Examples with MathDescription cbit.vcell.math.MathDescription used on opensource projects

Example 71 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class XmlReader method getMathDescription.

/**
 * This method returns a MathDescription from a XML element.
 * Creation date: (4/26/2001 12:11:14 PM)
 * @return cbit.vcell.math.MathDescription
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
MathDescription getMathDescription(Element param, Geometry geometry) throws XmlParseException {
    MathDescription mathdes = null;
    Element tempelement;
    // Retrieve Metadata(Version)
    Version version = getVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // Retrieve attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // Create new MathDescription
    if (version != null) {
        mathdes = new MathDescription(version);
    } else {
        mathdes = new MathDescription(name);
    }
    try {
        // this step is needed!
        mathdes.setGeometry(geometry);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("a PropertyVetoException was fired when setting the Geometry to the Mathdescription in the simContext " + name, e);
    }
    // set attributes
    try {
        mathdes.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // mathdes.setDescription(unMangle(annotation));
        // }
        // add Annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            mathdes.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the name " + name + ", to a new MathDescription!", e);
    }
    VariableHash varHash = new VariableHash();
    // Retrieve Constant
    Iterator<Element> iterator = param.getChildren(XMLTags.ConstantTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getConstant(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve FilamentRegionVariables
    iterator = param.getChildren(XMLTags.FilamentRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFilamentRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve FilamentVariables
    iterator = param.getChildren(XMLTags.FilamentVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFilamentVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // retrieve InsideVariables
    // **** This variables are for internal USE ******
    // Retrieve MembraneRegionVariable
    iterator = param.getChildren(XMLTags.MembraneRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMembraneRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve MembraneVariable
    iterator = param.getChildren(XMLTags.MembraneVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMemVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve PointVariable
    iterator = param.getChildren(XMLTags.PointVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getPointVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // retrieve OutsideVariables
    // **** This variables are for internal USE ******
    // Retrieve Volume Region variable
    iterator = param.getChildren(XMLTags.VolumeRegionVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeRegionVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve VolumeVariable
    iterator = param.getChildren(XMLTags.VolumeVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve StochVolVariable
    iterator = param.getChildren(XMLTags.StochVolVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getStochVolVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // Retrieve all the Functions //This needs to be processed before all the variables are read!
    iterator = param.getChildren(XMLTags.FunctionTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getFunction(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.VolumeRandomVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getRandomVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.MembraneRandomVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getRandomVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.VolumeParticleVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticalVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.MembraneParticleVariableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getMembraneParticalVariable(tempelement));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // ParticleMolecularTypeTag       getParticleMolecularTypes
    // has to be done before VolumeParticleSpeciesPattern and VolumeParticleObservable
    iterator = param.getChildren(XMLTags.ParticleMolecularTypeTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        mathdes.addParticleMolecularType(getParticleMolecularType(tempelement));
    }
    // VolumeParticleSpeciesPatternTag
    iterator = param.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticleSpeciesPattern(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // VolumeParticleObservableTag    getParticleObservables
    iterator = param.getChildren(XMLTags.VolumeParticleObservableTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            varHash.addVariable(getVolumeParticleObservable(tempelement, varHash));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException(e);
        }
    }
    // 
    try {
        mathdes.setAllVariables(varHash.getAlphabeticallyOrderedVariables());
    } catch (MathException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e);
    } catch (ExpressionBindingException e) {
        e.printStackTrace();
        throw new XmlParseException("Error adding the Function variables to the MathDescription " + name, e);
    }
    // Retrieve CompartmentsSubdomains
    iterator = param.getChildren(XMLTags.CompartmentSubDomainTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            mathdes.addSubDomain(getCompartmentSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new CompartmentSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve MembraneSubdomains
    iterator = param.getChildren(XMLTags.MembraneSubDomainTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        try {
            mathdes.addSubDomain(getMembraneSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new MembraneSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve the FilamentSubdomain (if any)
    tempelement = param.getChild(XMLTags.FilamentSubDomainTag, vcNamespace);
    if (tempelement != null) {
        try {
            mathdes.addSubDomain(getFilamentSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new FilamentSubDomain to the MathDescription " + name, e);
        }
    }
    // Retrieve the PointSubdomain (if any)
    tempelement = param.getChild(XMLTags.PointSubDomainTag, vcNamespace);
    if (tempelement != null) {
        try {
            mathdes.addSubDomain(getPointSubDomain(tempelement, mathdes));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("Error adding a new PointSubDomain to the MathDescription " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.EventTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        Event event = getEvent(mathdes, tempelement);
        try {
            mathdes.addEvent(event);
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new XmlParseException(e);
        }
    }
    iterator = param.getChildren(XMLTags.PostProcessingBlock, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempelement = (Element) iterator.next();
        getPostProcessingBlock(mathdes, tempelement);
    }
    return mathdes;
}

Example 72 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class MathTestingUtilities method comparePDEResults.

