Examples with UShortImage cbit.vcell.VirtualMicroscopy.UShortImage used on opensource projects

Example 26 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class PhotoactivationExperimentTest method main.

public static void main(String[] args) {
    try {
        File baseDir = new File(".");
        // File baseDir = new File("/Users/schaff/Documents/workspace/VCell_5.4");
        // initialize computing environment
        // 
        File workingDirectory = new File(baseDir, "workingDir");
        LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
        // 
        // import raw image time series data from VFRAP file format (can have noise, background, etc ... can be actual microscopy data)
        // 
        ClientTaskStatusSupport progressListener = new ClientTaskStatusSupport() {

            String message = "";

            int progress = 0;

            @Override
            public void setProgress(int progress) {
                this.progress = progress;
            }

            @Override
            public void setMessage(String message) {
                this.message = message;
            }

            @Override
            public boolean isInterrupted() {
                return false;
            }

            @Override
            public int getProgress() {
                return progress;
            }

            @Override
            public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
            }
        };
        // 
        // generate fake data (and save?)
        // 
        // ImageTimeSeries<UShortImage> simulatedFluorescence = generateFakeData(localWorkspace, progressListener);
        // new ExportRawTimeSeriesToVFrapOp().exportToVFRAP(vfrapFile, simulatedFluorescence, null);
        // 
        // analyze raw data (from file?) using Keyworthy method.
        // 
        // File vfrapFile = new File(baseDir, "vfrapPaper/photoactivation/Actin.vfrap");
        File vfrapFile = new File(baseDir, "vfrapPaper/photoactivation/Actin_binding_protein.vfrap");
        ImageTimeSeries<UShortImage> fluorTimeSeriesImages = new ImportRawTimeSeriesFromVFrapOp().importRawTimeSeriesFromVFrap(vfrapFile);
        analyzePhotoactivation(fluorTimeSeriesImages, localWorkspace);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 27 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class PhotoactivationExperimentTest method blurTimeSeries.

private static ImageTimeSeries<UShortImage> blurTimeSeries(ImageTimeSeries<UShortImage> rawTimeSeriesImages) throws ImageException {
    UShortImage[] blurredImages = new UShortImage[rawTimeSeriesImages.getAllImages().length];
    for (int i = 0; i < blurredImages.length; i++) {
        blurredImages[i] = new UShortImage(rawTimeSeriesImages.getAllImages()[i]);
        blurredImages[i].blur();
        blurredImages[i].blur();
    }
    ImageTimeSeries<UShortImage> blurredRaw = new ImageTimeSeries<UShortImage>(UShortImage.class, blurredImages, rawTimeSeriesImages.getImageTimeStamps(), rawTimeSeriesImages.getSizeZ());
    return blurredRaw;
}

Example 28 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage 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);
}

Example 29 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class GenerateNormalizedFrapData method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    ImageTimeSeries<UShortImage> rawTimeSeries = context.getData(rawImageTimeSeries);
    ROI backgroundROI = context.getData(backgroundROI_2D);
    Integer indexPostbleach = context.getData(indexOfFirstPostbleach);
    // do op
    GenerateNormalizedFrapDataOp op = new GenerateNormalizedFrapDataOp();
    NormalizedFrapDataResults results = op.generate(rawTimeSeries, backgroundROI, indexPostbleach);
    // set output
    context.setData(normalizedFrapData, results.normalizedFrapData);
    context.setData(this.prebleachAverage, results.prebleachAverage);
}

Example 30 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage in project vcell by virtualcell.

the class ImportRawTimeSeriesFrom2DVCellConcentrations method compute0.

@Override
protected void compute0(TaskContext context, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // set inputs
    File vcellSimLog = context.getData(vcellSimLogFile);
    String fluorFuncName = context.getData(fluorFunctionName);
    Double maximumIntensity = context.getData(maxIntensity);
    Boolean enableNoise = context.getData(bNoise);
    // do op
    ImportRawTimeSeriesFrom2DVCellConcentrationsOp op = new ImportRawTimeSeriesFrom2DVCellConcentrationsOp();
    ImageTimeSeries<UShortImage> imageTimeSeries = op.importRawTimeSeries(vcellSimLog, fluorFuncName, maximumIntensity, enableNoise);
    // set output
    context.setData(rawTimeSeriesImages, imageTimeSeries);
}