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

Example 26 with Extent

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

the class RunRefSimulationFastOp method runRefSimulation.

private RowColumnResultSet runRefSimulation(ROI cellROI, ROI[] imageDataROIs, UShortImage psf, FloatImage initRefConc, double experimentalRecoveryTime, LocalWorkspace localWorkspace, ClientTaskStatusSupport progressListener) throws Exception {
    User owner = LocalWorkspace.getDefaultOwner();
    KeyValue simKey = LocalWorkspace.createNewKeyValue();
    // 
    // save first image from normalized time series as the initial concentration field data
    // 
    ExternalDataInfo initialConcentrationExtData = createNewExternalDataInfo(localWorkspace, INITCONC_EXTDATA_NAME);
    Extent extent = initRefConc.getExtent();
    Origin origin = initRefConc.getOrigin();
    ISize isize = new ISize(initRefConc.getNumX(), initRefConc.getNumY(), initRefConc.getNumZ());
    saveExternalData(initRefConc, INITCONC_EXTDATA_VARNAME, initialConcentrationExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments initConditionFFA = new FieldFunctionArguments(INITCONC_EXTDATA_NAME, INITCONC_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    // 
    // save ROIs as a multivariate field data
    // 
    ExternalDataInfo roiExtData = createNewExternalDataInfo(localWorkspace, ROI_EXTDATA_NAME);
    saveROIsAsExternalData(imageDataROIs, localWorkspace, roiExtData.getExternalDataIdentifier());
    ArrayList<FieldFunctionArguments> roiFFAs = new ArrayList<FieldFunctionArguments>();
    for (ROI roi : imageDataROIs) {
        roiFFAs.add(new FieldFunctionArguments(ROI_EXTDATA_NAME, ROI_MASK_NAME_PREFIX + roi.getROIName(), new Expression(0.0), VariableType.VOLUME));
    }
    // 
    // save PSF as a field data
    // 
    ExternalDataInfo psfExtData = createNewExternalDataInfo(localWorkspace, PSF_EXTDATA_NAME);
    savePsfAsExternalData(psf, PSF_EXTDATA_VARNAME, psfExtData.getExternalDataIdentifier(), localWorkspace);
    FieldFunctionArguments psfFFA = new FieldFunctionArguments(PSF_EXTDATA_NAME, PSF_EXTDATA_VARNAME, new Expression(0.0), VariableType.VOLUME);
    TimeBounds timeBounds = getEstimatedRefTimeBound(experimentalRecoveryTime);
    double timeStepVal = REFERENCE_DIFF_DELTAT;
    Expression chirpedDiffusionRate = new Expression(REFERENCE_DIFF_RATE_COEFFICIENT + "*(t+" + REFERENCE_DIFF_DELTAT + ")");
    BioModel bioModel = createRefSimBioModel(simKey, owner, origin, extent, cellROI, timeStepVal, timeBounds, VAR_NAME, new Expression(initConditionFFA.infix()), psfFFA, chirpedDiffusionRate);
    if (progressListener != null) {
        progressListener.setMessage("Running Reference Simulation...");
    }
    // run simulation
    Simulation simulation = bioModel.getSimulation(0);
    ROIDataGenerator roiDataGenerator = getROIDataGenerator(localWorkspace, imageDataROIs);
    simulation.getMathDescription().getPostProcessingBlock().addDataGenerator(roiDataGenerator);
    runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), simulation, initialConcentrationExtData.getExternalDataIdentifier(), roiExtData.getExternalDataIdentifier(), psfExtData.getExternalDataIdentifier(), progressListener, true);
    KeyValue referenceSimKeyValue = simulation.getVersion().getVersionKey();
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(referenceSimKeyValue, LocalWorkspace.getDefaultOwner());
    VCSimulationDataIdentifier vcSimDataID = new VCSimulationDataIdentifier(vcSimID, 0);
    File hdf5File = new File(localWorkspace.getDefaultSimDataDirectory(), vcSimDataID.getID() + SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5);
    // get post processing info (time points, variable sizes)
    DataOperation.DataProcessingOutputInfoOP dataOperationInfo = new DataOperation.DataProcessingOutputInfoOP(null, /*no vcDataIdentifier OK*/
    false, null);
    DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(dataOperationInfo, hdf5File);
    // get post processing data
    DataOperation.DataProcessingOutputDataValuesOP dataOperationDataValues = new DataOperation.DataProcessingOutputDataValuesOP(null, /*no vcDataIdentifier OK*/
    ROI_EXTDATA_NAME, TimePointHelper.createAllTimeTimePointHelper(), DataIndexHelper.createSliceDataIndexHelper(0), null, null);
    DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataOperationResults.DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataOperationDataValues, hdf5File);
    // 
    // delete the simulation files
    // 
    // 
    // remove reference simulation files and field data files
    // 
    File userDir = new File(localWorkspace.getDefaultSimDataDirectory());
    File[] oldSimFilesToDelete = getSimulationFileNames(userDir, referenceSimKeyValue);
    for (int i = 0; oldSimFilesToDelete != null && i < oldSimFilesToDelete.length; i++) {
        oldSimFilesToDelete[i].delete();
    }
    deleteCanonicalExternalData(localWorkspace, initialConcentrationExtData.getExternalDataIdentifier());
    deleteCanonicalExternalData(localWorkspace, roiExtData.getExternalDataIdentifier());
    deleteCanonicalExternalData(localWorkspace, roiExtData.getExternalDataIdentifier());
    // get ref sim time points (distorted by time dilation acceleration)
    double[] rawRefDataTimePoints = dataProcessingOutputInfo.getVariableTimePoints();
    // get shifted time points
    double[] correctedRefDataTimePoints = shiftTimeForBaseDiffRate(rawRefDataTimePoints);
    double[][] refData = dataProcessingOutputDataValues.getDataValues();
    // 
    // for rowColumnResultSet with { "t", "roi1", .... , "roiN" } for reference data
    // 
    int numROIs = imageDataROIs.length;
    String[] columnNames = new String[numROIs + 1];
    columnNames[0] = "t";
    for (int i = 0; i < numROIs; i++) {
        columnNames[i + 1] = imageDataROIs[i].getROIName();
    }
    RowColumnResultSet reducedData = new RowColumnResultSet(columnNames);
    for (int i = 0; i < correctedRefDataTimePoints.length; i++) {
        double[] row = new double[numROIs + 1];
        row[0] = correctedRefDataTimePoints[i];
        double[] roiData = refData[i];
        for (int j = 0; j < numROIs; j++) {
            // roiData[0] is the average over the cell .. postbleach this shouldn't change for pure diffusion
            row[j + 1] = roiData[j + 1];
        }
        reducedData.addRow(row);
    }
    return reducedData;
}

