Package qupath.lib.objects

Class PathObjects

java.lang.Object

qupath.lib.objects.PathObjects

public class PathObjects
extends Object

Helper class to create PathObject. This should be used in preference of any constructors, which linger only for historical reasons and compatibility.

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
PathObjects()

Method Summary

Modifier and Type	Method	Description
static PathObject	createAnnotationObject(ROI roi)	Create an unclassified annotation object.
static PathObject	createAnnotationObject(ROI roi, PathClass pathClass)	Create a classified annotation object.
static PathObject	createAnnotationObject(ROI roi, PathClass pathClass, MeasurementList measurements)	Create a classified annotation object with a specified measurement list.
static PathObject	createCellObject(ROI roiCell, ROI roiNucleus)	Create a cell object.
static PathObject	createCellObject(ROI roiCell, ROI roiNucleus, PathClass pathClass)	Create a cell object with an optional classification.
static PathObject	createCellObject(ROI roiCell, ROI roiNucleus, PathClass pathClass, MeasurementList measurements)	Create a cell object with an optional classification and measurements list.
static PathObject	createDetectionObject(ROI roi)	Create an unclassified detection object.
static PathObject	createDetectionObject(ROI roi, PathClass pathClass)	Create a classified detection object.
static PathObject	createDetectionObject(ROI roi, PathClass pathClass, MeasurementList measurements)	Create a classified detection object with a specified measurement list.
static PathObject	createTileObject(ROI roi)	Create an unclassified tile object.
static PathObject	createTileObject(ROI roi, PathClass pathClass)	Create a tile object.
static PathObject	createTileObject(ROI roi, PathClass pathClass, MeasurementList measurements)	Create a tile object, with a classification and measurements list.
static TMACoreObject	createTMACoreObject(double xCenter, double yCenter, double diameter, boolean isMissing)	Create a TMA core object with an circular ROI.
static TMACoreObject	createTMACoreObject(double xCenter, double yCenter, double diameter, boolean isMissing, ImagePlane plane)	Create a TMA core object with an circular ROI.
static TMACoreObject	createTMACoreObject(double x, double y, double width, double height, boolean isMissing)	Create a TMA core object with an ellipse ROI.
static TMACoreObject	createTMACoreObject(double x, double y, double width, double height, boolean isMissing, ImagePlane plane)	Create a TMA core object with an ellipse ROI.

Methods inherited from class java.lang.Object

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

Constructor Details

PathObjects

public PathObjects()

Method Details

createAnnotationObject

public static PathObject createAnnotationObject(ROI roi,
 PathClass pathClass,
 MeasurementList measurements)

Create a classified annotation object with a specified measurement list.

Annotation objects are used to represent mutable objects, prizing flexibility over efficiency.

Parameters:

roi -

pathClass -

measurements -

Returns:

createAnnotationObject

public static PathObject createAnnotationObject(ROI roi,
 PathClass pathClass)

Create a classified annotation object.

Annotation objects are used to represent mutable objects, prizing flexibility over efficiency.

Parameters:

roi -

pathClass -

Returns:

createAnnotationObject

public static PathObject createAnnotationObject(ROI roi)

Create an unclassified annotation object.

Annotation objects are used to represent mutable objects, prizing flexibility over efficiency.

Parameters:

roi -

Returns:

createTMACoreObject

public static TMACoreObject createTMACoreObject(double xCenter,
 double yCenter,
 double diameter,
 boolean isMissing,
 ImagePlane plane)

Create a TMA core object with an circular ROI.

Parameters:

xCenter -

yCenter -

diameter -

isMissing -

plane -

Returns:

createTMACoreObject

public static TMACoreObject createTMACoreObject(double xCenter,
 double yCenter,
 double diameter,
 boolean isMissing)

Create a TMA core object with an circular ROI.

Parameters:

xCenter -

yCenter -

diameter -

isMissing -

Returns:

createTMACoreObject

public static TMACoreObject createTMACoreObject(double x,
 double y,
 double width,
 double height,
 boolean isMissing)

Create a TMA core object with an ellipse ROI.

Parameters:

x -

y -

width -

height -

isMissing -

Returns:

createTMACoreObject

public static TMACoreObject createTMACoreObject(double x,
 double y,
 double width,
 double height,
 boolean isMissing,
 ImagePlane plane)

Create a TMA core object with an ellipse ROI.