/**
 * Insert the method's description here.
 * Creation date: (8/20/2003 12:58:10 PM)
 */
public static SimulationComparisonSummary comparePDEResults(SimulationSymbolTable testSimSymbolTable, PDEDataManager testDataManager, SimulationSymbolTable refSimSymbolTable, PDEDataManager refDataManager, String[] varsToCompare, double absErrorThreshold, double relErrorThreshold, VCDocument refDocument, DataInfoProvider refDataInfoProvider, VCDocument testDocument, DataInfoProvider testDataInfoProvider) throws DataAccessException, ExpressionException {
    java.util.Hashtable<String, DataErrorSummary> tempVarHash = new java.util.Hashtable<String, DataErrorSummary>();
    boolean bTimesEqual = true;
    double[] testTimeArray = testDataManager.getDataSetTimes();
    double[] refTimeArray = refDataManager.getDataSetTimes();
    if (testTimeArray.length != refTimeArray.length) {
        bTimesEqual = false;
    // throw new RuntimeException("Data times for reference and test simulations don't match, cannot compare the two simulations!");
    } else {
        for (int i = 0; i < testTimeArray.length; i++) {
            if (testTimeArray[i] != refTimeArray[i]) {
                bTimesEqual = false;
            }
        }
    }
    // if (!checkSimVars(testSim, refSim)) {
    // //String errorS = "TestVars - ";
    // Variable[] testVars = testSim.getVariables();
    // //for(int i =0;i<vars.length;i+= 1){
    // //errorS+= vars[i].getName()+" ";
    // //}
    // //errorS+=" <<>> RefVars - ";
    // Variable[] refVars = refSim.getVariables();
    // //for(int i =0;i<vars.length;i+= 1){
    // //errorS+= vars[i].getName()+" ";
    // //}
    // throw new RuntimeException(
    // "VarNotMatch testLength="+(testVars != null?testVars.length+"":"null")+" refLength="+(refVars != null?refVars.length+"":"null"));
    // }
    CartesianMesh testMesh = testDataManager.getMesh();
    MathDescription testMathDesc = testSimSymbolTable.getSimulation().getMathDescription();
    // Variable[] refVars = refSim.getVariables();
    MathDescription refMathDesc = refSimSymbolTable.getSimulation().getMathDescription();
    CartesianMesh refMesh = refDataManager.getMesh();
    int[] membraneIndexMapping = null;
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable for testSimulation
    int testNumVol = testMesh.getSizeX() * testMesh.getSizeY() * testMesh.getSizeZ();
    CompartmentSubDomain[] testVolSubDomainLookup = new CompartmentSubDomain[testNumVol];
    for (int i = 0; i < testNumVol; i++) {
        int subVolumeIndex = testMesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = testMathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = testMathDesc.getCompartmentSubDomain(subVolume.getName());
        testVolSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable for testSimulation
    int testNumMem = testMesh.getMembraneElements().length;
    MembraneSubDomain[] testMemSubDomainLookup = new MembraneSubDomain[testNumMem];
    for (int i = 0; i < testNumMem; i++) {
        int insideVolIndex = testMesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = testMesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = testMathDesc.getMembraneSubDomain(testVolSubDomainLookup[insideVolIndex], testVolSubDomainLookup[outsideVolIndex]);
        testMemSubDomainLookup[i] = memSubDomain;
    }
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable for refSimulation
    int refNumVol = refMesh.getSizeX() * refMesh.getSizeY() * refMesh.getSizeZ();
    CompartmentSubDomain[] refVolSubDomainLookup = new CompartmentSubDomain[refNumVol];
    for (int i = 0; i < refNumVol; i++) {
        int subVolumeIndex = refMesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = refMathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = refMathDesc.getCompartmentSubDomain(subVolume.getName());
        refVolSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable for refSimulation
    int refNumMem = refMesh.getMembraneElements().length;
    MembraneSubDomain[] refMemSubDomainLookup = new MembraneSubDomain[refNumMem];
    for (int i = 0; i < refNumMem; i++) {
