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:152
colorbarVisible	boolean	undefined	NVMesh.colorbarVisible	nvmesh.ts:153
colormap?	| string | ColorMap | LegacyConnectome	undefined	NVMesh.colormap	nvmesh.ts:188
colormapInvert	boolean	false	NVMesh.colormapInvert	nvmesh.ts:162
connectome?	| string | LegacyConnectome	undefined	NVMesh.connectome	nvmesh.ts:194
data_type?	string	undefined	NVMesh.data_type	nvmesh.ts:175
dpg?	ValuesArray	undefined	NVMesh.dpg	nvmesh.ts:189
dps?	ValuesArray	undefined	NVMesh.dps	nvmesh.ts:190
dpv?	ValuesArray	undefined	NVMesh.dpv	nvmesh.ts:191
edgeColormap	string	'warm'	NVMesh.edgeColormap	nvmesh.ts:204
edgeColormapNegative?	string	undefined	NVMesh.edgeColormapNegative	nvmesh.ts:206
edgeMax?	number	undefined	NVMesh.edgeMax	nvmesh.ts:210
edgeMin?	number	undefined	NVMesh.edgeMin	nvmesh.ts:209
edges?	number[] | NVConnectomeEdge[]	undefined	NVMesh.edges	nvmesh.ts:214
edgeScale	number	1	NVMesh.edgeScale	nvmesh.ts:200
extentsMax	number | number[]	undefined	NVMesh.extentsMax	nvmesh.ts:156
extentsMin	number | number[]	undefined	NVMesh.extentsMin	nvmesh.ts:155
f32PerVertex	number	5	NVMesh.f32PerVertex	nvmesh.ts:186
fiberColor	string	'Global'	NVMesh.fiberColor	nvmesh.ts:181
fiberDecimationStride	number	1	NVMesh.fiberDecimationStride	nvmesh.ts:182
fiberDensity?	Float32Array	undefined	NVMesh.fiberDensity	nvmesh.ts:179
fiberDither	number	0.1	NVMesh.fiberDither	nvmesh.ts:180
fiberGroupColormap	ColorMap	null	NVMesh.fiberGroupColormap	nvmesh.ts:163
fiberLength?	number	undefined	NVMesh.fiberLength	nvmesh.ts:177
fiberLengths?	Uint32Array	undefined	NVMesh.fiberLengths	nvmesh.ts:178
fiberMask?	unknown[]	undefined	NVMesh.fiberMask	nvmesh.ts:187
fiberOcclusion	number	0	NVMesh.fiberOcclusion	nvmesh.ts:185
fiberRadius	number	0	NVMesh.fiberRadius	nvmesh.ts:184
fiberSides	number	5	NVMesh.fiberSides	nvmesh.ts:183
furthestVertexFromOrigin	number	undefined	NVMesh.furthestVertexFromOrigin	nvmesh.ts:154
gl	WebGL2RenderingContext	undefined	-	nvconnectome.ts:45
hasConnectome	boolean	false	NVMesh.hasConnectome	nvmesh.ts:193
id	string	undefined	NVMesh.id	nvmesh.ts:150
indexBuffer	WebGLBuffer	undefined	NVMesh.indexBuffer	nvmesh.ts:165
indexCount?	number	undefined	NVMesh.indexCount	nvmesh.ts:197
layers	NVMeshLayer[]	undefined	NVMesh.layers	nvmesh.ts:172
legendLineThickness	number	0	NVMesh.legendLineThickness	nvmesh.ts:201
meshShaderIndex	number	0	NVMesh.meshShaderIndex	nvmesh.ts:159
name	string	undefined	NVMesh.name	nvmesh.ts:151
nodeColormap	string	'warm'	NVMesh.nodeColormap	nvmesh.ts:203
nodeColormapNegative?	string	undefined	NVMesh.nodeColormapNegative	nvmesh.ts:205
nodeMaxColor?	number	undefined	NVMesh.nodeMaxColor	nvmesh.ts:208
nodeMinColor?	number	undefined	NVMesh.nodeMinColor	nvmesh.ts:207
nodes?	| LegacyNodes | NVConnectomeNode[]	undefined	NVMesh.nodes	nvmesh.ts:212
nodeScale	number	4	NVMesh.nodeScale	nvmesh.ts:199
nodesChanged	EventTarget	undefined	-	nvconnectome.ts:46
offsetPt0	Uint32Array	null	NVMesh.offsetPt0	nvmesh.ts:160
opacity	number	undefined	NVMesh.opacity	nvmesh.ts:157
points?	Point[]	undefined	NVMesh.points	nvmesh.ts:216
pts	Float32Array	undefined	NVMesh.pts	nvmesh.ts:170
rgba255	Uint8Array	undefined	NVMesh.rgba255	nvmesh.ts:176
showLegend	boolean	true	NVMesh.showLegend	nvmesh.ts:202
tris?	Uint32Array	undefined	NVMesh.tris	nvmesh.ts:171
type	MeshType	MeshType.MESH	NVMesh.type	nvmesh.ts:173
vao	WebGLVertexArrayObject	undefined	NVMesh.vao	nvmesh.ts:167
vaoFiber	WebGLVertexArrayObject	undefined	NVMesh.vaoFiber	nvmesh.ts:168
vertexBuffer	WebGLBuffer	undefined	NVMesh.vertexBuffer	nvmesh.ts:166
vertexCount	number	1	NVMesh.vertexCount	nvmesh.ts:198
visible	boolean	undefined	NVMesh.visible	nvmesh.ts:158

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:1073

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:527

Returns

void

Inherited from

NVMesh.createFiberDensityMap

---

decimateFaces()

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

Defined in: nvmesh.ts:1502

Parameters

Parameter	Type
n	number
ntarget	number

Returns

void

Inherited from

NVMesh.decimateFaces

---

decimateHierarchicalMesh()

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

Defined in: nvmesh.ts:1536

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:1619

Parameters

Parameter	Type
pts	Float32Array
tris	Uint32Array
rgba255	Uint8Array

Returns

Float32Array

Inherited from

NVMesh.generatePosNormClr

---

hierarchicalOrder()

hierarchicalOrder(): number;

Defined in: nvmesh.ts:1469

Returns

number

Inherited from

NVMesh.hierarchicalOrder

---

indexNearestXYZmm()

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

Defined in: nvmesh.ts:955

Parameters

Parameter	Type
Xmm	number
Ymm	number
Zmm	number

Returns

number[]

Inherited from

NVMesh.indexNearestXYZmm

---

initValuesArray()

initValuesArray(va: ValuesArray): ValuesArray;

Defined in: nvmesh.ts:347

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:360

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:2058

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:1453

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:1007

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:1567

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:1600

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:976

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:653

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:2023

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:1944

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:1847

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:2004

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:1665

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