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

Example 26 with Measurement

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

the class TrackObjects method linkObjects.

public static void linkObjects(Obj prevObj, Obj currObj, String trackObjectsName) {
    // Getting the track object from the previous-frame object
    Obj track = prevObj.getParent(trackObjectsName);
    // Setting relationship between the current object and track
    track.addChild(currObj);
    currObj.addParent(track);
    // Adding partner relationships between adjacent points in the track
    prevObj.addPartner(currObj);
    currObj.addPartner(prevObj);
    // Adding references to each other
    prevObj.addMeasurement(new Measurement(Measurements.TRACK_NEXT_ID, currObj.getID()));
    currObj.addMeasurement(new Measurement(Measurements.TRACK_PREV_ID, prevObj.getID()));
}

Example 27 with Measurement

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

the class ExtractObjectCrossSection method process.

@Override
public Status process(Workspace workspace) {
    // Getting input objects
    String inputObjectsName = parameters.getValue(INPUT_OBJECTS);
    Objs inputObjects = workspace.getObjects().get(inputObjectsName);
    // Getting parameters
    String outputObjectsName = parameters.getValue(OUTPUT_OBJECTS);
    String referenceMode = parameters.getValue(REFERENCE_MODE);
    String imageForMeasurementName = parameters.getValue(IMAGE_FOR_MEASUREMENT);
    String imageMeasurementName = parameters.getValue(IMAGE_MEASUREMENT);
    String objectMeasurementName = parameters.getValue(OBJECT_MEASUREMENT);
    String indicesString = parameters.getValue(RELATIVE_SLICE_INDICES);
    Objs outputObjects = new Objs(outputObjectsName, inputObjects);
    workspace.addObjects(outputObjects);
    int[] indices = CommaSeparatedStringInterpreter.interpretIntegers(indicesString, true, inputObjects.getNSlices());
    // same for all objects
    switch(referenceMode) {
        case ReferenceModes.IMAGE_MEASUREMENT:
            Image imageForMeasurement = workspace.getImage(imageForMeasurementName);
            Measurement imageMeasurement = imageForMeasurement.getMeasurement(imageMeasurementName);
            indices = applyIndexOffset(indices, imageMeasurement);
            break;
    }
    for (Obj inputObject : inputObjects.values()) {
        int[] finalIndices = indices;
        switch(referenceMode) {
            case ReferenceModes.OBJECT_MEASUREMENT:
                Measurement objectMeasurement = inputObject.getMeasurement(objectMeasurementName);
                finalIndices = applyIndexOffset(indices, objectMeasurement);
                break;
        }
        process(inputObject, outputObjects, finalIndices);
    }
    if (showOutput)
        outputObjects.convertToImageRandomColours().showImage();
    return Status.PASS;
}

Example 28 with Measurement

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

the class MeasureTrackMotion method calculateInstantaneousVelocity.

public static void calculateInstantaneousVelocity(Obj trackObject, Track track, String inputSpotObjectsName, boolean averageSubtracted) {
    double distPerPxXY = trackObject.getDppXY();
    double distPerPxZ = trackObject.getDppZ();
    TreeMap<Integer, Double> xVelocity = track.getInstantaneousXVelocity();
    TreeMap<Integer, Double> yVelocity = track.getInstantaneousYVelocity();
    TreeMap<Integer, Double> zVelocity = track.getInstantaneousZVelocity();
    TreeMap<Integer, Double> speed = track.getInstantaneousSpeed();
    // Getting the first timepoint
    int minT = Integer.MAX_VALUE;
    for (Obj spotObject : trackObject.getChildren(inputSpotObjectsName).values()) {
        minT = Math.min(minT, spotObject.getT());
    }
    for (Obj spotObject : trackObject.getChildren(inputSpotObjectsName).values()) {
        int t = spotObject.getT();
        // (rather than zero)
        if (t == minT) {
            String name = getFullName(Measurements.X_VELOCITY_PX, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, Double.NaN));
            name = getFullName(Measurements.X_VELOCITY_CAL, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, Double.NaN));
            name = getFullName(Measurements.Y_VELOCITY_PX, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, Double.NaN));
            name = getFullName(Measurements.Y_VELOCITY_CAL, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, Double.NaN));
            name = getFullName(Measurements.Z_VELOCITY_SLICES, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, Double.NaN));
            name = getFullName(Measurements.Z_VELOCITY_CAL, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, Double.NaN));
            name = getFullName(Measurements.INSTANTANEOUS_SPEED_PX, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, Double.NaN));
            name = getFullName(Measurements.INSTANTANEOUS_SPEED_CAL, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, Double.NaN));
        } else {
            String name = getFullName(Measurements.X_VELOCITY_PX, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, xVelocity.get(t)));
            name = getFullName(Measurements.X_VELOCITY_CAL, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, xVelocity.get(t) * distPerPxXY));
            name = getFullName(Measurements.Y_VELOCITY_PX, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, yVelocity.get(t)));
            name = getFullName(Measurements.Y_VELOCITY_CAL, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, yVelocity.get(t) * distPerPxXY));
            name = getFullName(Measurements.Z_VELOCITY_SLICES, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, zVelocity.get(t) * distPerPxXY / distPerPxZ));
            name = getFullName(Measurements.Z_VELOCITY_CAL, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, zVelocity.get(t) * distPerPxXY));
            name = getFullName(Measurements.INSTANTANEOUS_SPEED_PX, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, speed.get(t)));
            name = getFullName(Measurements.INSTANTANEOUS_SPEED_CAL, averageSubtracted);
            spotObject.addMeasurement(new Measurement(name, speed.get(t) * distPerPxXY));
        }
    }
}