Parameters:

x -

y -

width -

height -

isMissing -

plane -

Returns:

createDetectionObject

public static PathObject createDetectionObject(ROI roi,
 PathClass pathClass,
 MeasurementList measurements)

Create a classified detection object with a specified measurement list.

Detection objects are used to represent immutable objects that could be very numerous, prizing efficiency over flexibility.

Parameters:

roi -

pathClass -

measurements -

Returns:

See Also:

• createCellObject(ROI, ROI, PathClass, MeasurementList)

createDetectionObject

public static PathObject createDetectionObject(ROI roi,
 PathClass pathClass)

Create a classified detection object.

Detection objects are used to represent immutable objects that could be very numerous, prizing efficiency over flexibility.

Parameters:

roi -

pathClass -

Returns:

createDetectionObject

public static PathObject createDetectionObject(ROI roi)

Create an unclassified detection object.

Detection objects are used to represent immutable objects that could be very numerous, prizing efficiency over flexibility.

Parameters:

roi -

Returns:

createTileObject

public static PathObject createTileObject(ROI roi,
 PathClass pathClass,
 MeasurementList measurements)

Create a tile object, with a classification and measurements list.

Tile objects represent a special case of a detection objects, were the ROI doesn't represent any particular structure (e.g. it is a superpixel or square tile representing a local collection of pixels used on the path to region segmentation).

Parameters:

roi -

pathClass -

measurements -

Returns:

See Also:

• createDetectionObject(qupath.lib.roi.interfaces.ROI, qupath.lib.objects.classes.PathClass, qupath.lib.measurements.MeasurementList)

createTileObject

public static PathObject createTileObject(ROI roi,
 PathClass pathClass)

Create a tile object.

Tile objects represent a special case of a detection objects, were the ROI doesn't represent any particular structure (e.g. it is a superpixel or square tile representing a local collection of pixels used on the path to region segmentation).

Parameters:

roi -

pathClass -

Returns:

Since:

v0.5.0

See Also:

• createDetectionObject(qupath.lib.roi.interfaces.ROI, qupath.lib.objects.classes.PathClass, qupath.lib.measurements.MeasurementList)

createTileObject

public static PathObject createTileObject(ROI roi)

Create an unclassified tile object.

Tile objects represent a special case of a detection objects, were the ROI doesn't represent any particular structure (e.g. it is a superpixel or square tile representing a local collection of pixels used on the path to region segmentation).

Parameters:

roi -

Returns:

See Also:

• createDetectionObject(qupath.lib.roi.interfaces.ROI, qupath.lib.objects.classes.PathClass, qupath.lib.measurements.MeasurementList)

createCellObject

public static PathObject createCellObject(ROI roiCell,
 ROI roiNucleus,
 PathClass pathClass,
 MeasurementList measurements)

Create a cell object with an optional classification and measurements list.

Cell objects represent a special case of a detection objects, where an additional ROI can be stored representing the cell nucleus.

Parameters:

roiCell -

roiNucleus -

pathClass -

measurements -

Returns:

See Also:

• createDetectionObject(qupath.lib.roi.interfaces.ROI, qupath.lib.objects.classes.PathClass, qupath.lib.measurements.MeasurementList)

createCellObject

public static PathObject createCellObject(ROI roiCell,
 ROI roiNucleus,
 PathClass pathClass)

Create a cell object with an optional classification.

Cell objects represent a special case of a detection objects, where an additional ROI can be stored representing the cell nucleus.

Parameters:

roiCell -

roiNucleus -

pathClass -

Returns:

Since:

v0.5.0

See Also:

• createDetectionObject(qupath.lib.roi.interfaces.ROI, qupath.lib.objects.classes.PathClass, qupath.lib.measurements.MeasurementList)

createCellObject

public static PathObject createCellObject(ROI roiCell,
 ROI roiNucleus)

Create a cell object.

Cell objects represent a special case of a detection objects, where an additional ROI can be stored representing the cell nucleus.

Parameters:

roiCell -

roiNucleus -

Returns:

Since:

v0.5.0

See Also:

• createDetectionObject(qupath.lib.roi.interfaces.ROI, qupath.lib.objects.classes.PathClass, qupath.lib.measurements.MeasurementList)