Examples with Species cbit.vcell.model.Species used on opensource projects

Example 31 with Species

use of cbit.vcell.model.Species in project vcell by virtualcell.

the class SBMLImporter method createSBMLUnitSystemForVCModel.

private ModelUnitSystem createSBMLUnitSystemForVCModel() throws Exception {
    if (sbmlModel == null) {
        throw new SBMLImportException("SBML model is NULL");
    }
    ListOf listofUnitDefns = sbmlModel.getListOfUnitDefinitions();
    if (listofUnitDefns == null) {
        System.out.println("No Unit Definitions");
        // @TODO: deal with SBML level < 3.
        return ModelUnitSystem.createDefaultVCModelUnitSystem();
    }
    @SuppressWarnings("serial") VCUnitSystem tempVCUnitSystem = new VCUnitSystem() {
    };
    sbmlUnitIdentifierHash = new HashMap<String, VCUnitDefinition>();
    // add base SI unit identifiers (as defined in SBML spec) to hash
    sbmlUnitIdentifierHash.put("ampere", tempVCUnitSystem.getInstance("A"));
    sbmlUnitIdentifierHash.put("avogadro", tempVCUnitSystem.getInstance("6.02e23"));
    // sbmlUnitIdentifierHash.put("becquerel",
    // tempVCUnitSystem.getInstance("becquerel"));
    // sbmlUnitIdentifierHash.put("candela",
    // tempVCUnitSystem.getInstance("candela"));
    sbmlUnitIdentifierHash.put("coulomb", tempVCUnitSystem.getInstance("C"));
    sbmlUnitIdentifierHash.put("dimensionless", tempVCUnitSystem.getInstance("1"));
    sbmlUnitIdentifierHash.put("farad", tempVCUnitSystem.getInstance("F"));
    sbmlUnitIdentifierHash.put("gram", tempVCUnitSystem.getInstance("g"));
    // sbmlUnitIdentifierHash.put("gray",
    // tempVCUnitSystem.getInstance("gray"));
    sbmlUnitIdentifierHash.put("henry", tempVCUnitSystem.getInstance("H"));
    sbmlUnitIdentifierHash.put("hertz", tempVCUnitSystem.getInstance("Hz"));
    sbmlUnitIdentifierHash.put("item", tempVCUnitSystem.getInstance("molecules"));
    sbmlUnitIdentifierHash.put("joule", tempVCUnitSystem.getInstance("J"));
    // sbmlUnitIdentifierHash.put("katal",
    // tempVCUnitSystem.getInstance("katal"));
    sbmlUnitIdentifierHash.put("kelvin", tempVCUnitSystem.getInstance("K"));
    sbmlUnitIdentifierHash.put("kilogram", tempVCUnitSystem.getInstance("kg"));
    sbmlUnitIdentifierHash.put("litre", tempVCUnitSystem.getInstance("litre"));
    // sbmlUnitIdentifierHash.put("lumen",
    // tempVCUnitSystem.getInstance("lumen"));
    // sbmlUnitIdentifierHash.put("lux",
    // tempVCUnitSystem.getInstance("lux"));
    sbmlUnitIdentifierHash.put("metre", tempVCUnitSystem.getInstance("m"));
    sbmlUnitIdentifierHash.put("mole", tempVCUnitSystem.getInstance("mol"));
    sbmlUnitIdentifierHash.put("newton", tempVCUnitSystem.getInstance("N"));
    // sbmlUnitIdentifierHash.put("ohm",
    // tempVCUnitSystem.getInstance("ohm"));
    // sbmlUnitIdentifierHash.put("pascal",
    // tempVCUnitSystem.getInstance("pascal"));
    // sbmlUnitIdentifierHash.put("radian",
    // tempVCUnitSystem.getInstance("radian"));
    sbmlUnitIdentifierHash.put("second", tempVCUnitSystem.getInstance("s"));
    sbmlUnitIdentifierHash.put("siemens", tempVCUnitSystem.getInstance("S"));
    // sbmlUnitIdentifierHash.put("sievert",
    // tempVCUnitSystem.getInstance("sievert"));
    // sbmlUnitIdentifierHash.put("steradian",
    // tempVCUnitSystem.getInstance("steradian"));
    // sbmlUnitIdentifierHash.put("tesla",
    // tempVCUnitSystem.getInstance("tesla"));
    sbmlUnitIdentifierHash.put("volt", tempVCUnitSystem.getInstance("V"));
    sbmlUnitIdentifierHash.put("watt", tempVCUnitSystem.getInstance("W"));
    sbmlUnitIdentifierHash.put("weber", tempVCUnitSystem.getInstance("Wb"));
    long sbmlLevel = sbmlModel.getLevel();
    if (sbmlLevel < 3) {
