Class: NVConnectome

Defined in: nvconnectome.ts:44

Represents a connectome

Extends

• NVMesh

Constructors

Constructor

new NVConnectome(gl: WebGL2RenderingContext, connectome: LegacyConnectome): NVConnectome;

Defined in: nvconnectome.ts:48

Parameters

Parameter	Type
gl	WebGL2RenderingContext
connectome	LegacyConnectome

Returns

NVConnectome

Overrides

NVMesh.constructor

Properties

Property	Type	Default value	Inherited from	Defined in
anatomicalStructurePrimary	string	undefined	NVMesh.anatomicalStructurePrimary	nvmesh.ts:155
colorbarVisible	boolean	undefined	NVMesh.colorbarVisible	nvmesh.ts:156
colormap?	| string | ColorMap | LegacyConnectome	undefined	NVMesh.colormap	nvmesh.ts:191
colormapInvert	boolean	false	NVMesh.colormapInvert	nvmesh.ts:165
connectome?	| string | LegacyConnectome	undefined	NVMesh.connectome	nvmesh.ts:197
data_type?	string	undefined	NVMesh.data_type	nvmesh.ts:178
dpg?	ValuesArray	undefined	NVMesh.dpg	nvmesh.ts:192
dps?	ValuesArray	undefined	NVMesh.dps	nvmesh.ts:193
dpv?	ValuesArray	undefined	NVMesh.dpv	nvmesh.ts:194
edgeColormap	string	'warm'	NVMesh.edgeColormap	nvmesh.ts:207
edgeColormapNegative?	string	undefined	NVMesh.edgeColormapNegative	nvmesh.ts:209
edgeMax?	number	undefined	NVMesh.edgeMax	nvmesh.ts:213
edgeMin?	number	undefined	NVMesh.edgeMin	nvmesh.ts:212
edges?	number[] | NVConnectomeEdge[]	undefined	NVMesh.edges	nvmesh.ts:217
edgeScale	number	1	NVMesh.edgeScale	nvmesh.ts:203
extentsMax	number | number[]	undefined	NVMesh.extentsMax	nvmesh.ts:159
extentsMin	number | number[]	undefined	NVMesh.extentsMin	nvmesh.ts:158
f32PerVertex	number	5	NVMesh.f32PerVertex	nvmesh.ts:189
fiberColor	string	'Global'	NVMesh.fiberColor	nvmesh.ts:184
fiberDecimationStride	number	1	NVMesh.fiberDecimationStride	nvmesh.ts:185
fiberDensity?	Float32Array	undefined	NVMesh.fiberDensity	nvmesh.ts:182
fiberDither	number	0.1	NVMesh.fiberDither	nvmesh.ts:183
fiberGroupColormap	ColorMap	null	NVMesh.fiberGroupColormap	nvmesh.ts:166
fiberLength?	number	undefined	NVMesh.fiberLength	nvmesh.ts:180
fiberLengths?	Uint32Array	undefined	NVMesh.fiberLengths	nvmesh.ts:181
fiberMask?	unknown[]	undefined	NVMesh.fiberMask	nvmesh.ts:190
fiberOcclusion	number	0	NVMesh.fiberOcclusion	nvmesh.ts:188
fiberRadius	number	0	NVMesh.fiberRadius	nvmesh.ts:187
fiberSides	number	5	NVMesh.fiberSides	nvmesh.ts:186
furthestVertexFromOrigin	number	undefined	NVMesh.furthestVertexFromOrigin	nvmesh.ts:157
gl	WebGL2RenderingContext	undefined	-	nvconnectome.ts:45
hasConnectome	boolean	false	NVMesh.hasConnectome	nvmesh.ts:196
id	string	undefined	NVMesh.id	nvmesh.ts:153
indexBuffer	WebGLBuffer	undefined	NVMesh.indexBuffer	nvmesh.ts:168
indexCount?	number	undefined	NVMesh.indexCount	nvmesh.ts:200
layers	NVMeshLayer[]	undefined	NVMesh.layers	nvmesh.ts:175
legendLineThickness	number	0	NVMesh.legendLineThickness	nvmesh.ts:204
meshShaderIndex	number	0	NVMesh.meshShaderIndex	nvmesh.ts:162
name	string	undefined	NVMesh.name	nvmesh.ts:154
nodeColormap	string	'warm'	NVMesh.nodeColormap	nvmesh.ts:206
nodeColormapNegative?	string	undefined	NVMesh.nodeColormapNegative	nvmesh.ts:208
nodeMaxColor?	number	undefined	NVMesh.nodeMaxColor	nvmesh.ts:211
nodeMinColor?	number	undefined	NVMesh.nodeMinColor	nvmesh.ts:210
nodes?	| LegacyNodes | NVConnectomeNode[]	undefined	NVMesh.nodes	nvmesh.ts:215
nodeScale	number	4	NVMesh.nodeScale	nvmesh.ts:202
nodesChanged	EventTarget	undefined	-	nvconnectome.ts:46
offsetPt0	Uint32Array	null	NVMesh.offsetPt0	nvmesh.ts:163
opacity	number	undefined	NVMesh.opacity	nvmesh.ts:160
points?	Point[]	undefined	NVMesh.points	nvmesh.ts:219
pts	Float32Array	undefined	NVMesh.pts	nvmesh.ts:173
rgba255	Uint8Array	undefined	NVMesh.rgba255	nvmesh.ts:179
showLegend	boolean	true	NVMesh.showLegend	nvmesh.ts:205
tris?	Uint32Array	undefined	NVMesh.tris	nvmesh.ts:174
type	MeshType	MeshType.MESH	NVMesh.type	nvmesh.ts:176
vao	WebGLVertexArrayObject	undefined	NVMesh.vao	nvmesh.ts:170
vaoFiber	WebGLVertexArrayObject	undefined	NVMesh.vaoFiber	nvmesh.ts:171
vertexBuffer	WebGLBuffer	undefined	NVMesh.vertexBuffer	nvmesh.ts:169
vertexCount	number	1	NVMesh.vertexCount	nvmesh.ts:201
visible	boolean	undefined	NVMesh.visible	nvmesh.ts:161

