Examples with SimulationVersion org.vcell.util.document.SimulationVersion used on opensource projects

Example 11 with SimulationVersion

use of org.vcell.util.document.SimulationVersion in project vcell by virtualcell.

the class SimulationDbDriver method insertVersionableInit.

/**
 * This method was created in VisualAge.
 * @return cbit.image.VCImage
 * @param user cbit.vcell.server.User
 * @param image cbit.image.VCImage
 */
protected SimulationVersion insertVersionableInit(InsertHashtable hash, Connection con, User user, Versionable versionable, String name, String annot, boolean bVersion, boolean bMathematicallyEquivalent) throws DataAccessException, SQLException, RecordChangedException {
    SimulationVersion dbSimulationVersion = ((Simulation) versionable).getSimulationVersion();
    Version newVersion = insertVersionableInit(hash, con, user, versionable, name, annot, bVersion);
    // 
    // point to oldest mathematically equivalent ancestor, this will be used for all identification (status/data).
    // 
    KeyValue parentSimRef = null;
    if (bMathematicallyEquivalent) {
        if (dbSimulationVersion == null) {
            throw new RuntimeException("Simulation must have been saved for bMathematicallyEquivalent to be true");
        }
        if (dbSimulationVersion.getParentSimulationReference() != null) {
            // //
            // // mathematically equivalent, prior link is transitive  (B->C and A==B, then A->C)
            // //
            parentSimRef = dbSimulationVersion.getParentSimulationReference();
        } else {
            // //
            // // mathematically equivalent, no prior link (A==B, then A->B)
            // //
            parentSimRef = dbSimulationVersion.getVersionKey();
        }
    }
    return new SimulationVersion(newVersion.getVersionKey(), newVersion.getName(), newVersion.getOwner(), newVersion.getGroupAccess(), newVersion.getBranchPointRefKey(), newVersion.getBranchID(), newVersion.getDate(), newVersion.getFlag(), newVersion.getAnnot(), parentSimRef);
}

Example 12 with SimulationVersion

use of org.vcell.util.document.SimulationVersion in project vcell by virtualcell.

the class SimulationDbDriver method updateVersionableInit.

/**
 * This method was created in VisualAge.
 * @return cbit.image.VCImage
 * @param user cbit.vcell.server.User
 * @param image cbit.image.VCImage
 */
protected SimulationVersion updateVersionableInit(InsertHashtable hash, Connection con, User user, Versionable versionable, boolean bVersion, boolean bMathematicallyEquivalent) throws DataAccessException, SQLException, RecordChangedException {
    SimulationVersion dbSimulationVersion = ((Simulation) versionable).getSimulationVersion();
    Version newVersion = updateVersionableInit(hash, con, user, versionable, bVersion);
    // 
    // point to oldest mathematically equivalent ancestor, this will be used for all identification (status/data).
    // 
    KeyValue parentSimRef = null;
    if (bMathematicallyEquivalent) {
        if (dbSimulationVersion == null) {
            throw new RuntimeException("Simulation must have been saved for bMathematicallyEquivalent to be true");
        }
        if (dbSimulationVersion.getParentSimulationReference() != null) {
            // //
            // // mathematically equivalent, prior link is transitive  (B->C and A==B, then A->C)
            // //
            parentSimRef = dbSimulationVersion.getParentSimulationReference();
        } else {
            // //
            // // mathematically equivalent, no prior link (A==B, then A->B)
            // //
            parentSimRef = dbSimulationVersion.getVersionKey();
        }
    }
    return new SimulationVersion(newVersion.getVersionKey(), newVersion.getName(), newVersion.getOwner(), newVersion.getGroupAccess(), newVersion.getBranchPointRefKey(), newVersion.getBranchID(), newVersion.getDate(), newVersion.getFlag(), newVersion.getAnnot(), parentSimRef);
}

Example 13 with SimulationVersion

use of org.vcell.util.document.SimulationVersion in project vcell by virtualcell.