        // SBML predefined unit identifiers
        sbmlUnitIdentifierHash.put(UnitDefinition.SUBSTANCE, tempVCUnitSystem.getInstance("mole"));
        sbmlUnitIdentifierHash.put(UnitDefinition.VOLUME, tempVCUnitSystem.getInstance("litre"));
        sbmlUnitIdentifierHash.put(UnitDefinition.AREA, tempVCUnitSystem.getInstance("m2"));
        sbmlUnitIdentifierHash.put(UnitDefinition.LENGTH, tempVCUnitSystem.getInstance("m"));
        sbmlUnitIdentifierHash.put(UnitDefinition.TIME, tempVCUnitSystem.getInstance("s"));
    }
    if (sbmlModel.isSetSubstanceUnits()) {
        UnitDefinition ud = sbmlModel.getSubstanceUnitsInstance();
        VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
        sbmlUnitIdentifierHash.put(UnitDefinition.SUBSTANCE, vcUnitDef);
    }
    if (sbmlModel.isSetVolumeUnits()) {
        UnitDefinition ud = sbmlModel.getVolumeUnitsInstance();
        VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
        sbmlUnitIdentifierHash.put(UnitDefinition.VOLUME, vcUnitDef);
    }
    if (sbmlModel.isSetAreaUnits()) {
        UnitDefinition ud = sbmlModel.getAreaUnitsInstance();
        VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
        sbmlUnitIdentifierHash.put(UnitDefinition.AREA, vcUnitDef);
    }
    if (sbmlModel.isSetLengthUnits()) {
        UnitDefinition ud = sbmlModel.getLengthUnitsInstance();
        VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
        sbmlUnitIdentifierHash.put(UnitDefinition.LENGTH, vcUnitDef);
    }
    if (sbmlModel.isSetTimeUnits()) {
        UnitDefinition ud = sbmlModel.getTimeUnitsInstance();
        VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
        sbmlUnitIdentifierHash.put(UnitDefinition.TIME, vcUnitDef);
    }
    // read unit definition (identifiers) declared in SBML model
    for (int i = 0; i < sbmlModel.getNumUnitDefinitions(); i++) {
        UnitDefinition ud = (org.sbml.jsbml.UnitDefinition) listofUnitDefns.get(i);
        String unitName = ud.getId();
        VCUnitDefinition vcUnitDef = SBMLUnitTranslator.getVCUnitDefinition(ud, tempVCUnitSystem);
        sbmlUnitIdentifierHash.put(unitName, vcUnitDef);
    }
    // For SBML level 2
    // default units
    VCUnitDefinition defaultSubstanceUnit = sbmlUnitIdentifierHash.get(UnitDefinition.SUBSTANCE);
    VCUnitDefinition defaultVolumeUnit = sbmlUnitIdentifierHash.get(UnitDefinition.VOLUME);
    VCUnitDefinition defaultAreaUnit = sbmlUnitIdentifierHash.get(UnitDefinition.AREA);
    VCUnitDefinition defaultLengthUnit = sbmlUnitIdentifierHash.get(UnitDefinition.LENGTH);
    VCUnitDefinition defaultTimeUnit = sbmlUnitIdentifierHash.get(UnitDefinition.TIME);
    VCUnitDefinition modelSubstanceUnit = null;
    VCUnitDefinition modelVolumeUnit = null;
    VCUnitDefinition modelAreaUnit = null;
    VCUnitDefinition modelLengthUnit = null;
    VCUnitDefinition modelTimeUnit = null;
    // units in SBML model
    // compartments
    ListOf<Compartment> listOfCompartments = sbmlModel.getListOfCompartments();
    for (int i = 0; i < listOfCompartments.size(); i++) {
        Compartment sbmlComp = listOfCompartments.get(i);
        double dim = 3;
        if (sbmlComp.isSetSpatialDimensions()) {
            dim = sbmlComp.getSpatialDimensions();
        }
        String unitStr = sbmlComp.getUnits();
        VCUnitDefinition sbmlUnitDefinition = null;
        if (unitStr != null && unitStr.length() > 0) {
            sbmlUnitDefinition = sbmlUnitIdentifierHash.get(unitStr);
        } else {
            // applying default unit if not defined for this compartment
            if (dim == 3) {
                sbmlUnitDefinition = defaultVolumeUnit;
            } else if (dim == 2) {
