Examples with Measurement io.github.mianalysis.mia.object.Measurement used on opensource projects

Example 41 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class RegisterImages method addManualMeasurements.

static void addManualMeasurements(Image image, AbstractAffineModel2D model) {
    AffineTransform transform = model.createAffine();
    image.addMeasurement(new Measurement(Measurements.TRANSLATE_X, transform.getTranslateX()));
    image.addMeasurement(new Measurement(Measurements.TRANSLATE_Y, transform.getTranslateY()));
    image.addMeasurement(new Measurement(Measurements.SCALE_X, transform.getScaleX()));
    image.addMeasurement(new Measurement(Measurements.SCALE_Y, transform.getScaleY()));
    image.addMeasurement(new Measurement(Measurements.SHEAR_X, transform.getShearX()));
    image.addMeasurement(new Measurement(Measurements.SHEAR_Y, transform.getShearY()));
}

Example 42 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class RectangleHoughDetection method process.

@Override
public Status process(Workspace workspace) {
    // Getting input image
    String inputImageName = parameters.getValue(INPUT_IMAGE);
    Image inputImage = workspace.getImage(inputImageName);
    ImagePlus ipl = inputImage.getImagePlus();
    // Getting parameters
    String outputObjectsName = parameters.getValue(OUTPUT_OBJECTS);
    boolean outputTransformImage = parameters.getValue(OUTPUT_TRANSFORM_IMAGE);
    String outputImageName = parameters.getValue(OUTPUT_IMAGE);
    // Getting parameters
    String xRange = parameters.getValue(X_RANGE);
    String yRange = parameters.getValue(Y_RANGE);
    String widthRange = parameters.getValue(WIDTH_RANGE);
    String lengthRange = parameters.getValue(LENGTH_RANGE);
    String oriRange = parameters.getValue(ORIENTATION_RANGE);
    int samplingRate = parameters.getValue(DOWNSAMPLE_FACTOR);
    boolean multithread = parameters.getValue(ENABLE_MULTITHREADING);
    boolean normaliseScores = parameters.getValue(NORMALISE_SCORES);
    String detectionMode = parameters.getValue(DETECTION_MODE);
    double detectionThreshold = parameters.getValue(DETECTION_THRESHOLD);
    int nObjects = parameters.getValue(NUMBER_OF_OBJECTS);
    int exclusionRadius = parameters.getValue(EXCLUSION_RADIUS);
    boolean showTransformImage = parameters.getValue(SHOW_TRANSFORM_IMAGE);
    boolean showDetectionImage = parameters.getValue(SHOW_DETECTION_IMAGE);
    boolean showHoughScore = parameters.getValue(SHOW_HOUGH_SCORE);
    int labelSize = parameters.getValue(LABEL_SIZE);
    // Storing the image calibration
    SpatCal cal = SpatCal.getFromImage(ipl);
    int nFrames = ipl.getNFrames();
    double frameInterval = ipl.getCalibration().frameInterval;
    Objs outputObjects = new Objs(outputObjectsName, cal, nFrames, frameInterval, TemporalUnit.getOMEUnit());
    xRange = resampleRange(xRange, samplingRate);
    yRange = resampleRange(yRange, samplingRate);
    widthRange = resampleRange(widthRange, samplingRate);
    lengthRange = resampleRange(lengthRange, samplingRate);
    int nThreads = multithread ? Prefs.getThreads() : 1;
    // Iterating over all images in the ImagePlus
    int count = 1;
    int total = ipl.getNChannels() * ipl.getNSlices() * ipl.getNFrames();
    for (int c = 0; c < ipl.getNChannels(); c++) {
        for (int z = 0; z < ipl.getNSlices(); z++) {
            for (int t = 0; t < ipl.getNFrames(); t++) {
                ipl.setPosition(c + 1, z + 1, t + 1);
                // Applying scaling
                ImageProcessor ipr = ipl.getProcessor();
                if (samplingRate != 1)
                    ipr = ipr.resize(ipr.getWidth() / samplingRate);
                // Initialising the Hough transform
                String[] paramRanges = new String[] { xRange, yRange, widthRange, lengthRange, oriRange };
