Package qupath.opencv.dnn

Class DnnObjectClassifier

java.lang.Object

qupath.lib.classifiers.object.AbstractObjectClassifier<BufferedImage>

qupath.opencv.dnn.DnnObjectClassifier

All Implemented Interfaces:

ObjectClassifier<BufferedImage>, UriResource

public class DnnObjectClassifier
extends AbstractObjectClassifier<BufferedImage>
implements UriResource

Initial implementation of a patch-based ObjectClassifier using an OpenCV-compatible DNN.

Warning! This implementation is likely to change in the future.

Author:

Pete Bankhead

Field Summary

Fields inherited from interface qupath.lib.classifiers.object.ObjectClassifier

PROJECT_LOCATION

Constructor Summary

Constructors

Constructor	Description
DnnObjectClassifier(PathObjectFilter filter, DnnModel model, List<PathClass> pathClasses, int width, int height, double requestedPixelSize)	Constructor.

Method Summary

Modifier and Type	Method	Description
int	classifyObjects(ImageData<BufferedImage> imageData, Collection<? extends PathObject> pathObjects, boolean resetExistingClass)	Classify the objects in the specified collection.
Map<String,Integer>	getMissingFeatures(ImageData<BufferedImage> imageData, Collection<? extends PathObject> pathObjects)	Check for missing features, returning the names and number of input objects missing the specified features.
Collection<PathClass>	getPathClasses()	Get the classifications set by this classifier.
Collection<URI>	getURIs()	Get all the URIs required for this resource.
protected int	tryToClassify(List<? extends PathObject> pathObjects, ImageServer<BufferedImage> server, double downsample, IntFunction<PathClass> classifier)	Try to classify a batch of objects.
protected boolean	tryToClassify(PathObject pathObject, ImageServer<BufferedImage> server, double downsample, IntFunction<PathClass> classifier)
boolean	updateURIs(Map<URI,URI> replacements)	Update the specified URIs.

Methods inherited from class qupath.lib.classifiers.object.AbstractObjectClassifier

classifyObjects, getCompatibleObjects

Methods inherited from class java.lang.Object

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

Methods inherited from interface qupath.lib.io.UriResource

getUris, updateUris

Constructor Details

DnnObjectClassifier

public DnnObjectClassifier(PathObjectFilter filter,
 DnnModel model,
 List<PathClass> pathClasses,
 int width,
 int height,
 double requestedPixelSize)

Constructor.

Parameters:

filter - filter to select compatible options

model - wrapper for the DNN model, including optional preprocessing

pathClasses - ordered list of classifications, corresponding to the predicted labels

width - patch width, in pixels, at the classification size

height - patch height, in pixels, at the classification side

requestedPixelSize - requested pixel size, in calibrated units, used to calculate the downsample value

Method Details

getPathClasses

public Collection<PathClass> getPathClasses()

Description copied from interface: ObjectClassifier

Get the classifications set by this classifier.

Specified by:

getPathClasses in interface ObjectClassifier<BufferedImage>

Returns:

classifyObjects

public int classifyObjects(ImageData<BufferedImage> imageData,
 Collection<? extends PathObject> pathObjects,
 boolean resetExistingClass)

Description copied from interface: ObjectClassifier

Classify the objects in the specified collection. This provides a means to specify exactly which objects should be classified, avoiding reliance on ObjectClassifier.getCompatibleObjects(ImageData).

Note: this method does not typically fire any hierarchy change/object classification events. It is up to the caller to fire these events if required.

Specified by:

classifyObjects in interface ObjectClassifier<BufferedImage>

Parameters:

imageData - data that may or may not be required for classification depending upon how features are extracted

pathObjects - the objects to classify

resetExistingClass -

Returns:

the number of objects whose classification was changed.

See Also:

• ObjectClassifier.classifyObjects(ImageData, boolean)
• ObjectClassifier.getCompatibleObjects(ImageData)

tryToClassify

protected boolean tryToClassify(PathObject pathObject,
 ImageServer<BufferedImage> server,
 double downsample,
 IntFunction<PathClass> classifier)

tryToClassify

protected int tryToClassify(List<? extends PathObject> pathObjects,
 ImageServer<BufferedImage> server,
 double downsample,
 IntFunction<PathClass> classifier)

Try to classify a batch of objects.

Parameters:

pathObjects -

server -

downsample -

classifier -

Returns:

number of classified objects

getMissingFeatures

public Map<String,Integer> getMissingFeatures(ImageData<BufferedImage> imageData,
 Collection<? extends PathObject> pathObjects)

Description copied from interface: ObjectClassifier

Check for missing features, returning the names and number of input objects missing the specified features. This is useful as a warning that the input for the classifier may not be valid. Default implementation returns an empty map; however, implementations should attempt to provide a meaningful output if possible. Features that are not missing should not be included in the output.

Specified by:

getMissingFeatures in interface ObjectClassifier<BufferedImage>

Parameters:

imageData - image containing the objects to test

pathObjects - objects to test for missing features; if not available, ObjectClassifier.getCompatibleObjects(ImageData) will be called.

Returns:

a map of feature names and the number of objects missing the corresponding features.

getURIs

public Collection<URI> getURIs()
                        throws IOException

Description copied from interface: UriResource

Get all the URIs required for this resource. This is often an empty or singleton list.

Specified by:

getURIs in interface UriResource

Returns:

the required URIs

Throws:

IOException

updateURIs

public boolean updateURIs(Map<URI,URI> replacements)
                   throws IOException

Description copied from interface: UriResource

Update the specified URIs.

Warning! This should be used sparingly, particularly for objects that are otherwise immutable. It is intended only for correcting paths that have become invalid (e.g. because of files being relocated or transferred between computers) before first use of the object. It should not be used to manipulate an object after construction. Indeed, some implementations may throw an UnsupportedOperationException if called too late.

Specified by:

updateURIs in interface UriResource

Parameters:

replacements - replacement map, where the key gives the current URI and the value gives its replacement.

Returns:

true if URIs were changed, false otherwise

Throws:

IOException