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 Details

    • IMAGE_TYPE

      public static final String IMAGE_TYPE
      Key for an ImagePlus property to store a string representing a QuPath ImageData.ImageType.
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    • 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.
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    • BACKGROUND_DARK

      public static final String BACKGROUND_DARK
      Property value for IMAGE_BACKGROUND when an image is known to have a dark background.
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    • BACKGROUND_LIGHT

      public static final String BACKGROUND_LIGHT
      Property value for IMAGE_BACKGROUND when an image is known to have a light background.
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    • 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.
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    • 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.
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    • OBJECT_CLASSIFICATION

      public static final String OBJECT_CLASSIFICATION
      Set property for PathObject.getClassification() ()}
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    • OBJECT_NAME

      public static final String OBJECT_NAME
      Set property for PathObject.getName()
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    • OBJECT_TYPE

      public static final String OBJECT_TYPE
      Set property that stores the type of an object.
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    • OBJECT_ID

      public static final String OBJECT_ID
      Set property for PathObject.getID() ()}
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    • 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.
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    • DEFAULT_ROI_NAME

      public static final String DEFAULT_ROI_NAME
      Property to store the name for a Roi. The purpose of this is to allow QuPath to set the name of a Roi for processing within ImageJ, but then identify whether that name has been changed within ImageJ or not.

      It addresses the problem of figuring out when the name of a Roi should be used to update a QuPath object (because the name was intentionally set elsewhere), and when it should not.

      See Also:

  • Constructor Details

    • IJProperties

      public IJProperties()

  • Method Details

    • setImageRegion

      public static String setImageRegion(ImagePlus imp, ImageRegion region)
      Set the IMAGE_REGION_ROOT 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)
      Get the IMAGE_REGION_ROOT property, if set.
      Parameters:
      imp -
      Returns:
      the image region stored in the image properties, or null if a valid region could not be found

    • 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
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    • 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
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    • 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
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    • 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
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    • 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
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    • 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
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    • 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
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    • 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
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    • setDefaultRoiName

      public static String setDefaultRoiName(Roi roi, String name)
      Set the value of the DEFAULT_ROI_NAME property.
      Parameters:
      roi - the roi
      name - the name to set
      Returns:
      the name that was set

    • getDefaultRoiName

      public static String getDefaultRoiName(Roi roi)
      Get the value of the DEFAULT_ROI_NAME property.
      Parameters:
      roi - the roi to query
      Returns:
      the value of the property, or null if no value is found

    • hasDefaultRoiName

      public static boolean hasDefaultRoiName(Roi roi)
      Check whether the name of a Roi matches any (non-null) value of DEFAULT_ROI_NAME.
      Parameters:
      roi - the roi to query
      Returns:
      true if the default Roi name is not null, and matches the name of the Roi

    • 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
      Returns:
      a string representation of the object id
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    • 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
      Returns:
      a string representation of the object id
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    • 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
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    • setObjectType

      public static String setObjectType(Roi roi, PathObject pathObject)
      Set a property storing the type of an object (e.g. annotation, detection, cell), optionally appending an additional string.
      Parameters:
      roi - the roi with the property to set
      pathObject - the object whose type should be set
      Returns:
      a string representation of the object type
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    • setObjectTypeAnnotation

      public static String setObjectTypeAnnotation(Roi roi)
      Set the object type property of a Roi to indicate it should be an annotation in QuPath.
      Parameters:
      roi - the ImageJ roi
      Returns:
      the string representing the object type

    • setObjectTypeDetection

      public static String setObjectTypeDetection(Roi roi)
      Set the object type property of a Roi to indicate it should be an detection in QuPath.
      Parameters:
      roi - the ImageJ roi
      Returns:
      the string representing the object type

    • setObjectTypeTile

      public static String setObjectTypeTile(Roi roi)
      Set the object type property of a Roi to indicate it should be a tile in QuPath.
      Parameters:
      roi - the ImageJ roi
      Returns:
      the string representing the object type

    • setObjectTypeCell

      public static String setObjectTypeCell(Roi roi)
      Set the object type property of a Roi to indicate it should be a cell in QuPath.
      Parameters:
      roi - the ImageJ roi
      Returns:
      the string representing the object type

    • setObjectTypeCellNucleus

      public static String setObjectTypeCellNucleus(Roi roi)
      Set the object type property of a Roi to indicate it should be a cell nucleus in QuPath.

      Note that this may be useful for ImageJ, but it is not possible to create a QuPath cell object from a single nucleus ROI.

      Parameters:
      roi - the ImageJ roi
      Returns:
      the string representing the object type

    • getObjectType

      public static String getObjectType(Roi roi)
      Get the value of a Roi's OBJECT_TYPE property.
      Parameters:
      roi - the roi
      Returns:
      the value of OBJECT_TYPE, or null if no type property is set

    • getObjectCreator

      public static Optional<Function<ROI, PathObject>> getObjectCreator(Roi roi)
      Get a function to create a new object based upon the stored object type property, if available.

      Note that not all object types can be created in this way (e.g., it isn't possible to create a root object or TMA core object; it also isn't possible to create a cell containing a nucleus only, but rather only a detection).

      Parameters:
      roi - the Roi that may contain an object type property
      Returns:
      an optional that contains an object creator, if known

    • getObjectCreator

      public static Optional<Function<ROI, PathObject>> getObjectCreator(String typeString)
      Get a function to create a new object based upon a property value of OBJECT_TYPE.

      Note that not all object types can be created in this way (e.g., it isn't possible to create a root object or TMA core object; it also isn't possible to create a cell containing a nucleus only, but rather only a detection).

      Parameters:
      typeString - the type string, as would be set by setObjectType(Roi, PathObject)
      Returns:
      an optional that contains an object creator, if known

    • 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
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    • 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
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    • 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
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