Package qupath.lib.images.servers.openslide

Class OpenslideImageServer

java.lang.Object

qupath.lib.images.servers.AbstractImageServer<BufferedImage>

qupath.lib.images.servers.AbstractTileableImageServer

qupath.lib.images.servers.openslide.OpenslideImageServer

All Implemented Interfaces:

AutoCloseable, ImageServer<BufferedImage>

public class OpenslideImageServer
extends AbstractTileableImageServer

ImageServer implementation using OpenSlide.

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
OpenslideImageServer(URI uri, String... args)	Create an ImageServer using OpenSlide for the specified file.

Method Summary

Modifier and Type	Method	Description
void	close()
protected String	createID()	Create a unique ID for the server, which can be returned as the default value of AbstractImageServer.getPath().
protected ImageServerBuilder.ServerBuilder<BufferedImage>	createServerBuilder()	Create a ServerBuilder, which can be used to construct an identical ImageServer.
String	dumpMetadata()	Retrieve a JSON string representation of the properties, as stored as key-value pairs by OpenSlide.
BufferedImage	getAssociatedImage(String name)	Get the image for a given associated image name.
List<String>	getAssociatedImageList()	Get a list of 'associated images', e.g.
ImageServerMetadata	getOriginalMetadata()	Get the original metadata read during creation of the server.
String	getServerType()	A string describing the type of server, for example the name of the library used (Openslide, Bioformats...)
Collection<URI>	getURIs()	Get the URIs for images required for this server.
BufferedImage	readTile(TileRequest tileRequest)	Read a single image tile.

Methods inherited from class qupath.lib.images.servers.AbstractTileableImageServer

allowSmoothInterpolation, createDefaultRGBImage, getDefaultColorModel, getEmptyTile, getEmptyTile, getTile, readRegion

Methods inherited from class qupath.lib.images.servers.AbstractImageServer

finalize, getBuilder, getCache, getCachedTile, getChannel, getDefaultThumbnail, getDownsampleForResolution, getHeight, getImageClass, getMetadata, getPath, getPixelType, getPreferredDownsamples, getThumbnailDownsampleFactor, getTileRequestManager, getWidth, isEmptyRegion, isRGB, nChannels, nResolutions, nTimepoints, nZSlices, setMetadata, toString

Methods inherited from class java.lang.Object

clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface qupath.lib.images.servers.ImageServer

getPixelCalibration, readBufferedImage, readRegion, readRegion

Constructor Details

OpenslideImageServer

public OpenslideImageServer(URI uri,
 String... args)
                     throws IOException

Create an ImageServer using OpenSlide for the specified file.

The only supported arg is --no-crop, to specify that any bounding box should not be applied (which was the default in QuPath <= v0.1.2).

Parameters:

uri -

args -

Throws:

IOException

Method Details

getURIs

public Collection<URI> getURIs()

Description copied from interface: ImageServer

Get the URIs for images required for this server. In the simplest case, this is a singleton list returning a URI representing a local file. However, some ImageServers may not have an associated URI at all, whereas others may depend upon multiple URIs (e.g. if concatenating images).

Note: A URI alone may not be sufficient to recreate even a simple ImageServer; see ImageServer.getBuilder().

Returns:

createID

protected String createID()

Description copied from class: AbstractImageServer

Create a unique ID for the server, which can be returned as the default value of AbstractImageServer.getPath(). A suggested implementation is

  getClass().getName() + ": " + URI + parameters
 

This will be called on demand whenever AbstractImageServer.getPath() is first required.

Specified by:

createID in class AbstractImageServer<BufferedImage>

Returns:

close

public void close()

Specified by:

close in interface AutoCloseable

Overrides:

close in class AbstractImageServer<BufferedImage>

dumpMetadata

public String dumpMetadata()

Retrieve a JSON string representation of the properties, as stored as key-value pairs by OpenSlide.

Returns:

getServerType

public String getServerType()

Description copied from interface: ImageServer

A string describing the type of server, for example the name of the library used (Openslide, Bioformats...)

Returns:

readTile

public BufferedImage readTile(TileRequest tileRequest)
                       throws IOException

Description copied from class: AbstractTileableImageServer

Read a single image tile.

Specified by:

readTile in class AbstractTileableImageServer

Parameters:

tileRequest -

Returns:

Throws:

IOException

getAssociatedImageList

public List<String> getAssociatedImageList()

Description copied from interface: ImageServer

Get a list of 'associated images', e.g. thumbnails or slide overview images.

Each associated image is simply a T that does not warrant (or require) a full ImageServer, and most likely would never be analyzed.

Specified by:

getAssociatedImageList in interface ImageServer<BufferedImage>

Overrides:

getAssociatedImageList in class AbstractImageServer<BufferedImage>

Returns:

See Also:

• ImageServer.getAssociatedImage(String)

createServerBuilder

protected ImageServerBuilder.ServerBuilder<BufferedImage> createServerBuilder()

Description copied from class: AbstractImageServer

Create a ServerBuilder, which can be used to construct an identical ImageServer. This should also include the current metadata. It is permissible to return null for an ImageServer that cannot be recreated via a ImageServerBuilder.ServerBuilder.

Specified by:

createServerBuilder in class AbstractImageServer<BufferedImage>

Returns:

getAssociatedImage

public BufferedImage getAssociatedImage(String name)

Description copied from interface: ImageServer

Get the image for a given associated image name.

Specified by:

getAssociatedImage in interface ImageServer<BufferedImage>

Overrides:

getAssociatedImage in class AbstractImageServer<BufferedImage>

Parameters:

name -

Returns:

See Also:

• ImageServer.getAssociatedImageList()

getOriginalMetadata

public ImageServerMetadata getOriginalMetadata()

Description copied from interface: ImageServer

Get the original metadata read during creation of the server. This may or may not be correct.

Returns:

See Also:

• ImageServer.getMetadata()