Package qupath.imagej.images.servers

Class ImageJServer

java.lang.Object

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

qupath.lib.images.servers.AbstractTileableImageServer

qupath.imagej.images.servers.ImageJServer

All Implemented Interfaces:

AutoCloseable, ImageServer<BufferedImage>, PathObjectReader

public class ImageJServer
extends AbstractTileableImageServer
implements PathObjectReader

ImageServer that uses ImageJ's image-reading capabilities.

Constructor Summary

Constructors

Constructor	Description
ImageJServer(URI uri, String... args)	Constructor.

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()	Get a String representing the image metadata.
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.
Collection<PathObject>	readPathObjects()	Read a collection of objects from the source.
BufferedImage	readTile(TileRequest tile)	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

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

Constructor Details

ImageJServer

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

Constructor.

Parameters:

uri - URI representing the local file or an ImageJ-compatible URL

args - optional arguments (not currently used)

Throws:

IOException

Method Details

readPathObjects

public Collection<PathObject> readPathObjects()

Description copied from interface: PathObjectReader

Read a collection of objects from the source.

Specified by:

readPathObjects in interface PathObjectReader

Returns:

a collection of objects, or empty list if no objects are available.

dumpMetadata

public String dumpMetadata()

Get a String representing the image metadata.

Currently, this reflects the contents of the ImageJ 'Show info' command, which is tied to the 'current' slice and therefore not complete for all slices of a multichannel/multidimensional image. This behavior may change in the future.

Returns:

a String representing image metadata in ImageJ's own form

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()

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:

readTile

public BufferedImage readTile(TileRequest tile)

Description copied from class: AbstractTileableImageServer

Read a single image tile.

Specified by:

readTile in class AbstractTileableImageServer

Parameters:

tile -

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...)

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()

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