Package qupath.lib.images.servers

Class AffineTransformImageServer

java.lang.Object

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

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

qupath.lib.images.servers.AffineTransformImageServer

All Implemented Interfaces:

AutoCloseable, ImageServer<BufferedImage>

public class AffineTransformImageServer
extends TransformingImageServer<BufferedImage>

ImageServer that dynamically applies an AffineTransform to an existing ImageServer.

Warning! This is incomplete and will be changed/removed in the future.

Author:

Pete Bankhead

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AffineTransformImageServer(ImageServer<BufferedImage> server, AffineTransform transform)

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...)
AffineTransform	getTransform()	Get the affine transform for this server.
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

Constructor Details

AffineTransformImageServer

protected AffineTransformImageServer(ImageServer<BufferedImage> server,
 AffineTransform transform)
                              throws NoninvertibleTransformException

Throws:

NoninvertibleTransformException

Method Details

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)

getTransform

public AffineTransform getTransform()

Get the affine transform for this server.

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()

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:

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: