class is responsible for keeping 3d lines and skeletons More...

Inheritance diagram for Lines3D:

Collaboration diagram for Lines3D:

Public Member Functions
	Lines3D (Gin, activeNodeId, options)
	Constructor for the class.

function	clearContents ()
	Set all elements of the class to default values.

function	replaceGraph (Graph)
	replace the current graph object with a new graph

function Graph =	calculateLengthOfNodes (Graph, options)
	calculate length of nodes

function options =	getOptions ()
	get options of the class

function	setOptions (options)
	update options of the class

function [ Graph , nodeIds , EdgesTable , NodesTable ] =	getTree (treeId)
	[Graph, nodeIds, EdgesTable, NodesTable] = function getTree(obj, treeId) return graph with the tree specified in treeId

function treeNames =	getTreeNames (index)
	return name of trees

function [ noTrees , nodeByTree ] =	updateNumberOfTrees ()
	update number of trees in the graph and get array of nodes by tree index

function	deleteTree (treeId)
	delete tree from the graph

function	insertNode (nodeId, x, y, z)
	insert node to a tree after nodeId, the inserted node becomes an active node

function	updateNodeCoordinate (nodeId, x, y, z)
	update coordinate of the node

function	addNode (x, y, z, newTreeSwitch, options)
	add a new node(s) to the graph; when x,y,z are columns of coordinates they are considered to be connected with edges

function	connectNodes (s, t)
	make an edge between two nodes

function nodeId =	findClosestNode (x, y, z, orientation)
	find the closest node to a point with coordinates x, y, z

function	setActiveNode (x, y, z, orientation)
	set active the node which is closest to a point with coordinates x, y, z as the active node

function	splitAtNode (x, y, z, orientation)
	split tree at the node that is closest to the point with coordinates x, y, z the node and its edges will be removed

function result =	deleteNode (x, y, z, orientation)
	delete node that is closest to the point with coordinates x, y, z the previous and following nodes get connected after remove of the node

function	makeDummyGraph ()
	generate a dummy graph for developmental purposes

function	updateNodeStrel (nodeStrelSize)
	update strel element for showing nodes as circles

function [ edge , edgeIds ] =	clipEdge (Box)
	clip the edge using the Box matrix

function [ nodes , indices ] =	findSliceNodes (z, orientation)
	find nodes that are shown on the current slice

function img =	addLinesToImage (img, Box, options)
	add lines to the image

function	saveToFile (filename, options)
	save Lines3D to a file

Public Attributes
	G
	a graph with lines .Edges - a table containing information about edges of the graph .EndNodes - connectivity table [edgeId][Node1 Node2], each row defines an edge with indices of nodes that form the edge .Edges - matrix with coordinates of the edges, [edgeId][x1 y1 z1 x2 y2 z2], IN PHYSICAL UNITS .Weight - weights of edges .Length - length of nodes, IN PHYSICAL UNITS .Nodes - a table containing information about nodes of the graph .PointsXYZ - coordinates of nodes [NodeId][x, y, z] IN PHYSICAL UNITS to recalculate from pixels to the imaging units use mibImage.convertPixelsToUnits: .TreeName - a cell array where each nodes has name of tree to which the node belong, [NodeId]{`TreeName`} .NodeName - a cell array with names for the nodes, [NodeId]{`NodeName`} .Radius - a vector with radii of nodes .Properties.VariableUnits - a cell array with units for each variable, when coordinate are `pixels`, MIB suggest recompute them to image units .Properties.UserData.pixSize - a structure with pixSize of the underlying dataset .x - x resoulution, um/px .y - x resoulution, um/px .z - x resoulution, um/px .Properties.UserData.BoundingBox - a vector with the bounding box information [xmin, width, ymin, height, zmin, depth]

	activeNodeId = "[]"

	clipExtraThickness = 1
	index of the active node

	defaultNodeName = "Node"
	a number, extend clipping of the edges with additional thickness +/- this number sections default name for nodes

	defaultTreeName = "Tree"
	default name for trees

	edgeActiveColor = "[0.984, 0.549, 0.000]"

	edgeColor = "[1.000, 0.800, 0.502]"
	color of edges for the active tree [R, G, B], from 0 to 1