Example 27 with Extent

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

the class RunRefSimulationFastOp method saveROIsAsExternalData.

private void saveROIsAsExternalData(ROI[] rois, LocalWorkspace localWorkspace, ExternalDataIdentifier newROIExtDataID) throws ObjectNotFoundException, ImageException, IOException {
    ISize isize = rois[0].getISize();
    Origin origin = rois[0].getRoiImages()[0].getOrigin();
    Extent extent = rois[0].getRoiImages()[0].getExtent();
    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 cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    int NumTimePoints = 1;
    int NumChannels = rois.length;
    // dimensions: time points, channels, whole image ordered by z slices.
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    int index = 0;
    for (ROI roi : rois) {
        pixData[0][index++] = createDoubleArray(roi.getBinaryPixelsXYZ(1));
    }
    // Origin origin = new Origin(0,0,0);
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = cartesianMesh;
    fdos.doubleSpecData = pixData;
    fdos.specEDI = newROIExtDataID;
    ArrayList<String> varNames = new ArrayList<String>();
    ArrayList<VariableType> varTypes = new ArrayList<VariableType>();
    for (ROI roi : rois) {
        varNames.add(ROI_MASK_NAME_PREFIX + roi.getROIName());
        varTypes.add(VariableType.VOLUME);
    }
    fdos.varNames = varNames.toArray(new String[0]);
    fdos.owner = LocalWorkspace.getDefaultOwner();
    fdos.times = new double[] { 0.0 };
    fdos.variableTypes = varTypes.toArray(new VariableType[0]);
    fdos.origin = origin;
    fdos.extent = extent;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}

Example 28 with Extent

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

the class RunRefSimulationFastOp method savePsfAsExternalData.

private void savePsfAsExternalData(UShortImage psf, String varName, ExternalDataIdentifier newPsfExtDataID, LocalWorkspace localWorkspace) throws IOException, ImageException, ObjectNotFoundException {
    Origin origin = new Origin(0, 0, 0);
    Extent ext = new Extent(1, 1, 1);
    ISize isize = new ISize(3, 3, 1);
    VCImageUncompressed vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], ext, isize.getX(), isize.getY(), isize.getZ());
    RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
    CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, ext, isize, regionImage);
    int NumTimePoints = 1;
    // 8 rois integrated into 1 image
    int NumChannels = 1;
    short[][][] pixData = new short[NumTimePoints][NumChannels][1];
    pixData[0][0] = psf.getPixels();
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = cartesianMesh;
    fdos.shortSpecData = pixData;
    fdos.specEDI = newPsfExtDataID;
    fdos.varNames = new String[] { varName };
    fdos.owner = LocalWorkspace.getDefaultOwner();
    fdos.times = new double[] { 0.0 };
    fdos.variableTypes = new VariableType[] { VariableType.VOLUME };
    fdos.origin = origin;
    fdos.extent = ext;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}

Example 29 with Extent

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

the class RunSimulation2DOp method runRefSimulation.

public ImageTimeSeries<FloatImage> runRefSimulation(LocalWorkspace localWorkspace, Simulation simulation, String varName, 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(simKey, owner), 0);
    CartesianMesh mesh = localWorkspace.getDataSetControllerImpl().getMesh(vcDataIdentifier);
    ISize isize = new ISize(mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ());
    double[] dataTimes = localWorkspace.getDataSetControllerImpl().getDataSetTimes(vcDataIdentifier);
    FloatImage[] solutionImages = new FloatImage[dataTimes.length];
    for (int i = 0; i < dataTimes.length; i++) {
        SimDataBlock simDataBlock = localWorkspace.getDataSetControllerImpl().getSimDataBlock(null, vcDataIdentifier, varName, dataTimes[i]);
        double[] doubleData = simDataBlock.getData();
        float[] floatPixels = new float[doubleData.length];
        for (int j = 0; j < doubleData.length; j++) {
            floatPixels[j] = (float) doubleData[j];
        }
        solutionImages[i] = new FloatImage(floatPixels, origin, extent, isize.getX(), isize.getY(), isize.getZ());
    }
    ImageTimeSeries<FloatImage> solution = new ImageTimeSeries<FloatImage>(FloatImage.class, solutionImages, dataTimes, 1);
    return solution;
}

Example 30 with Extent

use of org.vcell.util.Extent 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);
}