        int insideVolIndex = refMesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = refMesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = refMathDesc.getMembraneSubDomain(refVolSubDomainLookup[insideVolIndex], refVolSubDomainLookup[outsideVolIndex]);
        refMemSubDomainLookup[i] = memSubDomain;
    }
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    String hashKey = new String("");
    DataErrorSummary tempVar = null;
    DataIdentifier[] refDataIDs = refDataManager.getDataIdentifiers();
    // for each var, do the following :
    for (int i = 0; i < varsToCompare.length; i++) {
        DataIdentifier refDataID = null;
        for (int j = 0; j < refDataIDs.length; j++) {
            if (refDataIDs[j].getName().equals(varsToCompare[i])) {
                refDataID = refDataIDs[j];
                break;
            }
        }
        // 
        // Find REFERENCE variable
        // 
        Variable refVar = getSimVar(refSimSymbolTable, varsToCompare[i]);
        if (refVar == null) {
            // Should only happen if TEST sims were generated 'post-domains' and REFERENCE sims were generated 'pre-domains'
            if (refDataID != null) {
                throw new RuntimeException("Unexpected reference condition: '" + varsToCompare[i] + "' not found in symboltable but was found in dataidentifiers");
            }
            if (testDocument instanceof BioModel) {
                // Only BioModels need to be checked
                // Look in TEST for a speciescontext with matching species name
                System.out.println("ReferenceVariable: using alternate method to find '" + varsToCompare[i] + "'");
                BioModel refBioModel = (BioModel) refDocument;
                BioModel testBioModel = (BioModel) testDocument;
                SpeciesContext testSpeciesContext = testBioModel.getModel().getSpeciesContext(varsToCompare[i]);
                if (testSpeciesContext != null) {
                    refVar = refSimSymbolTable.getVariable(testSpeciesContext.getSpecies().getCommonName());
                    for (int j = 0; j < refDataIDs.length; j++) {
                        if (refDataIDs[j].getName().equals(testSpeciesContext.getSpecies().getCommonName())) {
                            refDataID = refDataIDs[j];
                            break;
                        }
                    }
                }
            }
            if (refVar == null || refDataID == null) {
                Simulation refSim = refSimSymbolTable.getSimulation();
                throw new RuntimeException("The variable " + varsToCompare[i] + " was not found in Simulation (" + refSim.getName() + " " + refSim.getVersion().getDate() + ")\n");
            }
        }
        // 
        // Find TEST variable (assumed to have sims generated with a software version later than REFERENCE)
        // 
        Variable testVar = getSimVar(testSimSymbolTable, varsToCompare[i]);
        if (testVar == null) {
            // Should only happen if TEST sims were generated 'post-domains' and REFERENCE sims were generated 'pre-domains'
            System.out.println("TestVariable: using alternate method to find '" + varsToCompare[i] + "'");
            BioModel testBioModel = (BioModel) testDocument;
            SpeciesContext[] speciesContexts = testBioModel.getModel().getSpeciesContexts();
            boolean bSkip = false;
            for (int j = 0; j < speciesContexts.length; j++) {
                if (speciesContexts[j].getSpecies().getCommonName().equals(varsToCompare[i])) {
                    testVar = testSimSymbolTable.getVariable(speciesContexts[j].getName());
                    if (testVar == null) {
                        throw new RuntimeException("Speciescontext name '" + speciesContexts[j].getName() + "' not found in testsimsymboltable");
                    }
                    // If we got here it means at least one matching speciescontext was found in TEST with
                    // a species name matching varsToCompare[i].  We can skip because the matching speciesconetext
                    // will be used to do a comparison at some point.