Methods

addConnectomeEdge()

addConnectomeEdge(
   first: number,
   second: number,
   colorValue: number): NVConnectomeEdge;

Defined in: nvconnectome.ts:255

Parameters

Parameter	Type
first	number
second	number
colorValue	number

Returns

NVConnectomeEdge

---

addConnectomeNode()

addConnectomeNode(node: NVConnectomeNode): void;

Defined in: nvconnectome.ts:209

Parameters

Parameter	Type
node	NVConnectomeNode

Returns

void

---

blendColormap()

blendColormap(
   u8: Uint8Array,
   additiveRGBA: Uint8Array,
   layer: NVMeshLayer,
   mn: number,
   mx: number,
   lut: Uint8ClampedArray,
   invert: boolean): void;

Defined in: nvmesh.ts:1076

Parameters

Parameter	Type	Default value
u8	Uint8Array	undefined
additiveRGBA	Uint8Array	undefined
layer	NVMeshLayer	undefined
mn	number	undefined
mx	number	undefined
lut	Uint8ClampedArray	undefined
invert	boolean	false

Returns

void

Inherited from

NVMesh.blendColormap

---

createFiberDensityMap()

createFiberDensityMap(): void;

Defined in: nvmesh.ts:530

Returns

void

Inherited from

NVMesh.createFiberDensityMap

---

decimateFaces()

decimateFaces(n: number, ntarget: number): void;

Defined in: nvmesh.ts:1527

Parameters

Parameter	Type
n	number
ntarget	number

Returns

void

Inherited from

NVMesh.decimateFaces

---

decimateHierarchicalMesh()

decimateHierarchicalMesh(gl: WebGL2RenderingContext, order: number): boolean;

Defined in: nvmesh.ts:1561

Parameters

Parameter	Type	Default value
gl	WebGL2RenderingContext	undefined
order	number	4

Returns

boolean

Inherited from

NVMesh.decimateHierarchicalMesh

---

deleteConnectomeEdge()

deleteConnectomeEdge(first: number, second: number): NVConnectomeEdge;

Defined in: nvconnectome.ts:267

Parameters

Parameter	Type
first	number
second	number

Returns

NVConnectomeEdge

---

deleteConnectomeNode()

deleteConnectomeNode(node: NVConnectomeNode): void;

Defined in: nvconnectome.ts:220

Parameters

Parameter	Type
node	NVConnectomeNode

Returns

void

---

findClosestConnectomeNode()

findClosestConnectomeNode(point: number[], distance: number): NVConnectomeNode;

