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

Example 96 with UShortImage

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

the class ImportRawTimeSeriesFromVFrapOp method importRawTimeSeriesFromVFrap.

public ImageTimeSeries<UShortImage> importRawTimeSeriesFromVFrap(File vfrapFile) throws Exception {
    String xmlString = XmlUtil.getXMLString(vfrapFile.getAbsolutePath());
    MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
    Element vFrapRoot = XmlUtil.stringToXML(xmlString, null).getRootElement();
    // loading frap images and a ROIs subset for display purposes only (see next task)
    AnnotatedImageDataset annotatedImages = xmlReader.getAnnotatedImageDataset(vFrapRoot, null);
    ImageDataset imageDataset = annotatedImages.getImageDataset();
    UShortImage[] allImages = imageDataset.getAllImages();
    double[] imageTimeStamps = imageDataset.getImageTimeStamps();
    ImageTimeSeries<UShortImage> imageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, allImages, imageTimeStamps, 1);
    return imageTimeSeries;
}

Example 97 with UShortImage

use of cbit.vcell.VirtualMicroscopy.UShortImage 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 98 with UShortImage

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

the class ImportRawTimeSeriesFromHdf5FluorOp method importTimeSeriesFromHDF5Data.

public ImageTimeSeries<UShortImage> importTimeSeriesFromHDF5Data(File inputHDF5File, String fluorDataName, Double maxIntensity, boolean bNoise, int zSliceIndex) throws Exception {
    // if(progressListener != null){
    // progressListener.setMessage("Loading HDF5 file " + inputHDF5File.getAbsolutePath() + "...");
    // }
    DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(null, /*no vcDataIdentifier OK*/
    false, null), inputHDF5File);
    DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataOperationResults.DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputDataValuesOP(null, /*no vcDataIdentifier OK*/
    SimulationContext.FLUOR_DATA_NAME, TimePointHelper.createAllTimeTimePointHelper(), DataIndexHelper.createSliceDataIndexHelper(0), null, null), inputHDF5File);
    ArrayList<SourceDataInfo> sdiArr = dataProcessingOutputDataValues.createSourceDataInfos(dataProcessingOutputInfo.getVariableISize(SimulationContext.FLUOR_DATA_NAME), dataProcessingOutputInfo.getVariableOrigin(SimulationContext.FLUOR_DATA_NAME), dataProcessingOutputInfo.getVariableExtent(SimulationContext.FLUOR_DATA_NAME));
    double[] times = dataProcessingOutputInfo.getVariableTimePoints();
    if (sdiArr.size() != times.length) {
        throw new ImageException("Error FRAPData.createFrapData: times array length must equal SourceDataInfo vector size");
    }
    // construct
    int XY_SIZE = sdiArr.get(0).getXSize() * sdiArr.get(0).getYSize();
    int SLICE_OFFSET = 0 * XY_SIZE;
    // slice always 2D data
    int Z_SIZE = 1;
    // find scale factor to scale up the data to avoid losing precision when casting double to short
    double linearScaleFactor = 1;
    if (maxIntensity != null) {
        double maxDataValue = 0;
        for (int i = 0; i < times.length; i++) {
            if (sdiArr.get(i).getMinMax() != null) {
                maxDataValue = Math.max(maxDataValue, sdiArr.get(i).getMinMax().getMax());
            } else {
                double[] doubleData = (double[]) sdiArr.get(i).getData();
                for (int j = 0; j < doubleData.length; j++) {
                    maxDataValue = Math.max(maxDataValue, doubleData[j]);
                }
            }
        }
        linearScaleFactor = maxIntensity.doubleValue() / maxDataValue;
    }
    // saving each time step 2D double array to a UShortImage
    UShortImage[] dataImages1 = new UShortImage[times.length];
    for (int i = 0; i < times.length; i++) {
        double[] doubleData = (double[]) sdiArr.get(i).getData();
        short[] shortData = new short[XY_SIZE];
        for (int j = 0; j < shortData.length; j++) {
            shortData[j] = (short) (doubleData[j + (SLICE_OFFSET)] * linearScaleFactor);
        }
        dataImages1[i] = new UShortImage(shortData, sdiArr.get(i).getOrigin(), sdiArr.get(i).getExtent(), sdiArr.get(i).getXSize(), sdiArr.get(i).getYSize(), Z_SIZE);
    // if(progressListener != null){
    // int progress = (int)(((i+1)*1.0/times.length)*100);
    // progressListener.setProgress(progress);
    // }
    }
    ImageDataset imageDataSet = new ImageDataset(dataImages1, times, Z_SIZE);
    UShortImage[] dataImages = imageDataSet.getAllImages();
    double[] timeStamps = imageDataSet.getImageTimeStamps();
    ImageTimeSeries<UShortImage> rawImageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, dataImages, timeStamps, 1);
    return rawImageTimeSeries;
}