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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.util.HashMap;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.ThreadPoolExecutor;
import java.util.concurrent.TimeUnit;
import java.util.concurrent.atomic.AtomicInteger;
import org.scijava.Priority;
import org.scijava.plugin.Plugin;
import ij.ImagePlus;
import ij.Prefs;
import ij.gui.Roi;
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.object.Obj;
import io.github.mianalysis.mia.object.Objs;
import io.github.mianalysis.mia.object.Workspace;
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.InputImageP;
import io.github.mianalysis.mia.object.parameters.InputObjectsP;
import io.github.mianalysis.mia.object.parameters.OutputImageP;
import io.github.mianalysis.mia.object.parameters.Parameters;
import io.github.mianalysis.mia.object.parameters.SeparatorP;
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.ColourFactory;
/**
* Adds an overlay to the specified input image showing the extent of each specified input object as a filled shape. The opacity of the filled shape can be varied to see the image underneath.
*/
@Plugin(type = Module.class, priority = Priority.LOW, visible = true)
public class AddObjectFill extends AbstractOverlay {
/**
*
*/
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 RENDERING_SEPARATOR = "Overlay rendering";
/**
* Display the overlay elements in all frames (time axis) of the input image stack, irrespective of whether the object was 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 AddObjectFill(Modules modules) {
super("Add object fill", modules);
}
public interface ColourModes extends AbstractOverlay.ColourModes {
}
public interface SingleColours extends ColourFactory.SingleColours {
}
public static void addOverlay(ImagePlus ipl, Objs inputObjects, HashMap colours,
boolean renderInAllFrames, boolean multithread) {
String name = new AddObjectFill(null).getName();
// Adding the overlay element
try {
// 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());
}
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
AtomicInteger count = new AtomicInteger(1);
int total = inputObjects.size();
for (Obj object : inputObjects.values()) {
ImagePlus finalIpl = ipl;
Runnable task = () -> {
Color colour = colours.get(object.getID());
addOverlay(object, finalIpl, colour, renderInAllFrames);
writeProgressStatus(count.getAndIncrement(), total, "objects", name);
};
pool.submit(task);
}
pool.shutdown();
pool.awaitTermination(Integer.MAX_VALUE, TimeUnit.DAYS); // i.e. never terminate early
ipl.setPosition(1, 1, 1);
ipl.updateAndDraw();
} catch (InterruptedException e) {
// Do nothing as the user has selected this
return;
}
}
public static void addOverlay(Obj object, ImagePlus ipl, Color colour, boolean renderInAllFrames) {
if (ipl.getOverlay() == null)
ipl.setOverlay(new ij.gui.Overlay());
int t1 = object.getT() + 1;
int t2 = object.getT() + 1;
if (renderInAllFrames) {
t1 = 1;
t2 = ipl.getNFrames();
}
// Running through each slice of this object
double[][] range = object.getExtents(true, false);
// If this is a 2D object, add it to all slices
int minZ = (int) Math.floor(range[2][0]);
int maxZ = (int) Math.floor(range[2][1]);
if (object.is2D()) {
minZ = 0;
maxZ = ipl.getNSlices() - 1;
}
for (int t = t1; t <= t2; t++) {
for (int z = minZ; z <= maxZ; z++) {
Roi polyRoi = null;
if (object.is2D()) {
polyRoi = object.getRoi(0);
} else {
polyRoi = object.getRoi(z);
}
// If the object doesn't have any pixels in this plane, skip it
if (polyRoi == null)
continue;
if (ipl.isHyperStack()) {
polyRoi.setPosition(1, z + 1, t);
ipl.setPosition(1, z + 1, t);
} else {
int pos = Math.max(Math.max(1, z + 1), t);
polyRoi.setPosition(pos);
ipl.setPosition(pos);
}
polyRoi.setFillColor(colour);
ipl.getOverlay().addElement(polyRoi);
}
}
}
@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 showing the extent of each specified input object as a filled shape. The opacity of the filled shape can be varied to see the image underneath.";
}
@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();
boolean renderInAllFrames = parameters.getValue(RENDER_IN_ALL_FRAMES, workspace);
boolean multithread = parameters.getValue(ENABLE_MULTITHREADING, workspace);
// 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);
addOverlay(ipl, inputObjects, colours, renderInAllFrames, multithread);
Image outputImage = ImageFactory.createImage(outputImageName, ipl);
// If necessary, adding output image to workspace. This also allows us to show
// it.
if (!applyToInput && 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(RENDERING_SEPARATOR, this));
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);
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.addAll(super.updateAndGetParameters(inputObjectsName));
returnedParameters.add(parameters.getParameter(RENDERING_SEPARATOR));
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.getParameter(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.getParameter(INPUT_OBJECTS).setDescription("Objects to represent as overlays.");
parameters.getParameter(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.getParameter(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.getParameter(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.getParameter(RENDER_IN_ALL_FRAMES).setDescription(
"Display the overlay elements in all frames (time axis) of the input image stack, irrespective of whether the object was present in that frame.");
parameters.getParameter(ENABLE_MULTITHREADING).setDescription(
"Process multiple overlay elements simultaneously. This can provide a speed improvement when working on a computer with a multi-core CPU.");
}
}