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

Example 16 with UShortImage

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

the class ROIAssistPanel method resolveCurrentROI.

private void resolveCurrentROI() {
    final String CELL_ROI = "CELL_ROI";
    AsynchClientTask keepRegionsTask = new AsynchClientTask("Pick Region", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // TODO Auto-generated method stub
            RegionInfo[] keepRegionInfos = pickKeepRegionInfoFromCurrentROI();
            if (keepRegionInfos == null) {
                throw UserCancelException.CANCEL_GENERIC;
            }
            // dataToThreshold.getCurrentlyDisplayedROI().getPixelsXYZ();
            short[] keepPixels = new short[dataToThreshold.getCurrentlyDisplayedROI().getISize().getXYZ()];
            for (int i = 0; i < keepPixels.length; i++) {
                for (int j = 0; j < keepRegionInfos.length; j++) {
                    if (keepRegionInfos[j].isIndexInRegion(i)) {
                        keepPixels[i] = 1;
                    }
                }
            }
            UShortImage ushortImage = new UShortImage(keepPixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
            ROI newCellROI = new ROI(ushortImage, originalROI.getROIName());
            hashTable.put(CELL_ROI, newCellROI);
        }
    };
    AsynchClientTask updateDisplayTask = new AsynchClientTask("Updating display", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            dataToThreshold.addReplaceRoi((ROI) hashTable.get(CELL_ROI));
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { keepRegionsTask, updateDisplayTask }, false, false, null, true);
}

Example 17 with UShortImage

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

the class ROIMultiPaintManager method initImageDataSet.

private void initImageDataSet(short[][] dataToSegmentChannels, ISize uncroppedISize) throws Exception {
    initImageDataSetChannels = new ImageDataset[(dataToSegmentChannels != null ? dataToSegmentChannels.length : 1)];
    for (int c = 0; c < initImageDataSetChannels.length; c++) {
        UShortImage[] zImageSet = new UShortImage[uncroppedISize.getZ()];
        for (int i = 0; i < zImageSet.length; i++) {
            short[] shortData = new short[uncroppedISize.getX() * uncroppedISize.getY()];
            if (dataToSegmentChannels != null) {
                System.arraycopy(dataToSegmentChannels[c], shortData.length * i, shortData, 0, shortData.length);
            }
            zImageSet[i] = new UShortImage(shortData, DEFAULT_ORIGIN, DEFAULT_EXTENT, uncroppedISize.getX(), uncroppedISize.getY(), 1);
        }
        initImageDataSetChannels[c] = new ImageDataset(zImageSet, new double[] { 0.0 }, uncroppedISize.getZ());
    }
}

Example 18 with UShortImage

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

the class ROIMultiPaintManager method calculateAllPixelValuesRangeChannels0.

private static OverlayEditorPanelJAI.AllPixelValuesRange[] calculateAllPixelValuesRangeChannels0(ImageDataset[] sourceImageDatasetChannels) {
    OverlayEditorPanelJAI.AllPixelValuesRange[] pixelValuesRangeChannels = new OverlayEditorPanelJAI.AllPixelValuesRange[sourceImageDatasetChannels.length];
    for (int c = 0; c < sourceImageDatasetChannels.length; c++) {
        UShortImage[] allImages = sourceImageDatasetChannels[c].getAllImages();
        double min = 0;
        double max = min;
        for (int i = 0; i < allImages.length; i++) {
            ImageStatistics imageStats = allImages[i].getImageStatistics();
            if (i == 0 || imageStats.minValue < min) {
                min = imageStats.minValue;
            }
            if (i == 0 || imageStats.maxValue > max) {
                max = imageStats.maxValue;
            }
        }
        pixelValuesRangeChannels[c] = new OverlayEditorPanelJAI.AllPixelValuesRange((int) min, (int) max);
    }
    return pixelValuesRangeChannels;
}

Example 19 with UShortImage

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

the class FluorescenceNoiseTest method testBrownianDynamics.

private void testBrownianDynamics() throws ImageException {
    Origin origin = new Origin(0, 0, 0);
    Extent extent = new Extent(10, 10, 1);
    double psfVar = 0.25 * 0.25;
    // typically 10000 or 100000;
    int numParticles = 10000;
    double diffusionRate = 1;
    double bleachRadius = 0.25;
    final double bleachAmplitude = 0.5;
    final double bleachRadius2 = bleachRadius * bleachRadius;
    double endTime = 10;
    int numTimes = 1000;
    final BrownianDynamics2DSolver solver = new BrownianDynamics2DSolver(origin, extent, numParticles);
    boolean initiallyFluorescent = true;
    solver.initializeUniform(initiallyFluorescent);
    double totalBleachTime = 0.00001;
    int numBleachSteps = 1;
    double bleachCenterX = origin.getX() + 0.5 * extent.getX();
    double bleachCenterY = origin.getY() + 0.5 * extent.getY();
    double bleachPsfVariance = psfVar;
    double bleachFactor_K = 1000000;
    solver.bleachGuassian(diffusionRate, totalBleachTime, numBleachSteps, bleachCenterX, bleachCenterY, bleachPsfVariance, bleachFactor_K);
    // ParticleVisitor bleachGaussian = new ParticleVisitor() {
    // UniformRealDistribution uniform = new UniformRealDistribution();
    // 
    // @Override
    // public void visit(double x, double y, boolean bFluorescent, int index) {
    // // TODO Auto-generated method stub
    // double radius2 = x*x + y*y;
    // double bleachProb = bleachAmplitude * FastMath.exp(-radius2/bleachRadius2);
    // if (uniform.sample() < bleachProb){
    // solver.setFluorescence(index,false);
    // }else{
    // solver.setFluorescence(index,true);
    // }
    // }
    // };
    // solver.visit(bleachGaussian);
    double totalSampleTime = 0.1;
    int numSampleSteps = 1;
    double samplePsfVariance = psfVar;
    double detectorGainAndQuantumYeild = 100;
    boolean bNoise = true;
    boolean bConvolve = true;
    UShortImage sampledImage = solver.sampleImage(100, 100, origin, extent, diffusionRate, totalSampleTime, numSampleSteps, samplePsfVariance, detectorGainAndQuantumYeild, bConvolve, bNoise);
    new DisplayImageOp().displayImage(sampledImage, "initialBleach", null);
}

Example 20 with UShortImage

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

the class VFrapProcess 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/rawData/sim3/workflow.txt.save");
        ImageTimeSeries<UShortImage> fluorTimeSeriesImages = new ImportRawTimeSeriesFromVFrapOp().importRawTimeSeriesFromVFrap(vfrapFile);
        VFrapProcessResults results = compute(fluorTimeSeriesImages, 0.85, 0.4, localWorkspace, progressListener);
        new DisplayTimeSeriesOp().displayImageTimeSeries(fluorTimeSeriesImages, "raw data", null);
        new DisplayImageOp().displayImage(results.cellROI_2D.getRoiImages()[0], "cell ROI", null);
        new DisplayImageOp().displayImage(results.bleachROI_2D.getRoiImages()[0], "bleach ROI", null);
        new DisplayDependentROIsOp().displayDependentROIs(results.imageDataROIs, results.cellROI_2D, "data rois", null);
        new DisplayTimeSeriesOp().displayImageTimeSeries(results.normalizedTimeSeries, "normalized data", null);
        new DisplayProfileLikelihoodPlotsOp().displayProfileLikelihoodPlots(results.profileDataOne, "one fluorescent pool", null);
        new DisplayProfileLikelihoodPlotsOp().displayProfileLikelihoodPlots(results.profileDataTwoWithPenalty, "too pools", null);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}