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

Example 31 with UShortImage

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

the class RunFakeSim method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // set input
    Simulation sim = context.getData(simulation_2D);
    Double max_intensity = context.getData(maxIntensity);
    Double bleachLockingBegin = context.getData(bleachBlackoutBeginTime);
    Double bleachLockoutEnd = context.getData(bleachBlackoutEndTime);
    Boolean hasNoise = context.getData(bNoise);
    // do op
    RunFakeSimOp op = new RunFakeSimOp();
    ImageTimeSeries<UShortImage> solution = op.runRefSimulation(context.getLocalWorkspace(), sim, max_intensity, bleachLockingBegin, bleachLockoutEnd, hasNoise, clientTaskStatusSupport);
    // set output
    context.setData(simTimeSeries, solution);
}

Example 32 with UShortImage

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

the class GenerateActivationRoiOp method generateActivatedRoi.

public ROI generateActivatedRoi(Image firstPostactivation, ROI cellROI_2D, Double activationThreshold) throws ImageException {
    int numPixels = firstPostactivation.getNumXYZ();
    short[] scaledActivatedDataShort = new short[numPixels];
    short[] erodedCellUShort = cellROI_2D.getRoiImages()[0].getBinaryPixels(1);
    // input is already normalized to 1.0 ... if relative to max, then crazy values from outside cell can interfere.
    double activationThresholdValue = activationThreshold;
    double[] firstPostactivationImage = firstPostactivation.getDoublePixels();
    for (int j = 0; j < numPixels; j++) {
        boolean isCell = (erodedCellUShort[j] == 1);
        boolean isActivation = firstPostactivationImage[j] > activationThresholdValue;
        if (isCell && isActivation) {
            scaledActivatedDataShort[j] = 1;
        }
    }
    UShortImage activatedImage = new UShortImage(scaledActivatedDataShort, firstPostactivation.getOrigin(), firstPostactivation.getExtent(), firstPostactivation.getNumX(), firstPostactivation.getNumY(), firstPostactivation.getNumZ());
    ROI bleachedROI = new ROI(activatedImage, "bleachedROI");
    return bleachedROI;
}

Example 33 with UShortImage

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

the class GenerateCellROIsFromRawFrapTimeSeriesOp method generate.

public GeometryRoisAndBleachTiming generate(ImageTimeSeries rawTimeSeriesImages, double cellThreshold) throws Exception {
    Image[] allImages = rawTimeSeriesImages.getAllImages();
    int numPixels = allImages[0].getNumXYZ();
    int numTimes = allImages.length;
    ImageStatistics[] imageStats = new ImageStatistics[numTimes];
    for (int i = 0; i < numTimes; i++) {
        imageStats[i] = allImages[i].getImageStatistics();
    }
    // 
    // find largest change in fluorescence (ratio of total[n]/total[n+1]
    // 
    int indexPostbleach = -1;
    double largestRatio = 0.0;
    for (int tIndex = 0; tIndex < numTimes - 1; tIndex++) {
        double currentRatio = imageStats[tIndex].meanValue / imageStats[tIndex + 1].meanValue;
        if (currentRatio > largestRatio) {
            largestRatio = currentRatio;
            indexPostbleach = tIndex + 1;
        }
    }
    double[] firstImagePixels = allImages[0].getDoublePixels();
    short[] scaledCellDataShort = new short[numPixels];
    short[] scaledBackgoundDataShort = new short[numPixels];
    short[] wholeDomainDataShort = new short[numPixels];
    // 
    // find cell and background by thresholding the first image
    // 
    double cellThresholdValue = cellThreshold * imageStats[0].maxValue;
    for (int j = 0; j < numPixels; j++) {
        boolean isCell = firstImagePixels[j] > cellThresholdValue;
        if (isCell) {
            scaledCellDataShort[j] = 1;
        } else {
            scaledBackgoundDataShort[j] = 1;
        }
    }
    UShortImage cellImage = new UShortImage(scaledCellDataShort, allImages[0].getOrigin(), allImages[0].getExtent(), allImages[0].getNumX(), allImages[0].getNumY(), allImages[0].getNumZ());
    UShortImage backgroundImage = new UShortImage(scaledBackgoundDataShort, allImages[0].getOrigin(), allImages[0].getExtent(), allImages[0].getNumX(), allImages[0].getNumY(), allImages[0].getNumZ());
    Arrays.fill(wholeDomainDataShort, (short) 1);
    UShortImage wholeDomainImage = new UShortImage(wholeDomainDataShort, allImages[0].getOrigin(), allImages[0].getExtent(), allImages[0].getNumX(), allImages[0].getNumY(), allImages[0].getNumZ());
    UShortImage reverseCell = UShortImage.fastDilate(cellImage, 15, wholeDomainImage);
    reverseCell.reverse();
    reverseCell.and(backgroundImage);
    backgroundImage = reverseCell;
    ROI cellROI = new ROI(cellImage, "cellROI");
    ROI backgroundROI = new ROI(backgroundImage, "backgroundROI");
    GeometryRoisAndBleachTiming results = new GeometryRoisAndBleachTiming();
    results.cellROI_2D = cellROI;
    results.backgroundROI_2D = backgroundROI;
    results.indexOfFirstPostbleach = indexPostbleach;
    return results;
}

