Package qupath.lib.images.servers

Class ZProjectedImageServer

java.lang.Object

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

qupath.lib.images.servers.AbstractTileableImageServer

qupath.lib.images.servers.ZProjectedImageServer

All Implemented Interfaces:

AutoCloseable, ImageServer<BufferedImage>

public class ZProjectedImageServer
extends AbstractTileableImageServer

An image server that converts a z-stack into a 2D image with a projection.

Note that if the z-stack has the RGB format, transparency is not taken into account (all alpha values will be set to 255).

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ZProjectedImageServer.Projection	A type of projection on the Z-axis.

Field Summary

Fields

Modifier and Type	Field	Description
static final int	NO_RUNNING_OFFSET	Constant indicating that a full z-projection should be made using all slices, rather than a running z-projection made across a group of adjacent slices.

Method Summary

Modifier and Type	Method	Description
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.
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.

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

close, 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

Field Details

NO_RUNNING_OFFSET

public static final int NO_RUNNING_OFFSET

Constant indicating that a full z-projection should be made using all slices, rather than a running z-projection made across a group of adjacent slices.

See Also:

• Constant Field Values

Method Details

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:

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

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

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:

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()