	edgeThickness = 2
	color of edges [R, G, B], from 0 to 1

	extraEdgeFields = "[]"
	thickness of edges

	extraEdgeFieldsNumeric = "[]"
	a cell array with names of additional fields in the Edges table of the graph object

	extraNodeFields = "[]"
	a vector with indicator whether the field in extraEdgeFields is numeric (1) or not (0)

	extraNodeFieldsNumeric = "[]"
	a cell array with names of additional fields in the Nodes table of the graph object

	filename = "[]"
	a vector with indicator whether the field in extraNodeFields is numeric (1) or not (0)

	nodeActiveColor = "[1.0000 0.0000 0]"
	filename of the Lines3D file

	nodeColor = "[1.0000 1.0000 0]"
	color of the active node [R, G, B], from 0 to 1

	nodeRadius = 5
	color of nodes [R, G, B], from 0 to 1

	nodeStrel
	radius of nodes

	noTrees = 0
	strel element for making nodes

	treeLengths
	number of trees of the graph total length of each tree, numeric array

Detailed Description

class is responsible for keeping 3d lines and skeletons

Constructor & Destructor Documentation

◆ Lines3D()

Lines3D.Lines3D	(	Gin,
		activeNodeId,
		options )

Constructor for the class.

Constructor for the Lines3D class. Create a new instance of the class with default parameters

Parameters

Gin	[optional] graph with 3d lines .Edges - a table containing information about edges of the graph .EndNodes - connectivity table [edgeId][Node1 Node2], each row defines an edge with indices of nodes that form the edge .Edges - matrix with coordinates of the edges, [edgeId][x1 y1 z1 x2 y2 z2] .Nodes - a table containing information about nodes of the graph .PointsXYZ - coordinates of nodes [NodeId][x, y, z] to recalculate from pixels to the imaging units use mibImage.convertPixelsToUnits .Properties.UserData.pixSize - pixSize structure .Properties.UserData.BoundingBox - bounding box [xmin, width, ymin, height, zmin, depth] .Properties.VariableUnits - a cell array with units for each variable, when coordinate are `pixels`, MIB suggest recompute them to image units
activeNodeId	[optional] index of the active node, can be empty
options	[optional] a structure with additional settings .edgeColor - color of edges [R, G, B], from 0 to 1 .edgeThickness - thickness of edges .nodeColor - color of nodes [R, G, B], from 0 to 1 .nodeActiveColor - color of the active node [R, G, B], from 0 to 1 .nodeRadius - radius of nodes

References activeNodeId.

Member Function Documentation

◆ addLinesToImage()

function img = Lines3D.addLinesToImage	(	img,
		Box,
		options )

add lines to the image

Parameters

img	image where lines should be added
Box	a vector with a clipping box [xmin xmax ymin ymax zmin zmax]
options	an optional structure with additional parameters .orientation - a number that specifies desired orientation, 4-yx, 1-xz, 2-yz

Return values

img	an image with fused lines

Required fields of options:

References max, and min.

◆ addNode()

function Lines3D.addNode	(	x,
		y,
		z,
		newTreeSwitch,
		options )

add a new node(s) to the graph; when x,y,z are columns of coordinates they are considered to be connected with edges

Parameters

x	a column of x coordinates of nodes (in physical units)
y	a column of y coordinates of nodes (in physical units)
z	a column of z coordinates of nodes (in physical units)
newTreeSwitch	an optional switch to start a new tree
options	a structure with optional parameters .pixSize - structure with pixel sizes of the dataset .BoundingBox - a vector with the bounding box information [xmin, width, ymin, height, zmin, depth]

Required fields of options:

◆ calculateLengthOfNodes()

function Graph = Lines3D.calculateLengthOfNodes	(		Graph,
			options )

calculate length of nodes

Parameters

Graph	a graph object
options	[optional] - an optional structure with additional parameters .nodeId - ids of nodes that include edges that should be recalculated

Return values

Graph the graph object with added/modified Length field

Required fields of Graph:

Required fields of options:

Generated fields of Graph:

◆ clearContents()

function Lines3D.clearContents ( )

Set all elements of the class to default values.

