Examples with SubVolume cbit.vcell.geometry.SubVolume used on opensource projects

Example 61 with SubVolume

use of cbit.vcell.geometry.SubVolume in project vcell by virtualcell.

the class XmlReader method getGeometrySurfaceDescription.

private GeometrySurfaceDescription getGeometrySurfaceDescription(Element param, Geometry geom) throws XmlParseException {
    GeometrySurfaceDescription gsd = geom.getGeometrySurfaceDescription();
    String cutoffStr = param.getAttributeValue(XMLTags.CutoffFrequencyAttrTag);
    String xDim = param.getAttributeValue(XMLTags.NumSamplesXAttrTag);
    String yDim = param.getAttributeValue(XMLTags.NumSamplesYAttrTag);
    String zDim = param.getAttributeValue(XMLTags.NumSamplesZAttrTag);
    if (cutoffStr == null || xDim == null || yDim == null || zDim == null) {
        throw new XmlParseException("Attributes for element Surface Description not properly set, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
    }
    try {
        ISize isize = new ISize(Integer.parseInt(xDim), Integer.parseInt(yDim), Integer.parseInt(zDim));
        gsd.setVolumeSampleSize(isize);
        gsd.setFilterCutoffFrequency(new Double(cutoffStr));
        // these lists are allowed to be empty.
        ArrayList<Element> memRegions = new ArrayList<Element>(param.getChildren(XMLTags.MembraneRegionTag, vcNamespace));
        ArrayList<Element> volRegions = new ArrayList<Element>(param.getChildren(XMLTags.VolumeRegionTag, vcNamespace));
        ArrayList<GeometricRegion> regions = new ArrayList<GeometricRegion>();
        GeometryUnitSystem geometryUnitSystem = geom.getUnitSystem();
        for (Element temp : volRegions) {
            String regionID = temp.getAttributeValue(XMLTags.RegionIDAttrTag);
            String name = temp.getAttributeValue(XMLTags.NameAttrTag);
            String subvolumeRef = temp.getAttributeValue(XMLTags.SubVolumeAttrTag);
            if (regionID == null || name == null || subvolumeRef == null) {
                throw new XmlParseException("Attributes for element Volume Region not properly set, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
            }
            SubVolume subvolume = geom.getGeometrySpec().getSubVolume(subvolumeRef);
            if (subvolume == null) {
                throw new XmlParseException("The subvolume " + subvolumeRef + " could not be resolved.");
            }
            double size = -1;
            VCUnitDefinition unit = null;
            String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag);
            if (sizeStr != null) {
                size = Double.parseDouble(sizeStr);
                String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                if (unitSymbol != null) {
                    unit = geometryUnitSystem.getInstance(unitSymbol);
                }
            }
            VolumeGeometricRegion vgr = new VolumeGeometricRegion(name, size, unit, subvolume, Integer.parseInt(regionID));
            regions.add(vgr);
        }
        for (Element temp : memRegions) {
            String volRegion_1 = temp.getAttributeValue(XMLTags.VolumeRegion_1AttrTag);
            String volRegion_2 = temp.getAttributeValue(XMLTags.VolumeRegion_2AttrTag);
            String name = temp.getAttributeValue(XMLTags.NameAttrTag);
            if (volRegion_1 == null || volRegion_2 == null || name == null) {
                throw new XmlParseException("Attributes for element Membrane Region not properly set, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
            }
            VolumeGeometricRegion region1 = getAdjacentVolumeRegion(regions, volRegion_1);
            VolumeGeometricRegion region2 = getAdjacentVolumeRegion(regions, volRegion_2);
            if (region1 == null || region2 == null) {
                throw new XmlParseException("Element Membrane Region refernces invalid volume regions, under geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
            }
            double size = -1;
            VCUnitDefinition unit = null;
            String sizeStr = temp.getAttributeValue(XMLTags.SizeAttrTag);
            if (sizeStr != null) {
                size = Double.parseDouble(sizeStr);
                String unitSymbol = temp.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
                if (unitSymbol != null) {
                    unit = geometryUnitSystem.getInstance(unitSymbol);
                }
            }
            SurfaceGeometricRegion rsl = new SurfaceGeometricRegion(name, size, unit);
            rsl.addAdjacentGeometricRegion(region1);
            region1.addAdjacentGeometricRegion(rsl);
            rsl.addAdjacentGeometricRegion(region2);
            region2.addAdjacentGeometricRegion(rsl);
            regions.add(rsl);
        }
        if (regions.size() > 0) {
            gsd.setGeometricRegions((GeometricRegion[]) regions.toArray(new GeometricRegion[regions.size()]));
        }
    } catch (Exception e) {
        System.err.println("Unable to read geometry surface description from XML, for geometry: " + ((Element) param.getParent()).getAttributeValue(XMLTags.NameAttrTag));
        e.printStackTrace();
    }
    return gsd;
}

Example 62 with SubVolume

use of cbit.vcell.geometry.SubVolume in project vcell by virtualcell.

the class XmlReader method getMembraneSubDomain.

