io.github.mianalysis.mia.module.visualise.overlays.AddLabels Maven / Gradle / Ivy
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ModularImageAnalysis (MIA) is an ImageJ plugin which provides a modular framework for assembling image and object analysis workflows. Detected objects can be transformed, filtered, measured and related. Analysis workflows are batch-enabled by default, allowing easy processing of high-content datasets.
package io.github.mianalysis.mia.module.visualise.overlays;
import java.awt.Color;
import java.awt.Font;
import java.text.DecimalFormat;
import java.util.HashMap;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
import org.scijava.Priority;
import org.scijava.plugin.Plugin;
import com.drew.lang.annotations.Nullable;
import ij.ImagePlus;
import ij.ImageStack;
import ij.Prefs;
import ij.gui.TextRoi;
import ij.plugin.Duplicator;
import ij.plugin.HyperStackConverter;
import io.github.mianalysis.mia.module.Categories;
import io.github.mianalysis.mia.module.Category;
import io.github.mianalysis.mia.module.Module;
import io.github.mianalysis.mia.module.Modules;
import io.github.mianalysis.mia.module.images.process.binary.BinaryOperations2D;
import io.github.mianalysis.mia.module.images.process.binary.DistanceMap;
import io.github.mianalysis.mia.object.Obj;
import io.github.mianalysis.mia.object.Objs;
import io.github.mianalysis.mia.object.Workspace;
import io.github.mianalysis.mia.object.coordinates.Point;
import io.github.mianalysis.mia.object.image.Image;
import io.github.mianalysis.mia.object.image.ImageFactory;
import io.github.mianalysis.mia.object.parameters.BooleanP;
import io.github.mianalysis.mia.object.parameters.ChildObjectsP;
import io.github.mianalysis.mia.object.parameters.ChoiceP;
import io.github.mianalysis.mia.object.parameters.InputImageP;
import io.github.mianalysis.mia.object.parameters.InputObjectsP;
import io.github.mianalysis.mia.object.parameters.ObjectMeasurementP;
import io.github.mianalysis.mia.object.parameters.ObjectMetadataP;
import io.github.mianalysis.mia.object.parameters.OutputImageP;
import io.github.mianalysis.mia.object.parameters.Parameters;
import io.github.mianalysis.mia.object.parameters.ParentObjectsP;
import io.github.mianalysis.mia.object.parameters.PartnerObjectsP;
import io.github.mianalysis.mia.object.parameters.SeparatorP;
import io.github.mianalysis.mia.object.parameters.text.IntegerP;
import io.github.mianalysis.mia.object.parameters.text.StringP;
import io.github.mianalysis.mia.object.refs.collections.ImageMeasurementRefs;
import io.github.mianalysis.mia.object.refs.collections.MetadataRefs;
import io.github.mianalysis.mia.object.refs.collections.ObjMeasurementRefs;
import io.github.mianalysis.mia.object.refs.collections.ObjMetadataRefs;
import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
import io.github.mianalysis.mia.object.system.Status;
import io.github.mianalysis.mia.process.LabelFactory;
/**
* Adds an overlay to the specified input image with each object represented by
* a text label. The label can include information such as measurements,
* associated object counts or ID numbers.
*/
@Plugin(type = Module.class, priority = Priority.LOW, visible = true)
public class AddLabels extends AbstractOverlay {
TextRoi textRoi = null;
/**
*
*/
public static final String INPUT_SEPARATOR = "Image and object input";
/**
* Image onto which overlay will be rendered. Input image will only be updated
* if "Apply to input image" is enabled, otherwise the image containing the
* overlay will be stored as a new image with name specified by "Output image".
*/
public static final String INPUT_IMAGE = "Input image";
/**
* Objects to represent as overlays.
*/
public static final String INPUT_OBJECTS = "Input objects";
/**
*
*/
public static final String OUTPUT_SEPARATOR = "Image output";
/**
* Determines if the modifications made to the input image (added overlay
* elements) will be applied to that image or directed to a new image. When
* selected, the input image will be updated.
*/
public static final String APPLY_TO_INPUT = "Apply to input image";
/**
* If the modifications (overlay) aren't being applied directly to the input
* image, this control will determine if a separate image containing the overlay
* should be saved to the workspace.
*/
public static final String ADD_OUTPUT_TO_WORKSPACE = "Add output image to workspace";
/**
* The name of the new image to be saved to the workspace (if not applying the
* changes directly to the input image).
*/
public static final String OUTPUT_IMAGE = "Output image";
/**
*
*/
public static final String CONTENT_SEPARATOR = "Overlay content";
/**
* Controls what information each label displays:
*
* - "Child count" The number of children from a specific object collection
* for each object. The children to summarise are selected using the "Child
* objects for label" parameter.
* - "ID" The ID number of the object.