                    bSkip = true;
                    break;
                }
            }
            if (bSkip) {
                // these are tested already using full simcontext names
                System.out.println("Skipping '" + varsToCompare[i] + "' as lookup in testSimSymbolTable");
                continue;
            }
            Simulation refSim = refSimSymbolTable.getSimulation();
            throw new RuntimeException("The variable " + varsToCompare[i] + " was not found in Simulation (" + refSim.getName() + " " + refSim.getVersion().getDate() + ")\n");
        }
        // for each time in timeArray. ('t' is used to index the testTimeArray, for interpolation purposes.)
        int t = 0;
        for (int j = 0; j < refTimeArray.length; j++) {
            // get data block from varName, data from datablock
            SimDataBlock refSimDataBlock = refDataManager.getSimDataBlock(refVar.getName(), refTimeArray[j]);
            double[] refData = refSimDataBlock.getData();
            double[] resampledTestData = null;
            if (bTimesEqual) {
                // If time arrays for both sims are equal, no need to resample/interpolate, just obtain the datablock from dataManager
                SimDataBlock testSimDataBlock = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[j]);
                resampledTestData = testSimDataBlock.getData();
            } else {
                // Time resampling (interpolation) needed.
                while ((t < testTimeArray.length - 2) && (refTimeArray[j] >= testTimeArray[t + 1])) {
                    t++;
                }
                SimDataBlock testSimDataBlock_1 = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[t]);
                double[] testData_1 = testSimDataBlock_1.getData();
                SimDataBlock testSimDataBlock_2 = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[t + 1]);
                double[] testData_2 = testSimDataBlock_2.getData();
                resampledTestData = new double[testData_1.length];
                // 
                for (int m = 0; m < testData_1.length; m++) {
                    resampledTestData[m] = testData_1[m] + (testData_2[m] - testData_1[m]) * (refTimeArray[j] - testTimeArray[t]) / (testTimeArray[t + 1] - testTimeArray[t]);
                }
            }
            // Spatial resampling (interpolation) ...
            double[] spaceResampledData = new double[refData.length];
            if (!testMathDesc.getGeometry().getExtent().compareEqual(refMathDesc.getGeometry().getExtent()) || !testMathDesc.getGeometry().getOrigin().compareEqual(refMathDesc.getGeometry().getOrigin())) {
                throw new RuntimeException("Different origins and/or extents for the 2 geometries. Cannot compare the 2 simulations");
            }
            if (testMesh.getSizeX() != refMesh.getSizeX() || testMesh.getSizeY() != refMesh.getSizeY() || testMesh.getSizeZ() != refMesh.getSizeZ()) {
                if (testVar instanceof VolVariable) {
                    if (testMathDesc.getGeometry().getDimension() == 1 && refMathDesc.getGeometry().getDimension() == 1) {
                        spaceResampledData = resample1DSpatial(resampledTestData, testMesh, refMesh);
                    } else if (testMathDesc.getGeometry().getDimension() == 2 && refMathDesc.getGeometry().getDimension() == 2) {
                        spaceResampledData = resample2DSpatial(resampledTestData, testMesh, refMesh);
                    } else if (testMathDesc.getGeometry().getDimension() == 3 && refMathDesc.getGeometry().getDimension() == 3) {
                        spaceResampledData = resample3DSpatial(resampledTestData, testMesh, refMesh);
                    } else {
                        throw new RuntimeException("Comparison of 2 simulations with different geometry dimensions are not handled at this time!");
                    }
                } else {
                    throw new RuntimeException("spatial resampling for variable type: " + testVar.getClass().getName() + " not supported");
                }
            } else {
                // no space resampling required
                if (testVar instanceof MemVariable) {
                    // 
                    if (membraneIndexMapping == null) {
                        membraneIndexMapping = testMesh.getMembraneIndexMapping(refMesh);
                    }
                    spaceResampledData = new double[resampledTestData.length];
                    for (int k = 0; k < resampledTestData.length; k++) {
                        spaceResampledData[k] = resampledTestData[membraneIndexMapping[k]];
                    }
                } else {
                    // 
                    // no reordering needed for other variable types.