Examples:

obj.mibModel.I{obj.mibModel.Id}.Lines3D.clearContents();

◆ clipEdge()

function [ edge , edgeIds ] = Lines3D.clipEdge ( Box )

clip the edge using the Box matrix

Parameters

Box	a vector used for cliping the edges [xMin, xMax, yMin, yMax, zMin, zMax]

Return values

edge	a matrix of edges shown inside the clipping box, [x1 y1 z1 x2 y2 z2]
edgeIds	indices of the returned edges

References clipEdge3d().

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◆ connectNodes()

function Lines3D.connectNodes	(		s,
			t )

make an edge between two nodes

Parameters

s	index of the first node
t	index of the second node

References max.

◆ deleteNode()

function result = Lines3D.deleteNode	(	x,
		y,
		z,
		orientation )

delete node that is closest to the point with coordinates x, y, z the previous and following nodes get connected after remove of the node

Return value: results: type of the node that was deleted removed tree - the last node of a tree was removed, so the tree middle node - the removed node was in a middle of a tree multiple split - the node had more than 2 connections and as result multiple new trees were formed

Parameters

x	x coordinate of a point next to the node, or index of the node (in this case, y and z should be empty)
y	y coordinate of a point next to the node
z	z coordinate of a point next to the node
orientation	[optional] a number with orientation of the dataset, 4-yx, 1-xz, 2-yz, default 4

References N.

◆ deleteTree()

function Lines3D.deleteTree ( treeId )

delete tree from the graph

Parameters

treeId index of the tree to delete, or string with name of the tree

◆ findClosestNode()

function nodeId = Lines3D.findClosestNode	(	x,
		y,
		z,
		orientation )

find the closest node to a point with coordinates x, y, z

Parameters

x	x coordinate of a point next to the node
y	y coordinate of a point next to the node
z	z coordinate of a point next to the node
orientation	[optional] a number with orientation of the dataset, 4-yx, 1-xz, 2-yz, default 4

References distancePoints(), and min.

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◆ findSliceNodes()

function [ nodes , indices ] = Lines3D.findSliceNodes	(		z,
			orientation )

find nodes that are shown on the current slice

Parameters

z	Z-value to obtain the nodes
orientation	[optional, default 4 for XY] a number that specifies desired orientation, 4-yx, 1-xz, 2-yz

Return values

nodes	a matrix with coordinates of nodes [node; x, y, z]
indices	a vector with indices of returned nodes

◆ getOptions()

function options = Lines3D.getOptions ( )

get options of the class

Generated fields of options:

Referenced by mibLines3DController.saveBtn_Callback().

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◆ getTree()

function [ Graph , nodeIds , EdgesTable , NodesTable ] = Lines3D.getTree ( treeId )

[Graph, nodeIds, EdgesTable, NodesTable] = function getTree(obj, treeId) return graph with the tree specified in treeId

Parameters

treeId index of tree to get

Return values

Graph	graph object containing tree specified in treeId
nodeIds	indices of nodes belonging to this tree
EdgesTable	a table with edges that belong to treeId
NodesTable	a table with nodes that belong to treeId

◆ getTreeNames()

function treeNames = Lines3D.getTreeNames ( index )

return name of trees

Parameters

index [optional] indices of the trees

Return values

treeNames a cell array with names of trees

◆ insertNode()

function Lines3D.insertNode	(	nodeId,
		x,
		y,
		z )

insert node to a tree after nodeId, the inserted node becomes an active node

Parameters

nodeId	index of the node after which a new node should be inserted
x	new x coordinate
y	new y coordinate
z	new z coordinate

◆ makeDummyGraph()

function Lines3D.makeDummyGraph ( )

generate a dummy graph for developmental purposes

◆ replaceGraph()

function Lines3D.replaceGraph ( Graph )

replace the current graph object with a new graph

.Edges - a table containing information about edges of the graph .EndNodes - connectivity table [edgeId][Node1 Node2], each row defines an edge with indices of nodes that form the edge .Edges - [optional] a matrix with coordinates of the edges, [edgeId][x1 y1 z1 x2 y2 z2], (in physical units) .Weight - [optional] a vector of weights for each edge .Length - [optional] a vector of length for each edge (in physical units)

