Package qupath.lib.images.servers

Class LabeledImageServer

java.lang.Object

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

qupath.lib.images.servers.AbstractTileableImageServer

qupath.lib.images.servers.LabeledImageServer

All Implemented Interfaces:

AutoCloseable, GeneratingImageServer<BufferedImage>, ImageServer<BufferedImage>

public class LabeledImageServer
extends AbstractTileableImageServer
implements GeneratingImageServer<BufferedImage>

A special ImageServer implementation that doesn't have a backing image, but rather constructs tiles from a PathObjectHierarchy where pixel values are integer labels corresponding stored and classified annotations.

Warning! This is intend for temporary use when exporting labelled images. No attempt is made to respond to changes within the hierarchy. For consistent results, the hierarchy must remain static for the time in which this server is being used.

Author:

Pete Bankhead

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	LabeledImageServer.Builder	Helper class for building a LabeledImageServer.

Method Summary

Modifier and Type	Method	Description
void	close()
protected BufferedImage	createDefaultRGBImage(int width, int height)	Create the default (blank) RGB image for this server.
protected String	createID()	Returns a UUID.
protected ImageServerBuilder.ServerBuilder<BufferedImage>	createServerBuilder()	Returns null (does not support ServerBuilders).
Map<PathClass,Integer>	getBoundaryLabels()	Get an unmodifiable map of classifications and their corresponding boundary labels, if available.
Map<PathObject,Integer>	getInstanceLabels()	Get a mapping between objects and instance labels.
Map<PathClass,Integer>	getLabels()	Get an unmodifiable map of classifications and their corresponding labels.
List<PathObject>	getObjectsForRegion(ImageRegion region)	Get the objects to be painted that fall within a specified region.
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.
boolean	isEmptyRegion(RegionRequest request)	Returns true if there are no objects to be painted within the requested region.
protected BufferedImage	readTile(TileRequest tileRequest)	Read a single image tile.
void	setMetadata(ImageServerMetadata metadata)	Throws an exception - metadata should not be set for a hierarchy image server directly.

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

allowSmoothInterpolation, getDefaultColorModel, getEmptyTile, getEmptyTile, getTile, readRegion

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

finalize, getAssociatedImage, getAssociatedImageList, getBuilder, getCache, getCachedTile, getChannel, getDefaultThumbnail, getDownsampleForResolution, getHeight, getImageClass, getMetadata, getPath, getPixelType, getPreferredDownsamples, getThumbnailDownsampleFactor, getTileRequestManager, getWidth, 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

getAssociatedImage, getAssociatedImageList, getBuilder, getCachedTile, getChannel, getDefaultThumbnail, getDownsampleForResolution, getHeight, getImageClass, getMetadata, getPath, getPixelCalibration, getPixelType, getPreferredDownsamples, getTileRequestManager, getWidth, isRGB, nChannels, nResolutions, nTimepoints, nZSlices, readBufferedImage, readRegion, readRegion, readRegion

Method Details

getInstanceLabels

public Map<PathObject,Integer> getInstanceLabels()

Get a mapping between objects and instance labels.

Returns:

the instance label map, or an empty map if no objects are available or LabeledImageServer.Builder.useInstanceLabels() was not selected.

getLabels

public Map<PathClass,Integer> getLabels()

Get an unmodifiable map of classifications and their corresponding labels. Note that multiple classifications may use the same integer label.

Returns:

a map of labels, or empty map if none are available or useInstanceLabels() was selected.

getBoundaryLabels

public Map<PathClass,Integer> getBoundaryLabels()

Get an unmodifiable map of classifications and their corresponding boundary labels, if available. Note that multiple classifications may use the same integer label.

Returns:

a map of boundary labels, or empty map if none are available or useInstanceLabels() was selected.

createServerBuilder

protected ImageServerBuilder.ServerBuilder<BufferedImage> createServerBuilder()

Returns null (does not support ServerBuilders).

Specified by:

createServerBuilder 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().

Specified by:

getURIs in interface ImageServer<BufferedImage>

Returns:

createID

protected String createID()

Returns a UUID.

Specified by:

createID in class AbstractImageServer<BufferedImage>

Returns:

isEmptyRegion

public boolean isEmptyRegion(RegionRequest request)

Returns true if there are no objects to be painted within the requested region.

Specified by:

isEmptyRegion in interface ImageServer<BufferedImage>

Overrides:

isEmptyRegion in class AbstractImageServer<BufferedImage>

Parameters:

request -

Returns:

getObjectsForRegion

public List<PathObject> getObjectsForRegion(ImageRegion region)

Get the objects to be painted that fall within a specified region. Note that this does not take into consideration line thickness, and therefore results are not guaranteed to match isEmptyRegion(RegionRequest); in other worse, an object might fall outside the region but still influence an image type because of thick lines being drawn. If thicker lines should influence the result, the region should be padded accordingly.

Parameters:

region -

Returns:

a list of objects with ROIs that intersect the specified region

close

public void close()

Specified by:

close in interface AutoCloseable

Overrides:

close in class AbstractImageServer<BufferedImage>

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...)

Specified by:

getServerType in interface ImageServer<BufferedImage>

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.

Specified by:

getOriginalMetadata in interface ImageServer<BufferedImage>

Returns:

See Also:

• ImageServer.getMetadata()

setMetadata

public void setMetadata(ImageServerMetadata metadata)

Throws an exception - metadata should not be set for a hierarchy image server directly. Any changes should be made to the underlying image server for which this server represents an object hierarchy.

Specified by:

setMetadata in interface ImageServer<BufferedImage>

Overrides:

setMetadata in class AbstractImageServer<BufferedImage>

Parameters:

metadata -

createDefaultRGBImage

protected BufferedImage createDefaultRGBImage(int width,
 int height)

Description copied from class: AbstractTileableImageServer

Create the default (blank) RGB image for this server.

By default this will have TYPE_INT_RGB but a subclass may change this if necessary (e.g. to incorporate an alpha channel).

Overrides:

createDefaultRGBImage in class AbstractTileableImageServer

Parameters:

width -

height -

Returns:

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