Examples with Origin org.vcell.util.Origin used on opensource projects

Example 61 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class GenerateTrivial2DPsfOp method generateTrivial2D_Psf.

public UShortImage generateTrivial2D_Psf() {
    // psf image is now expecting a 3x3 image that are all zeros with a 1 in the middle (Kronecker delta)
    short[] pixels = new short[] { 0, 0, 0, 0, 1, 0, 0, 0, 0 };
    Origin origin = new Origin(0, 0, 0);
    Extent extent = new Extent(1, 1, 1);
    ISize isize = new ISize(3, 3, 1);
    UShortImage psfImage;
    try {
        psfImage = new UShortImage(pixels, origin, extent, isize.getX(), isize.getY(), isize.getZ());
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("unexpected image exception: " + e.getMessage(), e);
    }
    return psfImage;
}

Example 62 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class FitBleachSpotOp method main.

public static void main(String[] args) {
    try {
        int numX = 100;
        int numY = 100;
        double center_i = 52.44;
        double center_j = 51.39;
        double K = 30;
        double high = 0.9;
        double sigma2 = 4;
        float[] pixels = new float[numX * numY];
        Origin origin = new Origin(0, 0, 0);
        Extent extent = new Extent(1, 1, 1);
        FloatImage image = new FloatImage(pixels, origin, extent, numX, numY, 1);
        int index = 0;
        for (int j = 0; j < numY; j++) {
            for (int i = 0; i < numX; i++) {
                double radius = ((i - center_i) * (i - center_i) + (j - center_j) * (j - center_j));
                pixels[index++] = (float) (high - FastMath.exp(-K * FastMath.exp(-radius / sigma2)));
            }
        }
        double init_center_i = 50;
        double init_center_j = 50;
        double init_sigma2 = 2;
        GaussianFitResults fitResults = fitToGaussian(init_center_i, init_center_j, init_sigma2, image);
        System.out.println(fitResults);
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 63 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class FitBleachSpotOp method fit.

public FitBleachSpotOpResults fit(NormalizedSampleFunction bleachROI, FloatImage normImage) {
    // 
    // find initial guess by centroid from bleach ROI and total area of bleach ROI (assuming a circle of radius R)
    // 
    ISize size = bleachROI.getISize();
    if (size.getZ() > 1) {
        throw new RuntimeException("expecting 2D bleach region ROI");
    }
    short[] pixels = bleachROI.toROI(1e-5).getBinaryPixelsXYZ(1);
    long numPixelsInROI = 0;
    Extent extent = bleachROI.getExtent();
    double totalX_um = 0.0;
    double totalY_um = 0.0;
    double total_I = 0.0;
    double total_J = 0.0;
    int pixelIndex = 0;
    for (int i = 0; i < size.getX(); i++) {
        double x = extent.getX() * (i + 0.5) / (size.getX() - 1);
        for (int j = 0; j < size.getY(); j++) {
            if (pixels[pixelIndex] != 0) {
                double y = extent.getY() * (j + 0.5) / (size.getY() - 1);
                totalX_um += x;
                totalY_um += y;
                total_I += i;
                total_J += j;
                numPixelsInROI++;
            }
            pixelIndex++;
        }
    }
    Origin origin = bleachROI.getOrigin();
    double roiCenterX_um = origin.getX() + totalX_um / numPixelsInROI;
    double roiCenterY_um = origin.getY() + totalY_um / numPixelsInROI;
    double roiCenterI_pixelscale = total_I / numPixelsInROI;
    double roiCenterJ_pixelscale = total_J / numPixelsInROI;
    // Area = PI * R^2
    // R = sqrt(Area/PI)
    double roiBleachSpotArea_um2 = (extent.getX() * extent.getY() * numPixelsInROI) / (size.getX() * size.getY());
    double roiBleachRadius_um = Math.sqrt(roiBleachSpotArea_um2 / Math.PI);
    double roiBleachRadius_pixelscale = Math.sqrt(numPixelsInROI / Math.PI);
    FitBleachSpotOpResults results = new FitBleachSpotOpResults();
    results.bleachRadius_ROI = roiBleachRadius_um;
    results.centerX_ROI = roiCenterX_um;
    results.centerY_ROI = roiCenterY_um;
    GaussianFitResults gfresults = fitToGaussian(roiCenterI_pixelscale, roiCenterJ_pixelscale, roiBleachRadius_pixelscale * roiBleachRadius_pixelscale, normImage);
    results.bleachFactorK_GaussianFit = gfresults.K;
    results.bleachRadius_GaussianFit = Math.sqrt(gfresults.radius2);
    results.centerX_GaussianFit = origin.getX() + extent.getX() * (gfresults.centerI + 0.5) / size.getX();
    results.centerY_GaussianFit = origin.getY() + extent.getY() * (gfresults.centerJ + 0.5) / size.getY();
    return results;
}