the class SimulationTable method getSimulation.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.math.MathDescription
 * @param user cbit.vcell.server.User
 * @param rset java.sql.ResultSet
 */
public Simulation getSimulation(QueryHashtable dbc, ResultSet rset, Connection con, User user, MathDescriptionDbDriver mathDB, DatabaseSyntax dbSyntax) throws SQLException, DataAccessException, PropertyVetoException {
    // 
    // get TaskDescription Data into parsable form
    // 
    // 
    // String taskDescriptionString = new String(solverTaskDescData);
    // 
    // System.out.println("taskDescriptionString '"+taskDescriptionString+"'");
    String taskDescriptionString = rset.getString(SimulationTable.table.taskDescription.getUnqualifiedColName());
    taskDescriptionString = TokenMangler.getSQLRestoredString(taskDescriptionString);
    CommentStringTokenizer solverTaskDescTokens = new CommentStringTokenizer(taskDescriptionString);
    // 
    // get MathOverride Data (language) (MUST BE READ FIRST)
    // 
    /*
	byte[] mathOverridesData = null;
	mathOverridesData = rset.getBytes(SimulationTable.table.mathOverrides.toString());
	if (rset.wasNull() || mathOverridesData==null || mathOverridesData.length==0){
		throw new DataAccessException("no data stored for MathOverrides");
	}
	String mathOverridesString = new String(mathOverridesData);
	*/
    // 
    CommentStringTokenizer mathOverrideTokens = getMathOverridesTokenizer(rset, dbSyntax);
    String dataProcessingInstructionString = rset.getString(dataProcInstr.getUnqualifiedColName());
    DataProcessingInstructions dpi = null;
    if (!rset.wasNull() && dataProcessingInstructionString != null && dataProcessingInstructionString.length() > 0) {
        dataProcessingInstructionString = TokenMangler.getSQLRestoredString(dataProcessingInstructionString);
        dpi = DataProcessingInstructions.fromDbXml(dataProcessingInstructionString);
    }
    // 
    // Get Version
    // 
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    SimulationVersion simulationVersion = (SimulationVersion) getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    java.math.BigDecimal bigD = rset.getBigDecimal(SimulationTable.table.mathRef.toString());
    KeyValue mathKey = null;
    if (!rset.wasNull()) {
        mathKey = new KeyValue(bigD);
    } else {
        throw new DataAccessException("Error:  MathDescription Reference Cannot be Null for Simulation");
    }
    MathDescription mathDesc = (MathDescription) mathDB.getVersionable(dbc, con, user, VersionableType.MathDescription, mathKey);
    Simulation simulation = new Simulation(simulationVersion, mathDesc, mathOverrideTokens, solverTaskDescTokens);
    simulation.setDataProcessingInstructions(dpi);
    // MeshSpec (Is This Correct?????)
    if (mathDesc != null && mathDesc.getGeometry() != null && mathDesc.getGeometry().getDimension() > 0) {
        int msX = rset.getInt(SimulationTable.table.meshSpecX.getUnqualifiedColName());
        int msY = rset.getInt(SimulationTable.table.meshSpecY.getUnqualifiedColName());
        int msZ = rset.getInt(SimulationTable.table.meshSpecZ.getUnqualifiedColName());
        MeshSpecification meshSpec = new MeshSpecification(simulation.getMathDescription().getGeometry());
        meshSpec.setSamplingSize(new ISize(msX, msY, msZ));
        simulation.getMeshSpecification().copyFrom(meshSpec);
    }
    return simulation;
}

Example 14 with SimulationVersion

use of org.vcell.util.document.SimulationVersion in project vcell by virtualcell.

the class SimulationTable method getInfo.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.geometry.GeometryInfo
 * @param rset java.sql.ResultSet
 * @param log cbit.vcell.server.SessionLog
 */
public VersionInfo getInfo(ResultSet rset, Connection con) throws SQLException, DataAccessException {
    KeyValue mathRef = new KeyValue(rset.getBigDecimal(SimulationTable.table.mathRef.toString()));
    java.math.BigDecimal groupid = rset.getBigDecimal(VersionTable.privacy_ColumnName);
    Version version = getVersion(rset, DbDriver.getGroupAccessFromGroupID(con, groupid));
    SimulationVersion simulationVersion = (SimulationVersion) version;
    String softwareVersion = rset.getString(SoftwareVersionTable.table.softwareVersion.toString());
    return new SimulationInfo(mathRef, simulationVersion, VCellSoftwareVersion.fromString(softwareVersion));
}

Example 15 with SimulationVersion

use of org.vcell.util.document.SimulationVersion 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;
}