* - "Measurement value" A measurement associated with the object. The
* measurement is selected using the "Measurement for label" parameter.
* - "Parent ID" The ID number of a parent of the object. The parent object is
* selected using the "Parent object for label" parameter.
* - "Parent measurement value" A measurement associated with a parent of the
* object. The measurement is selected using the "Measurement for label"
* parameter and the parent object with the "Parent object for label"
* parameter.
* - "Partner count" The number of partners from a specific object collection
* for each object. The partners to summarise are selected using the "Partner
* objects for label" parameter.
*
*/
public static final String LABEL_MODE = "Label mode";
/**
* Number of decimal places to use when displaying numeric values.
*/
public static final String DECIMAL_PLACES = "Decimal places";
/**
* When enabled, numeric values will be displayed in the format 1.23E-3.
* Otherwise, the same value would appear as 0.00123.
*/
public static final String USE_SCIENTIFIC = "Use scientific notation";
/**
* Font size of the text label.
*/
public static final String LABEL_SIZE = "Label size";
/**
* Offset the label by this number of pixels horizontally (along the x-axis).
* Increasingly positive numbers move the label right.
*/
public static final String X_OFFSET = "X-offset";
/**
* Offset the label by this number of pixels vertically (along the y-axis).
* Increasingly positive numbers move the label down.
*/
public static final String Y_OFFSET = "Y-offset";
/**
*
*/
public static final String CENTRE_TEXT = "Centre text";
/**
* If "Label mode" is set to "Child count", these are the child objects which
* will be counted and displayed on the label. These objects will be children of
* the input objects.
*/
public static final String CHILD_OBJECTS_FOR_LABEL = "Child objects for label";
/**
* If "Label mode" is set to either "Parent ID" or "Parent measurement value",
* these are the parent objects which will be used. These objects will be
* parents of the input objects.
*/
public static final String PARENT_OBJECT_FOR_LABEL = "Parent object for label";
/**
* If "Label mode" is set to "Partner count", these are the partner objects
* which will be counted and displayed on the label. These objects will be
* partners of the input objects.
*/
public static final String PARTNER_OBJECTS_FOR_LABEL = "Partner objects for label";
/**
* If "Label mode" is set to either "Measurement value" or "Parent measurement
* value", these are the measurements which will be used.
*/
public static final String MEASUREMENT_FOR_LABEL = "Measurement for label";
public static final String OBJECT_METADATA_FOR_LABEL = "Metadata item for label";
/**
* Text to display at beginning of every label
*/
public static final String PREFIX = "Prefix";
/**
* Text to display at end of every label
*/
public static final String SUFFIX = "Suffix";
/**
*
*/
public static final String LOCATION_SEPARATOR = "Overlay location";
/**
* Determines the method used for placing the label overlay for each object:
*
* - "Centre of object" Labels will be placed at the centroid (average
* coordinate location) of each object. This position won't necessarily coincide
* with a region corresponding to that object. For example, the centroid of a
* crescent shape won't lie on the crescent itself.
* - "Fixed value" Labels will be placed at the x,y,z location specified by
* the user.
* - "Inside largest part of object" Labels will be placed coincident with the
* largest region of each object. This ensures the label is placed directly over
* the relevant object.
* - "Object measurement" Labels will be placed coincident with the specified
* measurements for each object.
*
*/
public static final String LABEL_POSITION = "Label position";
/**
* Object measurement specifying the X-position of the label. Measurement value
* must be specified in pixel units.
*/
public static final String X_POSITION_MEASUREMENT = "X-position measurement";
/**
* Object measurement specifying the Y-position of the label. Measurement value
* must be specified in pixel units.
*/
public static final String Y_POSITION_MEASUREMENT = "Y-position measurement";
/**
* Object measurement specifying the Z-position (slice) of the label.
* Measurement value must be specified in slice units.
*/
public static final String Z_POSITION_MEASUREMENT = "Z-position measurement";
/**
* Fixed value specifying the X-position of the label. Specified in pixel units.
*/
public static final String X_POSITION = "X-position";
/**
* Fixed value specifying the Y-position of the label. Specified in pixel units.
*/
public static final String Y_POSITION = "Y-position";
/**
* Fixed value specifying the Z-position of the label. Specified in pixel units.
*/
public static final String Z_POSITION = "Z-position";
/**
* Display overlay elements in all slices corresponding to that object.
*/
public static final String RENDER_IN_ALL_OBJECT_SLICES = "Render in all object slices";
/**
* Display overlay elements in all frames, irrespective of whether each object
* is present in that frame.
*/
public static final String RENDER_IN_ALL_FRAMES = "Render in all frames";
/**
*
*/
public static final String EXECUTION_SEPARATOR = "Execution controls";
/**
* Process multiple overlay elements simultaneously. This can provide a speed
* improvement when working on a computer with a multi-core CPU.
