOptions options, Mesh3D mesh, java.util.ArrayList<java.lang.Double> scales)
static java.util.ArrayList<MguiNumber>	NeuroMeshFunctions.mapGrid3DToCortexGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, double thickness, boolean normalize)
java.util.ArrayList<MguiNumber>	NeuroMeshEngine.mapVolumeToCortex(Mesh3D mesh, Volume3DInt volume, java.lang.Object thickness, ProgressUpdater progress)	Maps a volume to a cortical surface
static java.util.ArrayList<MguiNumber>	NeuroMeshFunctions.mapVolumeToCortexGaussian(Mesh3D mesh, Volume3DInt volume, java.lang.String channel, double sigma_normal, double sigma_tangent, double sigma_max_normal, double sigma_max_tangent, java.lang.Object _thickness, boolean normalize, ProgressUpdater progress, boolean output_matrix, java.lang.String matrix_file)	Maps values from a Grid3D object to a mesh object representing a middle cortical surface, by applying a Gaussian kernal to voxels in the vicinity of each mesh vertex.
static Mesh3D	NeuroMeshFunctions.resampleMesh(Mesh3D source_mesh, Mesh3D resample_mesh)	Resamples the source mesh with the vertices of the resample mesh (typically a sphere).

Uses of Mesh3D in mgui.geometry.util

Methods in mgui.geometry.util that return Mesh3D

Modifier and Type	Method	Description
static Mesh3D	ConvexHullFunctions.getConvexHull(java.util.ArrayList<org.jogamp.vecmath.Point3f> nodes, java.lang.String method, ProgressUpdater progress)	Returns a Mesh3D which is the

Uses of Mesh3D in mgui.interfaces.graphs.util

Methods in mgui.interfaces.graphs.util with parameters of type Mesh3D

Modifier and Type	Method	Description
static InterfaceAbstractGraph	GraphFunctions.getDistanceWeightedGraphForMesh(Mesh3D mesh)	Converts mesh to a weighted graph.

Uses of Mesh3D in mgui.interfaces.shapes

Methods in mgui.interfaces.shapes that return Mesh3D

Modifier and Type	Method	Description
Mesh3D	Mesh3DInt.getMesh()

Methods in mgui.interfaces.shapes with parameters of type Mesh3D

Modifier and Type	Method	Description
void	Mesh3DInt.setMesh(Mesh3D mesh)

Constructors in mgui.interfaces.shapes with parameters of type Mesh3D

Constructor	Description
Mesh3DInt(Mesh3D mesh)
Mesh3DInt(Mesh3D mesh, java.lang.String name)

Uses of Mesh3D in mgui.interfaces.shapes.util

Methods in mgui.interfaces.shapes.util that return Mesh3D

Modifier and Type	Method	Description
static Mesh3D	ShapeFunctions.getConvexHull(Shape3DInt shape)	Returns a new mesh which is the convex hull of the given mesh.
static Mesh3D	ShapeFunctions.getConvexHull(Shape3DInt shape, java.lang.String method)
static Mesh3D	ShapeFunctions.getConvexHull(Shape3DInt shape, java.lang.String method, ProgressUpdater progress)	Returns a new mesh which is the convex hull of the given mesh.
static Mesh3D	ShapeFunctions.getConvexHull(Shape3DInt shape, ProgressUpdater progress)
protected static Mesh3D	ShapeFunctions.getConvexHullBlocking(Shape3DInt shape, java.lang.String method, ProgressUpdater progress)

Methods in mgui.interfaces.shapes.util with parameters of type Mesh3D

Modifier and Type	Method	Description
static Mesh2DInt	ShapeFunctions.getIntersectionMesh(Mesh3D mesh, Plane3D plane)	Returns a Mesh2DInt object representing the intersection of the given 3D mesh with plane p.
static Mesh2DInt	ShapeFunctions.getIntersectionMesh(Mesh3D mesh, Plane3D plane, java.util.ArrayList<MguiNumber> data, ColourMap cmap)	Returns a Mesh2DInt object representing the intersection of the given 3D mesh with plane p.

Uses of Mesh3D in mgui.io.standard.gifti

Methods in mgui.io.standard.gifti with parameters of type Mesh3D

Modifier and Type	Method	Description
protected void	GiftiSurfaceWriter.writeAsciiCoords(java.io.BufferedWriter writer, Mesh3D mesh, int decimals)	Write coordinates as ASCII data to an XML writer; formats to decimals decimal places.
protected void	GiftiSurfaceWriter.writeAsciiFaces(java.io.BufferedWriter writer, Mesh3D mesh)	Write faces as ASCII data to an XML writer; formats to decimals decimal places.
protected void	GiftiSurfaceWriter.writeBinaryCoords(java.io.BufferedWriter writer, Mesh3D mesh, boolean compress, java.nio.ByteOrder b_order)	Write mesh coordinates as Base64 encoded binary data to an XML writer, in row major order.
protected void	GiftiSurfaceWriter.writeBinaryFaces(java.io.BufferedWriter writer, Mesh3D mesh, boolean compress, java.nio.ByteOrder b_order)	Write mesh faces as Base64 encoded binary data to an XML writer, in row major order.