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

Example 31 with Measurement

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

the class MeasureTrackMotion method calculateSpatialMeasurements.

public static void calculateSpatialMeasurements(Obj trackObject, Track track, boolean averageSubtracted) {
    if (track.size() == 0) {
        // Adding measurements to track objects
        String name = getFullName(Measurements.EUCLIDEAN_DISTANCE_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.EUCLIDEAN_DISTANCE_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.TOTAL_PATH_LENGTH_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.TOTAL_PATH_LENGTH_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.DIRECTIONALITY_RATIO, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
    } else {
        // If the track has a single time-point there's no velocity to measure
        double distPerPxXY = trackObject.getDppXY();
        double euclideanDistance = track.getEuclideanDistance();
        double totalPathLength = track.getTotalPathLength();
        String name = getFullName(Measurements.EUCLIDEAN_DISTANCE_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, euclideanDistance));
        name = getFullName(Measurements.EUCLIDEAN_DISTANCE_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, euclideanDistance * distPerPxXY));
        name = getFullName(Measurements.TOTAL_PATH_LENGTH_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, totalPathLength));
        name = getFullName(Measurements.TOTAL_PATH_LENGTH_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, totalPathLength * distPerPxXY));
        name = getFullName(Measurements.DIRECTIONALITY_RATIO, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, track.getDirectionalityRatio()));
    }
}

Example 32 with Measurement

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

the class FitLongestChord method processObject.

public void processObject(Obj object, boolean measureWidth, boolean measureOrientation, boolean storeEndPoints) {
    double dppXY = object.getDppXY();
    LongestChordCalculator calculator = new LongestChordCalculator(object);
    double longestChordLength = calculator.getLCLength();
    object.addMeasurement(new Measurement(Measurements.LENGTH_PX, longestChordLength));
    object.addMeasurement(new Measurement(Measurements.LENGTH_CAL, longestChordLength * dppXY));
    if (storeEndPoints) {
        double[][] LC = calculator.getLC();
        object.addMeasurement(new Measurement(Measurements.X1_PX, LC[0][0]));
        object.addMeasurement(new Measurement(Measurements.Y1_PX, LC[0][1]));
        object.addMeasurement(new Measurement(Measurements.Z1_SLICE, LC[0][2]));
        object.addMeasurement(new Measurement(Measurements.X2_PX, LC[1][0]));
        object.addMeasurement(new Measurement(Measurements.Y2_PX, LC[1][1]));
        object.addMeasurement(new Measurement(Measurements.Z2_SLICE, LC[1][2]));
    }
    if (measureWidth) {
        CumStat cumStat = calculator.calculateAverageDistanceFromLC();
        if (cumStat == null) {
            object.addMeasurement(new Measurement(Measurements.MEAN_SURF_DIST_PX, Double.NaN));
            object.addMeasurement(new Measurement(Measurements.MEAN_SURF_DIST_CAL, Double.NaN));
            object.addMeasurement(new Measurement(Measurements.STD_SURF_DIST_PX, Double.NaN));
            object.addMeasurement(new Measurement(Measurements.STD_SURF_DIST_CAL, Double.NaN));
            object.addMeasurement(new Measurement(Measurements.MAX_SURF_DIST_PX, Double.NaN));
            object.addMeasurement(new Measurement(Measurements.MAX_SURF_DIST_CAL, Double.NaN));
        } else {
            object.addMeasurement(new Measurement(Measurements.MEAN_SURF_DIST_PX, cumStat.getMean()));
            object.addMeasurement(new Measurement(Measurements.MEAN_SURF_DIST_CAL, cumStat.getMean() * dppXY));
            object.addMeasurement(new Measurement(Measurements.STD_SURF_DIST_PX, cumStat.getStd()));
            object.addMeasurement(new Measurement(Measurements.STD_SURF_DIST_CAL, cumStat.getStd() * dppXY));
            object.addMeasurement(new Measurement(Measurements.MAX_SURF_DIST_PX, cumStat.getMax()));
            object.addMeasurement(new Measurement(Measurements.MAX_SURF_DIST_CAL, cumStat.getMax() * dppXY));
        }
    }
    if (measureOrientation) {
        double orientationDegs = Math.toDegrees(calculator.getXYOrientationRads());
        // Ensuring the orientation is positive
        while (orientationDegs < 0) orientationDegs += 360;
        // Fitting to range -90 to + 90 degrees
        orientationDegs = (orientationDegs + 90) % 180 - 90;
        object.addMeasurement(new Measurement(Measurements.ORIENTATION_XY_DEGS, orientationDegs));
    }
}

Example 33 with Measurement

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

the class GetLocalObjectRegion method getCentroid.

