Examples with ImageTimeSeries org.vcell.vmicro.workflow.data.ImageTimeSeries used on opensource projects

Example 6 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class WorkflowObjectsPanel method displayData.

private void displayData(TaskContext taskContext, WorkflowObject workflowObject) {
    if (workflowObject instanceof DataInput || workflowObject instanceof DataOutput) {
        String title = parametersFunctionsTableModel.getName(workflowObject);
        WindowListener listener = new WindowAdapter() {
        };
        Object data = null;
        if (workflowObject instanceof WorkflowDataSource) {
            WorkflowDataSource dataHolder = (WorkflowDataSource) workflowObject;
            data = taskContext.getRepository().getData(dataHolder);
        } else if (workflowObject instanceof DataInput) {
            DataInput dataInput = (DataInput) workflowObject;
            data = taskContext.getData(dataInput);
        }
        if (data instanceof RowColumnResultSet) {
            RowColumnResultSet rc = (RowColumnResultSet) data;
            try {
                new DisplayPlotOp().displayPlot(rc, title, listener);
            } catch (ExpressionException e) {
                e.printStackTrace();
            }
        } else if (data instanceof ROI) {
            ROI roi = (ROI) data;
            Image image = roi.getRoiImages()[0];
            new DisplayImageOp().displayImage(image, title, listener);
        } else if (data instanceof ProfileData[]) {
            ProfileData[] profileData = (ProfileData[]) data;
            new DisplayProfileLikelihoodPlotsOp().displayProfileLikelihoodPlots(profileData, title, listener);
        } else if (data instanceof Image) {
            Image image = (Image) data;
            new DisplayImageOp().displayImage(image, title, listener);
        } else if (data instanceof ImageTimeSeries) {
            ImageTimeSeries imageTimeSeries = (ImageTimeSeries) data;
            try {
                DisplayTimeSeries.displayImageTimeSeries(imageTimeSeries, title, listener);
            } catch (ImageException | IOException e) {
                e.printStackTrace();
            }
        }
    }
}

Example 7 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class WorkflowObjectsPanel method hasDisplayData.

private boolean hasDisplayData(TaskContext taskContext, WorkflowObject workflowObject) {
    if (workflowObject instanceof DataInput || workflowObject instanceof DataOutput) {
        String title = parametersFunctionsTableModel.getName(workflowObject);
        WindowListener listener = new WindowAdapter() {
        };
        Object data = null;
        if (workflowObject instanceof WorkflowDataSource) {
            WorkflowDataSource dataHolder = (WorkflowDataSource) workflowObject;
            data = taskContext.getRepository().getData(dataHolder);
        } else if (workflowObject instanceof DataInput) {
            DataInput dataInput = (DataInput) workflowObject;
            data = taskContext.getData(dataInput);
        }
        if (data instanceof RowColumnResultSet || data instanceof ROI || data instanceof ProfileData[] || data instanceof Image || data instanceof ImageTimeSeries) {
            return true;
        }
    }
    return false;
}

Example 8 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class GenerateReducedData method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    ROI[] rois = context.getData(imageDataROIs);
    ImageTimeSeries<? extends Image> simData = (ImageTimeSeries<? extends Image>) context.getData(imageTimeSeries);
    // do op
    GenerateReducedDataOp op = new GenerateReducedDataOp();
    RowColumnResultSet reducedData = op.generateReducedData(simData, rois);
    // set output
    context.setData(reducedROIData, reducedData);
}

Example 9 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class ImportRawTimeSeriesFromExperimentImageOp method importRawTimeSeries.

public ImageTimeSeries<UShortImage> importRawTimeSeries(File expTimeSeriesFile) throws Exception {
    ClientTaskStatusSupport clientTaskStatusSupport = null;
    ImageDataset rawTimeData = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(expTimeSeriesFile.getAbsolutePath(), clientTaskStatusSupport);
    ImageTimeSeries<UShortImage> imageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, rawTimeData.getAllImages(), rawTimeData.getImageTimeStamps(), 1);
    return imageTimeSeries;
}

Example 10 with ImageTimeSeries

use of org.vcell.vmicro.workflow.data.ImageTimeSeries in project vcell by virtualcell.

the class FluorescenceNoiseTest method generateTestData.

private ImageTimeSeries<UShortImage> generateTestData(Origin origin, Extent extent, int numX, int numY, int numParticles, double diffusionRate, double psfVar, double bleachRadius, boolean bNoise, boolean bConvolve) throws ImageException {
    double detectorGainAndQuantumYeild = 100;
    double totalSampleTime = 0.5;
    int numSampleSteps = 1;
    int numPrebleach = 2;
    ArrayList<UShortImage> images = new ArrayList<UShortImage>();
    ArrayList<Double> times = new ArrayList<Double>();
    final BrownianDynamics2DSolver solver = new BrownianDynamics2DSolver(origin, extent, numParticles);
    boolean initiallyFluorescent = true;
    solver.initializeUniform(initiallyFluorescent);
    // simulate and write prebleach images
    for (int i = 0; i < numPrebleach; i++) {
        images.add(solver.sampleImage(numX, numY, origin, extent, diffusionRate, totalSampleTime, numSampleSteps, psfVar, detectorGainAndQuantumYeild, bConvolve, bNoise));
        times.add(solver.currentTime());
    }
    // bleach
    double totalBleachTime = 0.1;
    int numBleachSteps = 5;
    double bleachCenterX = origin.getX() + 0.5 * extent.getX();
    double bleachCenterY = origin.getY() + 0.5 * extent.getY();
    double bleachPsfVariance = bleachRadius;
    double bleachFactor_K = 10;
    solver.bleachGuassian(diffusionRate, totalBleachTime, numBleachSteps, bleachCenterX, bleachCenterY, bleachPsfVariance, bleachFactor_K);
    // wait
    double postbleachDelay = 0.1;
    solver.step(diffusionRate, postbleachDelay);
    while (solver.currentTime() < 5) {
        double samplePsfVariance = psfVar;
        images.add(solver.sampleImage(numX, numY, origin, extent, diffusionRate, totalSampleTime, numSampleSteps, psfVar, detectorGainAndQuantumYeild, bConvolve, bNoise));
        times.add(solver.currentTime());
    // solver.step(diffusionRate, 1-totalSampleTime);
    }
    double[] timeArray = new double[times.size()];
    for (int i = 0; i < timeArray.length; i++) {
        timeArray[i] = times.get(i);
    }
    UShortImage[] imageArray = images.toArray(new UShortImage[images.size()]);
    return new ImageTimeSeries<UShortImage>(UShortImage.class, imageArray, timeArray, 1);
}