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

Example 51 with Measurement

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

the class MeasureObjectCurvature method measureCurvature.

public static void measureCurvature(Obj inputObject, TreeMap<Double, Double> curvature, boolean absoluteCurvature, boolean signedCurvature) {
    double dppXY = inputObject.getDppXY();
    CumStat cumStatSigned = new CumStat();
    CumStat cumStatAbsolute = new CumStat();
    for (double value : curvature.values()) {
        if (absoluteCurvature)
            cumStatAbsolute.addMeasure(Math.abs(value));
        if (signedCurvature)
            cumStatSigned.addMeasure(value);
    }
    // Adding measurements
    if (absoluteCurvature) {
        inputObject.addMeasurement(new Measurement(Measurements.MEAN_ABSOLUTE_CURVATURE_PX, cumStatAbsolute.getMean()));
        inputObject.addMeasurement(new Measurement(Measurements.MIN_ABSOLUTE_CURVATURE_PX, cumStatAbsolute.getMin()));
        inputObject.addMeasurement(new Measurement(Measurements.MAX_ABSOLUTE_CURVATURE_PX, cumStatAbsolute.getMax()));
        inputObject.addMeasurement(new Measurement(Measurements.STD_ABSOLUTE_CURVATURE_PX, cumStatAbsolute.getStd()));
        inputObject.addMeasurement(new Measurement(Measurements.MEAN_ABSOLUTE_CURVATURE_CAL, cumStatAbsolute.getMean() / dppXY));
        inputObject.addMeasurement(new Measurement(Measurements.MIN_ABSOLUTE_CURVATURE_CAL, cumStatAbsolute.getMin() / dppXY));
        inputObject.addMeasurement(new Measurement(Measurements.MAX_ABSOLUTE_CURVATURE_CAL, cumStatAbsolute.getMax() / dppXY));
        inputObject.addMeasurement(new Measurement(Measurements.STD_ABSOLUTE_CURVATURE_CAL, cumStatAbsolute.getStd() / dppXY));
    }
    if (signedCurvature) {
        inputObject.addMeasurement(new Measurement(Measurements.MEAN_SIGNED_CURVATURE_PX, cumStatSigned.getMean()));
        inputObject.addMeasurement(new Measurement(Measurements.MIN_SIGNED_CURVATURE_PX, cumStatSigned.getMin()));
        inputObject.addMeasurement(new Measurement(Measurements.MAX_SIGNED_CURVATURE_PX, cumStatSigned.getMax()));
        inputObject.addMeasurement(new Measurement(Measurements.STD_SIGNED_CURVATURE_PX, cumStatSigned.getStd()));
        inputObject.addMeasurement(new Measurement(Measurements.MEAN_SIGNED_CURVATURE_CAL, cumStatSigned.getMean() / dppXY));
        inputObject.addMeasurement(new Measurement(Measurements.MIN_SIGNED_CURVATURE_CAL, cumStatSigned.getMin() / dppXY));
        inputObject.addMeasurement(new Measurement(Measurements.MAX_SIGNED_CURVATURE_CAL, cumStatSigned.getMax() / dppXY));
        inputObject.addMeasurement(new Measurement(Measurements.STD_SIGNED_CURVATURE_CAL, cumStatSigned.getStd() / dppXY));
    }
}

Example 52 with Measurement

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

the class MeasureObjectColocalisation method setObjectMeasurements.

public void setObjectMeasurements(Obj obj, HashMap<String, Double> measurements, String imageName1, String imageName2) {
    for (String measurementName : measurements.keySet()) {
        String fullName = getFullName(imageName1, imageName2, measurementName);
        obj.addMeasurement(new Measurement(fullName, measurements.get(measurementName)));
    }
}

Example 53 with Measurement

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

the class MeasureObjectTexture method processObject.

public static void processObject(Obj object, Image image, TextureCalculator textureCalculator, double[] offs, boolean calibratedOffset) {
    ImagePlus ipl = image.getImagePlus();
    // If the input stack is a single timepoint and channel, there's no need to
    // create a new ImageStack
    ImageStack timeStack = null;
    if (ipl.getNChannels() == 1 && ipl.getNFrames() == 1) {
        timeStack = ipl.getStack();
    } else {
        int t = object.getT() + 1;
        int nSlices = ipl.getNSlices();
        timeStack = SubHyperstackMaker.makeSubhyperstack(ipl, "1-1", "1-" + nSlices, t + "-" + t).getStack();
    }
    textureCalculator.calculate(timeStack, object, (int) offs[0], (int) offs[1], (int) offs[2]);
    // Acquiring measurements
    String name = getFullName(image.getName(), Measurements.ASM, offs, calibratedOffset);
    object.addMeasurement(new Measurement(name, textureCalculator.getASM()));
    name = getFullName(image.getName(), Measurements.CONTRAST, offs, calibratedOffset);
    object.addMeasurement(new Measurement(name, textureCalculator.getContrast()));
    name = getFullName(image.getName(), Measurements.CORRELATION, offs, calibratedOffset);
    object.addMeasurement(new Measurement(name, textureCalculator.getCorrelation()));
    name = getFullName(image.getName(), Measurements.ENTROPY, offs, calibratedOffset);
    object.addMeasurement(new Measurement(name, textureCalculator.getEntropy()));
}

Example 54 with Measurement

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

the class FilterByChildren method process.