                sbmlUnitDefinition = defaultAreaUnit;
            } else if (dim == 1) {
                sbmlUnitDefinition = defaultLengthUnit;
            }
        }
        if (dim == 3) {
            if (sbmlUnitDefinition == null) {
                sbmlUnitDefinition = defaultVolumeUnit;
            }
            if (modelVolumeUnit == null) {
                modelVolumeUnit = sbmlUnitDefinition;
            } else if (!sbmlUnitDefinition.isEquivalent(modelVolumeUnit)) {
                localIssueList.add(new Issue(new SBMLIssueSource(sbmlComp), issueContext, IssueCategory.Units, "unit for compartment '" + sbmlComp.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current vol unit (" + modelVolumeUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
            // logger.sendMessage(VCLogger.Priority.MediumPriority,
            // VCLogger.ErrorType.UnitError, "unit for compartment '" +
            // sbmlComp.getId() + "' (" + unitStr + ") : (" +
            // sbmlUnitDefinition.getSymbol() +
            // ") not compatible with current vol unit (" +
            // modelVolumeUnit.getSymbol() + ")");
            }
        } else if (dim == 2) {
            if (modelAreaUnit == null) {
                modelAreaUnit = sbmlUnitDefinition;
            } else if (!sbmlUnitDefinition.isEquivalent(modelAreaUnit)) {
                localIssueList.add(new Issue(new SBMLIssueSource(sbmlComp), issueContext, IssueCategory.Units, "unit for compartment '" + sbmlComp.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current area unit (" + modelAreaUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
            // logger.sendMessage(VCLogger.Priority.MediumPriority,
            // VCLogger.ErrorType.UnitError, "unit for compartment '" +
            // sbmlComp.getId() + "' (" + unitStr + ") : (" +
            // sbmlUnitDefinition.getSymbol() +
            // ") not compatible with current area unit (" +
            // modelAreaUnit.getSymbol() + ")");
            }
        }
    }
    // species
    ListOf<org.sbml.jsbml.Species> listOfSpecies = sbmlModel.getListOfSpecies();
    for (int i = 0; i < listOfSpecies.size(); i++) {
        org.sbml.jsbml.Species sbmlSpecies = listOfSpecies.get(i);
        String unitStr = sbmlSpecies.getSubstanceUnits();
        VCUnitDefinition sbmlUnitDefinition = null;
        if (unitStr != null && unitStr.length() > 0) {
            sbmlUnitDefinition = sbmlUnitIdentifierHash.get(unitStr);
        } else {
            // apply default substance unit
            sbmlUnitDefinition = defaultSubstanceUnit;
        }
        if (modelSubstanceUnit == null) {
            modelSubstanceUnit = sbmlUnitDefinition;
        } else if (!sbmlUnitDefinition.isEquivalent(modelSubstanceUnit)) {
            localIssueList.add(new Issue(new SBMLIssueSource(sbmlSpecies), issueContext, IssueCategory.Units, "unit for species '" + sbmlSpecies.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current substance unit (" + modelSubstanceUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
        // logger.sendMessage(VCLogger.Priority.MediumPriority,
        // VCLogger.ErrorType.UnitError, "unit for species '" +
        // sbmlSpecies.getId() + "' (" + unitStr + ") : (" +
        // sbmlUnitDefinition.getSymbol() +
        // ") not compatible with current substance unit (" +
        // modelSubstanceUnit.getSymbol() + ")");
        }
    }
    // reactions for SBML level 2 version < 3
    long sbmlVersion = sbmlModel.getVersion();
    if (sbmlVersion < 3) {
        ListOf<Reaction> listOfReactions = sbmlModel.getListOfReactions();
        for (int i = 0; i < listOfReactions.size(); i++) {
            Reaction sbmlReaction = listOfReactions.get(i);