*/
public static final String ENABLE_MULTITHREADING = "Enable multithreading";
public AddLabels(Modules modules) {
super("Add labels", modules);
}
public interface LabelModes extends LabelFactory.LabelModes {
}
public interface LabelPositions {
String CENTRE = "Centre of object";
String FIXED_VALUE = "Fixed value";
String INSIDE = "Inside largest part of object";
String OBJECT_MEASUREMENT = "Object measurement";
String[] ALL = new String[] { CENTRE, FIXED_VALUE, INSIDE, OBJECT_MEASUREMENT };
}
public static double[] getMeanObjectLocation(Obj object) {
double xMean = object.getXMean(true);
double yMean = object.getYMean(true);
double zMean = object.getZMean(true, false);
int z = (int) Math.round(zMean + 1);
return new double[] { xMean, yMean, z };
}
public static double[] getInsideObjectLocation(Obj obj) {
// Binarise object and calculate its distance map
Image binaryImage = obj.getAsImage("Binary", false);
BinaryOperations2D.process(binaryImage, BinaryOperations2D.OperationModes.ERODE, 1, 1, true);
ImagePlus distanceIpl = DistanceMap
.process(binaryImage, "Distance", true, DistanceMap.WeightModes.WEIGHTS_3_4_5_7, true, false)
.getImagePlus();
ImageStack distanceIst = distanceIpl.getStack();
// Get location of largest value
Point bestPoint = null;
double distance = Double.MIN_VALUE;
for (Point point : obj.getCoordinateSet()) {
int idx = distanceIpl.getStackIndex(1, point.getZ() + 1, obj.getT() + 1);
float currDistance = distanceIst.getProcessor(idx).getf(point.getX(), point.getY());
if (currDistance > distance) {
distance = currDistance;
bestPoint = point;
}
}
// Returning this point
return new double[] { bestPoint.getX(), bestPoint.getY(), bestPoint.getZ() + 1 };
}
public static double[] getMeasurementObjectLocation(Obj obj, String[] measurements) {
double x;
double y;
double z;
if (obj.getMeasurement(measurements[0]) != null)
x = obj.getMeasurement(measurements[0]).getValue();
else
x = 0;
if (obj.getMeasurement(measurements[1]) != null)
y = obj.getMeasurement(measurements[1]).getValue();
else
y = 0;
if (obj.getMeasurement(measurements[2]) != null)
z = obj.getMeasurement(measurements[2]).getValue();
else
z = 0;
// Returning this point
return new double[] { x, y, z };
}
public static void addOverlay(ImagePlus ipl, Objs inputObjects, String labelPosition,
HashMap labels, int labelSize, int xOffset, int yOffset, boolean centreText,
HashMap colours,
boolean renderInAllSlices, boolean renderInAllFrames, boolean multithread,
@Nullable String[] measurementNames, @Nullable int[] positions) {
// If necessary, turning the image into a HyperStack (if 2 dimensions=1 it will
// be a standard ImagePlus)
if (!ipl.isComposite() & (ipl.getNSlices() > 1 | ipl.getNFrames() > 1 | ipl.getNChannels() > 1))
ipl = HyperStackConverter.toHyperStack(ipl, ipl.getNChannels(), ipl.getNSlices(), ipl.getNFrames());
// Adding the overlay element
try {
int nThreads = multithread ? Prefs.getThreads() : 1;
ThreadPoolExecutor pool = new ThreadPoolExecutor(nThreads, nThreads, 0L, TimeUnit.MILLISECONDS,
new LinkedBlockingQueue<>());
// Running through each object, adding it to the overlay along with an ID label
for (Obj object : inputObjects.values()) {
ImagePlus finalIpl = ipl;
Runnable task = () -> {
int t1 = object.getT() + 1;
int t2 = object.getT() + 1;
if (renderInAllFrames) {
t1 = 1;
t2 = finalIpl.getNFrames();
}
Color colour = colours.get(object.getID());
String label = labels == null ? "" : labels.get(object.getID());
double[] location;
switch (labelPosition) {
case LabelPositions.CENTRE:
default:
location = getMeanObjectLocation(object);
break;
case LabelPositions.FIXED_VALUE:
location = new double[] { positions[0], positions[1], positions[2] };
break;
case LabelPositions.INSIDE:
location = getInsideObjectLocation(object);
break;
case LabelPositions.OBJECT_MEASUREMENT:
location = getMeasurementObjectLocation(object, measurementNames);
break;
}
location[0] = location[0] + xOffset;
location[1] = location[1] + yOffset;
for (int t = t1; t <= t2; t++) {
if (renderInAllSlices) {
