Examples with ImageException cbit.image.ImageException used on opensource projects

Example 26 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class GeomDbDriver method updateVersionable.

/**
 * This method was created in VisualAge.
 * @return cbit.image.VCImage
 * @param user cbit.vcell.server.User
 * @param image cbit.image.VCImage
 */
public KeyValue updateVersionable(InsertHashtable hash, QueryHashtable dbc, Connection con, User user, Geometry geometry, KeyValue updatedImageKey, boolean bVersion) throws DataAccessException, SQLException, RecordChangedException {
    Version newVersion = null;
    try {
        newVersion = updateVersionableInit(hash, con, user, geometry, bVersion);
        insertGeometry(hash, dbc, con, user, geometry, updatedImageKey, newVersion, bVersion);
    } catch (ImageException e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("ImageException: " + e.getMessage());
    }
    return newVersion.getVersionKey();
}

Example 27 with ImageException

use of cbit.image.ImageException 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;
}

Example 28 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class RunRefSimulationFastOp method createRefSimBioModel.

private BioModel createRefSimBioModel(KeyValue simKey, User owner, Origin origin, Extent extent, ROI cellROI_2D, double timeStepVal, TimeBounds timeBounds, String varName, Expression initialConcentration, FieldFunctionArguments psfFFA, Expression chirpedDiffusionRate) throws Exception {
    int numX = cellROI_2D.getRoiImages()[0].getNumX();
    int numY = cellROI_2D.getRoiImages()[0].getNumY();
    int numZ = cellROI_2D.getRoiImages().length;
    short[] shortPixels = cellROI_2D.getRoiImages()[0].getPixels();
    byte[] bytePixels = new byte[numX * numY * numZ];
    final byte EXTRACELLULAR_PIXVAL = 0;
    final byte CYTOSOL_PIXVAL = 1;
    for (int i = 0; i < bytePixels.length; i++) {
        if (shortPixels[i] != 0) {
            bytePixels[i] = CYTOSOL_PIXVAL;
        }
    }
    VCImage maskImage;
    try {
        maskImage = new VCImageUncompressed(null, bytePixels, extent, numX, numY, numZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to create mask image for geometry");
    }
    Geometry geometry = new Geometry("geometry", maskImage);
    geometry.getGeometrySpec().setOrigin(origin);
    if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
        throw new Exception("Cell ROI has no ExtraCellular.");
    }
    String EXTRACELLULAR_NAME = "ec";
    String CYTOSOL_NAME = "cyt";
    String PLASMAMEMBRANE_NAME = "pm";
    ImageSubVolume subVolume0 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0);
    ImageSubVolume subVolume1 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1);
    if (subVolume0.getPixelValue() == EXTRACELLULAR_PIXVAL) {
        subVolume0.setName(EXTRACELLULAR_NAME);
        subVolume1.setName(CYTOSOL_NAME);
    } else {
        subVolume0.setName(CYTOSOL_NAME);
        subVolume1.setName(EXTRACELLULAR_NAME);
    }
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    Feature extracellular = model.addFeature(EXTRACELLULAR_NAME);
    Feature cytosol = model.addFeature(CYTOSOL_NAME);
    Membrane plasmaMembrane = model.addMembrane(PLASMAMEMBRANE_NAME);
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    MembraneMapping plasmaMembraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(plasmaMembrane);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    plasmaMembraneMapping.setGeometryClass(pmSurfaceClass);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    plasmaMembraneMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    // Mobile Species
    Species diffusingSpecies = model.addSpecies(new Species("species", "Mobile bleachable species"));
    SpeciesContext diffusingSpeciesContext = model.addSpeciesContext(diffusingSpecies, cytosol);
    diffusingSpeciesContext.setName(varName);
    SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(diffusingSpeciesContext);
    scs.getInitialConditionParameter().setExpression(initialConcentration);
    chirpedDiffusionRate.bindExpression(scs);
    scs.getDiffusionParameter().setExpression(chirpedDiffusionRate);
    // simContext.getMicroscopeMeasurement().addFluorescentSpecies(speciesContexts[0]);
    // simContext.getMicroscopeMeasurement().setConvolutionKernel(new MicroscopeMeasurement.ProjectionZKernel());
    MathDescription mathDescription = simContext.createNewMathMapping().getMathDescription();
    // maybe there is a way that works for simContext.getMicroscopeMeasurement().... but this is needed now.
    mathDescription.addVariable(new Function(Simulation.PSF_FUNCTION_NAME, new Expression(psfFFA.infix()), null));
    simContext.setMathDescription(mathDescription);
    SimulationVersion simVersion = new SimulationVersion(simKey, "sim1", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation newSimulation = new Simulation(simVersion, simContext.getMathDescription());
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    newSimulation.getMeshSpecification().setSamplingSize(cellROI_2D.getISize());
    newSimulation.getSolverTaskDescription().setTimeStep(new TimeStep(timeStepVal, timeStepVal, timeStepVal));
    return bioModel;
}

Example 29 with ImageException

use of cbit.image.ImageException in project vcell by virtualcell.

the class RunRefSimulationOp method createRefSimBioModel.

