Package qupath.imagej.tools

Class IJProperties

java.lang.Object

qupath.imagej.tools.IJProperties

public class IJProperties
extends Object

Store QuPath-related information within the properties of ImageJ objects.

Note that these use ImagePlus.setProp(String, String) rather than the tempting ImagePlus.setProperty(String, Object), as this seems necessary to be able to access the properties later from a macro.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BACKGROUND_DARK	Property value for IMAGE_BACKGROUND when an image is known to have a dark background.
static final String	BACKGROUND_LIGHT	Property value for IMAGE_BACKGROUND when an image is known to have a light background.
static final String	IMAGE_BACKGROUND	Key for an ImagePlus property storing either "light" or "dark depending upon whether an image is known to be brightfield of fluorescence respectively.
static final String	IMAGE_REGION_ROOT	Key for a ImagePlus properties to store the bounding box of a QuPath ImageRegion.
static final String	IMAGE_REQUEST	Key for an ImagePlus property to store a json representation of a RegionRequest used to request the image.
static final String	IMAGE_TYPE	Key for an ImagePlus property to store a string representing a QuPath ImageData.ImageType.
static final String	OBJECT_CLASSIFICATION	Set property for PathObject.getClassification() ()}
static final String	OBJECT_ID	Set property for PathObject.getID() ()}
static final String	OBJECT_MEASUREMENT_ROOT	Base for property names that store measurements to be added to PathObject.getMeasurements().
static final String	OBJECT_NAME	Set property for PathObject.getName()

Constructor Summary

Constructors

Constructor	Description
IJProperties()

Method Summary

Modifier and Type	Method	Description
static Map<String,Number>	getAllMeasurements(Roi roi)	Get all QuPath object measurements found in the properties of a Roi.
static String	getClassification(Roi roi)	Get a QuPath classification, as stored in a roi's properties.
static String	getImageBackground(ImagePlus imp)	Get the image background property value
static ImageRegion	getImageRegion(ImagePlus imp)
static Double	getMeasurement(Roi roi, String name)	Get a measurement stored as a property.
static UUID	getObjectId(Roi roi)	Get a QuPath object ID from the Roi properties.
static String	getObjectName(Roi roi)	Get a QuPath object name, as stored in a roi's properties.
static RegionRequest	getRegionRequest(ImagePlus imp)	Get a RegionRequest by reading the json representation stored as a property in the image.
static void	putMeasurement(Roi roi, String name, double value)	Set a property storing a QuPath object measurement within a specified Roi.
static String	setClassification(Roi roi, String classification)	Set a property storing a QuPath object classification within a specified Roi.
static String	setClassification(Roi roi, PathObject pathObject)	Set a property storing a QuPath object classification within a specified Roi.
static String	setImageBackground(ImagePlus imp, ImageData.ImageType imageType)	Set the IMAGE_BACKGROUND property as "dark" for fluorescence images or "light" for brightield images; otherwise, do nothing.
static String	setImageRegion(ImagePlus imp, ImageRegion region)	Set the IMAGE_REGION property as a string representation of the region's bounding box.
static String	setImageType(ImagePlus imp, ImageData.ImageType imageType)	Set the IMAGE_TYPE property based on the name of QuPath's image type, if available.
static String	setObjectId(Roi roi, UUID id)	Set a property storing a QuPath object ID within a specified Roi.
static String	setObjectId(Roi roi, PathObject pathObject)	Set a property storing a QuPath object ID within a specified Roi.
static String	setObjectName(Roi roi, String name)	Set a property storing a QuPath object name within a specified Roi.
static String	setObjectName(Roi roi, PathObject pathObject)	Set a property storing a QuPath object name within a specified Roi.
static String	setRegionRequest(ImagePlus imp, RegionRequest request)	Store a json representation of a RegionRequest as a property in an image.

Methods inherited from class java.lang.Object

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

Field Details

IMAGE_TYPE

public static final String IMAGE_TYPE

Key for an ImagePlus property to store a string representing a QuPath ImageData.ImageType.

See Also:

• Constant Field Values

IMAGE_BACKGROUND

public static final String IMAGE_BACKGROUND

Key for an ImagePlus property storing either "light" or "dark depending upon whether an image is known to be brightfield of fluorescence respectively.

See Also:

• Constant Field Values

BACKGROUND_DARK

public static final String BACKGROUND_DARK

Property value for IMAGE_BACKGROUND when an image is known to have a dark background.

See Also:

• Constant Field Values

BACKGROUND_LIGHT

public static final String BACKGROUND_LIGHT

Property value for IMAGE_BACKGROUND when an image is known to have a light background.

See Also:

• Constant Field Values

IMAGE_REGION_ROOT

public static final String IMAGE_REGION_ROOT

Key for a ImagePlus properties to store the bounding box of a QuPath ImageRegion. Each value (x, y, width, height) is stored as a separate entry.

See Also:

• Constant Field Values

IMAGE_REQUEST

public static final String IMAGE_REQUEST

Key for an ImagePlus property to store a json representation of a RegionRequest used to request the image.

See Also:

• Constant Field Values

OBJECT_CLASSIFICATION

public static final String OBJECT_CLASSIFICATION

Set property for PathObject.getClassification() ()}

See Also:

• Constant Field Values

OBJECT_NAME

public static final String OBJECT_NAME

Set property for PathObject.getName()

See Also:

• Constant Field Values

OBJECT_ID

public static final String OBJECT_ID

Set property for PathObject.getID() ()}

See Also:

• Constant Field Values

OBJECT_MEASUREMENT_ROOT

public static final String OBJECT_MEASUREMENT_ROOT

Base for property names that store measurements to be added to PathObject.getMeasurements(). The measurement name should be in the format OBJECT_MEASUREMENT_ROOT + name where name must not contain any spaces or newlines.