/**
 * This method returns a MembraneSubDomain object from a XML Element.
 * Creation date: (5/18/2001 4:23:30 PM)
 * @return cbit.vcell.math.MembraneSubDomain
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
@SuppressWarnings("unchecked")
private MembraneSubDomain getMembraneSubDomain(Element param, MathDescription mathDesc) throws XmlParseException {
    // no need to do anything with the 'Name' attribute : constructor of MembraneSubDomain creates name from inside/outside compartmentSubDomains.
    // String msdName = unMangle( param.getAttributeValue(XMLTags.NameAttrTag) );
    // if ( msdName != null) {
    // }
    // get compartmentSubDomain references
    // inside
    String name = unMangle(param.getAttributeValue(XMLTags.InsideCompartmentTag));
    CompartmentSubDomain insideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(name);
    if (insideRef == null) {
        throw new XmlParseException("The reference to the inside CompartmentSubDomain " + name + ", could not be resolved!");
    }
    // outside
    name = unMangle(param.getAttributeValue(XMLTags.OutsideCompartmentTag));
    CompartmentSubDomain outsideRef = (CompartmentSubDomain) mathDesc.getCompartmentSubDomain(name);
    if (outsideRef == null) {
        throw new XmlParseException("The reference to the outside CompartmentSubDomain " + name + ", could not be resolved!");
    }
    // *** create new Membrane SubDomain ***
    SubVolume insideSubVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(insideRef.getName());
    SubVolume outsideSubVolume = mathDesc.getGeometry().getGeometrySpec().getSubVolume(outsideRef.getName());
    SurfaceClass surfaceClass = mathDesc.getGeometry().getGeometrySurfaceDescription().getSurfaceClass(insideSubVolume, outsideSubVolume);
    MembraneSubDomain subDomain = new MembraneSubDomain(insideRef, outsideRef, surfaceClass.getName());
    transcribeComments(param, subDomain);
    // Process BoundaryConditions
    Iterator<Element> iterator = param.getChildren(XMLTags.BoundaryTypeTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        // create BoundaryConditionType
        String temp = tempelement.getAttributeValue(XMLTags.BoundaryTypeAttrTag);
        BoundaryConditionType bType = new BoundaryConditionType(temp);
        // Process Xm
        if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXm)) {
            subDomain.setBoundaryConditionXm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueXp)) {
            // Process Xp
            subDomain.setBoundaryConditionXp(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYm)) {
            // Process Ym
            subDomain.setBoundaryConditionYm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueYp)) {
            // Process Yp
            subDomain.setBoundaryConditionYp(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZm)) {
            // Process Zm
            subDomain.setBoundaryConditionZm(bType);
        } else if (tempelement.getAttributeValue(XMLTags.BoundaryAttrTag).equalsIgnoreCase(XMLTags.BoundaryAttrValueZp)) {
            // Process Zp
            subDomain.setBoundaryConditionZp(bType);
        } else {
            // If not indentified throw an exception!!
            throw new XmlParseException("Unknown BoundaryConditionType: " + tempelement.getAttributeValue(XMLTags.BoundaryAttrTag));
        }
    }
    // Add OdeEquations
    iterator = param.getChildren(XMLTags.OdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = (Element) iterator.next();
        OdeEquation odeEquation = getOdeEquation(tempElement, mathDesc);
        try {
            subDomain.addEquation(odeEquation);
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an OdeEquation to a MembraneSubDomain!", e);
        }
    }
    // process PdeEquations
    iterator = param.getChildren(XMLTags.PdeEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = (Element) iterator.next();
        try {
            subDomain.addEquation(getPdeEquation(tempElement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an PdeEquation to the MembraneSubDomain " + name, e);
        }
    }
    // Add JumpConditions
    iterator = param.getChildren(XMLTags.JumpConditionTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempElement = (Element) iterator.next();
        try {
            subDomain.addJumpCondition(getJumpCondition(tempElement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a JumpCondition to a MembraneSubDomain!", e);
        }
    }
    // Add the FastSystem (if any)
    Element tempElement = param.getChild(XMLTags.FastSystemTag, vcNamespace);
    if (tempElement != null) {
        subDomain.setFastSystem(getFastSystem(tempElement, mathDesc));
    }
    // add MembraneRegionEquation
    iterator = param.getChildren(XMLTags.MembraneRegionEquationTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        tempElement = (Element) iterator.next();
        try {
            subDomain.addEquation(getMembraneRegionEquation(tempElement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a MembraneRegionEquation to a MEmbraneSubDomain!", e);
        }
    }
    iterator = param.getChildren(XMLTags.ParticleJumpProcessTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addParticleJumpProcess(getParticleJumpProcess(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e);
        }
    }
    iterator = param.getChildren(XMLTags.ParticlePropertiesTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addParticleProperties(getParticleProperties(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding a jump process to the MembraneSubDomain " + name, e);
        }
    }
    // process ComputeNormal "equations"
    iterator = param.getChildren(XMLTags.ComputeNormalTag, vcNamespace).iterator();
    while (iterator.hasNext()) {
        Element tempelement = (Element) iterator.next();
        try {
            subDomain.addEquation(getComputeNormal(tempelement, mathDesc));
        } catch (MathException e) {
            e.printStackTrace();
            throw new XmlParseException("A MathException was fired when adding an ComputeNormal 'equation' to the MembraneSubDomain " + name, e);
        }
    }
    Element velElem = param.getChild(XMLTags.VelocityTag, vcNamespace);
    setMembraneSubdomainVelocity(velElem, XMLTags.XAttrTag, subDomain::setVelocityX);
    setMembraneSubdomainVelocity(velElem, XMLTags.YAttrTag, subDomain::setVelocityY);
    return subDomain;
}

