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271
...ules/src/main/java/io/github/mianalysis/mia/module/visualise/plots/PlotTrackMotility.java
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| package io.github.mianalysis.mia.module.visualise.plots; | ||
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| import java.awt.Color; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
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| import org.scijava.Priority; | ||
| import org.scijava.plugin.Plugin; | ||
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| import com.google.common.primitives.Doubles; | ||
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| import ij.gui.Plot; | ||
| 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.visualise.overlays.AbstractOverlay; | ||
| 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.ChoiceP; | ||
| import io.github.mianalysis.mia.object.parameters.ObjectMeasurementP; | ||
| import io.github.mianalysis.mia.object.parameters.ObjectMetadataP; | ||
| 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.ChildObjectsP; | ||
| import io.github.mianalysis.mia.object.parameters.InputObjectsP; | ||
| import io.github.mianalysis.mia.object.parameters.OutputImageP; | ||
| import io.github.mianalysis.mia.object.parameters.SeparatorP; | ||
| import io.github.mianalysis.mia.object.parameters.text.DoubleP; | ||
| 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; | ||
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| @Plugin(type = Module.class, priority = Priority.LOW, visible = true) | ||
| public class PlotTrackMotility extends AbstractOverlay { | ||
| public static final String INPUT_SEPARATOR = "Object input/image output"; | ||
| public static final String INPUT_TRACKS = "Input tracks"; | ||
| public static final String INPUT_OBJECTS = "Input objects"; | ||
| public static final String OUTPUT_IMAGE = "Output image"; | ||
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| public static final String PLOT_SEPARATOR = "Plot controls"; | ||
| public static final String LINE_WIDTH = "Line width"; | ||
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| // public static final String AXIS_SEPARATOR = "Axis controls"; | ||
| // public static final String X_RANGE_MODE = "X-range mode"; | ||
| // public static final String X_RANGE_MIN = "X-range min"; | ||
| // public static final String X_RANGE_MAX = "X-range max"; | ||
| // public static final String Y_RANGE_MODE = "Y-range mode"; | ||
| // public static final String Y_RANGE_MIN = "Y-range min"; | ||
| // public static final String Y_RANGE_MAX = "Y-range max"; | ||
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| public PlotTrackMotility(Modules modules) { | ||
| super("Plot track motility", modules); | ||
| } | ||
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| @Override | ||
| public Category getCategory() { | ||
| return Categories.VISUALISATION_PLOTS; | ||
| } | ||
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| @Override | ||
| public String getVersionNumber() { | ||
| return "1.0.0"; | ||
| } | ||
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| @Override | ||
| public String getDescription() { | ||
| return ""; | ||
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| } | ||
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| public static double[][] getPositionValues(Obj trackObject, String objectsName) { | ||
| Objs childObjects = trackObject.getChildren(objectsName); | ||
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| // Find first object in track | ||
| int minT = Integer.MAX_VALUE; | ||
| Obj currObj = null; | ||
| for (Obj childObject:childObjects.values()) { | ||
| if (childObject.getT() < minT) { | ||
| minT = childObject.getT(); | ||
| currObj = childObject; | ||
| } | ||
| } | ||
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| // Creating stores for the coordinates | ||
| ArrayList<Double> x = new ArrayList<>(); | ||
| ArrayList<Double> y = new ArrayList<>(); | ||
| x.add(0d); | ||
| y.add(0d); | ||
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| // Iterating over each timepoint instance, adding a link to the previous object | ||
| double x0 = currObj.getXMean(true); | ||
| double y0 = currObj.getYMean(true); | ||
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| Objs nextObjects = currObj.getNextPartners(objectsName); | ||
| while (nextObjects.size() > 0) { | ||
| Obj nextObject = nextObjects.getFirst(); | ||
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| x.add(nextObject.getXMean(true)-x0); | ||
| y.add(nextObject.getYMean(true)-y0); | ||
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| nextObjects = nextObject.getNextPartners(objectsName); | ||
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| } | ||
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| double[][] positions = new double[2][x.size()]; | ||
| positions[0] = Doubles.toArray(x); | ||
| positions[1] = Doubles.toArray(y); | ||
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| return positions; | ||
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| } | ||
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| @Override | ||
| protected Status process(Workspace workspace) { | ||
| // Getting parameters | ||
| String inputTracksName = parameters.getValue(INPUT_TRACKS, workspace); | ||
| String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace); | ||
| String outputImageName = parameters.getValue(OUTPUT_IMAGE, workspace); | ||
| double lineWidth = parameters.getValue(LINE_WIDTH, workspace); | ||
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| Objs trackObjects = workspace.getObjects(inputTracksName); | ||
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| // Creating plot | ||
| Plot plot = new Plot("Motility", "x-position (px)", "y-position (px)"); | ||
