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

Example 51 with ModelUnitSystem

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

the class XmlReader method getModelParameter.

public ModelParameter getModelParameter(Element paramElement, Model model) {
    // get its attributes : name, role and unit definition
    String glParamName = unMangle(paramElement.getAttributeValue(XMLTags.NameAttrTag));
    String role = paramElement.getAttributeValue(XMLTags.ParamRoleAttrTag);
    ModelUnitSystem modelUnitSystem = model.getUnitSystem();
    int glParamRole = -1;
    if (role.equals(XMLTags.ParamRoleUserDefinedTag)) {
        glParamRole = Model.ROLE_UserDefined;
    } else {
        throw new RuntimeException("unknown type of model parameter (not user-defined)");
    }
    // 
    // int glParamRole = -1;
    // if (role.equals(XMLTags.ParamRoleUserDefinedTag)) {
    // glParamRole = Model.ROLE_UserDefined;
    // } else	if (role.equals(XMLTags.RoleVariableRateTag)) {
    // glParamRole = Model.ROLE_VariableRate;
    // } else {
    // throw new RuntimeException("unknown type of model parameter (not user-defined or variable rate)");
    // }
    String unitSymbol = paramElement.getAttributeValue(XMLTags.VCUnitDefinitionAttrTag);
    VCUnitDefinition glParamUnit = null;
    if (unitSymbol != null) {
        glParamUnit = modelUnitSystem.getInstance(unitSymbol);
    }
    // get parameter contents : expression; annotation, if any.
    String glParamExpStr = paramElement.getText();
    Expression glParamExp = unMangleExpression(glParamExpStr);
    String glParamAnnotation = null;
    String annotationText = paramElement.getChildText(XMLTags.AnnotationTag, vcNamespace);
    if (annotationText != null && annotationText.length() > 0) {
        glParamAnnotation = unMangle(annotationText);
    }
    // create new global parameter
    ModelParameter newGlParam = model.new ModelParameter(glParamName, glParamExp, glParamRole, glParamUnit);
    newGlParam.setModelParameterAnnotation(glParamAnnotation);
    return newGlParam;
}

Example 52 with ModelUnitSystem

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

the class VFrapXmlHelper method CreateSaveVFrapDataSymbols.

public static void CreateSaveVFrapDataSymbols(Hashtable<String, Object> hashTable, BioModel bioModel, ExternalDataIdentifier vfrapMisc) {
    String[] channelNames = (String[]) hashTable.get("channelNames");
    DataSymbolType[] channelVFrapImageType = (DataSymbolType[]) hashTable.get("channelVFrapImageType");
    String initialFieldDataName = (String) hashTable.get("initialFieldDataName");
    SimulationContext simContext = bioModel.getSimulationContexts()[0];
    ModelUnitSystem modelUnitSystem = bioModel.getModel().getUnitSystem();
    for (int i = 0; i < channelNames.length; i++) {
        // TODO: construct dataSymbolName from vFrapConstants::nameFromToken()
        // item name postfixed with field data name
        String dataSymbolName = channelNames[i] + "_" + initialFieldDataName;
        DataSymbol dataSymbol = new FieldDataSymbol(dataSymbolName, channelVFrapImageType[i], simContext.getDataContext(), modelUnitSystem.getInstance_TBD(), vfrapMisc, channelNames[i], VariableType.VOLUME.getTypeName(), 0D);
        simContext.getDataContext().addDataSymbol(dataSymbol);
    }
}

Example 53 with ModelUnitSystem

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

the class ITextWriter method writeStructureMapping.

// boundary types ignored.
protected void writeStructureMapping(Section simContextSection, SimulationContext sc) throws DocumentException {
    GeometryContext gc = sc.getGeometryContext();
    if (gc == null) {
        return;
    }
    Section structMappSection = null;
    /*try {
			ByteArrayOutputStream bos = generateStructureMappingImage(sc);
			com.lowagie.text.Image structMapImage = com.lowagie.text.Image.getInstance(Toolkit.getDefaultToolkit().createImage(bos.toByteArray()), null);
			structMappSection = simContextSection.addSection("Structure Mapping For " + sc.getName(), simContextSection.numberDepth() + 1);
			structMappSection.add(structMapImage);
		} catch (Exception e) {
			System.err.println("Unable to add structure mapping image to report.");
			e.printStackTrace();
		}*/
    StructureMapping[] structMap = gc.getStructureMappings();
    Table structMapTable = null;
    ModelUnitSystem modelUnitSystem = sc.getModel().getUnitSystem();
    for (int i = 0; i < structMap.length; i++) {
        if (!(structMap[i] instanceof FeatureMapping)) {
            continue;
        }
        if (i == 0) {
            structMapTable = getTable(5, 100, 1, 3, 3);
            structMapTable.addCell(createCell("Structure Mapping", getBold(DEF_HEADER_FONT_SIZE), 5, 1, Element.ALIGN_CENTER, true));
            structMapTable.addCell(createHeaderCell("Structure", getBold(), 1));
            structMapTable.addCell(createHeaderCell("Subdomain", getBold(), 1));
            structMapTable.addCell(createHeaderCell("Resolved (T/F)", getBold(), 1));
            structMapTable.addCell(createHeaderCell("Surf/Vol", getBold(), 1));
            structMapTable.addCell(createHeaderCell("VolFract", getBold(), 1));
            structMapTable.endHeaders();
        }
        String structName = structMap[i].getStructure().getName();
        SubVolume subVol = (SubVolume) ((FeatureMapping) structMap[i]).getGeometryClass();
        String subDomain = "";
        if (subVol != null) {
            subDomain = subVol.getName();
        }
        // ((FeatureMapping)structMap[i]).getResolved();
        boolean isResolved = false;
        String surfVolStr = "", volFractStr = "";
        MembraneMapping mm = (MembraneMapping) gc.getStructureMapping(sc.getModel().getStructureTopology().getParentStructure(structMap[i].getStructure()));
        if (mm != null) {
            StructureMapping.StructureMappingParameter smp = mm.getSurfaceToVolumeParameter();
            if (smp != null) {
                Expression tempExp = smp.getExpression();
                VCUnitDefinition tempUnit = smp.getUnitDefinition();
                if (tempExp != null) {
                    surfVolStr = tempExp.infix();
                    if (tempUnit != null && !modelUnitSystem.getInstance_DIMENSIONLESS().compareEqual(tempUnit)) {
                        // no need to add '1' for dimensionless unit
                        surfVolStr += " " + tempUnit.getSymbolUnicode();
                    }
                }
            }
            smp = mm.getVolumeFractionParameter();
            if (smp != null) {
                Expression tempExp = smp.getExpression();
                VCUnitDefinition tempUnit = smp.getUnitDefinition();
                if (tempExp != null) {
                    volFractStr = tempExp.infix();
                    if (tempUnit != null && !modelUnitSystem.getInstance_DIMENSIONLESS().compareEqual(tempUnit)) {
                        volFractStr += " " + tempUnit.getSymbolUnicode();
                    }
                }
            }
        }
        structMapTable.addCell(createCell(structName, getFont()));
        structMapTable.addCell(createCell(subDomain, getFont()));
        structMapTable.addCell(createCell((isResolved ? " T " : " F "), getFont()));
        structMapTable.addCell(createCell(surfVolStr, getFont()));
        structMapTable.addCell(createCell(volFractStr, getFont()));
    }
    if (structMapTable != null) {
        if (structMappSection == null) {
            structMappSection = simContextSection.addSection("Structure Mapping For " + sc.getName(), simContextSection.numberDepth() + 1);
        }
        structMappSection.add(structMapTable);
    }
}