Package qupath.lib.images.servers.bioformats

Class BioFormatsImageServer

java.lang.Object

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

qupath.lib.images.servers.AbstractTileableImageServer

qupath.lib.images.servers.bioformats.BioFormatsImageServer

All Implemented Interfaces:

AutoCloseable, ImageServer<BufferedImage>, PathObjectReader

public class BioFormatsImageServer
extends AbstractTileableImageServer
implements PathObjectReader

QuPath ImageServer that uses the Bio-Formats library to read image data.

See http://www.openmicroscopy.org/site/products/bio-formats

See also https://docs.openmicroscopy.org/bio-formats/6.5.1/developers/matlab-dev.html#improving-reading-performance

Constructor Summary

Constructors

Constructor	Description
BioFormatsImageServer(URI uri, String... args)	Create an ImageServer using the Bio-Formats library.

Method Summary

Modifier and Type	Method	Description
void	close()
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 a builder capable of creating a server like this one.
String	dumpMetadata()	Retrieve a string representation of the metadata OME-XML.
BufferedImage	getAssociatedImage(String name)	Get the image for a given associated image name.
List<String>	getAssociatedImageList()	Get a list of 'associated images', e.g.
File	getFile()	Get the underlying file.
String	getFormat()	Get the format String, as returned by Bio-Formats IFormatReader.getFormat().
OMEPyramidStore	getMetadataStore()	Get the MetadataStore, as used by Bio-Formats.
ImageServerMetadata	getOriginalMetadata()	Get the original metadata read during creation of the server.
int	getSeries()	Get the series index, as used by Bio-Formats.
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 tileRequest)	Read a single image tile.
void	setMetadata(ImageServerMetadata metadata)	Set the metadata to use, e.g.

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

getBuilder, getCache, getCachedTile, getChannel, getDefaultThumbnail, getDownsampleForResolution, getHeight, getImageClass, getMetadata, getPath, getPixelType, getPreferredDownsamples, getThumbnailDownsampleFactor, getTileRequestManager, getWidth, isEmptyRegion, isRGB, nChannels, nResolutions, nTimepoints, nZSlices, 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

BioFormatsImageServer

public BioFormatsImageServer(URI uri,
 String... args)
                      throws FormatException,
IOException,
loci.common.services.DependencyException,
loci.common.services.ServiceException,
URISyntaxException

Create an ImageServer using the Bio-Formats library.

This requires an absolute URI, where an integer fragment can be used to define the series number.

Parameters:

uri - for the image that should be opened; this might include a sub-image as a query or fragment.

args - optional arguments

Throws:

FormatException

IOException

loci.common.services.DependencyException

loci.common.services.ServiceException

URISyntaxException

Method Details

getFormat

public String getFormat()

Get the format String, as returned by Bio-Formats IFormatReader.getFormat().

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().

Specified by:

getURIs in interface ImageServer<BufferedImage>

Returns:

createID

public 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:

setMetadata

public void setMetadata(ImageServerMetadata metadata)

Description copied from interface: ImageServer

Set the metadata to use, e.g. to change the pixel size in microns.

Specified by:

setMetadata in interface ImageServer<BufferedImage>

Overrides:

setMetadata in class AbstractImageServer<BufferedImage>

Parameters:

metadata -

createServerBuilder

protected ImageServerBuilder.ServerBuilder<BufferedImage> createServerBuilder()

Returns a builder capable of creating a server like this one.

Specified by:

createServerBuilder in class AbstractImageServer<BufferedImage>

Returns:

getSeries

public int getSeries()

Get the series index, as used by Bio-Formats.

Returns:

readTile

public 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

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:

close

public void close()
           throws Exception

Specified by:

close in interface AutoCloseable

Overrides:

close in class AbstractImageServer<BufferedImage>

Throws:

Exception

getMetadataStore

public OMEPyramidStore getMetadataStore()

Get the MetadataStore, as used by Bio-Formats. This can be used to query metadata values not otherwise accessible.

Returns:

dumpMetadata

public String dumpMetadata()

Retrieve a string representation of the metadata OME-XML.

Returns:

getAssociatedImageList

public List<String> getAssociatedImageList()

Description copied from interface: ImageServer

Get a list of 'associated images', e.g. thumbnails or slide overview images.

Each associated image is simply a T that does not warrant (or require) a full ImageServer, and most likely would never be analyzed.

Specified by:

getAssociatedImageList in interface ImageServer<BufferedImage>

Overrides:

getAssociatedImageList in class AbstractImageServer<BufferedImage>

Returns:

See Also:

• ImageServer.getAssociatedImage(String)

getAssociatedImage

public BufferedImage getAssociatedImage(String name)

Description copied from interface: ImageServer

Get the image for a given associated image name.

Specified by:

getAssociatedImage in interface ImageServer<BufferedImage>

Overrides:

getAssociatedImage in class AbstractImageServer<BufferedImage>

Parameters:

name -

Returns:

See Also:

• ImageServer.getAssociatedImageList()

getFile

public File getFile()

Get the underlying file.

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()

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.