double[][] extents = object.getExtents(true, false);
int zMin = (int) Math.round(extents[2][0]);
int zMax = (int) Math.round(extents[2][1]);
for (int z = zMin; z <= zMax; z++) {
location[2] = z + 1;
addOverlay(finalIpl, label, location, t, colour, labelSize, centreText);
}
} else {
addOverlay(finalIpl, label, location, t, colour, labelSize, centreText);
}
}
};
pool.submit(task);
}
pool.shutdown();
pool.awaitTermination(Integer.MAX_VALUE, TimeUnit.DAYS); // i.e. never terminate early
} catch (InterruptedException e) {
// Do nothing as the user has selected this
}
}
public static void addOverlay(ImagePlus ipl, String label, double[] labelCoords, int t, Color colour, int labelSize,
boolean centreText) {
if (ipl.getOverlay() == null)
ipl.setOverlay(new ij.gui.Overlay());
// Adding text label
TextRoi text = new TextRoi(labelCoords[0], labelCoords[1], label,
new Font(Font.SANS_SERIF, Font.PLAIN, labelSize));
text.setStrokeColor(colour);
text.setAntialiased(true);
if (ipl.isHyperStack()) {
text.setPosition(1, (int) labelCoords[2], t);
} else {
text.setPosition((int) Math.max(Math.max(1, labelCoords[2]), t));
}
if (centreText) {
text.setLocation(text.getXBase() - text.getFloatWidth() / 2 + 1,
text.getYBase() - text.getFloatHeight() / 2 + 1);
}
ipl.getOverlay().addElement(text);
}
public HashMap getLabels(Objs inputObjects, String labelMode, DecimalFormat df,
String childObjectsForLabelName, String parentObjectsForLabelName, String partnerObjectsForLabelName,
String measurementForLabel, String objectMetadataForLabel) {
switch (labelMode) {
case LabelModes.CHILD_COUNT:
return LabelFactory.getChildCountLabels(inputObjects, childObjectsForLabelName, df);
case LabelModes.ID:
return LabelFactory.getIDLabels(inputObjects, df);
case LabelModes.MEASUREMENT_VALUE:
return LabelFactory.getMeasurementLabels(inputObjects, measurementForLabel, df);
case LabelModes.OBJECT_METADATA_ITEM:
return LabelFactory.getObjectMetadataLabels(inputObjects, objectMetadataForLabel, df);
case LabelModes.PARENT_ID:
return LabelFactory.getParentIDLabels(inputObjects, parentObjectsForLabelName, df);
case LabelModes.PARENT_MEASUREMENT_VALUE:
return LabelFactory.getParentMeasurementLabels(inputObjects, parentObjectsForLabelName,
measurementForLabel,
df);
case LabelModes.PARTNER_COUNT:
return LabelFactory.getPartnerCountLabels(inputObjects, partnerObjectsForLabelName, df);
}
return null;
}
public void appendPrefixSuffix(HashMap labels, String prefix, String suffix) {
if (prefix.equals("") && suffix.equals(""))
return;
for (int key : labels.keySet()) {
String label = labels.get(key);
labels.put(key, prefix + label + suffix);
}
}
@Override
public Category getCategory() {
return Categories.VISUALISATION_OVERLAYS;
}
@Override
public String getVersionNumber() {
return "1.0.0";
}
@Override
public String getDescription() {
return "Adds an overlay to the specified input image with each object represented by a text label. The label can include information such as measurements, associated object counts or ID numbers.";
}
@Override
protected Status process(Workspace workspace) {
// Getting parameters
boolean applyToInput = parameters.getValue(APPLY_TO_INPUT, workspace);
boolean addOutputToWorkspace = parameters.getValue(ADD_OUTPUT_TO_WORKSPACE, workspace);
String outputImageName = parameters.getValue(OUTPUT_IMAGE, workspace);
// Getting input objects
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
Objs inputObjects = workspace.getObjects().get(inputObjectsName);
// Getting input image
String inputImageName = parameters.getValue(INPUT_IMAGE, workspace);
Image inputImage = workspace.getImages().get(inputImageName);
ImagePlus ipl = inputImage.getImagePlus();
// Getting label settings
String labelMode = parameters.getValue(LABEL_MODE, workspace);
int labelSize = parameters.getValue(LABEL_SIZE, workspace);
int xOffset = parameters.getValue(X_OFFSET, workspace);
int yOffset = parameters.getValue(Y_OFFSET, workspace);
boolean centreText = parameters.getValue(CENTRE_TEXT, workspace);