                    // 
                    spaceResampledData = resampledTestData;
                }
            }
            // for each point in data block ...
            testDataInfoProvider.getPDEDataContext().setVariableName(testVar.getName());
            for (int k = 0; k < refData.length; k++) {
                if (!testDataInfoProvider.isDefined(k)) {
                    continue;
                }
                // Determine maxRef, minRef, maxAbsErr for variable
                // SubDomain testSubDomain = null;
                String sn = null;
                VariableType refVarType = refDataID.getVariableType();
                if (refVarType.equals(VariableType.VOLUME)) {
                    // testSubDomain = refVolSubDomainLookup[k];
                    sn = refVolSubDomainLookup[k].getName();
                } else if (refVarType.equals(VariableType.MEMBRANE)) {
                    // testSubDomain = refMemSubDomainLookup[k];
                    sn = refMemSubDomainLookup[k].getName();
                } else if (refVarType.equals(VariableType.MEMBRANE_REGION)) {
                    sn = "MRV_" + i;
                } else if (refVarType.equals(VariableType.VOLUME_REGION)) {
                    sn = "VRV_" + i;
                } else {
                    throw new RuntimeException("Var " + refVar.getName() + " not supported yet!");
                }
                // hashKey = refVar.getName()+":"+testSubDomain.getName();
                hashKey = refVar.getName() + ":" + sn;
                tempVar = tempVarHash.get(hashKey);
                if (tempVar == null) {
                    tempVar = new DataErrorSummary(null);
                    tempVarHash.put(hashKey, tempVar);
                }
                tempVar.addDataValues(refData[k], spaceResampledData[k], refTimeArray[j], k, absErrorThreshold, relErrorThreshold);
            }
        // end for (k)
        }
    // end for (j)
    }
    // end for (i)
    Enumeration<String> enumKeys = tempVarHash.keys();
    while (enumKeys.hasMoreElements()) {
        String key = enumKeys.nextElement();
        DataErrorSummary tempVarSummary = tempVarHash.get(key);
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(key, tempVarSummary.getMinRef(), tempVarSummary.getMaxRef(), tempVarSummary.getMaxAbsoluteError(), tempVarSummary.getMaxRelativeError(), tempVarSummary.getL2Norm(), tempVarSummary.getTimeAtMaxAbsoluteError(), tempVarSummary.getIndexAtMaxAbsoluteError(), tempVarSummary.getTimeAtMaxRelativeError(), tempVarSummary.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}

Example 73 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writeModelDescription.

/**
 *# Model description: FEATURE name handle priority boundary_conditions
 *MODEL_BEGIN
 *FEATURE Nucleus 0 value value value value
 *FEATURE Cytosol 1 flux flux value value
 *FEATURE ExtraCellular 2 flux flux value value
 *MEMBRANE Nucleus_Cytosol_membrane Nucleus Cytosol value value value value
 *MEMBRANE Cytosol_ExtraCellular_membrane Cytosol ExtraCellular flux flux value value
 *MODEL_END
 * @throws MathException
 */
private void writeModelDescription() throws MathException {
    Simulation simulation = simTask.getSimulation();
    printWriter.println("# Model description: FEATURE name handle boundary_conditions");
    printWriter.println(FVInputFileKeyword.MODEL_BEGIN);
    MathDescription mathDesc = simulation.getMathDescription();
    Enumeration<SubDomain> enum1 = mathDesc.getSubDomains();
    while (enum1.hasMoreElements()) {
        SubDomain sd = enum1.nextElement();
        if (sd instanceof CompartmentSubDomain) {
            CompartmentSubDomain csd = (CompartmentSubDomain) sd;
            printWriter.print(FVInputFileKeyword.FEATURE + " " + csd.getName() + " " + mathDesc.getHandle(csd) + " ");
            writeFeature_boundaryConditions(csd);
        } else if (sd instanceof MembraneSubDomain) {
            MembraneSubDomain msd = (MembraneSubDomain) sd;
            printWriter.print(FVInputFileKeyword.MEMBRANE + " " + msd.getName() + " " + msd.getInsideCompartment().getName() + " " + msd.getOutsideCompartment().getName() + " ");
            writeMembrane_boundaryConditions(msd);
        }
    }
    printWriter.println(FVInputFileKeyword.MODEL_END);
    printWriter.println();
}

Example 74 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writeVariables.

