Package qupath.lib.gui.images.servers

Class ChannelDisplayTransformServer

java.lang.Object

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

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

qupath.lib.gui.images.servers.ChannelDisplayTransformServer

All Implemented Interfaces:

AutoCloseable, ImageServer<BufferedImage>, PathObjectReader

public class ChannelDisplayTransformServer
extends TransformingImageServer<BufferedImage>
implements PathObjectReader

ImageServer that applies a color transform to an image. This can either be a single RGB transform, or one or more single-channel (float) transforms.

Note: This class may move or be removed in a later version.

Author:

Pete Bankhead

Method Summary

Modifier and Type	Method	Description
static ImageServer<BufferedImage>	createColorTransformServer(ImageServer<BufferedImage> server, List<ChannelDisplayInfo> channels)	Create an ImageServer for which the channels are created dynamically from a list of ChannelDisplayInfos.
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()	Returns null (does not support ServerBuilders).
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<PathObject>	readPathObjects()	Read a collection of objects from the source.
BufferedImage	readRegion(RegionRequest request)	Read a 2D(+C) image region for a specified RegionRequest.

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

getURIs, getWrappedServer

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

close, finalize, 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, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

getPixelCalibration, readBufferedImage, readRegion, readRegion

Method Details

createColorTransformServer

public static ImageServer<BufferedImage> createColorTransformServer(ImageServer<BufferedImage> server,
 List<ChannelDisplayInfo> channels)

Create an ImageServer for which the channels are created dynamically from a list of ChannelDisplayInfos.

Parameters:

server - the server providing the underlying data

channels - ChannelDisplayInfo objects defining how the pixels from the wrapped server should be converted to channels in the new server

Returns:

createServerBuilder

protected ImageServerBuilder.ServerBuilder<BufferedImage> createServerBuilder()

Returns null (does not support ServerBuilders).

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:

readRegion

public BufferedImage readRegion(RegionRequest request)
                         throws IOException

Description copied from interface: ImageServer

Read a 2D(+C) image region for a specified RegionRequest. Coordinates and bounding box dimensions from the request are in pixel units, at the full image resolution (i.e. when downsample = 1).

All channels are always returned.

No specific checking is guaranteed to ensure that the request is valid, e.g. if it extends beyond the image boundary then it is likely (but not certain) that the returned image will be cropped accordingly - but some implementations may contain empty padding instead. Therefore it is up to the caller to ensure that the requests are within range.

However, it is expected that any returnable region will be at least 1x1 pixel in size, even if via high downsampling one might otherwise expect a 0x0 image. This is consistent with the idea of pixels representing point samples rather than little squares.

Note: One should avoid returning null, as this cannot be stored as a value in some map implementations that may be used for caching.

Specified by:

readRegion in interface ImageServer<BufferedImage>

Overrides:

readRegion in class TransformingImageServer<BufferedImage>

Parameters:

request - the region for which pixels are requested

Returns:

pixels for the region being requested

Throws:

IOException

See Also:

• ImageServer.readRegion(double, int, int, int, int, int, int)
• ImageServer.readRegion(double, int, int, int, int)
• ImageServer.readBufferedImage(RegionRequest)

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>

Overrides:

getOriginalMetadata in class TransformingImageServer<BufferedImage>

Returns:

See Also:

• ImageServer.getMetadata()

readPathObjects

public Collection<PathObject> readPathObjects()
                                       throws IOException

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.

Throws:

IOException