int decimalPlaces = parameters.getValue(DECIMAL_PLACES, workspace);
boolean useScientific = parameters.getValue(USE_SCIENTIFIC, workspace);
String childObjectsForLabelName = parameters.getValue(CHILD_OBJECTS_FOR_LABEL, workspace);
String parentObjectsForLabelName = parameters.getValue(PARENT_OBJECT_FOR_LABEL, workspace);
String partnerObjectsForLabelName = parameters.getValue(PARTNER_OBJECTS_FOR_LABEL, workspace);
String measurementForLabel = parameters.getValue(MEASUREMENT_FOR_LABEL, workspace);
String objectMetadataForLabel = parameters.getValue(OBJECT_METADATA_FOR_LABEL, workspace);
String prefix = parameters.getValue(PREFIX, workspace);
String suffix = parameters.getValue(SUFFIX, workspace);
String labelPosition = parameters.getValue(LABEL_POSITION, workspace);
String xPosMeas = parameters.getValue(X_POSITION_MEASUREMENT, workspace);
String yPosMeas = parameters.getValue(Y_POSITION_MEASUREMENT, workspace);
String zPosMeas = parameters.getValue(Z_POSITION_MEASUREMENT, workspace);
int xPos = parameters.getValue(X_POSITION, workspace);
int yPos = parameters.getValue(Y_POSITION, workspace);
int zPos = parameters.getValue(Z_POSITION, workspace);
boolean renderInAllSlices = parameters.getValue(RENDER_IN_ALL_OBJECT_SLICES, workspace);
boolean renderInAllFrames = parameters.getValue(RENDER_IN_ALL_FRAMES, workspace);
boolean multithread = parameters.getValue(ENABLE_MULTITHREADING, workspace);
String[] measurementNames = new String[] { xPosMeas, yPosMeas, zPosMeas };
int[] positions = new int[] { xPos, yPos, zPos };
// Only add output to workspace if not applying to input
if (applyToInput)
addOutputToWorkspace = false;
// Duplicating the image, so the original isn't altered
if (!applyToInput)
ipl = new Duplicator().run(ipl);
// Generating colours for each object
HashMap colours = getColours(inputObjects, workspace);
DecimalFormat df = LabelFactory.getDecimalFormat(decimalPlaces, useScientific);
HashMap labels = getLabels(inputObjects, labelMode, df, childObjectsForLabelName,
parentObjectsForLabelName, partnerObjectsForLabelName, measurementForLabel, objectMetadataForLabel);
appendPrefixSuffix(labels, prefix, suffix);
addOverlay(ipl, inputObjects, labelPosition, labels, labelSize, xOffset, yOffset, centreText, colours,
renderInAllSlices,
renderInAllFrames, multithread, measurementNames, positions);
Image outputImage = ImageFactory.createImage(outputImageName, ipl);
// If necessary, adding output image to workspace. This also allows us to show
// it.
if (addOutputToWorkspace)
workspace.addImage(outputImage);
if (showOutput)
outputImage.show();
return Status.PASS;
}
@Override
protected void initialiseParameters() {
super.initialiseParameters();
parameters.add(new SeparatorP(INPUT_SEPARATOR, this));
parameters.add(new InputImageP(INPUT_IMAGE, this));
parameters.add(new InputObjectsP(INPUT_OBJECTS, this));
parameters.add(new SeparatorP(OUTPUT_SEPARATOR, this));
parameters.add(new BooleanP(APPLY_TO_INPUT, this, false));
parameters.add(new BooleanP(ADD_OUTPUT_TO_WORKSPACE, this, false));
parameters.add(new OutputImageP(OUTPUT_IMAGE, this));
parameters.add(new SeparatorP(CONTENT_SEPARATOR, this));
parameters.add(new ChoiceP(LABEL_MODE, this, LabelModes.ID, LabelModes.ALL));
parameters.add(new IntegerP(DECIMAL_PLACES, this, 0));
parameters.add(new BooleanP(USE_SCIENTIFIC, this, false));
parameters.add(new IntegerP(LABEL_SIZE, this, 8));
parameters.add(new IntegerP(X_OFFSET, this, 0));
parameters.add(new IntegerP(Y_OFFSET, this, 0));
parameters.add(new BooleanP(CENTRE_TEXT, this, true));
parameters.add(new ChildObjectsP(CHILD_OBJECTS_FOR_LABEL, this));
parameters.add(new ParentObjectsP(PARENT_OBJECT_FOR_LABEL, this));
parameters.add(new PartnerObjectsP(PARTNER_OBJECTS_FOR_LABEL, this));
parameters.add(new ObjectMeasurementP(MEASUREMENT_FOR_LABEL, this));
parameters.add(new ObjectMetadataP(OBJECT_METADATA_FOR_LABEL, this));
parameters.add(new StringP(PREFIX, this));
parameters.add(new StringP(SUFFIX, this));
parameters.add(new SeparatorP(LOCATION_SEPARATOR, this));