Example 63 with SubVolume

use of cbit.vcell.geometry.SubVolume 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 64 with SubVolume

use of cbit.vcell.geometry.SubVolume in project vcell by virtualcell.

the class XmlReader method getSubVolume.

/**
 * This method returns a SubVolume element type from a XML representation.
 * Creation date: (4/26/2001 4:14:01 PM)
 * @return SubVolume
 * @param param org.jdom.Element
 */
private SubVolume getSubVolume(Element param) throws XmlParseException {
    String typeString = param.getAttributeValue(XMLTags.TypeAttrTag);
    SubVolume newsubvolume = null;
    if (typeString != null) {
        // process the subvolume upon the 'type'
        if (typeString.equalsIgnoreCase(XMLTags.CompartmentBasedTypeTag)) {
            // Process compartmental based
            newsubvolume = getCompartmentSubVolume(param);
        } else if (typeString.equalsIgnoreCase(XMLTags.AnalyticBasedTypeTag)) {
            // Process Analytic based
            newsubvolume = getAnalyticSubVolume(param);
        } else if (typeString.equalsIgnoreCase(XMLTags.ImageBasedTypeTag)) {
            // Process Image based
            newsubvolume = getImageSubVolume(param);
        } else if (typeString.equalsIgnoreCase(XMLTags.CSGBasedTypeTag)) {
            // Process Constructed Solid Geometry based
            newsubvolume = getCSGObject(param, null);
        } else {
            // Throw an exception
            throw new XmlParseException("Parse Error! Unknown Subvolume type:" + typeString);
        }
    } else {
        System.out.println("Invalid VCML format! Error in <Subvolume name=\"" + param.getAttributeValue(XMLTags.NameAttrTag) + "\"/>");
        System.out.println("Valid format is:");
        System.out.println("<SubVolume Name=\"??\" Handle=\"?\" ImagePixelValue=\"?\"/>");
        throw new XmlParseException("Invalid VCML syntax in <Subvolume name=\"" + param.getAttributeValue(XMLTags.NameAttrTag) + "\"/>");
    }
    return newsubvolume;
}

Example 65 with SubVolume

use of cbit.vcell.geometry.SubVolume in project vcell by virtualcell.

the class XmlReader method getSurfaceClass.

private SurfaceClass getSurfaceClass(Element param, Geometry geom) throws XmlParseException {
    Set<SubVolume> surfaceClassSubVolumeSet = new HashSet<SubVolume>();
    KeyValue surfaceClassKey = null;
    String surfaceClassName = null;
    surfaceClassName = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String surfaceClassKeyStr = param.getAttributeValue(XMLTags.KeyValueAttrTag);
    surfaceClassKey = (surfaceClassKeyStr == null ? null : new KeyValue(surfaceClassKeyStr));
    String subVol1Ref = param.getAttributeValue(XMLTags.SubVolume1RefAttrTag);
    String subVol2Ref = param.getAttributeValue(XMLTags.SubVolume2RefAttrTag);
    if (subVol1Ref != null) {
        SubVolume subVolume = geom.getGeometrySpec().getSubVolume(subVol1Ref);
        if (subVolume == null) {
            throw new XmlParseException("SurfaceClass missing subvolume '" + subVol1Ref + "'");
        }
        surfaceClassSubVolumeSet.add(subVolume);
    }
    if (subVol2Ref != null) {
        SubVolume subVolume = geom.getGeometrySpec().getSubVolume(subVol2Ref);
        if (subVolume == null) {
            throw new XmlParseException("SurfaceClass missing subvolume '" + subVol2Ref + "'");
        }
        surfaceClassSubVolumeSet.add(subVolume);
    }
    return new SurfaceClass(surfaceClassSubVolumeSet, surfaceClassKey, surfaceClassName);
}