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

Example 11 with Measurement

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

the class AbstractMacroRunner method interceptMeasurement.

public static Measurement interceptMeasurement(ResultsTable table, String heading) {
    if (table == null || table.getColumn(0) == null)
        return new Measurement(getFullName(heading), Double.NaN);
    int nRows = table.getColumn(0).length;
    double value = table.getValue(heading, nRows - 1);
    return new Measurement(getFullName(heading), value);
}

Example 12 with Measurement

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

the class RunMacro method process.

@Override
public Status process(Workspace workspace) {
    // Getting input image
    boolean provideInputImage = parameters.getValue(PROVIDE_INPUT_IMAGE);
    String inputImageName = parameters.getValue(INPUT_IMAGE);
    String macroMode = parameters.getValue(MACRO_MODE);
    String macroText = parameters.getValue(MACRO_TEXT);
    String macroFile = parameters.getValue(MACRO_FILE);
    boolean interceptOutputImage = parameters.getValue(INTERCEPT_OUTPUT_IMAGE);
    boolean applyToInput = parameters.getValue(APPLY_TO_INPUT);
    String outputImageName = parameters.getValue(OUTPUT_IMAGE);
    // Getting a list of measurement headings
    ParameterGroup measurementGroup = parameters.getParameter(ADD_INTERCEPTED_VARIABLE);
    LinkedHashSet<String> expectedMeasurements = expectedMeasurements(measurementGroup, VARIABLE);
    // Setting the MacroHandler to the current workspace
    MacroHandler.setWorkspace(workspace);
    MacroHandler.setModules(modules);
    // Get current image
    Image inputImage = provideInputImage ? workspace.getImage(inputImageName) : null;
    ImagePlus inputImagePlus = (inputImage != null) ? inputImage.getImagePlus().duplicate() : null;
    // If the macro is stored as a file, load this to the macroText string
    if (macroMode.equals(MacroModes.MACRO_FILE)) {
        macroText = IJ.openAsString(macroFile);
        macroText = GlobalVariables.convertString(macroText, modules);
        macroText = TextType.applyCalculation(macroText);
    }
    // Appending variables to the front of the macro
    ParameterGroup variableGroup = parameters.getParameter(ADD_VARIABLE);
    String finalMacroText = addVariables(macroText, variableGroup);
    // If providing the input image direct from the workspace, hide all open windows
    // while the macro runs
    ArrayList<ImagePlus> openImages = null;
    if (provideInputImage)
        openImages = hideImages();
    // Running the macro
    Interpreter interpreter = new Interpreter();
    interpreter.setIgnoreErrors(true);
    try {
        inputImagePlus = interpreter.runBatchMacro(finalMacroText, inputImagePlus);
        if (interpreter.getErrorMessage() != null)
            throw new RuntimeException();
    } catch (RuntimeException e) {
        IJ.runMacro("setBatchMode(false)");
        if (provideInputImage)
            for (ImagePlus openImage : openImages) openImage.show();
        MIA.log.writeError("Macro failed with error \"" + interpreter.getErrorMessage() + "\".  Skipping file.");
        return Status.FAIL;
    }
    // windows
    if (provideInputImage)
        for (ImagePlus openImage : openImages) openImage.show();
    if (interceptOutputImage && inputImagePlus != null) {
        if (applyToInput && inputImage != null) {
            inputImage.setImagePlus(inputImagePlus);
            if (showOutput)
                inputImage.showImage();
        } else {
            Image outputImage = new Image(outputImageName, inputImagePlus);
            workspace.addImage(outputImage);
            if (showOutput)
                outputImage.showImage();
        }
    }
    // Intercepting measurements
    if (provideInputImage) {
        for (String expectedMeasurement : expectedMeasurements) {
            double value = interpreter.getVariable(expectedMeasurement);
            Measurement measurement = new Measurement(getFullName(expectedMeasurement), value);
            inputImage.addMeasurement(measurement);
        }
    }
    return Status.PASS;
}

Example 13 with Measurement

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

the class TrackEditor method addSingleTimepointTracks.

static void addSingleTimepointTracks(Set<Integer> trackIDs, Objs spotObjects, Objs trackObjects, String inputTrackObjectsName) {
    // Determining the maximum current track ID
    int maxID = 0;
    for (int trackID : trackIDs) maxID = Math.max(maxID, trackID);
    // Single timepoint "tracks" aren't assigned track IDs yet, so doing that now
    for (Obj obj : spotObjects.values()) {
        if (obj.getParent(inputTrackObjectsName) == null) {
            Obj trackObject = trackObjects.createAndAddNewObject(VolumeType.POINTLIST, ++maxID + 1);
            obj.addParent(trackObject);
            trackObject.addChild(obj);
            obj.addMeasurement(new Measurement(Measurements.TRACK_NEXT_ID, Double.NaN));
            obj.addMeasurement(new Measurement(Measurements.TRACK_PREV_ID, Double.NaN));
        }
    }
}

Example 14 with Measurement

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

the class CreateMeasurementMap method processParentMeasurements.

public static void processParentMeasurements(CumStat[] cumStats, Indexer indexer, Objs objects, String parentObjectsName, String measurementName, @Nullable String message) {
    // Adding objects
    int count = 0;
    int nTotal = objects.size();
    for (Obj object : objects.values()) {
        // Getting parent object
        Obj parentObject = object.getParent(parentObjectsName);
        if (parentObject == null)
            continue;
        // Getting measurement value. Skip if null or NaN.
        Measurement measurement = parentObject.getMeasurement(measurementName);
        if (measurement == null)
            continue;
        double measurementValue = measurement.getValue();
        if (Double.isNaN(measurementValue))
            continue;
        // Getting all object points
        for (Point<Integer> point : object.getCoordinateSet()) {
            // Getting index for this point
            int z = indexer.getDim()[2] == 1 ? 0 : point.getZ();
            int t = indexer.getDim()[3] == 1 ? 0 : object.getT();
            int idx = indexer.getIndex(new int[] { point.getX(), point.getY(), z, t });
            // Adding measurement
            cumStats[idx].addMeasure(measurementValue);
        }
        if (message != null)
            writeProgressStatus(++count, nTotal, "objects", message);
    }
}

Example 15 with Measurement

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

the class CreateMeasurementMap method processObjectMeasurement.

public static void processObjectMeasurement(CumStat[] cumStats, Indexer indexer, Objs objects, String measurementName, @Nullable String message) {
    // Adding objects
    int count = 0;
    int nTotal = objects.size();
    for (Obj object : objects.values()) {
        // Getting measurement value. Skip if null or NaN.
        Measurement measurement = object.getMeasurement(measurementName);
        if (measurement == null)
            continue;
        double measurementValue = measurement.getValue();
        if (Double.isNaN(measurementValue))
            continue;
        // Getting all object points
        for (Point<Integer> point : object.getCoordinateSet()) {
            // Getting index for this point
            int z = indexer.getDim()[2] == 1 ? 0 : point.getZ();
            int t = indexer.getDim()[3] == 1 ? 0 : object.getT();
            int idx = indexer.getIndex(new int[] { point.getX(), point.getY(), z, t });
            // Adding measurement
            cumStats[idx].addMeasure(measurementValue);
        }
        if (message != null)
            writeProgressStatus(++count, nTotal, "objects", message);
    }
}