Example 64 with Origin

use of org.vcell.util.Origin in project vcell by virtualcell.

the class RunFakeSimOp method runRefSimulation.

public ImageTimeSeries<UShortImage> runRefSimulation(LocalWorkspace localWorkspace, Simulation simulation, double max_intensity, double bleachBlackoutStartTime, double bleachBlackoutStopTime, boolean hasNoise, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, progressListener);
    Extent extent = simulation.getMathDescription().getGeometry().getExtent();
    Origin origin = simulation.getMathDescription().getGeometry().getOrigin();
    VCDataIdentifier vcDataIdentifier = new VCSimulationDataIdentifier(new VCSimulationIdentifier(simulation.getKey(), simulation.getVersion().getOwner()), 0);
    CartesianMesh mesh = localWorkspace.getDataSetControllerImpl().getMesh(vcDataIdentifier);
    ISize isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataProcessingOutputDataValues) localWorkspace.getDataSetControllerImpl().doDataOperation(new DataProcessingOutputDataValuesOP(vcDataIdentifier, SimulationContext.FLUOR_DATA_NAME, TimePointHelper.createAllTimeTimePointHelper(), DataIndexHelper.createSliceDataIndexHelper(0), null, null));
    ArrayList<SourceDataInfo> sourceDataInfoArr = dataProcessingOutputDataValues.createSourceDataInfos(new ISize(mesh.getSizeX(), mesh.getSizeY(), 1), origin, extent);
    // find scale factor to scale up the data to avoid losing precision when casting double to short
    double maxDataValue = 0;
    for (int i = 0; i < dataTimes.length; i++) {
        if (sourceDataInfoArr.get(i).getMinMax() != null) {
            maxDataValue = Math.max(maxDataValue, sourceDataInfoArr.get(i).getMinMax().getMax());
        } else {
            double[] doubleData = (double[]) sourceDataInfoArr.get(i).getData();
            for (int j = 0; j < doubleData.length; j++) {
                maxDataValue = Math.max(maxDataValue, doubleData[j]);
            }
        }
    }
    double scale = max_intensity / maxDataValue;
    ArrayList<UShortImage> outputImages = new ArrayList<UShortImage>();
    ArrayList<Double> outputTimes = new ArrayList<Double>();
    for (int i = 0; i < dataTimes.length; i++) {
        if (dataTimes[i] < bleachBlackoutStartTime || dataTimes[i] > bleachBlackoutStopTime) {
            // saving each time step 2D double array to a UShortImage
            double[] doubleData = (double[]) sourceDataInfoArr.get(i).getData();
            short[] shortData = new short[isize.getX() * isize.getY()];
            for (int j = 0; j < shortData.length; j++) {
                double dData = doubleData[j] * scale;
                if (dData < 0 || dData > 65535.0) {
                    throw new RuntimeException("scaled pixel out of range of unsigned 16 bit integer, original simulated value = " + doubleData[j] + ", scale = " + scale + ", scaled value = " + dData);
                }
                short sData = (short) (0x0000ffff & ((int) dData));
                if (hasNoise && dData > 0.0) {
                    if (dData > 20) {
                        shortData[j] = (short) (0x0000ffff & (int) RandomVariable.normal(dData, Math.sqrt(dData)));
                    } else {
                        shortData[j] = (short) (0x0000ffff & RandomVariable.poisson(dData));
                    }
                } else {
                    shortData[j] = sData;
                }
            }
            outputTimes.add(dataTimes[i]);
            outputImages.add(new UShortImage(shortData, sourceDataInfoArr.get(i).getOrigin(), sourceDataInfoArr.get(i).getExtent(), sourceDataInfoArr.get(i).getXSize(), sourceDataInfoArr.get(i).getYSize(), 1));
            if (progressListener != null) {
                int progress = (int) (((i + 1) * 1.0 / dataTimes.length) * 100);
                progressListener.setProgress(progress);
            }
        }
    }
    double[] outputTimesArray = new double[outputTimes.size()];
    for (int i = 0; i < outputTimes.size(); i++) {
        outputTimesArray[i] = outputTimes.get(i);
    }
    ImageTimeSeries<UShortImage> fakeFluorTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, outputImages.toArray(new UShortImage[0]), outputTimesArray, 1);
    return fakeFluorTimeSeries;
}