/**
 *# Variables : type name unit time_dependent_flag advection_flag solve_whole_mesh_flag solve_regions
 *VARIABLE_BEGIN
 *VOLUME_ODE rB uM
 *VOLUME_PDE rf uM false false
 *VOLUME_PDE r uM false false
 *VOLUME_ODE rfB uM
 *VARIABLE_END
 * @throws MathException
 * @throws ExpressionException
 * @throws IOException
 */
private void writeVariables() throws MathException, ExpressionException, IOException {
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    printWriter.println("# Variables : type name domain time_dependent_flag advection_flag grad_flag solve_whole_mesh_flag solve_regions");
    printWriter.println(FVInputFileKeyword.VARIABLE_BEGIN);
    MathDescription mathDesc = simSymbolTable.getSimulation().getMathDescription();
    Variable[] vars = simSymbolTable.getVariables();
    ArrayList<RandomVariable> rvList = new ArrayList<RandomVariable>();
    for (int i = 0; i < vars.length; i++) {
        String varName = vars[i].getName();
        String domainName = vars[i].getDomain() == null ? null : vars[i].getDomain().getName();
        if (vars[i] instanceof VolumeRandomVariable || vars[i] instanceof MembraneRandomVariable) {
            rvList.add((RandomVariable) vars[i]);
        } else if (vars[i] instanceof VolVariable) {
            if (bChomboSolver && domainName == null) {
                throw new MathException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " requires that every variable is defined in a single domain");
            }
            VolVariable volVar = (VolVariable) vars[i];
            if (mathDesc.isPDE(volVar)) {
                boolean hasTimeVaryingDiffusionOrAdvection = simSymbolTable.hasTimeVaryingDiffusionOrAdvection(volVar);
                final boolean hasVelocity = mathDesc.hasVelocity(volVar);
                final boolean hasGradient = mathDesc.hasGradient(volVar);
                if (mathDesc.isPdeSteady(volVar)) {
                    printWriter.print("VOLUME_PDE_STEADY ");
                } else {
                    printWriter.print("VOLUME_PDE ");
                }
                printWriter.print(varName + " " + domainName + " " + hasTimeVaryingDiffusionOrAdvection + " " + hasVelocity + " " + hasGradient);
            } else {
                printWriter.print("VOLUME_ODE " + varName + " " + domainName);
            }
            if (domainName == null) {
                Vector<SubDomain> listOfSubDomains = new Vector<SubDomain>();
                int totalNumCompartments = 0;
                Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
                while (subDomainEnum.hasMoreElements()) {
                    SubDomain subDomain = subDomainEnum.nextElement();
                    if (subDomain instanceof CompartmentSubDomain) {
                        CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) subDomain;
                        totalNumCompartments++;
                        Equation varEquation = subDomain.getEquation(vars[i]);
                        if (varEquation != null) {
                            if (!(varEquation instanceof PdeEquation) || !((PdeEquation) varEquation).isDummy(simSymbolTable, compartmentSubDomain)) {
                                listOfSubDomains.add(compartmentSubDomain);
                            }
                        }
                    }
                }
                if ((totalNumCompartments == listOfSubDomains.size()) || (listOfSubDomains.size() == 0 && simTask.getSimulation().getSolverTaskDescription().getSolverDescription().equals(SolverDescription.SundialsPDE))) {
                    printWriter.print(" true");
                } else {
                    printWriter.print(" false");
                    for (int j = 0; j < listOfSubDomains.size(); j++) {
                        CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) listOfSubDomains.elementAt(j);
                        printWriter.print(" " + compartmentSubDomain.getName());
                    }
                }
                printWriter.println();
            } else {
                printWriter.println(" false " + domainName);
            }
        } else if (vars[i] instanceof VolumeParticleVariable) {