protected int[] getCentroid(Obj inputObject) {
    String centroidSource = parameters.getValue(CENTROID_SOURCE);
    double xPosition = parameters.getValue(X_POSITION);
    double yPosition = parameters.getValue(Y_POSITION);
    double zPosition = parameters.getValue(Z_POSITION);
    String xMeasurementName = parameters.getValue(X_MEASUREMENT);
    String yMeasurementName = parameters.getValue(Y_MEASUREMENT);
    String zMeasurementName = parameters.getValue(Z_MEASUREMENT);
    String centroidParentObjectsName = parameters.getValue(PARENT_OBJECT_FOR_CENTROID);
    String centroidUnits = parameters.getValue(CENTROID_SPATIAL_UNITS);
    if (inputObject.is2D())
        zPosition = 0;
    switch(centroidSource) {
        case CentroidSources.MEASUREMENT:
            Measurement xMeasurement = inputObject.getMeasurement(xMeasurementName);
            Measurement yMeasurement = inputObject.getMeasurement(yMeasurementName);
            Measurement zMeasurement = inputObject.getMeasurement(zMeasurementName);
            if (xMeasurement == null || yMeasurement == null || (!inputObject.is2D() && zMeasurement == null))
                return null;
            xPosition = xMeasurement.getValue();
            yPosition = yMeasurement.getValue();
            if (!inputObject.is2D())
                zPosition = zMeasurement.getValue();
            break;
        case CentroidSources.OBJECT_CENTROID:
            xPosition = inputObject.getXMean(true);
            yPosition = inputObject.getYMean(true);
            if (!inputObject.is2D())
                zPosition = inputObject.getZMean(true, false);
            break;
        case CentroidSources.PARENT_MEASUREMENT:
            Obj parentObject = inputObject.getParent(centroidParentObjectsName);
            if (parentObject == null)
                return null;
            else {
                xMeasurement = parentObject.getMeasurement(xMeasurementName);
                yMeasurement = parentObject.getMeasurement(yMeasurementName);
                zMeasurement = parentObject.getMeasurement(zMeasurementName);
                if (xMeasurement == null || yMeasurement == null || (!inputObject.is2D() && zMeasurement == null))
                    return null;
                xPosition = xMeasurement.getValue();
                yPosition = yMeasurement.getValue();
                if (!inputObject.is2D())
                    zPosition = zMeasurement.getValue();
            }
            break;
    }
    switch(centroidUnits) {
        case SpatialUnits.CALIBRATED:
            xPosition = xPosition / inputObject.getDppXY();
            yPosition = yPosition / inputObject.getDppXY();
            if (!inputObject.is2D())
                zPosition = zPosition / inputObject.getDppXY();
            break;
    }
    return new int[] { (int) Math.round(xPosition), (int) Math.round(yPosition), (int) Math.round(zPosition) };
}

Example 34 with Measurement

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

the class FitGaussian2D method assignMeasurements.

static void assignMeasurements(Obj obj, ImageProcessor iprCrop, double[] p, int x, int y, int halfW) {
    double distPerPxXY = obj.getDppXY();
    double distPerPxZ = obj.getDppZ();
    double x0 = p[0] + x - halfW;
    double y0 = p[1] + y - halfW;
    double z0 = obj.getZMean(true, false);
    double sx = p[2];
    double sy = p[3];
    double A0 = p[4];
    double ABG = p[5];
    double th = p[6];
    double residual = calculateResidual(iprCrop, p);
    double ellipticity = sx > sy ? (sx - sy) / sx : (sy - sx) / sy;
    double sm = (sx + sy) / 2;
    // Storing the results as measurements
    obj.addMeasurement(new Measurement(Measurements.X0_PX, x0));
    obj.addMeasurement(new Measurement(Measurements.Y0_PX, y0));
    obj.addMeasurement(new Measurement(Measurements.Z0_SLICE, z0));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_X_PX, sx));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_Y_PX, sy));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_MEAN_PX, sm));
    obj.addMeasurement(new Measurement(Measurements.X0_CAL, x0 * distPerPxXY));
    obj.addMeasurement(new Measurement(Measurements.Y0_CAL, y0 * distPerPxXY));
    obj.addMeasurement(new Measurement(Measurements.Z0_CAL, z0 * distPerPxZ));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_X_CAL, sx * distPerPxXY));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_Y_CAL, sy * distPerPxXY));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_MEAN_CAL, sm * distPerPxXY));
    obj.addMeasurement(new Measurement(Measurements.A_0, A0));
    obj.addMeasurement(new Measurement(Measurements.A_BG, ABG));
    obj.addMeasurement(new Measurement(Measurements.THETA, th));
    obj.addMeasurement(new Measurement(Measurements.ELLIPTICITY, ellipticity));
    obj.addMeasurement(new Measurement(Measurements.RESIDUAL, residual));
}

Example 35 with Measurement

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

the class FitGaussian2D method assignMissingMeasurements.

static void assignMissingMeasurements(Obj obj) {
    obj.addMeasurement(new Measurement(Measurements.X0_PX, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.Y0_PX, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.Z0_SLICE, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_X_PX, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_Y_PX, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_MEAN_PX, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.X0_CAL, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.Y0_CAL, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.Z0_CAL, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_X_CAL, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_Y_CAL, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.SIGMA_MEAN_CAL, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.A_0, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.A_BG, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.THETA, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.ELLIPTICITY, Double.NaN));
    obj.addMeasurement(new Measurement(Measurements.RESIDUAL, Double.NaN));
}