parameters.add(new ChoiceP(LABEL_POSITION, this, LabelPositions.CENTRE, LabelPositions.ALL));
parameters.add(new ObjectMeasurementP(X_POSITION_MEASUREMENT, this));
parameters.add(new ObjectMeasurementP(Y_POSITION_MEASUREMENT, this));
parameters.add(new ObjectMeasurementP(Z_POSITION_MEASUREMENT, this));
parameters.add(new IntegerP(X_POSITION, this, 0));
parameters.add(new IntegerP(Y_POSITION, this, 0));
parameters.add(new IntegerP(Z_POSITION, this, 0));
parameters.add(new BooleanP(RENDER_IN_ALL_OBJECT_SLICES, this, false));
parameters.add(new BooleanP(RENDER_IN_ALL_FRAMES, this, false));
parameters.add(new SeparatorP(EXECUTION_SEPARATOR, this));
parameters.add(new BooleanP(ENABLE_MULTITHREADING, this, true));
addParameterDescriptions();
}
@Override
public Parameters updateAndGetParameters() {
Workspace workspace = null;
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
String parentObjectsName = parameters.getValue(PARENT_OBJECT_FOR_LABEL, workspace);
Parameters returnedParameters = new Parameters();
returnedParameters.add(parameters.getParameter(INPUT_SEPARATOR));
returnedParameters.add(parameters.getParameter(INPUT_IMAGE));
returnedParameters.add(parameters.getParameter(INPUT_OBJECTS));
returnedParameters.add(parameters.getParameter(OUTPUT_SEPARATOR));
returnedParameters.add(parameters.getParameter(APPLY_TO_INPUT));
if (!(boolean) parameters.getValue(APPLY_TO_INPUT, workspace)) {
returnedParameters.add(parameters.getParameter(ADD_OUTPUT_TO_WORKSPACE));
if ((boolean) parameters.getValue(ADD_OUTPUT_TO_WORKSPACE, workspace)) {
returnedParameters.add(parameters.getParameter(OUTPUT_IMAGE));
}
}
returnedParameters.add(parameters.getParameter(CONTENT_SEPARATOR));
returnedParameters.add(parameters.getParameter(LABEL_MODE));
switch ((String) parameters.getValue(LABEL_MODE, workspace)) {
case LabelModes.CHILD_COUNT:
returnedParameters.add(parameters.getParameter(CHILD_OBJECTS_FOR_LABEL));
((ChildObjectsP) parameters.getParameter(CHILD_OBJECTS_FOR_LABEL))
.setParentObjectsName(inputObjectsName);
break;
case LabelModes.MEASUREMENT_VALUE:
returnedParameters.add(parameters.getParameter(MEASUREMENT_FOR_LABEL));
((ObjectMeasurementP) parameters.getParameter(MEASUREMENT_FOR_LABEL)).setObjectName(inputObjectsName);
break;
case LabelModes.OBJECT_METADATA_ITEM:
returnedParameters.add(parameters.getParameter(OBJECT_METADATA_FOR_LABEL));
((ObjectMetadataP) parameters.getParameter(OBJECT_METADATA_FOR_LABEL)).setObjectName(inputObjectsName);
break;
case LabelModes.PARENT_ID:
returnedParameters.add(parameters.getParameter(PARENT_OBJECT_FOR_LABEL));
((ParentObjectsP) parameters.getParameter(PARENT_OBJECT_FOR_LABEL))
.setChildObjectsName(inputObjectsName);
break;
case LabelModes.PARENT_MEASUREMENT_VALUE:
returnedParameters.add(parameters.getParameter(PARENT_OBJECT_FOR_LABEL));
((ParentObjectsP) parameters.getParameter(PARENT_OBJECT_FOR_LABEL))
.setChildObjectsName(inputObjectsName);
returnedParameters.add(parameters.getParameter(MEASUREMENT_FOR_LABEL));
if (parentObjectsName != null) {
((ObjectMeasurementP) parameters.getParameter(MEASUREMENT_FOR_LABEL))
.setObjectName(parentObjectsName);
}
break;
case LabelModes.PARTNER_COUNT:
returnedParameters.add(parameters.getParameter(PARTNER_OBJECTS_FOR_LABEL));
((PartnerObjectsP) parameters.getParameter(PARTNER_OBJECTS_FOR_LABEL))
.setPartnerObjectsName(inputObjectsName);
break;
}
if (!((String) parameters.getValue(LABEL_MODE, workspace)).equals(LabelModes.OBJECT_METADATA_ITEM)) {
returnedParameters.add(parameters.getParameter(DECIMAL_PLACES));
returnedParameters.add(parameters.getParameter(USE_SCIENTIFIC));
}
returnedParameters.add(parameters.getParameter(LABEL_SIZE));
returnedParameters.add(parameters.getParameter(X_OFFSET));
returnedParameters.add(parameters.getParameter(Y_OFFSET));
returnedParameters.add(parameters.getParameter(CENTRE_TEXT));
returnedParameters.add(parameters.getParameter(PREFIX));
returnedParameters.add(parameters.getParameter(SUFFIX));
returnedParameters.addAll(super.updateAndGetParameters(inputObjectsName));