                RectangleTransform transform = new RectangleTransform(ipr, paramRanges);
                transform.setnThreads(nThreads);
                // Running the transforms
                transform.run();
                // Normalising scores based on the number of points in that rectangle
                if (normaliseScores)
                    transform.normaliseScores();
                // Getting the accumulator as an image
                if (outputTransformImage || (showOutput && showTransformImage)) {
                    ImagePlus showIpl = new Duplicator().run(transform.getAccumulatorAsImage());
                    if (outputTransformImage) {
                        Image outputImage = new Image(outputImageName, showIpl);
                        workspace.addImage(outputImage);
                    }
                    if (showOutput && showTransformImage) {
                        IntensityMinMax.run(showIpl, true);
                        showIpl.setTitle("Accumulator");
                        showIpl.show();
                    }
                }
                // Getting rectangle objects and adding to workspace
                ArrayList<double[]> rectangles;
                switch(detectionMode) {
                    default:
                    case DetectionModes.ALL_ABOVE_SCORE:
                        rectangles = transform.getObjects(detectionThreshold, exclusionRadius);
                        break;
                    case DetectionModes.N_HIGHEST_SCORES:
                        rectangles = transform.getNObjects(nObjects, exclusionRadius);
                        break;
                }
                for (double[] rectangle : rectangles) {
                    // Initialising the object
                    Obj outputObject = outputObjects.createAndAddNewObject(VolumeType.QUADTREE);
                    // Getting rectangle parameters
                    int x = (int) Math.round(rectangle[0]) * samplingRate;
                    int y = (int) Math.round(rectangle[1]) * samplingRate;
                    int w = (int) Math.round(rectangle[2]) * samplingRate;
                    int l = (int) Math.round(rectangle[3]) * samplingRate;
                    int ori = (int) Math.round(rectangle[4]);
                    double score = rectangle[5];
                    double thetaRads = -Math.toRadians((double) ori);
                    int x1 = (int) Math.round((-l / 2) * Math.cos(thetaRads));
                    int y1 = (int) Math.round(-(-l / 2) * Math.sin(thetaRads));
                    RotatedRectRoi roi = new RotatedRectRoi(x + x1, y + y1, x - x1, y - y1, w);
                    for (Point point : roi.getContainedPoints()) {
                        try {
                            try {
                                outputObject.add(point.x, point.y, z);
                            } catch (PointOutOfRangeException e) {
                            }
                        } catch (IntegerOverflowException e) {
                            return Status.FAIL;
                        }
                    }
                    // Adding measurements
                    outputObject.setT(t);
                    outputObject.addMeasurement(new Measurement(Measurements.SCORE, score));
                }
                writeProgressStatus(count++, total, "images");
            }
        }
    }
    ipl.setPosition(1, 1, 1);
    workspace.addObjects(outputObjects);
    if (showOutput && showDetectionImage)
        showDetectionImage(inputImage, outputObjects, showHoughScore, labelSize);
    return Status.PASS;
}

Example 43 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class ColourFactoryTest method testGetColoursMeasurementColour.