Parameters

Graph graph object with a new graph, required fields (may have more) .Nodes - a table containing information about nodes of the graph .PointsXYZ - matrix with coordinates of nodes [nodeId](x, y, z) (in physical units) to recalculate from pixels to the imaging units use mibImage.convertPixelsToUnits .TreeName - [optional] a cell array where each entry contains name of the node's parant tree .NodeName - [optional] a cell array where each entry has name of the corresponding node .Radius - [optional] a vector with radius parameter for each node .[name_of_field] - [optional] optional fields as either array of vectors or cells .Properties.UserData.pixSize - a structure with pixSize of the underlying dataset .x - x resoulution, um/px .y - x resoulution, um/px .z - x resoulution, um/px .Properties.UserData.BoundingBox - a vector with the bounding box information [xmin, width, ymin, height, zmin, depth] .Properties.VariableUnits - a cell array with units for each variable, when coordinate are pixels, MIB suggest recompute them to image units

Required fields of Graph:

References convertPixelsToUnits(), and max.

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◆ saveToFile()

function Lines3D.saveToFile	(		filename,
			options )

save Lines3D to a file

Parameters

filename full path to file

options a structure with optional paramters .format - a char string lines3d - MIB lines3d format amira-ascii - amira ascii amira-binary - amira binary excel - Microsoft Excel format .treeId - a number with index of a tree to save, when empty save all graph .NodeFieldName - [optional] name of variable for nodes to save, only for Amira .EdgeFieldName - [optional] name of variable for edges to save, only for Amira .showWaitbar - [optional] a number 1-show; 0-do not show the waitbar

Required fields of options:

References filename, graph2amiraSpatialGraph(), mibInputMultiDlg(), and xlswrite2().

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◆ setActiveNode()

function Lines3D.setActiveNode	(	x,
		y,
		z,
		orientation )

set active the node which is closest to a point with coordinates x, y, z as the active node

Parameters

x	x coordinate of a point next to the node
y	y coordinate of a point next to the node
z	z coordinate of a point next to the node
orientation	[optional] a number with orientation of the dataset, 4-yx, 1-xz, 2-yz, default 4

◆ setOptions()

function Lines3D.setOptions ( options )

update options of the class

◆ splitAtNode()

function Lines3D.splitAtNode	(	x,
		y,
		z,
		orientation )

split tree at the node that is closest to the point with coordinates x, y, z the node and its edges will be removed

Parameters

x	x coordinate of a point next to the node
y	y coordinate of a point next to the node
z	z coordinate of a point next to the node
orientation	[optional] a number with orientation of the dataset, 4-yx, 1-xz, 2-yz, default 4

References min, and N.

◆ updateNodeCoordinate()

function Lines3D.updateNodeCoordinate	(	nodeId,
		x,
		y,
		z )

update coordinate of the node

Parameters

nodeId	index of the node to update
x	new x coordinate
y	new y coordinate
z	new z coordinate

◆ updateNodeStrel()

function Lines3D.updateNodeStrel ( nodeStrelSize )

update strel element for showing nodes as circles

◆ updateNumberOfTrees()

function [ noTrees , nodeByTree ] = Lines3D.updateNumberOfTrees ( )

update number of trees in the graph and get array of nodes by tree index

Return values

noTrees	total number of isolated trees of the graph
nodeByTree	vector of nodes, where values indicate corresponding tree of the node

References max, and noTrees.

Member Data Documentation

◆ activeNodeId

Lines3D.activeNodeId = "[]"

Referenced by Lines3D(), mibLines3DController.loadBtn_Callback(), and mibLines3DController.saveBtn_Callback().

◆ clipExtraThickness

Lines3D.clipExtraThickness = 1

index of the active node

Default: 1

◆ defaultNodeName

Lines3D.defaultNodeName = "Node"

a number, extend clipping of the edges with additional thickness +/- this number sections default name for nodes

Default: "Node"

◆ defaultTreeName

Lines3D.defaultTreeName = "Tree"

default name for trees

Default: "Tree"

◆ edgeActiveColor

Lines3D.edgeActiveColor = "[0.984, 0.549, 0.000]"

◆ edgeColor

Lines3D.edgeColor = "[1.000, 0.800, 0.502]"

color of edges for the active tree [R, G, B], from 0 to 1

Default: "[1.000, 0.800, 0.502]"

◆ edgeThickness

Lines3D.edgeThickness = 2

color of edges [R, G, B], from 0 to 1

Default: 2

◆ extraEdgeFields

Lines3D.extraEdgeFields = "[]"

thickness of edges

Default: "[]"