Defined in: nvconnectome.ts:280

Parameters

Parameter	Type
point	number[]
distance	number

Returns

NVConnectomeNode

---

generatePosNormClr()

generatePosNormClr(
   pts: Float32Array,
   tris: Uint32Array,
   rgba255: Uint8Array): Float32Array;

Defined in: nvmesh.ts:1644

Parameters

Parameter	Type
pts	Float32Array
tris	Uint32Array
rgba255	Uint8Array

Returns

Float32Array

Inherited from

NVMesh.generatePosNormClr

---

hierarchicalOrder()

hierarchicalOrder(): number;

Defined in: nvmesh.ts:1494

Returns

number

Inherited from

NVMesh.hierarchicalOrder

---

indexNearestXYZmm()

indexNearestXYZmm(
   Xmm: number,
   Ymm: number,
   Zmm: number): number[];

Defined in: nvmesh.ts:958

Parameters

Parameter	Type
Xmm	number
Ymm	number
Zmm	number

Returns

number[]

Inherited from

NVMesh.indexNearestXYZmm

---

initValuesArray()

initValuesArray(va: ValuesArray): ValuesArray;

Defined in: nvmesh.ts:350

Parameters

Parameter	Type
va	ValuesArray

Returns

ValuesArray

Inherited from

NVMesh.initValuesArray

---

json()

json(): Connectome;

Defined in: nvconnectome.ts:435

Returns

Connectome

---

linesToCylinders()

linesToCylinders(
   gl: WebGL2RenderingContext,
   posClrF32: Float32Array,
   indices: number[]): void;

Defined in: nvmesh.ts:363

Parameters

Parameter	Type
gl	WebGL2RenderingContext
posClrF32	Float32Array
indices	number[]

Returns

void

Inherited from

NVMesh.linesToCylinders

---

loadFromBase64()

loadFromBase64(__namedParameters: Partial<LoadFromBase64Params>): Promise<NVMesh>;

Defined in: nvmesh.ts:2083

load and return a new NVMesh instance from a base64 encoded string

Parameters

Parameter	Type
__namedParameters	Partial<LoadFromBase64Params>

Returns

Promise<NVMesh>

Inherited from

NVMesh.loadFromBase64

---

reverseFaces()

reverseFaces(gl: WebGL2RenderingContext): void;

Defined in: nvmesh.ts:1478

Parameters

Parameter	Type
gl	WebGL2RenderingContext

Returns

void

Inherited from

NVMesh.reverseFaces

---

scalars2RGBA()

scalars2RGBA(
   rgba: Uint8ClampedArray,
   layer: NVMeshLayer,
   scalars: AnyNumberArray,
   isNegativeCmap: boolean): Uint8ClampedArray;

Defined in: nvmesh.ts:1010

Parameters

Parameter	Type	Default value
rgba	Uint8ClampedArray	undefined
layer	NVMeshLayer	undefined
scalars	AnyNumberArray	undefined
isNegativeCmap	boolean	false

Returns

Uint8ClampedArray

Inherited from

NVMesh.scalars2RGBA

---

setLayerProperty()

setLayerProperty(
   id: number,
   key: keyof NVMeshLayer,
   val: string | number | boolean,
gl: WebGL2RenderingContext): Promise<void>;

Defined in: nvmesh.ts:1592

Parameters

Parameter	Type
id	number
key	keyof NVMeshLayer
val	string | number | boolean
gl	WebGL2RenderingContext

Returns

Promise<void>

Inherited from

NVMesh.setLayerProperty

---

setProperty()

setProperty(
   key: keyof NVConnectome,
   val:
  | string
  | number
  | boolean
  | number[]
  | ColorMap
  | Float32Array
  | Uint8Array
  | LegacyConnectome,
   gl: WebGL2RenderingContext): void;

Defined in: nvmesh.ts:1625

Parameters

Parameter	Type
key	keyof NVConnectome
val	| string | number | boolean | number[] | ColorMap | Float32Array | Uint8Array | LegacyConnectome
gl	WebGL2RenderingContext

Returns

void

Inherited from

NVMesh.setProperty

---

unloadMesh()

unloadMesh(gl: WebGL2RenderingContext): void;

Defined in: nvmesh.ts:979

Parameters

Parameter	Type
gl	WebGL2RenderingContext

Returns

void

Inherited from

NVMesh.unloadMesh

---

updateConnectome()

updateConnectome(gl: WebGL2RenderingContext): void;