@ParameterizedTest
@EnumSource(VolumeType.class)
public void testGetColoursMeasurementColour(VolumeType volumeType) {
    // Setting calibration parameters
    double dppXY = 0.02;
    double dppZ = 0.1;
    String calibratedUnits = "µm";
    SpatCal calibration = new SpatCal(dppXY, dppZ, calibratedUnits, 1, 1, 1);
    // Creating the Objs
    Objs collection = new Objs("Obj", calibration, 1, 0.02, UNITS.SECOND);
    // Adding objects
    Obj obj = collection.createAndAddNewObject(volumeType, 0);
    Measurement meas = new Measurement("Meas", 3.2);
    obj.addMeasurement(meas);
    collection.add(obj);
    obj = collection.createAndAddNewObject(volumeType, 1);
    meas = new Measurement("Meas", -0.1);
    obj.addMeasurement(meas);
    collection.add(obj);
    obj = collection.createAndAddNewObject(volumeType, 2);
    meas = new Measurement("Meas", Double.NaN);
    obj.addMeasurement(meas);
    collection.add(obj);
    HashMap<Integer, Float> hues = ColourFactory.getMeasurementValueHues(collection, "Meas", false, new double[] { Double.NaN, Double.NaN });
    HashMap<Integer, Color> actual = ColourFactory.getColours(hues, 100);
    // For random numbers we don't know what value they will have
    assertEquals(3, actual.size());
    assertEquals(Color.getHSBColor(3.2f, 1f, 1f), actual.get(0));
    assertEquals(Color.getHSBColor(-0.1f, 1f, 1f), actual.get(1));
    assertEquals(Color.getHSBColor(1f, 1f, 1f), actual.get(2));
}

Example 44 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class ColourFactoryTest method testGetHuesIDColourNormalised.

@ParameterizedTest
@EnumSource(VolumeType.class)
public void testGetHuesIDColourNormalised(VolumeType volumeType) {
    // Setting calibration parameters
    double dppXY = 0.02;
    double dppZ = 0.1;
    String calibratedUnits = "µm";
    SpatCal calibration = new SpatCal(dppXY, dppZ, calibratedUnits, 1, 1, 1);
    // Creating the Objs
    Objs collection = new Objs("Obj", calibration, 1, 0.02, UNITS.SECOND);
    // Adding objects
    Obj obj = collection.createAndAddNewObject(volumeType, 0);
    Measurement meas = new Measurement("Meas", 3.2);
    obj.addMeasurement(meas);
    collection.add(obj);
    obj = collection.createAndAddNewObject(volumeType, 1);
    meas = new Measurement("Meas", -0.1);
    obj.addMeasurement(meas);
    collection.add(obj);
    obj = collection.createAndAddNewObject(volumeType, 2);
    meas = new Measurement("Meas", Double.NaN);
    obj.addMeasurement(meas);
    collection.add(obj);
    HashMap<Integer, Float> actual = ColourFactory.getIDHues(collection, true);
    // For random numbers we don't know what value they will have
    assertEquals(3, actual.size());
    assertEquals(0f, actual.get(0), tolerance);
    assertEquals(0.06f, actual.get(1), tolerance);
    assertEquals(0.13f, actual.get(2), tolerance);
}

Example 45 with Measurement

use of io.github.mianalysis.mia.object.Measurement in project mia by mianalysis.

the class LabelFactoryTest method testGetIDsMeasurement.

@ParameterizedTest
@EnumSource(VolumeType.class)
public void testGetIDsMeasurement(VolumeType volumeType) {
    // Setting calibration parameters
    double dppXY = 0.02;
    double dppZ = 0.1;
    String calibratedUnits = "µm";
    SpatCal calibration = new SpatCal(dppXY, dppZ, calibratedUnits, 1, 1, 1);
    // Creating the Objs
    Objs collection = new Objs("Obj", calibration, 1, 0.02, UNITS.SECOND);
    // Adding objects
    Obj obj = collection.createAndAddNewObject(volumeType, 0);
    Measurement meas = new Measurement("Meas", 3.2);
    obj.addMeasurement(meas);
    obj = collection.createAndAddNewObject(volumeType, 1);
    meas = new Measurement("Meas", -0.1);
    obj.addMeasurement(meas);
    obj = collection.createAndAddNewObject(volumeType, 2);
    meas = new Measurement("Meas", Double.NaN);
    obj.addMeasurement(meas);
    DecimalFormat df = LabelFactory.getDecimalFormat(2, false);
    HashMap<Integer, String> actual = LabelFactory.getMeasurementLabels(collection, "Meas", df);
    assertEquals(3, actual.size());
    assertEquals("3.20", actual.get(0));
    assertEquals("-0.10", actual.get(1));
    assertEquals("NA", actual.get(2));
}