Package qupath.lib.images.servers

Class SparseImageServer

java.lang.Object

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

qupath.lib.images.servers.AbstractTileableImageServer

qupath.lib.images.servers.SparseImageServer

All Implemented Interfaces:

AutoCloseable, ImageServer<BufferedImage>

public class SparseImageServer
extends AbstractTileableImageServer

An ImageServer that combines regions from multiple separate ImageServers, repositioning these as necessary to generate one larger field of view.

Regions are currently defined within a JSON file passed as the 'path' argument, and this also contains the full paths to the other ImageServers.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SparseImageServer.Builder	Builder to create a new SparseImageServer.
static class	SparseImageServer.SparseImageServerManager	Helper class for SparseImageServers, capable of returning the appropriate ImageServer for different ImageRegions and different resolutions.

Method Summary

Modifier and Type	Method	Description
void	close()
protected String	createID()	Returns a UUID.
protected ImageServerBuilder.ServerBuilder<BufferedImage>	createServerBuilder()	Create a ServerBuilder, which can be used to construct an identical ImageServer.
protected ColorModel	getDefaultColorModel()	Get an appropriate colormodel that may be used.
SparseImageServer.SparseImageServerManager	getManager()	Get the manager, which defines from whence the regions originate.
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.
protected BufferedImage	readTile(TileRequest tileRequest)	Read a single image tile.
static List<SparseImageServer>	splitConnectedRegions(SparseImageServer server, double distancePixels, boolean permitBoundsOverlap)	Split a SparseImageServer into multiple servers, whereby each split server represents one connected region.

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

allowSmoothInterpolation, createDefaultRGBImage, getEmptyTile, getEmptyTile, getTile, readRegion

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

getAssociatedImage, getAssociatedImageList, 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, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

getPixelCalibration, readBufferedImage, readRegion, readRegion

Method Details

getDefaultColorModel

protected ColorModel getDefaultColorModel()

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:

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()

Returns a UUID.

Specified by:

createID in class AbstractImageServer<BufferedImage>

Returns:

getManager

public SparseImageServer.SparseImageServerManager getManager()

Get the manager, which defines from whence the regions originate.

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()

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:

close

public void close()
           throws Exception

Specified by:

close in interface AutoCloseable

Overrides:

close in class AbstractImageServer<BufferedImage>

Throws:

Exception

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

splitConnectedRegions

public static List<SparseImageServer> splitConnectedRegions(SparseImageServer server,
 double distancePixels,
 boolean permitBoundsOverlap)
                                                     throws IOException

Split a SparseImageServer into multiple servers, whereby each split server represents one connected region. This can be useful whenever a sparse server contains (for example) multiple pieces of tissue with a substantial gap between them, because it allows each piece to be treated as a separate image.

Parameters:

server - the sparse server to be split

distancePixels - the maximum separation between regions for them to be considered part of the same server after splitting. Must be a positive value or zero; suggested default is 1.

permitBoundsOverlap - if true, the bounding boxes for each server may overlap. If unsure, it is strongly advised to use 'false', since otherwise part of a returned server may be 'empty' because the corresponding region was assigned to another server, creating the misleading impression there was nothing there.

Returns:

Throws:

IOException