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:136
colorbarVisible	boolean	undefined	NVMesh.colorbarVisible	nvmesh.ts:137
colormap?	| string | ColorMap | LegacyConnectome	undefined	NVMesh.colormap	nvmesh.ts:173
colormapInvert	boolean	false	NVMesh.colormapInvert	nvmesh.ts:146
connectome?	| string | LegacyConnectome	undefined	NVMesh.connectome	nvmesh.ts:179
data_type?	string	undefined	NVMesh.data_type	nvmesh.ts:159
dpg?	ValuesArray	undefined	NVMesh.dpg	nvmesh.ts:174
dps?	ValuesArray	undefined	NVMesh.dps	nvmesh.ts:175
dpsThreshold	number	NaN	NVMesh.dpsThreshold	nvmesh.ts:171
dpv?	ValuesArray	undefined	NVMesh.dpv	nvmesh.ts:176
edgeColormap	string	'warm'	NVMesh.edgeColormap	nvmesh.ts:189
edgeColormapNegative?	string	undefined	NVMesh.edgeColormapNegative	nvmesh.ts:191
edgeMax?	number	undefined	NVMesh.edgeMax	nvmesh.ts:195
edgeMin?	number	undefined	NVMesh.edgeMin	nvmesh.ts:194
edges?	number[] | NVConnectomeEdge[]	undefined	NVMesh.edges	nvmesh.ts:199
edgeScale	number	1	NVMesh.edgeScale	nvmesh.ts:185
extentsMax	number | number[]	undefined	NVMesh.extentsMax	nvmesh.ts:140
extentsMin	number | number[]	undefined	NVMesh.extentsMin	nvmesh.ts:139
f32PerVertex	number	5	NVMesh.f32PerVertex	nvmesh.ts:170
fiberColor	string	'Global'	NVMesh.fiberColor	nvmesh.ts:165
fiberDecimationStride	number	1	NVMesh.fiberDecimationStride	nvmesh.ts:166
fiberDensity?	Float32Array	undefined	NVMesh.fiberDensity	nvmesh.ts:163
fiberDither	number	0.1	NVMesh.fiberDither	nvmesh.ts:164
fiberGroupColormap	ColorMap	null	NVMesh.fiberGroupColormap	nvmesh.ts:147
fiberLength?	number	undefined	NVMesh.fiberLength	nvmesh.ts:161
fiberLengths?	Uint32Array	undefined	NVMesh.fiberLengths	nvmesh.ts:162
fiberMask?	unknown[]	undefined	NVMesh.fiberMask	nvmesh.ts:172
fiberOcclusion	number	0	NVMesh.fiberOcclusion	nvmesh.ts:169
fiberRadius	number	0	NVMesh.fiberRadius	nvmesh.ts:168
fiberSides	number	5	NVMesh.fiberSides	nvmesh.ts:167
furthestVertexFromOrigin	number	undefined	NVMesh.furthestVertexFromOrigin	nvmesh.ts:138
gl	WebGL2RenderingContext	undefined	-	nvconnectome.ts:45
groups?	ValuesArray	undefined	NVMesh.groups	nvmesh.ts:177
hasConnectome	boolean	false	NVMesh.hasConnectome	nvmesh.ts:178
id	string	undefined	NVMesh.id	nvmesh.ts:134
indexBuffer	WebGLBuffer	undefined	NVMesh.indexBuffer	nvmesh.ts:149
indexCount?	number	undefined	NVMesh.indexCount	nvmesh.ts:182
layers	NVMeshLayer[]	undefined	NVMesh.layers	nvmesh.ts:156
legendLineThickness	number	0	NVMesh.legendLineThickness	nvmesh.ts:186
meshShaderIndex	number	0	NVMesh.meshShaderIndex	nvmesh.ts:143
name	string	undefined	NVMesh.name	nvmesh.ts:135
nodeColormap	string	'warm'	NVMesh.nodeColormap	nvmesh.ts:188
nodeColormapNegative?	string	undefined	NVMesh.nodeColormapNegative	nvmesh.ts:190
nodeMaxColor?	number	undefined	NVMesh.nodeMaxColor	nvmesh.ts:193
nodeMinColor?	number	undefined	NVMesh.nodeMinColor	nvmesh.ts:192
nodes?	| LegacyNodes | NVConnectomeNode[]	undefined	NVMesh.nodes	nvmesh.ts:197
nodeScale	number	4	NVMesh.nodeScale	nvmesh.ts:184
nodesChanged	EventTarget	undefined	-	nvconnectome.ts:46
offsetPt0	Uint32Array	null	NVMesh.offsetPt0	nvmesh.ts:144
opacity	number	undefined	NVMesh.opacity	nvmesh.ts:141
points?	Point[]	undefined	NVMesh.points	nvmesh.ts:201
pts	Float32Array	undefined	NVMesh.pts	nvmesh.ts:154
rgba255	Uint8Array	undefined	NVMesh.rgba255	nvmesh.ts:160
showLegend	boolean	true	NVMesh.showLegend	nvmesh.ts:187
tris?	Uint32Array	undefined	NVMesh.tris	nvmesh.ts:155
type	MeshType	MeshType.MESH	NVMesh.type	nvmesh.ts:157
vao	WebGLVertexArrayObject	undefined	NVMesh.vao	nvmesh.ts:151
vaoFiber	WebGLVertexArrayObject	undefined	NVMesh.vaoFiber	nvmesh.ts:152
vertexBuffer	WebGLBuffer	undefined	NVMesh.vertexBuffer	nvmesh.ts:150
vertexCount	number	1	NVMesh.vertexCount	nvmesh.ts:183
visible	boolean	undefined	NVMesh.visible	nvmesh.ts:142

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:1085

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:518

Returns

void

Inherited from

NVMesh.createFiberDensityMap

---

decimateFaces()

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

Defined in: nvmesh.ts:1521

Parameters

Parameter	Type
n	number
ntarget	number

Returns

void

Inherited from

NVMesh.decimateFaces

---

decimateHierarchicalMesh()

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

Defined in: nvmesh.ts:1555

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:1629

Parameters

Parameter	Type
pts	Float32Array
tris	Uint32Array
rgba255	Uint8Array

Returns

Float32Array

Inherited from

NVMesh.generatePosNormClr

---

hierarchicalOrder()

hierarchicalOrder(): number;

Defined in: nvmesh.ts:1488

Returns

number

Inherited from

NVMesh.hierarchicalOrder

---

indexNearestXYZmm()

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

Defined in: nvmesh.ts:972

Parameters

Parameter	Type
Xmm	number
Ymm	number
Zmm	number

Returns

number[]

Inherited from

NVMesh.indexNearestXYZmm

---

initValuesArray()

initValuesArray(va: ValuesArray): ValuesArray;

Defined in: nvmesh.ts:338

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:351

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:2051

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:1472

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:1024

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:1586

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:1614

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:993

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:644

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:2024

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:1939

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:1852

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:2005

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:1675

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