returnedParameters.add(parameters.getParameter(LOCATION_SEPARATOR));
returnedParameters.add(parameters.getParameter(LABEL_POSITION));
switch ((String) parameters.getValue(LABEL_POSITION, workspace)) {
default:
returnedParameters.add(parameters.getParameter(RENDER_IN_ALL_OBJECT_SLICES));
break;
case LabelPositions.FIXED_VALUE:
returnedParameters.add(parameters.getParameter(X_POSITION));
returnedParameters.add(parameters.getParameter(Y_POSITION));
returnedParameters.add(parameters.getParameter(RENDER_IN_ALL_OBJECT_SLICES));
if (!(boolean) parameters.getValue(RENDER_IN_ALL_OBJECT_SLICES, workspace))
returnedParameters.add(parameters.getParameter(Z_POSITION));
break;
case LabelPositions.OBJECT_MEASUREMENT:
returnedParameters.add(parameters.getParameter(X_POSITION_MEASUREMENT));
returnedParameters.add(parameters.getParameter(Y_POSITION_MEASUREMENT));
((ObjectMeasurementP) parameters.getParameter(X_POSITION_MEASUREMENT)).setObjectName(inputObjectsName);
((ObjectMeasurementP) parameters.getParameter(Y_POSITION_MEASUREMENT)).setObjectName(inputObjectsName);
returnedParameters.add(parameters.getParameter(RENDER_IN_ALL_OBJECT_SLICES));
if (!(boolean) parameters.getValue(RENDER_IN_ALL_OBJECT_SLICES, workspace)) {
returnedParameters.add(parameters.getParameter(Z_POSITION_MEASUREMENT));
((ObjectMeasurementP) parameters.getParameter(Z_POSITION_MEASUREMENT))
.setObjectName(inputObjectsName);
}
break;
}
returnedParameters.add(parameters.getParameter(RENDER_IN_ALL_FRAMES));
returnedParameters.add(parameters.getParameter(EXECUTION_SEPARATOR));
returnedParameters.add(parameters.getParameter(ENABLE_MULTITHREADING));
return returnedParameters;
}
@Override
public ImageMeasurementRefs updateAndGetImageMeasurementRefs() {
return null;
}
@Override
public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
return null;
}
@Override
public ObjMetadataRefs updateAndGetObjectMetadataRefs() {
return null;
}
@Override
public MetadataRefs updateAndGetMetadataReferences() {
return null;
}
@Override
public ParentChildRefs updateAndGetParentChildRefs() {
return null;
}
@Override
public PartnerRefs updateAndGetPartnerRefs() {
return null;
}
@Override
public boolean verify() {
return true;
}
@Override
protected void addParameterDescriptions() {
super.addParameterDescriptions();
parameters.get(INPUT_IMAGE)
.setDescription("Image onto which overlay will be rendered. Input image will only be updated if \""
+ APPLY_TO_INPUT
+ "\" is enabled, otherwise the image containing the overlay will be stored as a new image with name specified by \""
+ OUTPUT_IMAGE + "\".");
parameters.get(INPUT_OBJECTS).setDescription("Objects to represent as overlays.");
parameters.get(APPLY_TO_INPUT).setDescription(
"Determines if the modifications made to the input image (added overlay elements) will be applied to that image or directed to a new image. When selected, the input image will be updated.");
parameters.get(ADD_OUTPUT_TO_WORKSPACE).setDescription(
"If the modifications (overlay) aren't being applied directly to the input image, this control will determine if a separate image containing the overlay should be saved to the workspace.");
parameters.get(OUTPUT_IMAGE).setDescription(
"The name of the new image to be saved to the workspace (if not applying the changes directly to the input image).");
parameters.get(LABEL_MODE).setDescription("Controls what information each label displays:
"
+ "- \"" + LabelModes.CHILD_COUNT
+ "\" The number of children from a specific object collection for each object. The children to summarise are selected using the \""
+ CHILD_OBJECTS_FOR_LABEL + "\" parameter.
"
+ "- \"" + LabelModes.ID + "\" The ID number of the object.
"
+ "- \"" + LabelModes.MEASUREMENT_VALUE
+ "\" A measurement associated with the object. The measurement is selected using the \""
+ MEASUREMENT_FOR_LABEL + "\" parameter.
"
+ "- \"" + LabelModes.PARENT_ID
+ "\" The ID number of a parent of the object. The parent object is selected using the \""
+ PARENT_OBJECT_FOR_LABEL + "\" parameter.