◆ extraEdgeFieldsNumeric

Lines3D.extraEdgeFieldsNumeric = "[]"

a cell array with names of additional fields in the Edges table of the graph object

Default: "[]"

◆ extraNodeFields

Lines3D.extraNodeFields = "[]"

a vector with indicator whether the field in extraEdgeFields is numeric (1) or not (0)

Default: "[]"

◆ extraNodeFieldsNumeric

Lines3D.extraNodeFieldsNumeric = "[]"

a cell array with names of additional fields in the Nodes table of the graph object

Default: "[]"

◆ filename

Lines3D.filename = "[]"

a vector with indicator whether the field in extraNodeFields is numeric (1) or not (0)

Default: "[]"

Referenced by mibLines3DController.loadBtn_Callback(), and saveToFile().

◆ G

Lines3D.G

a graph with lines .Edges - a table containing information about edges of the graph .EndNodes - connectivity table [edgeId][Node1 Node2], each row defines an edge with indices of nodes that form the edge .Edges - matrix with coordinates of the edges, [edgeId][x1 y1 z1 x2 y2 z2], IN PHYSICAL UNITS .Weight - weights of edges .Length - length of nodes, IN PHYSICAL UNITS .Nodes - a table containing information about nodes of the graph .PointsXYZ - coordinates of nodes [NodeId][x, y, z] IN PHYSICAL UNITS to recalculate from pixels to the imaging units use mibImage.convertPixelsToUnits: .TreeName - a cell array where each nodes has name of tree to which the node belong, [NodeId]{TreeName} .NodeName - a cell array with names for the nodes, [NodeId]{NodeName} .Radius - a vector with radii of nodes .Properties.VariableUnits - a cell array with units for each variable, when coordinate are pixels, MIB suggest recompute them to image units .Properties.UserData.pixSize - a structure with pixSize of the underlying dataset .x - x resoulution, um/px .y - x resoulution, um/px .z - x resoulution, um/px .Properties.UserData.BoundingBox - a vector with the bounding box information [xmin, width, ymin, height, zmin, depth]

Referenced by mibLines3DController.loadBtn_Callback(), and mibLines3DController.saveBtn_Callback().

◆ nodeActiveColor

Lines3D.nodeActiveColor = "[1.0000 0.0000 0]"

filename of the Lines3D file

Default: "[1.0000 0.0000 0]"

◆ nodeColor

Lines3D.nodeColor = "[1.0000 1.0000 0]"

color of the active node [R, G, B], from 0 to 1

Default: "[1.0000 1.0000 0]"

◆ nodeRadius

Lines3D.nodeRadius = 5

color of nodes [R, G, B], from 0 to 1

Default: 5

◆ nodeStrel

Lines3D.nodeStrel

radius of nodes

◆ noTrees

Lines3D.noTrees = 0

strel element for making nodes

Default: 0

Referenced by updateNumberOfTrees().

◆ treeLengths

Lines3D.treeLengths

number of trees of the graph total length of each tree, numeric array

The documentation for this class was generated from the following file:

Classes/@Lines3D/Lines3D.m

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Lines3D()

Member Function Documentation

◆ addLinesToImage()

◆ addNode()

◆ calculateLengthOfNodes()

◆ clearContents()

◆ clipEdge()

◆ connectNodes()

◆ deleteNode()

◆ deleteTree()

◆ findClosestNode()

◆ findSliceNodes()

◆ getOptions()

◆ getTree()

◆ getTreeNames()

◆ insertNode()

◆ makeDummyGraph()

◆ replaceGraph()

◆ saveToFile()

◆ setActiveNode()

◆ setOptions()

◆ splitAtNode()

◆ updateNodeCoordinate()

◆ updateNodeStrel()

◆ updateNumberOfTrees()

Member Data Documentation

◆ activeNodeId

◆ clipExtraThickness

◆ defaultNodeName

◆ defaultTreeName

◆ edgeActiveColor

◆ edgeColor

◆ edgeThickness

◆ extraEdgeFields

◆ extraEdgeFieldsNumeric

◆ extraNodeFields

◆ extraNodeFieldsNumeric

◆ filename

◆ G

◆ nodeActiveColor

◆ nodeColor

◆ nodeRadius

◆ nodeStrel

◆ noTrees

◆ treeLengths