Examples with ExportRawTimeSeriesToVFrapOp org.vcell.vmicro.op.ExportRawTimeSeriesToVFrapOp used on opensource projects

Example 1 with ExportRawTimeSeriesToVFrapOp

use of org.vcell.vmicro.op.ExportRawTimeSeriesToVFrapOp in project vcell by virtualcell.

the class BrownianDynamicsTest method main.

public static void main(String[] args) {
    try {
        Options commandOptions = new Options();
        Option noiseOption = new Option(OPTION_NOISE, false, "sampled images use Poisson statistics for photons, default is to count particles");
        commandOptions.addOption(noiseOption);
        Option psfOption = new Option(OPTION_PSF, false, "sampled images are convolve with microscope psf, default is to bin");
        commandOptions.addOption(psfOption);
        Option imageFileOption = new Option(OPTION_IMAGEFILE, true, "file to store image time series");
        imageFileOption.setArgName("filename");
        imageFileOption.setValueSeparator('=');
        commandOptions.addOption(imageFileOption);
        Option plotFileOption = new Option(OPTION_PLOTFILE, true, "file to store CSV time series (reduced data for ROIs)");
        plotFileOption.setArgName("filename");
        plotFileOption.setValueSeparator('=');
        commandOptions.addOption(plotFileOption);
        Option displayImageOption = new Option(OPTION_DISPLAY_IMAGE, false, "display image time series");
        commandOptions.addOption(displayImageOption);
        Option displayPlotOption = new Option(OPTION_DISPLAY_PLOT, false, "display plot of bleach roi");
        commandOptions.addOption(displayPlotOption);
        Option extentOption = new Option(OPTION_EXTENT, true, "extent of entire domain (default " + DEFAULT_EXTENT_SCALE + ")");
        extentOption.setArgName("extent");
        extentOption.setValueSeparator('=');
        commandOptions.addOption(extentOption);
        Option imageSizeOption = new Option(OPTION_IMAGE_SIZE, true, "num pixels in x and y (default " + DEFAULT_IMAGE_SIZE + ")");
        imageSizeOption.setArgName("numPixels");
        imageSizeOption.setValueSeparator('=');
        commandOptions.addOption(imageSizeOption);
        Option numParticlesOption = new Option(OPTION_NUM_PARTICLES, true, "num particles (default " + DEFAULT_NUM_PARTICLES + ")");
        numParticlesOption.setArgName("num");
        numParticlesOption.setValueSeparator('=');
        commandOptions.addOption(numParticlesOption);
        Option diffusionOption = new Option(OPTION_DIFFUSION, true, "diffusion rate (default " + DEFAULT_DIFFUSION + ")");
        diffusionOption.setArgName("rate");
        diffusionOption.setValueSeparator('=');
        commandOptions.addOption(diffusionOption);
        Option bleachRadiusOption = new Option(OPTION_BLEACH_RADIUS, true, "bleach radius (default " + DEFAULT_BLEACH_RADIUS + ")");
        bleachRadiusOption.setArgName("radius");
        bleachRadiusOption.setValueSeparator('=');
        commandOptions.addOption(bleachRadiusOption);
        Option psfRadiusOption = new Option(OPTION_PSF_RADIUS, true, "psf radius (default " + DEFAULT_PSF_RADIUS + ")");
        psfRadiusOption.setArgName("radius");
        psfRadiusOption.setValueSeparator('=');
        commandOptions.addOption(psfRadiusOption);
        Option bleachDurationOption = new Option(OPTION_BLEACH_DURATION, true, "psf radius (default " + DEFAULT_BLEACH_DURATION + ")");
        bleachDurationOption.setArgName("duration");
        bleachDurationOption.setValueSeparator('=');
        commandOptions.addOption(bleachDurationOption);
        Option endTimeOption = new Option(OPTION_ENDTIME, true, "end time (default " + DEFAULT_ENDTIME + ")");
        endTimeOption.setArgName("time");
        endTimeOption.setValueSeparator('=');
        commandOptions.addOption(endTimeOption);
        CommandLine cmdLine = null;
        try {
            Parser parser = new BasicParser();
            cmdLine = parser.parse(commandOptions, args);
        } catch (ParseException e1) {
            e1.printStackTrace();
            HelpFormatter hf = new HelpFormatter();
            hf.printHelp("BrownianDynamicsTest", commandOptions);
            System.exit(2);
        }
        boolean bNoise = cmdLine.hasOption(OPTION_NOISE);
        boolean bConvolve = cmdLine.hasOption(OPTION_PSF);
        File imageFile = null;
        if (cmdLine.hasOption(OPTION_IMAGEFILE)) {
            imageFile = new File(cmdLine.getOptionValue(OPTION_IMAGEFILE));
        }
        File plotFile = null;
        if (cmdLine.hasOption(OPTION_PLOTFILE)) {
            plotFile = new File(cmdLine.getOptionValue(OPTION_PLOTFILE));
        }
        boolean bDisplayImage = cmdLine.hasOption(OPTION_DISPLAY_IMAGE);
        boolean bDisplayPlot = cmdLine.hasOption(OPTION_DISPLAY_PLOT);