            printWriter.println(FVInputFileKeyword.VOLUME_PARTICLE + " " + varName + " " + domainName);
        } else if (vars[i] instanceof MembraneParticleVariable) {
            printWriter.println(FVInputFileKeyword.MEMBRANE_PARTICLE + " " + varName + " " + domainName);
        } else if (vars[i] instanceof VolumeRegionVariable) {
            printWriter.println("VOLUME_REGION " + varName + " " + domainName);
        } else if (vars[i] instanceof MemVariable) {
            if (bChomboSolver && domainName == null) {
                throw new MathException(simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel() + " requires that every variable is defined in a single domain");
            }
            MemVariable memVar = (MemVariable) vars[i];
            if (mathDesc.isPDE(memVar)) {
                printWriter.println("MEMBRANE_PDE " + varName + " " + domainName + " " + simSymbolTable.hasTimeVaryingDiffusionOrAdvection(memVar));
            } else {
                printWriter.println("MEMBRANE_ODE " + varName + " " + domainName);
            }
        } else if (vars[i] instanceof MembraneRegionVariable) {
            printWriter.println("MEMBRANE_REGION " + varName + " " + domainName);
        } else if (vars[i] instanceof FilamentVariable) {
            throw new RuntimeException("Filament application not supported yet");
        }
    }
    int numRandomVariables = rvList.size();
    if (numRandomVariables > 0) {
        ISize samplingSize = simTask.getSimulation().getMeshSpecification().getSamplingSize();
        String[] varNameArr = new String[numRandomVariables];
        VariableType[] varTypeArr = new VariableType[numRandomVariables];
        double[][] dataArr = new double[numRandomVariables][];
        for (int i = 0; i < numRandomVariables; i++) {
            RandomVariable rv = rvList.get(i);
            varNameArr[i] = rv.getName();
            int numRandomNumbers = 0;
            if (rv instanceof VolumeRandomVariable) {
                printWriter.print("VOLUME_RANDOM");
                varTypeArr[i] = VariableType.VOLUME;
                numRandomNumbers = samplingSize.getXYZ();
            } else if (rv instanceof MembraneRandomVariable) {
                printWriter.print("MEMBRANE_RANDOM");
                varTypeArr[i] = VariableType.MEMBRANE;
                numRandomNumbers = resampledGeometry.getGeometrySurfaceDescription().getSurfaceCollection().getTotalPolygonCount();
            } else {
                throw new RuntimeException("Unknown RandomVariable type");
            }
            printWriter.println(" " + varNameArr[i]);
            dataArr[i] = generateRandomNumbers(rv, numRandomNumbers);
        }
        File rvFile = new File(workingDirectory, simTask.getSimulationJobID() + RANDOM_VARIABLE_FILE_EXTENSION);
        DataSet.writeNew(rvFile, varNameArr, varTypeArr, samplingSize, dataArr);
    }
    printWriter.println(FVInputFileKeyword.VARIABLE_END);
    printWriter.println();
}

Example 75 with MathDescription

use of cbit.vcell.math.MathDescription in project vcell by virtualcell.

the class XmlHelper method simToXML.

public static String simToXML(Simulation sim) throws XmlParseException {
    String simString = null;
    if (sim == null) {
        throw new XmlParseException("Invalid input for Simulation: " + sim);
    }
    Xmlproducer xmlProducer = new Xmlproducer(true);
    // cannot be null
    MathDescription md = sim.getMathDescription();
    Geometry geom = md.getGeometry();
    Element container = new Element(SIM_CONTAINER);
    Element mathElement = xmlProducer.getXML(md);
    Element simElement = xmlProducer.getXML(sim);
    if (geom != null) {
        Element geomElement = xmlProducer.getXML(geom);
        container.addContent(geomElement);
    } else {
        System.err.println("No corresponding geometry for the simulation: " + sim.getName());
    }
    container.addContent(mathElement);
    container.addContent(simElement);
    container = XmlUtil.setDefaultNamespace(container, Namespace.getNamespace(XMLTags.VCML_NS));
    simString = XmlUtil.xmlToString(container);
    return simString;
}