"
+ "- \"" + LabelModes.PARENT_MEASUREMENT_VALUE
+ "\" A measurement associated with a parent of the object. The measurement is selected using the \""
+ MEASUREMENT_FOR_LABEL + "\" parameter and the parent object with the \"" + PARENT_OBJECT_FOR_LABEL
+ "\" parameter.
"
+ "- \"" + LabelModes.PARTNER_COUNT
+ "\" The number of partners from a specific object collection for each object. The partners to summarise are selected using the \""
+ PARTNER_OBJECTS_FOR_LABEL + "\" parameter.
");
parameters.get(DECIMAL_PLACES)
.setDescription("Number of decimal places to use when displaying numeric values.");
parameters.get(USE_SCIENTIFIC).setDescription(
"When enabled, numeric values will be displayed in the format 1.23E-3. Otherwise, the same value would appear as 0.00123.");
parameters.get(LABEL_SIZE).setDescription("Font size of the text label.");
parameters.get(X_OFFSET).setDescription(
"Offset the label by this number of pixels horizontally (along the x-axis). Increasingly positive numbers move the label right.");
parameters.get(Y_OFFSET).setDescription(
"Offset the label by this number of pixels vertically (along the y-axis). Increasingly positive numbers move the label down.");
parameters.get(PREFIX).setDescription("Text to display at beginning of every label");
parameters.get(SUFFIX).setDescription("Text to display at end of every label");
parameters.get(CHILD_OBJECTS_FOR_LABEL).setDescription("If \"" + LABEL_MODE + "\" is set to \""
+ LabelModes.CHILD_COUNT
+ "\", these are the child objects which will be counted and displayed on the label. These objects will be children of the input objects.");
parameters.get(PARENT_OBJECT_FOR_LABEL).setDescription("If \"" + LABEL_MODE + "\" is set to either \""
+ LabelModes.PARENT_ID + "\" or \"" + LabelModes.PARENT_MEASUREMENT_VALUE
+ "\", these are the parent objects which will be used. These objects will be parents of the input objects.");
parameters.get(PARTNER_OBJECTS_FOR_LABEL).setDescription("If \"" + LABEL_MODE + "\" is set to \""
+ LabelModes.PARTNER_COUNT
+ "\", these are the partner objects which will be counted and displayed on the label. These objects will be partners of the input objects.");
parameters.get(MEASUREMENT_FOR_LABEL)
.setDescription("If \"" + LABEL_MODE + "\" is set to either \"" + LabelModes.MEASUREMENT_VALUE
+ "\" or \"" + LabelModes.PARENT_MEASUREMENT_VALUE
+ "\", these are the measurements which will be used.");
parameters.get(LABEL_POSITION)
.setDescription("Determines the method used for placing the label overlay for each object:
"
+ "- \"" + LabelPositions.CENTRE
+ "\" Labels will be placed at the centroid (average coordinate location) of each object. This position won't necessarily coincide with a region corresponding to that object. For example, the centroid of a crescent shape won't lie on the crescent itself.
"
+ "- \"" + LabelPositions.FIXED_VALUE
+ "\" Labels will be placed at the x,y,z location specified by the user.
"
+ "- \"" + LabelPositions.INSIDE
+ "\" Labels will be placed coincident with the largest region of each object. This ensures the label is placed directly over the relevant object.
"
+ "\"" + LabelPositions.OBJECT_MEASUREMENT
+ "\" Labels will be placed coincident with the specified measurements for each object. ");
parameters.get(X_POSITION_MEASUREMENT).setDescription(
"Object measurement specifying the X-position of the label. Measurement value must be specified in pixel units.");
parameters.get(Y_POSITION_MEASUREMENT).setDescription(
"Object measurement specifying the Y-position of the label. Measurement value must be specified in pixel units.");
parameters.get(Z_POSITION_MEASUREMENT).setDescription(
"Object measurement specifying the Z-position (slice) of the label. Measurement value must be specified in slice units.");
parameters.get(X_POSITION).setDescription(
"Fixed value specifying the X-position of the label. Specified in pixel units.");
parameters.get(Y_POSITION).setDescription(
"Fixed value specifying the Y-position of the label. Specified in pixel units.");
parameters.get(Z_POSITION).setDescription(
"Fixed value specifying the Z-position of the label. Specified in pixel units.");
parameters.get(RENDER_IN_ALL_OBJECT_SLICES)
.setDescription("Display overlay elements in all slices corresponding to that object.");
parameters.get(RENDER_IN_ALL_FRAMES).setDescription(
"Display overlay elements in all frames, irrespective of whether each object is present in that frame.");
parameters.get(ENABLE_MULTITHREADING).setDescription(
"Process multiple overlay elements simultaneously. This can provide a speed improvement when working on a computer with a multi-core CPU.");
}
}