            KineticLaw kineticLaw = sbmlReaction.getKineticLaw();
            if (kineticLaw != null) {
                // first check substance unit
                String unitStr = kineticLaw.getSubstanceUnits();
                VCUnitDefinition sbmlUnitDefinition = null;
                if (unitStr != null && unitStr.length() > 0) {
                    sbmlUnitDefinition = sbmlUnitIdentifierHash.get(unitStr);
                } else {
                    // apply default substance unit
                    sbmlUnitDefinition = defaultSubstanceUnit;
                }
                if (modelSubstanceUnit == null) {
                    modelSubstanceUnit = sbmlUnitDefinition;
                } else if (!sbmlUnitDefinition.isEquivalent(modelSubstanceUnit)) {
                    localIssueList.add(new Issue(new SBMLIssueSource(sbmlReaction), issueContext, IssueCategory.Units, "substance unit for reaction '" + sbmlReaction.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current substance unit (" + modelSubstanceUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
                // logger.sendMessage(VCLogger.Priority.MediumPriority,
                // VCLogger.ErrorType.UnitError,
                // "substance unit for reaction '" +
                // sbmlReaction.getId() + "' (" + unitStr + ") : (" +
                // sbmlUnitDefinition.getSymbol() +
                // ") not compatible with current substance unit (" +
                // modelSubstanceUnit.getSymbol() + ")");
                }
                // check time unit
                unitStr = kineticLaw.getTimeUnits();
                if (unitStr != null && unitStr.length() > 0) {
                    sbmlUnitDefinition = sbmlUnitIdentifierHash.get(unitStr);
                } else {
                    // apply default time unit
                    sbmlUnitDefinition = defaultTimeUnit;
                }
                if (modelTimeUnit == null) {
                    modelTimeUnit = sbmlUnitDefinition;
                } else if (!sbmlUnitDefinition.isEquivalent(modelTimeUnit)) {
                    localIssueList.add(new Issue(new SBMLIssueSource(sbmlReaction), issueContext, IssueCategory.Units, "time unit for reaction '" + sbmlReaction.getId() + "' (" + unitStr + ") : (" + sbmlUnitDefinition.getSymbol() + ") not compatible with current time unit (" + modelTimeUnit.getSymbol() + ")", Issue.SEVERITY_WARNING));
                // logger.sendMessage(VCLogger.Priority.MediumPriority,
                // VCLogger.ErrorType.UnitError,
                // "time unit for reaction '" + sbmlReaction.getId() +
                // "' (" + unitStr + ") : (" +
                // sbmlUnitDefinition.getSymbol() +
                // ") not compatible with current time unit (" +
                // modelTimeUnit.getSymbol() + ")");
                }
            }
        }
    }
    if (modelSubstanceUnit == null) {
        modelSubstanceUnit = defaultSubstanceUnit;
    }
    if (modelVolumeUnit == null) {
        modelVolumeUnit = defaultVolumeUnit;
    }
    if (modelAreaUnit == null) {
        modelAreaUnit = defaultAreaUnit;
    }
    if (modelLengthUnit == null) {
        modelLengthUnit = defaultLengthUnit;
    }
    if (modelTimeUnit == null) {
        modelTimeUnit = defaultTimeUnit;
    }
    if (modelSubstanceUnit == null && modelVolumeUnit == null && modelAreaUnit == null && modelLengthUnit == null && modelTimeUnit == null) {
        // default (VC)modelUnitSystem
        return ModelUnitSystem.createDefaultVCModelUnitSystem();
    } else {
        return ModelUnitSystem.createSBMLUnitSystem(modelSubstanceUnit, modelVolumeUnit, modelAreaUnit, modelLengthUnit, modelTimeUnit);
    }
}

