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

Example 91 with Extent

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

the class GenerateNormalizedFrapDataOp method generate.

public NormalizedFrapDataResults generate(ImageTimeSeries<UShortImage> rawImageTimeSeries, ROI backgroundROI_2D, Integer indexPostbleach) throws Exception {
    UShortImage firstImage = rawImageTimeSeries.getAllImages()[0];
    ISize isize = firstImage.getISize();
    int nX = isize.getX();
    int nY = isize.getY();
    int nZ = isize.getZ();
    int numTimes = rawImageTimeSeries.getSizeT();
    Extent extent = firstImage.getExtent();
    org.vcell.util.Origin origin = firstImage.getOrigin();
    if (indexPostbleach == 0) {
        throw new RuntimeException("no prebleach images found - indexOfFirstPostbleach is 0");
    }
    // 
    // find average "dark count" in background of pre-bleach images (for background subtraction)
    // 
    float avgBackground = 0.0f;
    int numPrebleach = indexPostbleach;
    for (int i = 0; i < numPrebleach; i++) {
        avgBackground += getAverage(rawImageTimeSeries.getAllImages()[i], backgroundROI_2D);
    }
    avgBackground /= numPrebleach;
    // 
    // find averaged prebleach image (corrected for background).
    // 
    int numPostbleachImages = numTimes - numPrebleach;
    // holds new averaged image pixels
    float[] prebleachAveragePixels = new float[nX * nY * nZ];
    for (int i = 0; i < numPrebleach; i++) {
        short[] currPrebleachImage = rawImageTimeSeries.getAllImages()[i].getPixels();
        for (int j = 0; j < isize.getXYZ(); j++) {
            float intPixel = 0x0000ffff & ((int) currPrebleachImage[j]);
            prebleachAveragePixels[j] += intPixel / numPrebleach;
        }
    }
    FloatImage prebleachAverageImage = new FloatImage(prebleachAveragePixels, origin, extent, nX, nY, nZ);
    // 
    // create normalized dataset
    // 
    // normalized postbleach = (origPostbleach - background)/(prebleach - background)
    // 
    FloatImage[] normalizedImages = new FloatImage[numPostbleachImages];
    double[] postbleachTimeStamps = new double[numPostbleachImages];
    for (int i = 0; i < numPostbleachImages; i++) {
        double[] origTimeStamps = rawImageTimeSeries.getImageTimeStamps();
        postbleachTimeStamps[i] = origTimeStamps[indexPostbleach + i] - origTimeStamps[indexPostbleach];
        float[] normalizedPixels = new float[isize.getXYZ()];
        normalizedImages[i] = new FloatImage(normalizedPixels, origin, extent, nX, nY, nZ);
        short[] uncorrectedPixels = rawImageTimeSeries.getAllImages()[i + indexPostbleach].getPixels();
        for (int j = 0; j < isize.getXYZ(); j++) {
            int intPixel = 0x0000ffff & ((int) uncorrectedPixels[j]);
            normalizedPixels[j] = (intPixel - avgBackground) / (Math.max(1, prebleachAveragePixels[j] - avgBackground));
        }
        normalizedImages[i] = new FloatImage(normalizedPixels, origin, extent, nX, nY, nZ);
    }
    ImageTimeSeries<FloatImage> normalizedData = new ImageTimeSeries<FloatImage>(FloatImage.class, normalizedImages, postbleachTimeStamps, nZ);
    NormalizedFrapDataResults results = new NormalizedFrapDataResults();
    results.normalizedFrapData = normalizedData;
    results.prebleachAverage = prebleachAverageImage;
    return results;
}

Example 92 with Extent

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

the class FitTimeSeries 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 93 with Extent

use of org.vcell.util.Extent 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 94 with Extent

use of org.vcell.util.Extent 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;
}

Example 95 with Extent

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

the class RunRefSimulationFastOp method getROIDataGenerator.

private ROIDataGenerator getROIDataGenerator(LocalContext localWorkspace, ROI[] rois) throws ImageException, IOException {
    // create ROI image
    short[] roiFieldData = null;
    if (rois.length > 0) {
        Origin origin = new Origin(0, 0, 0);
        Extent extent = rois[0].getRoiImages()[0].getExtent();
        ISize isize = rois[0].getISize();
        int numROIX = rois[0].getISize().getX();
        int numROIY = rois[0].getISize().getY();
        roiFieldData = new short[numROIX * numROIY];
        short regionCounter = 1;
        for (int roiIdx = 0; roiIdx < rois.length; roiIdx++) {
            short[] roiImg = rois[roiIdx].getPixelsXYZ();
            for (int pixelIdx = 0; pixelIdx < (numROIX * numROIY); pixelIdx++) {
                if (roiImg[pixelIdx] > 0) {
                    roiFieldData[pixelIdx] = regionCounter;
                }
            }
            regionCounter++;
        }
        // create field data
        int NumTimePoints = 1;
        // 8 rois integrated into 1 image
        int NumChannels = 1;
        short[][][] pixData = new short[NumTimePoints][NumChannels][];
        pixData[0][0] = roiFieldData;
        // get extental data id
        VCImage vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ());
        RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
        CartesianMesh simpleCartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
        ExternalDataIdentifier newROIExtDataID = createNewExternalDataInfo(localWorkspace, ROI_SUMDATA_NAME).getExternalDataIdentifier();
        try {
            FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
            fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
            fdos.cartesianMesh = simpleCartesianMesh;
            fdos.shortSpecData = pixData;
            fdos.specEDI = newROIExtDataID;
            fdos.varNames = new String[] { "roiSumDataVar" };
            fdos.owner = LocalWorkspace.getDefaultOwner();
            fdos.times = new double[] { 0.0 };
            fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
            fdos.origin = origin;
            fdos.extent = extent;
            fdos.isize = isize;
            localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return new ROIDataGenerator(ROI_EXTDATA_NAME, /*name*/
        new int[] { 0 }, /* volumePoints*/
        new int[0], /* membranePoints*/
        regionCounter, /*numRegions*/
        0, /*zSlice*/
        newROIExtDataID.getKey(), /* fieldDataKey, sample image*/
        new FieldFunctionArguments(ROI_SUMDATA_NAME, ROI_SUMDATA_VARNAME, new Expression(0), VariableType.VOLUME), /*FieldFunctionArguments, sample image*/
        false);
    }
    return null;
}