Package qupath.lib.analysis.heatmaps

Class DensityMaps

java.lang.Object

qupath.lib.analysis.heatmaps.DensityMaps

public class DensityMaps
extends Object

Class for constructing and using density maps.

A density map is an ImageServer with the channel type ImageServerMetadata.ChannelType.DENSITY. The pixel values relate to the density of objects of some kind, based upon applying one or more predicates.

Currently, only 2D density maps are supported. There are several supported density map types, defined with DensityMaps.DensityMapType.

Author:

Pete Bankhead

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DensityMaps.DensityMapBuilder	Builder for an ImageServer representing a density map or for DensityMaps.DensityMapParameters.
static class	DensityMaps.DensityMapParameters	Class for storing parameters to build a ImageServer representing a density map.
static enum	DensityMaps.DensityMapType	Density map types.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	CHANNEL_ALL_OBJECTS	Channel name for the channel with all object counts (not always present).
static final String	PROJECT_LOCATION	Default location to use when storing density maps in a project.

Constructor Summary

Constructors

Constructor	Description
DensityMaps()

Method Summary

Modifier and Type	Method	Description
static DensityMaps.DensityMapBuilder	builder(DensityMaps.DensityMapBuilder builder)	Create a new DensityMaps.DensityMapBuilder initialized with the same properties as an existing builder.
static DensityMaps.DensityMapBuilder	builder(PathObjectPredicates.PathObjectPredicate mainObjectFilter)	Create a new DensityMaps.DensityMapBuilder to generate a customized density map.
static void	findHotspots(PathObjectHierarchy hierarchy, ImageServer<BufferedImage> densityServer, int channel, int nHotspots, double radius, double minCount, PathClass hotspotClass, boolean deleteExisting, boolean peaksOnly)	Find hotspots in a density map.
static DensityMaps.DensityMapBuilder	loadDensityMap(Path path)	Load a DensityMaps.DensityMapBuilder from the specified path.
static boolean	threshold(PathObjectHierarchy hierarchy, ImageServer<BufferedImage> densityServer, int channel, double threshold, PixelClassifierTools.CreateObjectOptions... options)	Threshold a single channel of a density map to generate new annotations.
static boolean	threshold(PathObjectHierarchy hierarchy, ImageServer<BufferedImage> densityServer, Map<Integer,? extends Number> thresholds, String pathClassName, PixelClassifierTools.CreateObjectOptions... options)	Threshold one or more channels of a density map to generate new annotations.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

CHANNEL_ALL_OBJECTS

public static final String CHANNEL_ALL_OBJECTS

Channel name for the channel with all object counts (not always present).

See Also:

• Constant Field Values

PROJECT_LOCATION

public static final String PROJECT_LOCATION

Default location to use when storing density maps in a project.

See Also:

• Project.getResources(String, Class, String)
• Constant Field Values

Constructor Details

DensityMaps

public DensityMaps()

Method Details

builder

public static DensityMaps.DensityMapBuilder builder(PathObjectPredicates.PathObjectPredicate mainObjectFilter)

Create a new DensityMaps.DensityMapBuilder to generate a customized density map.

Parameters:

mainObjectFilter - predicate to identify which objects will be included in the density map

Returns:

the builder

builder

public static DensityMaps.DensityMapBuilder builder(DensityMaps.DensityMapBuilder builder)

Create a new DensityMaps.DensityMapBuilder initialized with the same properties as an existing builder.

Parameters:

builder - the existing builder

Returns:

the new builder

loadDensityMap

public static DensityMaps.DensityMapBuilder loadDensityMap(Path path)
                                                    throws IOException

Load a DensityMaps.DensityMapBuilder from the specified path.

Parameters:

path -

Returns:

Throws:

IOException

threshold

public static boolean threshold(PathObjectHierarchy hierarchy,
 ImageServer<BufferedImage> densityServer,
 int channel,
 double threshold,
 PixelClassifierTools.CreateObjectOptions... options)
                         throws IOException

Threshold a single channel of a density map to generate new annotations.

Parameters:

hierarchy - hierarchy to which objects should be added

densityServer - density map

channel - channel to threshold; this is also used to determine the class name for the created annotations

threshold - threshold value

options - additional objects when creating the annotations

Returns:

true if changes were made, false otherwise

Throws:

IOException

threshold

public static boolean threshold(PathObjectHierarchy hierarchy,
 ImageServer<BufferedImage> densityServer,
 Map<Integer,? extends Number> thresholds,
 String pathClassName,
 PixelClassifierTools.CreateObjectOptions... options)
                         throws IOException

Threshold one or more channels of a density map to generate new annotations.

Parameters:

hierarchy - hierarchy to which objects should be added

densityServer - density map

thresholds - map between channel numbers and thresholds

pathClassName - name of the classification to apply to the generated annotations

options - additional options to customize how annotations are created

Returns:

true if changes were made, false otherwise

Throws:

IOException

findHotspots

public static void findHotspots(PathObjectHierarchy hierarchy,
 ImageServer<BufferedImage> densityServer,
 int channel,
 int nHotspots,
 double radius,
 double minCount,
 PathClass hotspotClass,
 boolean deleteExisting,
 boolean peaksOnly)
                         throws IOException

Find hotspots in a density map.

Parameters:

hierarchy - hierarchy used to obtain selected objects and add hotspots

densityServer - the density map to query

channel - channel in which to find hotspots (usually 0)

nHotspots - maximum number of hotspots to find per selected annotation

radius - hotspot radius, in calibrated units

minCount - minimum value required in the 'count' channel (the last channel)

hotspotClass - the classification to apply to hotspots

deleteExisting - optionally delete existing annotations identified as hotspots

peaksOnly - optionally restrict hotspots to only include intensity peaks

Throws:

IOException