Example 34 with UShortImage

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

the class GenerateDependentImageROIsOp method generate.

public ROI[] generate(ROI cellROI_2d, ROI bleachedROI_2d) throws Exception {
    UShortImage cellROI_2D = null;
    UShortImage bleachedROI_2D = null;
    UShortImage dilatedROI_2D_1 = null;
    UShortImage dilatedROI_2D_2 = null;
    UShortImage dilatedROI_2D_3 = null;
    UShortImage dilatedROI_2D_4 = null;
    UShortImage dilatedROI_2D_5 = null;
    UShortImage erodedROI_2D_0 = null;
    UShortImage erodedROI_2D_1 = null;
    UShortImage erodedROI_2D_2 = null;
    cellROI_2D = cellROI_2d.getRoiImages()[0];
    bleachedROI_2D = bleachedROI_2d.getRoiImages()[0];
    dilatedROI_2D_1 = UShortImage.fastDilate(bleachedROI_2D, 4, cellROI_2D);
    dilatedROI_2D_2 = UShortImage.fastDilate(bleachedROI_2D, 10, cellROI_2D);
    dilatedROI_2D_3 = UShortImage.fastDilate(bleachedROI_2D, 18, cellROI_2D);
    dilatedROI_2D_4 = UShortImage.fastDilate(bleachedROI_2D, 28, cellROI_2D);
    dilatedROI_2D_5 = UShortImage.fastDilate(bleachedROI_2D, 40, cellROI_2D);
    erodedROI_2D_0 = new UShortImage(bleachedROI_2D);
    // The erode always causes problems if eroding without checking the bleached length and height.
    // we have to check the min length of the bleached area to make sure erode within the length.
    Rectangle bleachRect = bleachedROI_2D.getNonzeroBoundingBox();
    if (bleachRect == null || bleachRect.isEmpty()) {
        throw new RuntimeException("bleach ROI is null or empty");
    }
    int minLen = Math.min(bleachRect.height, bleachRect.width);
    if ((minLen / 2.0) < 5) {
        erodedROI_2D_1 = UShortImage.erodeDilate(bleachedROI_2D, UShortImage.createCircularBinaryKernel(1), bleachedROI_2D, true);
        erodedROI_2D_2 = UShortImage.erodeDilate(bleachedROI_2D, UShortImage.createCircularBinaryKernel(2), bleachedROI_2D, true);
    } else {
        erodedROI_2D_1 = UShortImage.erodeDilate(bleachedROI_2D, UShortImage.createCircularBinaryKernel(2), bleachedROI_2D, true);
        erodedROI_2D_2 = UShortImage.erodeDilate(bleachedROI_2D, UShortImage.createCircularBinaryKernel(5), bleachedROI_2D, true);
    }
    UShortImage reverseErodeROI_2D_1 = new UShortImage(erodedROI_2D_1);
    reverseErodeROI_2D_1.reverse();
    erodedROI_2D_0.and(reverseErodeROI_2D_1);
    UShortImage reverseErodeROI_2D_2 = new UShortImage(erodedROI_2D_2);
    reverseErodeROI_2D_2.reverse();
    erodedROI_2D_1.and(reverseErodeROI_2D_2);
    UShortImage reverseDilateROI_2D_4 = new UShortImage(dilatedROI_2D_4);
    reverseDilateROI_2D_4.reverse();
    dilatedROI_2D_5.and(reverseDilateROI_2D_4);
    UShortImage reverseDilateROI_2D_3 = new UShortImage(dilatedROI_2D_3);
    reverseDilateROI_2D_3.reverse();
    dilatedROI_2D_4.and(reverseDilateROI_2D_3);
    UShortImage reverseDilateROI_2D_2 = new UShortImage(dilatedROI_2D_2);
    reverseDilateROI_2D_2.reverse();
    dilatedROI_2D_3.and(reverseDilateROI_2D_2);
    UShortImage reverseDilateROI_2D_1 = new UShortImage(dilatedROI_2D_1);
    reverseDilateROI_2D_1.reverse();
    dilatedROI_2D_2.and(reverseDilateROI_2D_1);
    UShortImage reverseBleach_2D = new UShortImage(bleachedROI_2D);
    reverseBleach_2D.reverse();
    dilatedROI_2D_1.and(reverseBleach_2D);
    ArrayList<ROI> rois = new ArrayList<ROI>();
    // rois.add(new ROI(this.bleachedROI_2D.getData())); // copy this one through
    rois.add(new ROI(erodedROI_2D_2, VFRAP_ROI_ENUM.ROI_BLEACHED_RING1.name()));
    rois.add(new ROI(erodedROI_2D_1, VFRAP_ROI_ENUM.ROI_BLEACHED_RING2.name()));
    rois.add(new ROI(erodedROI_2D_0, VFRAP_ROI_ENUM.ROI_BLEACHED_RING3.name()));
    rois.add(new ROI(dilatedROI_2D_1, VFRAP_ROI_ENUM.ROI_BLEACHED_RING4.name()));
    rois.add(new ROI(dilatedROI_2D_2, VFRAP_ROI_ENUM.ROI_BLEACHED_RING5.name()));
    rois.add(new ROI(dilatedROI_2D_3, VFRAP_ROI_ENUM.ROI_BLEACHED_RING6.name()));
    rois.add(new ROI(dilatedROI_2D_4, VFRAP_ROI_ENUM.ROI_BLEACHED_RING7.name()));
    rois.add(new ROI(dilatedROI_2D_5, VFRAP_ROI_ENUM.ROI_BLEACHED_RING8.name()));
    Iterator<ROI> roiIter = rois.iterator();
    while (roiIter.hasNext()) {
        ROI roi = roiIter.next();
        short[] roiPixels = roi.getBinaryPixelsXYZ(1);
        int numPixels = roiPixels.length;
        int count = 0;
        for (int p = 0; p < numPixels; p++) {
            if (roiPixels[p] != 0) {
                count++;
            }
        }
        if (count == 0) {
            roiIter.remove();
        }
    }
    return rois.toArray(new ROI[0]);
}