@Override
protected Status process(Workspace workspace) {
    // Getting input objects
    String inputObjectsName = parameters.getValue(INPUT_OBJECTS);
    Objs inputObjects = workspace.getObjects().get(inputObjectsName);
    // Getting parameters
    String filterMode = parameters.getValue(FILTER_MODE);
    String outputObjectsName = parameters.getValue(OUTPUT_FILTERED_OBJECTS);
    String filterMethod = parameters.getValue(FILTER_METHOD);
    String childObjectsName = parameters.getValue(CHILD_OBJECTS);
    boolean storeSummary = parameters.getValue(STORE_SUMMARY_RESULTS);
    boolean storeIndividual = parameters.getValue(STORE_INDIVIDUAL_RESULTS);
    boolean moveObjects = filterMode.equals(FilterModes.MOVE_FILTERED);
    boolean remove = !filterMode.equals(FilterModes.DO_NOTHING);
    Objs outputObjects = moveObjects ? new Objs(outputObjectsName, inputObjects) : null;
    int count = 0;
    Iterator<Obj> iterator = inputObjects.values().iterator();
    while (iterator.hasNext()) {
        Obj inputObject = iterator.next();
        Objs childObjects = inputObject.getChildren(childObjectsName);
        // Removing the object if it has no children
        if (childObjects == null) {
            count++;
            if (remove)
                processRemoval(inputObject, outputObjects, iterator);
            continue;
        }
        double value = childObjects.size();
        double refValue = getReferenceValue(workspace, inputObject);
        boolean conditionMet = testFilter(value, refValue, filterMethod);
        // Adding measurements
        if (storeIndividual) {
            String measurementName = getIndividualMeasurementName(childObjectsName);
            inputObject.addMeasurement(new Measurement(measurementName, conditionMet ? 1 : 0));
        }
        // Removing the object if it has too few children
        if (conditionMet) {
            count++;
            if (remove)
                processRemoval(inputObject, outputObjects, iterator);
        }
    }
    // If moving objects, addRef them to the workspace
    if (moveObjects)
        workspace.addObjects(outputObjects);
    // If storing the result, create a new metadata item for it
    if (storeSummary) {
        String metadataName = getSummaryMeasurementName(childObjectsName);
        workspace.getMetadata().put(metadataName, count);
    }
    // Showing objects
    if (showOutput)
        inputObjects.convertToImageRandomColours().showImage();
    return Status.PASS;
}

Example 55 with Measurement

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

the class FilterByMeasurementExtremes method process.

@Override
protected Status process(Workspace workspace) {
    // Getting input objects
    String inputObjectsName = parameters.getValue(INPUT_OBJECTS);
    Objs inputObjects = workspace.getObjects().get(inputObjectsName);
    // Getting parameters
    String filterMode = parameters.getValue(FILTER_MODE);
    String outputObjectsName = parameters.getValue(OUTPUT_FILTERED_OBJECTS);
    String filterMethod = parameters.getValue(FILTER_METHOD);
    boolean perTimepoint = parameters.getValue(PER_TIMEPOINT);
    String measName = parameters.getValue(MEASUREMENT);
    boolean moveObjects = filterMode.equals(FilterModes.MOVE_FILTERED);
    boolean remove = !filterMode.equals(FilterModes.DO_NOTHING);
    Objs outputObjects = moveObjects ? new Objs(outputObjectsName, inputObjects) : null;
    // Getting reference limits
    HashMap<Integer, double[]> minMax = getMeasurementExtremes(inputObjects, measName, perTimepoint);
    Iterator<Obj> iterator = inputObjects.values().iterator();
    while (iterator.hasNext()) {
        Obj inputObject = iterator.next();
        Measurement measurement = inputObject.getMeasurement(measName);
        if (measurement == null)
            continue;
        // Getting the values to filter on
        double value = measurement.getValue();
        int t = perTimepoint ? inputObject.getT() : 0;
        double[] currMinMax = minMax.get(t);
        boolean conditionMet = testFilter(value, currMinMax, filterMethod);
        // Removing the object if it failed the test
        if (conditionMet && remove)
            processRemoval(inputObject, outputObjects, iterator);
    }
    // If moving objects, addRef them to the workspace
    if (moveObjects)
        workspace.addObjects(outputObjects);
    // Showing objects
    if (showOutput)
        inputObjects.convertToImageRandomColours().showImage();
    return Status.PASS;
}