Example 32 with Species

use of cbit.vcell.model.Species in project vcell by virtualcell.

the class SBMLImporter method checkIdentifiersNameLength.

private void checkIdentifiersNameLength() throws Exception {
    // Check compartment name lengths
    ListOf listofIds = sbmlModel.getListOfCompartments();
    boolean bLongCompartmentName = false;
    SBase issueSource = null;
    for (int i = 0; i < sbmlModel.getNumCompartments(); i++) {
        Compartment compartment = (Compartment) listofIds.get(i);
        String compartmentName = compartment.getId();
        if (compartmentName.length() > 64) {
            bLongCompartmentName = true;
            issueSource = compartment;
        }
    }
    // Check species name lengths
    listofIds = sbmlModel.getListOfSpecies();
    boolean bLongSpeciesName = false;
    for (int i = 0; i < sbmlModel.getNumSpecies(); i++) {
        org.sbml.jsbml.Species species = (org.sbml.jsbml.Species) listofIds.get(i);
        String speciesName = species.getId();
        if (speciesName.length() > 64) {
            bLongSpeciesName = true;
            issueSource = species;
        }
    }
    // Check parameter name lengths
    listofIds = sbmlModel.getListOfParameters();
    boolean bLongParameterName = false;
    for (int i = 0; i < sbmlModel.getNumParameters(); i++) {
        Parameter param = (Parameter) listofIds.get(i);
        String paramName = param.getId();
        if (paramName.length() > 64) {
            bLongParameterName = true;
            issueSource = param;
        }
    }
    // Check reaction name lengths
    listofIds = sbmlModel.getListOfReactions();
    boolean bLongReactionName = false;
    for (int i = 0; i < sbmlModel.getNumReactions(); i++) {
        Reaction rxn = (Reaction) listofIds.get(i);
        String rxnName = rxn.getId();
        if (rxnName.length() > 64) {
            bLongReactionName = true;
            issueSource = rxn;
        }
    }
    if (bLongCompartmentName || bLongSpeciesName || bLongParameterName || bLongReactionName) {
        String warningMsg = "WARNING: The imported model has one or more ";
        if (bLongCompartmentName) {
            warningMsg = warningMsg + "compartments, ";
        }
        if (bLongSpeciesName) {
            warningMsg = warningMsg + "species, ";
        }
        if (bLongParameterName) {
            warningMsg = warningMsg + "global parameters, ";
        }
        if (bLongReactionName) {
            warningMsg = warningMsg + "reactions ";
        }
        warningMsg = warningMsg + "that have ids/names that are longer than 64 characters. \n\nUser is STRONGLY recommeded to shorten " + "the names to avoid problems with the length of expressions these names might be used in.";
        localIssueList.add(new Issue(new SBMLIssueSource(issueSource), issueContext, IssueCategory.SBMLImport_UnsupportedAttributeOrElement, warningMsg, Issue.SEVERITY_WARNING));
    // logger.sendMessage(VCLogger.Priority.MediumPriority,
    // VCLogger.ErrorType.UnsupportedConstruct, warningMsg);
    }
}

Example 33 with Species

use of cbit.vcell.model.Species in project vcell by virtualcell.

the class SBMLImporter method setSpeciesInitialConditions.

