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Class: TIFFImageDataProvider

Defined in: @tissuumaps-storage/src/tiff/TIFFImageDataProvider.ts:34

Data provider for images stored in TIFF files

Opens a TIFFImageDataSource as TIFFImageData, with one tile source per channel for multi-channel files and a single one for files drawn in their own colors. The format is recognized from the file's metadata (see findTIFFParser), which provides the channel names and colors; the histograms the renderer stretches the channels over are read from the pixels.

Implements​

Constructors​

Constructor​

new TIFFImageDataProvider(): TIFFImageDataProvider

Returns​

TIFFImageDataProvider

Properties​

name​

readonly name: "TIFF" = "TIFF"

Defined in: @tissuumaps-storage/src/tiff/TIFFImageDataProvider.ts:51

The name of the data provider

Implementation of​

ImageDataProvider.name

schema​

readonly schema: object

Defined in: @tissuumaps-storage/src/tiff/TIFFImageDataProvider.ts:53

The JSON schema for the data source

properties​

properties: object

properties.source​

source: object

properties.source.type​

type: string = "string"

properties.t​

t: object

properties.t.minimum​

minimum: number = 0

properties.t.type​

type: string = "integer"

properties.z​

z: object

properties.z.minimum​

minimum: number = 0

properties.z.type​

type: string = "integer"

required​

required: string[]

type​

type: string = "object"

Implementation of​

ImageDataProvider.schema

uischema​

readonly uischema: object

Defined in: @tissuumaps-storage/src/tiff/TIFFImageDataProvider.ts:71

The JSON Forms UI schema for the data source

It must not contain a control for the data source's source, which the application renders itself if the schema declares it, as a string.

elements​

elements: object[]

type​

type: string = "VerticalLayout"

Implementation of​

ImageDataProvider.uischema

Methods​

load()​

load(normalizedDataSource, options?): Promise<TIFFImageData>

Defined in: @tissuumaps-storage/src/tiff/TIFFImageDataProvider.ts:170

Opens a TIFF image data source and returns the loaded image data

The file is opened with openTIFF, and its structure read by the parser of its format (see findTIFFParser), with z and t selecting the plane. The channel histograms are read afterwards, a few channels at a time (see TIFFImageDataProvider._computeChannelHistograms).

Parameters​

normalizedDataSource​

NormalizedTIFFImageDataSource

The normalized data source to open

options?​

DataProviderLoadOptions

See DataProviderLoadOptions; workspace is required for workspace-relative sources

Returns​

Promise<TIFFImageData>

A promise that resolves to the loaded image data

Throws​

Error if the source is workspace-relative while no workspace is open, or if the file holds a TIFF no parser recognizes

Implementation of​

ImageDataProvider.load

normalize()​

normalize(dataSource, workspace, projectSource): NormalizedTIFFImageDataSource

Defined in: @tissuumaps-storage/src/tiff/TIFFImageDataProvider.ts:101

Returns the data source with tiffImageDataSourceDefaults applied and its source normalized (see SourceUtils.normalizeSource)

Parameters​

dataSource​

TIFFImageDataSource

The data source to normalize

workspace​

FileSystemDirectoryHandle | null

The directory handle of the open workspace, if any

projectSource​

string | null

Where the project was loaded from, if anywhere

Returns​

NormalizedTIFFImageDataSource

The normalized data source

Implementation of​

ImageDataProvider.normalize

readName()​

readName(normalizedSource, workspace, options?): Promise<string | undefined>

Defined in: @tissuumaps-storage/src/tiff/TIFFImageDataProvider.ts:143

Reads the image's own name for a data object backed by a source, which only OME-TIFF files have (see OMETIFFParser.readImageName)

Parameters​

normalizedSource​

string

The normalized source

workspace​

FileSystemDirectoryHandle | null

The directory handle of the open workspace, if any

options?​

Optional abort signal

signal?​

AbortSignal

Returns​

Promise<string | undefined>

A promise that resolves to the name, if any

Throws​

Error if the source is workspace-relative while no workspace is open, or if the file cannot be read

Implementation of​

ImageDataProvider.readName

supports()​

supports(normalizedSource): Promise<boolean>

Defined in: @tissuumaps-storage/src/tiff/TIFFImageDataProvider.ts:124

Returns whether a source has a TIFF file extension (see TIFFImageDataProvider._extensions)

Parameters​

normalizedSource​

string

The normalized source to check

Returns​

Promise<boolean>

A promise that resolves to whether the source is supported

Implementation of​

ImageDataProvider.supports