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| // Generating colours for each object | ||
| HashMap<Integer, Color> colours = getColours(trackObjects, workspace); | ||
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| // Iterating over each track, creating the plot | ||
| int count = 0; | ||
| double extreme = 0; | ||
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| for (Obj trackObject : trackObjects.values()) { | ||
| // Getting values to plot | ||
| double[][] posDouble = getPositionValues(trackObject, inputObjectsName); | ||
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| for (int i=0;i<posDouble[0].length;i++) { | ||
| if (Math.abs(posDouble[0][i]) > extreme) | ||
| extreme = Math.abs(posDouble[0][i]); | ||
| if (Math.abs(posDouble[1][i]) > extreme) | ||
| extreme = Math.abs(posDouble[1][i]); | ||
| } | ||
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| plot.setLineWidth((float) lineWidth); | ||
| plot.setColor(colours.get(trackObject.getID())); | ||
| plot.add("Line", posDouble[0], posDouble[1]); | ||
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| writeProgressStatus(count, trackObjects.size(), "tracks"); | ||
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| } | ||
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| plot.setLimits(-extreme,extreme,-extreme,extreme); | ||
| plot.setSize(640,640); | ||
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| Image outputImage = ImageFactory.createImage(outputImageName, plot.getImagePlus()); | ||
| workspace.addImage(outputImage); | ||
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| if (showOutput) | ||
| outputImage.show(); | ||
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| return Status.PASS; | ||
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| } | ||
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| @Override | ||
| protected void initialiseParameters() { | ||
| super.initialiseParameters(); | ||
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| parameters.add(new SeparatorP(INPUT_SEPARATOR, this)); | ||
| parameters.add(new InputObjectsP(INPUT_TRACKS, this)); | ||
| parameters.add(new ChildObjectsP(INPUT_OBJECTS, this)); | ||
| parameters.add(new OutputImageP(OUTPUT_IMAGE, this)); | ||
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| parameters.add(new SeparatorP(PLOT_SEPARATOR, this)); | ||
| parameters.add(new DoubleP(LINE_WIDTH, this, 1.0)); | ||
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| // parameters.add(new SeparatorP(AXIS_SEPARATOR, this)); | ||
| // parameters.add(new IntegerP(X_RANGE_MIN, this, 0)); | ||
| // parameters.add(new IntegerP(X_RANGE_MAX, this, 1)); | ||
| // parameters.add(new DoubleP(Y_RANGE_MIN, this, 0.0)); | ||
| // parameters.add(new DoubleP(Y_RANGE_MAX, this, 1.0)); | ||
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| } | ||
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| @Override | ||
| public Parameters updateAndGetParameters() { | ||
| Workspace workspace = null; | ||
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| Parameters returnedParameters = new Parameters(); | ||
| String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace); | ||
| String trackObjectsName = parameters.getValue(INPUT_TRACKS, workspace); | ||
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| returnedParameters.add(parameters.getParameter(INPUT_SEPARATOR)); | ||
| returnedParameters.add(parameters.getParameter(INPUT_TRACKS)); | ||
| returnedParameters.add(parameters.getParameter(INPUT_OBJECTS)); | ||
| ((ChildObjectsP) parameters.getParameter(INPUT_OBJECTS)).setParentObjectsName(trackObjectsName); | ||
| returnedParameters.add(parameters.getParameter(OUTPUT_IMAGE)); | ||
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| returnedParameters.add(parameters.getParameter(PLOT_SEPARATOR)); | ||
| returnedParameters.add(parameters.getParameter(LINE_WIDTH)); | ||
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| returnedParameters.addAll(super.updateAndGetParameters(inputObjectsName)); | ||
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| // returnedParameters.add(parameters.getParameter(AXIS_SEPARATOR)); | ||
| // returnedParameters.add(parameters.getParameter(X_RANGE_MODE)); | ||
| // switch ((String) parameters.getValue(X_RANGE_MODE, workspace)) { | ||
| // case AxisRangeModes.FIXED: | ||
| // returnedParameters.add(parameters.getParameter(X_RANGE_MIN)); | ||
| // returnedParameters.add(parameters.getParameter(X_RANGE_MAX)); | ||
| // break; | ||
| // } | ||
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| // returnedParameters.add(parameters.getParameter(Y_RANGE_MODE)); | ||
| // switch ((String) parameters.getValue(Y_RANGE_MODE, workspace)) { | ||
| // case AxisRangeModes.FIXED: | ||
| // returnedParameters.add(parameters.getParameter(Y_RANGE_MIN)); | ||
| // returnedParameters.add(parameters.getParameter(Y_RANGE_MAX)); | ||
| // break; | ||
| // } | ||
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| return returnedParameters; | ||
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| } | ||
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| @Override | ||
| public ImageMeasurementRefs updateAndGetImageMeasurementRefs() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public ObjMetadataRefs updateAndGetObjectMetadataRefs() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public MetadataRefs updateAndGetMetadataReferences() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public ParentChildRefs updateAndGetParentChildRefs() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public PartnerRefs updateAndGetPartnerRefs() { | ||
| return null; | ||
| } | ||
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| @Override | ||
| public boolean verify() { | ||
| return true; | ||
| } | ||
| } |