private static BioModel createRefSimBioModel(KeyValue simKey, User owner, Origin origin, Extent extent, ROI cellROI_2D, double timeStepVal, TimeBounds timeBounds, String varName, Expression initialConcentration, double baseDiffusionRate) throws Exception {
    int numX = cellROI_2D.getRoiImages()[0].getNumX();
    int numY = cellROI_2D.getRoiImages()[0].getNumY();
    int numZ = cellROI_2D.getRoiImages().length;
    short[] shortPixels = cellROI_2D.getRoiImages()[0].getPixels();
    byte[] bytePixels = new byte[numX * numY * numZ];
    final byte EXTRACELLULAR_PIXVAL = 0;
    final byte CYTOSOL_PIXVAL = 1;
    for (int i = 0; i < bytePixels.length; i++) {
        if (shortPixels[i] != 0) {
            bytePixels[i] = CYTOSOL_PIXVAL;
        }
    }
    VCImage maskImage;
    try {
        maskImage = new VCImageUncompressed(null, bytePixels, extent, numX, numY, numZ);
    } catch (ImageException e) {
        e.printStackTrace();
        throw new RuntimeException("failed to create mask image for geometry");
    }
    Geometry geometry = new Geometry("geometry", maskImage);
    geometry.getGeometrySpec().setOrigin(origin);
    if (geometry.getGeometrySpec().getNumSubVolumes() != 2) {
        throw new Exception("Cell ROI has no ExtraCellular.");
    }
    String EXTRACELLULAR_NAME = "ec";
    String CYTOSOL_NAME = "cyt";
    String PLASMAMEMBRANE_NAME = "pm";
    ImageSubVolume subVolume0 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(0);
    ImageSubVolume subVolume1 = (ImageSubVolume) geometry.getGeometrySpec().getSubVolume(1);
    if (subVolume0.getPixelValue() == EXTRACELLULAR_PIXVAL) {
        subVolume0.setName(EXTRACELLULAR_NAME);
        subVolume1.setName(CYTOSOL_NAME);
    } else {
        subVolume0.setName(CYTOSOL_NAME);
        subVolume1.setName(EXTRACELLULAR_NAME);
    }
    geometry.getGeometrySurfaceDescription().updateAll();
    BioModel bioModel = new BioModel(null);
    bioModel.setName("unnamed");
    Model model = new Model("model");
    bioModel.setModel(model);
    Feature extracellular = model.addFeature(EXTRACELLULAR_NAME);
    Feature cytosol = model.addFeature(CYTOSOL_NAME);
    Membrane plasmaMembrane = model.addMembrane(PLASMAMEMBRANE_NAME);
    SimulationContext simContext = new SimulationContext(bioModel.getModel(), geometry);
    bioModel.addSimulationContext(simContext);
    FeatureMapping cytosolFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(cytosol);
    FeatureMapping extracellularFeatureMapping = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(extracellular);
    MembraneMapping plasmaMembraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(plasmaMembrane);
    SubVolume cytSubVolume = geometry.getGeometrySpec().getSubVolume(CYTOSOL_NAME);
    SubVolume exSubVolume = geometry.getGeometrySpec().getSubVolume(EXTRACELLULAR_NAME);
    SurfaceClass pmSurfaceClass = geometry.getGeometrySurfaceDescription().getSurfaceClass(exSubVolume, cytSubVolume);
    cytosolFeatureMapping.setGeometryClass(cytSubVolume);
    extracellularFeatureMapping.setGeometryClass(exSubVolume);
    plasmaMembraneMapping.setGeometryClass(pmSurfaceClass);
    cytosolFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    extracellularFeatureMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    plasmaMembraneMapping.getUnitSizeParameter().setExpression(new Expression(1.0));
    // Mobile Species
    Species diffusingSpecies = model.addSpecies(new Species("species", "Mobile bleachable species"));
    SpeciesContext diffusingSpeciesContext = model.addSpeciesContext(diffusingSpecies, cytosol);
    diffusingSpeciesContext.setName(varName);
    SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(diffusingSpeciesContext);
    scs.getInitialConditionParameter().setExpression(initialConcentration);
    scs.getDiffusionParameter().setExpression(new Expression(baseDiffusionRate));
    // simContext.getMicroscopeMeasurement().addFluorescentSpecies(speciesContexts[0]);
    // simContext.getMicroscopeMeasurement().setConvolutionKernel(new MicroscopeMeasurement.ProjectionZKernel());
    simContext.setMathDescription(simContext.createNewMathMapping().getMathDescription());
    SimulationVersion simVersion = new SimulationVersion(simKey, "sim1", owner, new GroupAccessNone(), new KeyValue("0"), new BigDecimal(0), new Date(), VersionFlag.Current, "", null);
    Simulation newSimulation = new Simulation(simVersion, simContext.getMathDescription());
    newSimulation.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
    simContext.addSimulation(newSimulation);
    newSimulation.getSolverTaskDescription().setTimeBounds(timeBounds);
    newSimulation.getSolverTaskDescription().setOutputTimeSpec(new UniformOutputTimeSpec(timeStepVal));
    newSimulation.getMeshSpecification().setSamplingSize(cellROI_2D.getISize());
    newSimulation.getSolverTaskDescription().setTimeStep(new TimeStep(timeStepVal, timeStepVal, timeStepVal));
    return bioModel;
}

Example 30 with ImageException

use of cbit.image.ImageException 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;
}