Package qupath.imagej.tools
Class IJProperties
java.lang.Object
qupath.imagej.tools.IJProperties
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
FieldsModifier and TypeFieldDescriptionstatic final StringProperty value for IMAGE_BACKGROUND when an image is known to have a dark background.static final StringProperty value for IMAGE_BACKGROUND when an image is known to have a light background.static final StringKey for anImagePlusproperty storing either"light"or"darkdepending upon whether an image is known to be brightfield of fluorescence respectively.static final StringKey for aImagePlusproperties to store the bounding box of a QuPathImageRegion.static final StringKey for anImagePlusproperty to store a json representation of aRegionRequestused to request the image.static final StringKey for anImagePlusproperty to store a string representing a QuPathImageData.ImageType.static final StringSet property forPathObject.getClassification()()}static final StringSet property forPathObject.getID()()}static final StringBase for property names that store measurements to be added toPathObject.getMeasurements().static final StringSet property forPathObject.getName() -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetAllMeasurements(Roi roi) Get all QuPath object measurements found in the properties of a Roi.static StringgetClassification(Roi roi) Get a QuPath classification, as stored in a roi's properties.static StringGet the image background property valuestatic qupath.lib.regions.ImageRegiongetImageRegion(ImagePlus imp) static DoublegetMeasurement(Roi roi, String name) Get a measurement stored as a property.static UUIDgetObjectId(Roi roi) Get a QuPath object ID from the Roi properties.static StringgetObjectName(Roi roi) Get a QuPath object name, as stored in a roi's properties.static qupath.lib.regions.RegionRequestGet a RegionRequest by reading the json representation stored as a property in the image.static voidputMeasurement(Roi roi, String name, double value) Set a property storing a QuPath object measurement within a specified Roi.static StringsetClassification(Roi roi, String classification) Set a property storing a QuPath object classification within a specified Roi.static StringsetClassification(Roi roi, qupath.lib.objects.PathObject pathObject) Set a property storing a QuPath object classification within a specified Roi.static StringsetImageBackground(ImagePlus imp, qupath.lib.images.ImageData.ImageType imageType) Set theIMAGE_BACKGROUNDproperty as"dark"for fluorescence images or"light"for brightield images; otherwise, do nothing.static StringsetImageRegion(ImagePlus imp, qupath.lib.regions.ImageRegion region) Set theIMAGE_REGIONproperty as a string representation of the region's bounding box.static StringsetImageType(ImagePlus imp, qupath.lib.images.ImageData.ImageType imageType) Set theIMAGE_TYPEproperty based on the name of QuPath's image type, if available.static StringsetObjectId(Roi roi, UUID id) Set a property storing a QuPath object ID within a specified Roi.static StringsetObjectId(Roi roi, qupath.lib.objects.PathObject pathObject) Set a property storing a QuPath object ID within a specified Roi.static StringsetObjectName(Roi roi, String name) Set a property storing a QuPath object name within a specified Roi.static StringsetObjectName(Roi roi, qupath.lib.objects.PathObject pathObject) Set a property storing a QuPath object name within a specified Roi.static StringsetRegionRequest(ImagePlus imp, qupath.lib.regions.RegionRequest request) Store a json representation of a RegionRequest as a property in an image.
-
Field Details
-
IMAGE_TYPE
Key for anImagePlusproperty to store a string representing a QuPathImageData.ImageType.- See Also:
-
IMAGE_BACKGROUND
Key for anImagePlusproperty storing either"light"or"darkdepending upon whether an image is known to be brightfield of fluorescence respectively.- See Also:
-
BACKGROUND_DARK
Property value for IMAGE_BACKGROUND when an image is known to have a dark background.- See Also:
-
BACKGROUND_LIGHT
Property value for IMAGE_BACKGROUND when an image is known to have a light background.- See Also:
-
IMAGE_REGION_ROOT
Key for aImagePlusproperties to store the bounding box of a QuPathImageRegion. Each value (x, y, width, height) is stored as a separate entry.- See Also:
-
IMAGE_REQUEST
Key for anImagePlusproperty to store a json representation of aRegionRequestused to request the image.- See Also:
-
OBJECT_CLASSIFICATION
Set property forPathObject.getClassification()()}- See Also:
-
OBJECT_NAME
Set property forPathObject.getName()- See Also:
-
OBJECT_ID
Set property forPathObject.getID()()}- See Also:
-
OBJECT_MEASUREMENT_ROOT
Base for property names that store measurements to be added toPathObject.getMeasurements(). The measurement name should be in the formatOBJECT_MEASUREMENT_ROOT + namewherenamemust not contain any spaces or newlines.- See Also:
-
-
Constructor Details
-
IJProperties
public IJProperties()
-
-
Method Details
-
setImageRegion
Set theIMAGE_REGIONproperty 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
-
setRegionRequest
Store a json representation of a RegionRequest as a property in an image.- Parameters:
imp- the imagerequest- the request that corresponds to the image- Returns:
- the json representation that is stored
- See Also:
-
getRegionRequest
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:
-
setImageType
Set theIMAGE_TYPEproperty 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, qupath.lib.images.ImageData.ImageType imageType) Set theIMAGE_BACKGROUNDproperty 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
Get the image background property value- Parameters:
imp-- Returns:
- one of
"dark","light"ornull.
-
setClassification
Set a property storing a QuPath object classification within a specified Roi.- Parameters:
roi- the roi with the property to setpathObject- the object whose classification should be stored- See Also:
-
setClassification
Set a property storing a QuPath object classification within a specified Roi.- Parameters:
roi- the roi with the property to setclassification- the classification string value- See Also:
-
getClassification
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:
-
setObjectName
Set a property storing a QuPath object name within a specified Roi.- Parameters:
roi- the roi with the property to setpathObject- the object whose name should be stored- See Also:
-
setObjectName
Set a property storing a QuPath object name within a specified Roi.- Parameters:
roi- the roi with the property to setname- the name value- See Also:
-
getObjectName
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:
-
setObjectId
Set a property storing a QuPath object ID within a specified Roi.- Parameters:
roi- the roi with the property to setpathObject- the object whose ID should be stored- See Also:
-
setObjectId
Set a property storing a QuPath object ID within a specified Roi.- Parameters:
roi- the roi with the property to setid- the id value- See Also:
-
getObjectId
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:
-
putMeasurement
Set a property storing a QuPath object measurement within a specified Roi.- Parameters:
roi- the roi with the property to setname- the name of the measurementvalue- the measurement value- See Also:
-
getMeasurement
Get a measurement stored as a property. The property name will begin withOBJECT_MEASUREMENT_ROOTbut the name supplied here need only be the measurement name appended to this.- Parameters:
roi- the roi that may contain the measurement as a propertyname- the measurement name- Returns:
- the measurement if it is found, or null otherwise
- See Also:
-
getAllMeasurements
Get all QuPath object measurements found in the properties of a Roi. These are properties with names that start withOBJECT_MEASUREMENT_ROOTand 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:
-