Package qupath.lib.classifiers.pixel

Class PixelClassificationImageServer

java.lang.Object

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

qupath.lib.images.servers.AbstractTileableImageServer

qupath.lib.classifiers.pixel.PixelClassificationImageServer

All Implemented Interfaces:

AutoCloseable, ImageServer<BufferedImage>

public class PixelClassificationImageServer
extends AbstractTileableImageServer

ImageServer that delivers pixels derived from applying a PixelClassifier to another ImageServer.

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
PixelClassificationImageServer(ImageData<BufferedImage> imageData, PixelClassifier classifier)	Constructor.
PixelClassificationImageServer(ImageData<BufferedImage> imageData, PixelClassifier classifier, String customID, ColorModel colorModel)	Constructor.

Method Summary

Modifier and Type	Method	Description
protected String	createID()	Returns a random UUID.
protected ImageServerBuilder.ServerBuilder<BufferedImage>	createServerBuilder()	Returns null (does not support ServerBuilders).
BufferedImage	getCachedTile(TileRequest tile)	Get a cached tile, or null if the tile has not been cached.
PixelClassifier	getClassifier()	Get the PixelClassifier performing the classification.
protected ColorModel	getDefaultColorModel()	Get an appropriate colormodel that may be used.
ImageData<BufferedImage>	getImageData()	Get the underlying ImageData used for classification.
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.
void	readAllTiles()	Read all the tiles.
protected BufferedImage	readTile(TileRequest tileRequest)	Read a single image tile.
void	setMetadata(ImageServerMetadata metadata)	Not allowed - throws an UnsupportedOperationException.

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

allowSmoothInterpolation, createDefaultRGBImage, getEmptyTile, getEmptyTile, getTile, readRegion

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

close, finalize, getAssociatedImage, getAssociatedImageList, getBuilder, getCache, getChannel, getDefaultThumbnail, getDownsampleForResolution, getHeight, getImageClass, getMetadata, getPath, getPixelType, getPreferredDownsamples, getThumbnailDownsampleFactor, getTileRequestManager, getWidth, isEmptyRegion, isRGB, nChannels, nResolutions, nTimepoints, nZSlices, 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

PixelClassificationImageServer

public PixelClassificationImageServer(ImageData<BufferedImage> imageData,
 PixelClassifier classifier)

Constructor.

An ImageData is required because some forms of classification may required additional image properties (e.g. image type, stains), not simply an ImageServer.

Parameters:

imageData -

classifier -

PixelClassificationImageServer

public PixelClassificationImageServer(ImageData<BufferedImage> imageData,
 PixelClassifier classifier,
 String customID,
 ColorModel colorModel)

Constructor.

Parameters:

imageData -

classifier -

customID - optionally provide a custom ID (path). This is when the default (based upon the ImageData and PixelClassifier isn't sufficient), e.g. because the classifier can change output based upon ImageData status.

colorModel - optional colormodel

Method Details

readAllTiles

public void readAllTiles()

Read all the tiles. This is useful for a classifier that can be applied in full to an image without causing memory issues (e.g. a density map), particularly if it is is dependent upon a changing property of the image (e.g. its object hierarchy). After calling this method, tiles will be returned from an internal cache rather than being computed anew.

getDefaultColorModel

protected ColorModel getDefaultColorModel()
                                   throws IOException

Description copied from class: AbstractTileableImageServer

Get an appropriate colormodel that may be used. The default implementation uses the default RGB color model for RGB images, or else requests a low-resolution thumbnail to extract the color model from it. If neither implementation is sufficient, subclasses should override this method.

Overrides:

getDefaultColorModel in class AbstractTileableImageServer

Returns:

Throws:

IOException

createID

protected String createID()

Returns a random UUID.

Specified by:

createID in class AbstractImageServer<BufferedImage>

Returns:

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:

getImageData

public ImageData<BufferedImage> getImageData()

Get the underlying ImageData used for classification.

Returns:

getClassifier

public PixelClassifier getClassifier()

Get the PixelClassifier performing the classification.

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:

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()

setMetadata

public void setMetadata(ImageServerMetadata metadata)
                 throws UnsupportedOperationException

Not allowed - throws an UnsupportedOperationException.

Specified by:

setMetadata in interface ImageServer<BufferedImage>

Overrides:

setMetadata in class AbstractImageServer<BufferedImage>

Parameters:

metadata -

Throws:

UnsupportedOperationException

getCachedTile

public BufferedImage getCachedTile(TileRequest tile)

Description copied from class: AbstractImageServer

Get a cached tile, or null if the tile has not been cached.

This is useful whenever it is important to return quickly rather than wait for a tile to be fetched or generated.

Warning! The cached tile is returned directly (with no defensive copying) for performance. This means that it must not be modified by the code that requests it. If there is any chance the tile may be modified (or passed to untrusted code), then make sure to make a defensive copy, e.g. using BufferedImageTools.duplicate(java.awt.image.BufferedImage) if using a buffered image.

Specified by:

getCachedTile in interface ImageServer<BufferedImage>

Overrides:

getCachedTile in class AbstractImageServer<BufferedImage>

Parameters:

tile -

Returns:

the tile if it has been cached, or null if no cached tile is available for the request.

readTile

protected 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

createServerBuilder

protected ImageServerBuilder.ServerBuilder<BufferedImage> createServerBuilder()

Returns null (does not support ServerBuilders).

Specified by:

createServerBuilder in class AbstractImageServer<BufferedImage>

Returns: