Class: OMEZarrImageDataProvider
Defined in: @tissuumaps-storage/src/ome-zarr/OMEZarrImageDataProvider.ts:28
Data provider for OME-Zarr images
Opens an OMEZarrImageDataSource as OMEZarrImageData with one tile source and one precomputed value histogram per channel if the image has a channel axis (even one of length one), and with a single tile source otherwise.
Implements
Constructors
Constructor
new OMEZarrImageDataProvider():
OMEZarrImageDataProvider
Returns
OMEZarrImageDataProvider
Properties
name
readonlyname:"OME-Zarr"="OME-Zarr"
Defined in: @tissuumaps-storage/src/ome-zarr/OMEZarrImageDataProvider.ts:41
The name of the data provider
Implementation of
schema
readonlyschema:object
Defined in: @tissuumaps-storage/src/ome-zarr/OMEZarrImageDataProvider.ts:43
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
uischema
readonlyuischema:object
Defined in: @tissuumaps-storage/src/ome-zarr/OMEZarrImageDataProvider.ts:61
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
Methods
load()
load(
normalizedDataSource,options?):Promise<OMEZarrImageData>
Defined in: @tissuumaps-storage/src/ome-zarr/OMEZarrImageDataProvider.ts:174
Opens an OME-Zarr image data source and returns the loaded image data
The OME-Zarr image and its arrays are loaded once with openOMEZarr
and shared between the tile sources opened for it: one per channel for
images with a channel axis, or a single one for images without one. Every
tile source renders exactly one channel (c), so that its tile data holds
a single tile (see OMEZarrImageData.getTileData) and its resolved
omero metadata is that channel's. The z and t of the data source
select the plane to open.
For images with a channel axis, the channels are opened concurrently, each computing the value histogram of its plane from a downsampled resolution level as soon as its tile source has opened (see OMEZarrImageDataProvider._computeChannelHistogram), so that OMEZarrImageData.getChannelHistogram can return it without computing anything.
Parameters
normalizedDataSource
NormalizedOMEZarrImageDataSource
The normalized data source to open
options?
See DataProviderLoadOptions; workspace is required
for workspace-relative sources
Returns
Promise<OMEZarrImageData>
A promise that resolves to the loaded image data
Throws
Error if the source is workspace-relative while no workspace is open
Implementation of
normalize()
normalize(
dataSource,workspace,projectSource):NormalizedOMEZarrImageDataSource
Defined in: @tissuumaps-storage/src/ome-zarr/OMEZarrImageDataProvider.ts:91
Returns the data source with omeZarrImageDataSourceDefaults applied
and its source normalized (see SourceUtils.normalizeSource)
Parameters
dataSource
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
NormalizedOMEZarrImageDataSource
The normalized data source
Implementation of
readName()
readName(
normalizedSource,workspace,options?):Promise<string|undefined>
Defined in: @tissuumaps-storage/src/ome-zarr/OMEZarrImageDataProvider.ts:141
Reads the image's own name from its metadata (see OMEZarrUtils.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, or to undefined if the
image has none
Throws
See OMEZarrUtils.readImageName
Implementation of
supports()
supports(
normalizedSource,workspace,options?):Promise<boolean>
Defined in: @tissuumaps-storage/src/ome-zarr/OMEZarrImageDataProvider.ts:117
Returns whether a source is an OME-Zarr image that is no label image (see OMEZarrUtils.inspectImage)
Parameters
normalizedSource
string
The normalized source to check
workspace
FileSystemDirectoryHandle | null
The directory handle of the open workspace, if any
options?
Optional abort signal
signal?
AbortSignal
Returns
Promise<boolean>
A promise that resolves to whether the source is supported
Throws
See OMEZarrUtils.inspectImage