See Also:

• Constant Field Values

Constructor Details

IJProperties

public IJProperties()

Method Details

setImageRegion

public static String setImageRegion(ImagePlus imp,
 ImageRegion region)

Set the IMAGE_REGION property as a string representation of the region's bounding box.

This also stores additional properties under "qupath.image.region.x", "qupath.image.region.y", "qupath.image.region.width" and "qupath.image.region.height" to encode the values separately, in addition to "qupath.image.region.downsample" if available.

Parameters:

imp -

region -

Returns:

the value that was set for the property, or null if the region was null

getImageRegion

public static ImageRegion getImageRegion(ImagePlus imp)

setRegionRequest

public static String setRegionRequest(ImagePlus imp,
 RegionRequest request)

Store a json representation of a RegionRequest as a property in an image.

Parameters:

imp - the image

request - the request that corresponds to the image

Returns:

the json representation that is stored

See Also:

• IMAGE_REQUEST

getRegionRequest

public static RegionRequest getRegionRequest(ImagePlus imp)

Get a RegionRequest by reading the json representation stored as a property in the image.

Parameters:

imp - the image

Returns:

the RegionRequest, or null if none is found

See Also:

• IMAGE_REQUEST

setImageType

public static String setImageType(ImagePlus imp,
 ImageData.ImageType imageType)

Set the IMAGE_TYPE property based on the name of QuPath's image type, if available.

Parameters:

imp -

imageType -

Returns:

the value that was set for the property, or null if it was not set

setImageBackground

public static String setImageBackground(ImagePlus imp,
 ImageData.ImageType imageType)

Set the IMAGE_BACKGROUND property as "dark" for fluorescence images or "light" for brightield images; otherwise, do nothing.

Parameters:

imp -

imageType -

Returns:

the value that was set for the property, or null if it was not set

getImageBackground

public static String getImageBackground(ImagePlus imp)

Get the image background property value

Parameters:

imp -

Returns:

one of "dark", "light" or null.

setClassification

public static String setClassification(Roi roi,
 PathObject pathObject)

Set a property storing a QuPath object classification within a specified Roi.

Parameters:

roi - the roi with the property to set

pathObject - the object whose classification should be stored

See Also:

• OBJECT_CLASSIFICATION

setClassification

public static String setClassification(Roi roi,
 String classification)

Set a property storing a QuPath object classification within a specified Roi.

Parameters:

roi - the roi with the property to set

classification - the classification string value

See Also:

• OBJECT_CLASSIFICATION

getClassification

public static String getClassification(Roi roi)

Get a QuPath classification, as stored in a roi's properties.

Parameters:

roi - the roi

Returns:

the classification if available, or null otherwise

See Also:

• OBJECT_CLASSIFICATION

setObjectName

public static String setObjectName(Roi roi,
 PathObject pathObject)

Set a property storing a QuPath object name within a specified Roi.

Parameters:

roi - the roi with the property to set

pathObject - the object whose name should be stored

See Also:

• OBJECT_NAME

setObjectName

public static String setObjectName(Roi roi,
 String name)

Set a property storing a QuPath object name within a specified Roi.

Parameters:

roi - the roi with the property to set

name - the name value

See Also:

• OBJECT_NAME

getObjectName

public static String getObjectName(Roi roi)

Get a QuPath object name, as stored in a roi's properties.

Parameters:

roi - the roi

Returns:

the name if available, or null otherwise

See Also:

• OBJECT_NAME

setObjectId

public static String setObjectId(Roi roi,
 PathObject pathObject)

Set a property storing a QuPath object ID within a specified Roi.

Parameters:

roi - the roi with the property to set

pathObject - the object whose ID should be stored

See Also:

• OBJECT_ID

setObjectId

public static String setObjectId(Roi roi,
 UUID id)

Set a property storing a QuPath object ID within a specified Roi.

Parameters:

roi - the roi with the property to set

id - the id value

See Also:

• OBJECT_ID

getObjectId

public static UUID getObjectId(Roi roi)

Get a QuPath object ID from the Roi properties.

Parameters:

roi - the roi

Returns:

a UUID if found in the Roi's properties, or null otherwise

See Also:

• OBJECT_ID

putMeasurement

public static void putMeasurement(Roi roi,
 String name,
 double value)

Set a property storing a QuPath object measurement within a specified Roi.

Parameters:

roi - the roi with the property to set

name - the name of the measurement

value - the measurement value

See Also:

• OBJECT_MEASUREMENT_ROOT

getMeasurement

public static Double getMeasurement(Roi roi,
 String name)

Get a measurement stored as a property. The property name will begin with OBJECT_MEASUREMENT_ROOT but the name supplied here need only be the measurement name appended to this.

Parameters:

roi - the roi that may contain the measurement as a property

name - the measurement name

Returns:

the measurement if it is found, or null otherwise

See Also:

• OBJECT_MEASUREMENT_ROOT

getAllMeasurements

public static Map<String,Number> getAllMeasurements(Roi roi)

Get all QuPath object measurements found in the properties of a Roi. These are properties with names that start with OBJECT_MEASUREMENT_ROOT and contain a numeric value that can be parsed.

Parameters:

roi - the Roi to query

Returns:

a map of all measurements that could be found, or an empty map if none are found

See Also:

• OBJECT_MEASUREMENT_ROOT