Example 35 with UShortImage

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

the class ComputeMeasurementErrorOp method computeNormalizedMeasurementError.

public RowColumnResultSet computeNormalizedMeasurementError(NormalizedSampleFunction[] rois, int indexPostbleach, ImageTimeSeries<UShortImage> rawImageDataset, FloatImage prebleachAvgImage, final ClientTaskStatusSupport clientTaskStatusSupport) throws ImageException {
    UShortImage[] rawImages = rawImageDataset.getAllImages();
    double[] timeStamps = rawImageDataset.getImageTimeStamps();
    double[][] sigma = refreshNormalizedMeasurementError(rawImages, timeStamps, prebleachAvgImage, rois, indexPostbleach);
    String[] columnNames = new String[rois.length + 1];
    columnNames[0] = "t";
    for (int i = 0; i < rois.length; i++) {
        columnNames[i + 1] = rois[i].getName();
    }
    RowColumnResultSet rowColumnResultSet = new RowColumnResultSet(columnNames);
    double[] allTimePoints = timeStamps;
    for (int time = 0; time < (allTimePoints.length - indexPostbleach); time++) {
        double[] rowValues = new double[rois.length + 1];
        rowValues[0] = allTimePoints[time + indexPostbleach];
        for (int col = 0; col < rois.length; col++) {
            rowValues[col + 1] = sigma[col][time];
        }
        rowColumnResultSet.addRow(rowValues);
    }
    return rowColumnResultSet;
}