Defined in: nvconnectome.ts:301

Parameters

Parameter	Type
gl	WebGL2RenderingContext

Returns

void

---

updateConnectomeNodeByIndex()

updateConnectomeNodeByIndex(index: number, updatedNode: NVConnectomeNode): void;

Defined in: nvconnectome.ts:234

Parameters

Parameter	Type
index	number
updatedNode	NVConnectomeNode

Returns

void

---

updateConnectomeNodeByPoint()

updateConnectomeNodeByPoint(point: [number, number, number], updatedNode: NVConnectomeNode): void;

Defined in: nvconnectome.ts:241

Parameters

Parameter	Type
point	[number, number, number]
updatedNode	NVConnectomeNode

Returns

void

---

updateFibers()

updateFibers(gl: WebGL2RenderingContext): void;

Defined in: nvmesh.ts:656

Parameters

Parameter	Type
gl	WebGL2RenderingContext

Returns

void

Inherited from

NVMesh.updateFibers

---

updateLabels()

updateLabels(): void;

Defined in: nvconnectome.ts:128

Returns

void

---

updateMesh()

updateMesh(gl: WebGL2RenderingContext): void;

Defined in: nvconnectome.ts:430

Parameters

Parameter	Type
gl	WebGL2RenderingContext

Returns

void

Overrides

NVMesh.updateMesh

---

convertFreeSurferConnectome()

static convertFreeSurferConnectome(json: FreeSurferConnectome, colormap: string): Connectome;

Defined in: nvconnectome.ts:95

Parameters

Parameter	Type	Default value
json	FreeSurferConnectome	undefined
colormap	string	'warm'

Returns

Connectome

---

convertLegacyConnectome()

static convertLegacyConnectome(json: LegacyConnectome): Connectome;

Defined in: nvconnectome.ts:61

Parameters

Parameter	Type
json	LegacyConnectome

Returns

Connectome

---

loadConnectomeFromUrl()

static loadConnectomeFromUrl(gl: WebGL2RenderingContext, url: string): Promise<NVConnectome>;

Defined in: nvconnectome.ts:449

Factory method to create connectome from options

Parameters

Parameter	Type
gl	WebGL2RenderingContext
url	string

Returns

Promise<NVConnectome>

---

loadFromFile()

static loadFromFile(__namedParameters: Partial<LoadFromFileParams>): Promise<NVMesh>;

Defined in: nvmesh.ts:2048

factory function to load and return a new NVMesh instance from a file in the browser

Parameters

Parameter	Type
__namedParameters	Partial<LoadFromFileParams>

Returns

Promise<NVMesh>

NVMesh instance

Inherited from

NVMesh.loadFromFile

---

loadFromUrl()

static loadFromUrl(__namedParameters: Partial<LoadFromUrlParams>): Promise<NVMesh>;

Defined in: nvmesh.ts:1969

factory function to load and return a new NVMesh instance from a given URL

Parameters

Parameter	Type
__namedParameters	Partial<LoadFromUrlParams>

Returns

Promise<NVMesh>

Inherited from

NVMesh.loadFromUrl

---

loadLayer()

static loadLayer(layer: NVMeshLayer, nvmesh: NVMesh): Promise<void>;

Defined in: nvmesh.ts:1872

Parameters

Parameter	Type
layer	NVMeshLayer
nvmesh	NVMesh

Returns

Promise<void>

Inherited from

NVMesh.loadLayer

---

readFileAsync()

static readFileAsync(file: Blob): Promise<ArrayBuffer>;

Defined in: nvmesh.ts:2029

Parameters

Parameter	Type
file	Blob

Returns

Promise<ArrayBuffer>

Inherited from

NVMesh.readFileAsync

---

readMesh()

static readMesh(
   buffer: ArrayBuffer,
   name: string,
   gl: WebGL2RenderingContext,
   opacity: number,
   rgba255: Uint8Array,
visible: boolean): Promise<NVMesh>;

Defined in: nvmesh.ts:1690

Parameters

Parameter	Type	Default value
buffer	ArrayBuffer	undefined
name	string	undefined
gl	WebGL2RenderingContext	undefined
opacity	number	1.0
rgba255	Uint8Array	...
visible	boolean	true

Returns

Promise<NVMesh>

Inherited from

NVMesh.readMesh