        double extentScale = DEFAULT_EXTENT_SCALE;
        if (cmdLine.hasOption(OPTION_EXTENT)) {
            extentScale = Double.parseDouble(cmdLine.getOptionValue(OPTION_EXTENT));
        }
        int imageSize = DEFAULT_IMAGE_SIZE;
        if (cmdLine.hasOption(OPTION_IMAGE_SIZE)) {
            imageSize = Integer.parseInt(cmdLine.getOptionValue(OPTION_IMAGE_SIZE));
        }
        int numParticles = DEFAULT_NUM_PARTICLES;
        if (cmdLine.hasOption(OPTION_NUM_PARTICLES)) {
            numParticles = Integer.parseInt(cmdLine.getOptionValue(OPTION_NUM_PARTICLES));
        }
        double diffusionRate = DEFAULT_DIFFUSION;
        if (cmdLine.hasOption(OPTION_DIFFUSION)) {
            diffusionRate = Double.parseDouble(cmdLine.getOptionValue(OPTION_DIFFUSION));
        }
        double bleachRadius = DEFAULT_BLEACH_RADIUS;
        if (cmdLine.hasOption(OPTION_BLEACH_RADIUS)) {
            bleachRadius = Double.parseDouble(cmdLine.getOptionValue(OPTION_BLEACH_RADIUS));
        }
        double psfRadius = DEFAULT_PSF_RADIUS;
        if (cmdLine.hasOption(OPTION_PSF_RADIUS)) {
            psfRadius = Double.parseDouble(cmdLine.getOptionValue(OPTION_PSF_RADIUS));
        }
        double bleachDuration = DEFAULT_BLEACH_DURATION;
        if (cmdLine.hasOption(OPTION_BLEACH_DURATION)) {
            bleachDuration = Double.parseDouble(cmdLine.getOptionValue(OPTION_BLEACH_DURATION));
        }
        double endTime = DEFAULT_ENDTIME;
        if (cmdLine.hasOption(OPTION_ENDTIME)) {
            endTime = Double.parseDouble(cmdLine.getOptionValue(OPTION_BLEACH_DURATION));
        }
        // 
        // hard coded parameters
        // 
        Origin origin = new Origin(0, 0, 0);
        Extent extent = new Extent(extentScale, extentScale, 1);
        int numX = imageSize;
        int numY = imageSize;
        double psfVar = psfRadius * psfRadius;
        BrownianDynamicsTest test = new BrownianDynamicsTest();
        ImageTimeSeries<UShortImage> rawTimeSeries = test.generateTestData(origin, extent, numX, numY, numParticles, diffusionRate, psfVar, bleachRadius * bleachRadius, bNoise, bConvolve, bleachDuration, endTime);
        // 
        if (imageFile != null) {
            new ExportRawTimeSeriesToVFrapOp().exportToVFRAP(imageFile, rawTimeSeries, null);
        }
        // 
        if (bDisplayImage) {
            new DisplayTimeSeriesOp().displayImageTimeSeries(rawTimeSeries, "time series", null);
        }
        // 
        // compute reduced data if needed for plotting or saving.
        // 
        RowColumnResultSet reducedData = null;
        if (bDisplayPlot || plotFile != null) {
            double muX = origin.getX() + 0.5 * extent.getX();
            double muY = origin.getY() + 0.5 * extent.getY();
            double sigma = Math.sqrt(psfVar);
            NormalizedSampleFunction gaussian = NormalizedSampleFunction.fromGaussian("psf", origin, extent, new ISize(numX, numY, 1), muX, muY, sigma);
            reducedData = new GenerateReducedDataOp().generateReducedData(rawTimeSeries, new NormalizedSampleFunction[] { gaussian });
        }
        // 
        if (plotFile != null) {
            FileOutputStream fos = new FileOutputStream(plotFile);
            new CSV().exportTo(fos, reducedData);
        }
        if (bDisplayPlot) {
            new DisplayPlotOp().displayPlot(reducedData, "bleached roi", null);
        }
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 2 with ExportRawTimeSeriesToVFrapOp

use of org.vcell.vmicro.op.ExportRawTimeSeriesToVFrapOp in project vcell by virtualcell.

the class ExportRawTimeSeriesToVFrap method compute0.

@Override
protected void compute0(TaskContext context, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get inputs
    File outputFile = context.getData(vfrapFile);
    ImageTimeSeries imageTimeSeries = context.getData(rawTimeSeriesImages);
    // validate that imageTimeSeries is of type ImageTimeSeries<UShortImage>
    Image[] images = imageTimeSeries.getAllImages();
    UShortImage[] usImages = new UShortImage[images.length];
    for (int i = 0; i < usImages.length; i++) {
        if (!(images[i] instanceof UShortImage)) {
            throw new Exception("type mismatch, expecting only UShortImages in time series");
        }
        usImages[i] = (UShortImage) images[i];
    }
    ImageTimeSeries<UShortImage> ushortImageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, usImages, imageTimeSeries.getImageTimeStamps(), imageTimeSeries.getSizeZ());
    ExportRawTimeSeriesToVFrapOp op = new ExportRawTimeSeriesToVFrapOp();
    op.exportToVFRAP(outputFile, ushortImageTimeSeries, clientTaskStatusSupport);
    // write output (just boolean "done" flag)
    context.setData(written, true);
}