Example 29 with Measurement

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

the class MeasureTrackMotion method calculateRelativeTimepoint.

public static void calculateRelativeTimepoint(Obj trackObject, Track track, String inputSpotObjectsName, boolean averageSubtracted) {
    if (track.size() == 0)
        return;
    int firstTimepoint = track.values().iterator().next().getF();
    for (Obj spotObject : trackObject.getChildren(inputSpotObjectsName).values()) {
        int currentTimepoint = spotObject.getT();
        String name = getFullName(Measurements.RELATIVE_FRAME, averageSubtracted);
        spotObject.addMeasurement(new Measurement(name, currentTimepoint - firstTimepoint));
    }
}

Example 30 with Measurement

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

the class MeasureTrackMotion method calculateVelocity.

public static void calculateVelocity(Obj trackObject, Track track, boolean averageSubtracted) {
    if (track.size() <= 1) {
        String name = getFullName(Measurements.MEAN_X_VELOCITY_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.MEAN_X_VELOCITY_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.MEAN_Y_VELOCITY_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.MEAN_Y_VELOCITY_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.MEAN_Z_VELOCITY_SLICES, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.MEAN_Z_VELOCITY_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.MEAN_INSTANTANEOUS_SPEED_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
        name = getFullName(Measurements.MEAN_INSTANTANEOUS_SPEED_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, Double.NaN));
    } else {
        // Calculating track motion
        double distPerPxXY = trackObject.getDppXY();
        double distPerPxZ = trackObject.getDppZ();
        TreeMap<Integer, Double> xVelocity = track.getInstantaneousXVelocity();
        TreeMap<Integer, Double> yVelocity = track.getInstantaneousYVelocity();
        TreeMap<Integer, Double> zVelocity = track.getInstantaneousZVelocity();
        TreeMap<Integer, Double> speed = track.getInstantaneousSpeed();
        CumStat cumStatX = new CumStat();
        CumStat cumStatY = new CumStat();
        CumStat cumStatZ = new CumStat();
        CumStat cumStatSpeed = new CumStat();
        for (int frame : xVelocity.keySet()) {
            // The first value is set to zero
            if (frame == 0)
                continue;
            cumStatX.addMeasure(xVelocity.get(frame));
            cumStatY.addMeasure(yVelocity.get(frame));
            cumStatZ.addMeasure(zVelocity.get(frame));
            cumStatSpeed.addMeasure(speed.get(frame));
        }
        String name = getFullName(Measurements.MEAN_X_VELOCITY_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatX.getMean()));
        name = getFullName(Measurements.MEAN_X_VELOCITY_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatX.getMean() * distPerPxXY));
        name = getFullName(Measurements.MEAN_Y_VELOCITY_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatY.getMean()));
        name = getFullName(Measurements.MEAN_Y_VELOCITY_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatY.getMean() * distPerPxXY));
        name = getFullName(Measurements.MEAN_Z_VELOCITY_SLICES, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatZ.getMean() * distPerPxXY / distPerPxZ));
        name = getFullName(Measurements.MEAN_Z_VELOCITY_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatZ.getMean() * distPerPxXY));
        name = getFullName(Measurements.MEAN_Z_VELOCITY_SLICES, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatZ.getMean() * distPerPxXY / distPerPxZ));
        name = getFullName(Measurements.MEAN_Z_VELOCITY_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatZ.getMean() * distPerPxXY));
        name = getFullName(Measurements.MEAN_INSTANTANEOUS_SPEED_PX, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatSpeed.getMean()));
        name = getFullName(Measurements.MEAN_INSTANTANEOUS_SPEED_CAL, averageSubtracted);
        trackObject.addMeasurement(new Measurement(name, cumStatSpeed.getMean() * distPerPxXY));
    }
}