Package qupath.lib.classifiers.object

Class ObjectClassifiers

java.lang.Object

qupath.lib.classifiers.object.ObjectClassifiers

public class ObjectClassifiers
extends Object

Helper class for creating ObjectClassifiers.

Author:

Pete Bankhead

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	ObjectClassifiers.ClassifyByMeasurementBuilder<T>	Builder to create a simple ObjectClassifier that assigns a classification based upon whether the measurement of an object is above, equal to or below a specified threshold.
static class	ObjectClassifiers.ObjectClassifierTypeAdapterFactory	TypeAdapterFactory to help with serializing ObjectClassifiers to and from JSON.

Constructor Summary

Constructors

Constructor	Description
ObjectClassifiers()

Method Summary

Modifier and Type	Method	Description
static <T> ObjectClassifier<T>	createChannelClassifier(PathObjectFilter filter, ImageChannel channel, String measurement, double threshold)	Create a classifier that thresholds a single measurement, assigning a class based on an ImageChannel if the value is ≥ threshold.
static <T> ObjectClassifier<T>	createCompositeClassifier(Collection<ObjectClassifier<T>> classifiers)	Create a composite ObjectClassifier, which sequentially applies multiple (usually single-class) classifiers.
static <T> ObjectClassifier<T>	createCompositeClassifier(ObjectClassifier<T>... classifiers)	Create a composite ObjectClassifier, which sequentially applies multiple (usually single-class) classifiers.
static TypeAdapterFactory	getTypeAdapterFactory()	Get a TypeAdapterFactory to handle ObjectClassifier instances.
static <T> ObjectClassifier<T>	readClassifier(Path path)	Read the classifier from a file.
static <T> void	writeClassifier(ObjectClassifier<T> classifier, Path path)	Write the classifier to a file.

Methods inherited from class java.lang.Object

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

Constructor Details

ObjectClassifiers

public ObjectClassifiers()

Method Details

getTypeAdapterFactory

public static TypeAdapterFactory getTypeAdapterFactory()

Get a TypeAdapterFactory to handle ObjectClassifier instances.

Returns:

createCompositeClassifier

public static <T> ObjectClassifier<T> createCompositeClassifier(ObjectClassifier<T>... classifiers)

Create a composite ObjectClassifier, which sequentially applies multiple (usually single-class) classifiers. This can be used for multiplexed images, where a single classifier may be trained for each marker.

Type Parameters:

T -

Parameters:

classifiers - an array of classifiers to combine

Returns:

the composite object classifier

createCompositeClassifier

public static <T> ObjectClassifier<T> createCompositeClassifier(Collection<ObjectClassifier<T>> classifiers)

Create a composite ObjectClassifier, which sequentially applies multiple (usually single-class) classifiers. This can be used for multiplexed images, where a single classifier may be trained for each marker.

Type Parameters:

T -

Parameters:

classifiers - a collection of classifiers to combine

Returns:

the composite object classifier

createChannelClassifier

public static <T> ObjectClassifier<T> createChannelClassifier(PathObjectFilter filter,
 ImageChannel channel,
 String measurement,
 double threshold)

Create a classifier that thresholds a single measurement, assigning a class based on an ImageChannel if the value is ≥ threshold.

Parameters:

filter - filter to apply, typically PathObjectFilter.CELLS

channel - ImageChannel from which the PathClass should be derived.

measurement - name of the measurement (within the object's MeasurementList)

threshold - threshold to apply to the measurement

Returns:

the object classifier

See Also:

• PathObjectFilter

readClassifier

public static <T> ObjectClassifier<T> readClassifier(Path path)
                                              throws IOException

Read the classifier from a file.

Type Parameters:

T -

Parameters:

path -

Returns:

Throws:

IOException

writeClassifier

public static <T> void writeClassifier(ObjectClassifier<T> classifier,
 Path path)
                                throws IOException

Write the classifier to a file.

Type Parameters:

T -

Parameters:

classifier -

path -

Throws:

IOException