/**
 * setSpeciesInitialConditions : called after speciesContexts and global
 * parameters have been set. Checks for init conditions set on species in
 * the Sbml model, and if it is set using an assignment rule, obtain the
 * corresponding expression. Obtain the sbml -> vc unit conversion factor
 * for species concentrations to adjust the species initial condition
 * units/factor.
 */
private void setSpeciesInitialConditions() {
    try {
        // fill in SpeciesContextSpec for each speciesContext
        Model vcModel = vcBioModel.getSimulationContext(0).getModel();
        SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
        for (int i = 0; i < vcSpeciesContexts.length; i++) {
            org.sbml.jsbml.Species sbmlSpecies = (org.sbml.jsbml.Species) sbmlModel.getSpecies(vcSpeciesContexts[i].getName());
            // Sometimes, the species name can be null or a blank string; in
            // that case, use species id as the name.
            String speciesName = sbmlSpecies.getId();
            Compartment compartment = (Compartment) sbmlModel.getCompartment(sbmlSpecies.getCompartment());
            Expression initExpr = null;
            if (sbmlSpecies.isSetInitialConcentration()) {
                // If initial
                // Concentration
                // is set
                Expression initConcentration = new Expression(sbmlSpecies.getInitialConcentration());
                // check if initConc is set by a (assignment) rule. That
                // takes precedence over initConc value set on species.
                initExpr = getValueFromAssignmentRule(speciesName);
                if (initExpr == null) {
                    initExpr = new Expression(initConcentration);
                }
            } else if (sbmlSpecies.isSetInitialAmount()) {
                // If initial
                // amount is set
                double initAmount = sbmlSpecies.getInitialAmount();
                // initConcentration. Else, throw exception.
                if (compartment.isSetSize()) {
                    double compartmentSize = compartment.getSize();
                    Expression initConcentration = new Expression(0.0);
                    if (compartmentSize != 0.0) {
                        initConcentration = new Expression(initAmount / compartmentSize);
                    } else {
                        logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.UnitError, "compartment '" + compartment.getId() + "' has zero size, unable to determine initial concentration for species " + speciesName);
                    }
                    // check if initConc is set by a (assignment) rule. That
                    // takes precedence over initConc/initAmt value set on
                    // species.
                    initExpr = getValueFromAssignmentRule(speciesName);
                    if (initExpr == null) {
                        initExpr = new Expression(initConcentration);
                    }
                } else {
                    logger.sendMessage(VCLogger.Priority.HighPriority, VCLogger.ErrorType.SpeciesError, " Compartment '" + compartment.getId() + "' size not set or is defined by a rule; cannot calculate initConc.");
                }
            } else {
                // initConc/initAmt not set; check if species has a
                // (assignment) rule.
                initExpr = getValueFromAssignmentRule(speciesName);
                if (initExpr == null) {
                    // warning and set it to 0.0
                    if (sbmlModel.getInitialAssignment(speciesName) == null) {
                        localIssueList.add(new Issue(new SBMLIssueSource(sbmlModel.getSpecies(speciesName)), issueContext, IssueCategory.SBMLImport_MissingSpeciesInitCondition, "no initial condition for species " + speciesName + ", assuming 0.0", Issue.SEVERITY_WARNING));
                    // logger.sendMessage(VCLogger.Priority.MediumPriority,
                    // VCLogger.ErrorType.UnitError,
                    // "no initial condition for species "+speciesName+", assuming 0.0");
                    }
                    initExpr = new Expression(0.0);
                }
            }
            // similar to the conversion that is done in reactions.
            if (initExpr != null) {
                // initExpr will be changed
                initExpr = adjustExpression(initExpr, vcModel);
            }
            // If any of the symbols in the expression for speciesConc is a
            // rule, expand it.
            substituteGlobalParamRulesInPlace(initExpr, false);
            SpeciesContextSpec speciesContextSpec = vcBioModel.getSimulationContext(0).getReactionContext().getSpeciesContextSpec(vcSpeciesContexts[i]);
            speciesContextSpec.getInitialConditionParameter().setExpression(initExpr);
            speciesContextSpec.setConstant(sbmlSpecies.getBoundaryCondition() || sbmlSpecies.getConstant());
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Error setting initial condition for species context; " + e.getMessage(), e);
    }
}

Example 34 with Species

use of cbit.vcell.model.Species in project vcell by virtualcell.

the class SpeciesTable method getSpecies.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionParticipant
 * @param rset java.sql.ResultSet
 */
public Species getSpecies(java.sql.ResultSet rset, DBSpecies dbSpecies) throws java.sql.SQLException, DataAccessException {
    String annotation = rset.getString(SpeciesTable.table.annotation.toString());
    if (annotation != null) {
        annotation = org.vcell.util.TokenMangler.getSQLRestoredString(annotation);
    }
    String cNameStr = TokenMangler.getSQLRestoredString(rset.getString(SpeciesTable.table.commonName.toString()));
    Species species = new Species(cNameStr, annotation, dbSpecies);
    return species;
}

Example 35 with Species

use of cbit.vcell.model.Species 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;
}