Examples with Domain cbit.vcell.math.Variable.Domain used on opensource projects

Example 46 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writePostProcessingBlock.

private void writePostProcessingBlock() throws Exception {
    // SolverException, ExpressionException and exceptions from roiDataGenerator.getROIDataGeneratorDescription()
    PostProcessingBlock postProcessingBlock = simTask.getSimulation().getMathDescription().getPostProcessingBlock();
    if (postProcessingBlock.getNumDataGenerators() == 0) {
        // to make c++ code write default var statisitcs, without the token it won't write anything
        printWriter.println(FVInputFileKeyword.POST_PROCESSING_BLOCK_BEGIN);
        printWriter.println(FVInputFileKeyword.POST_PROCESSING_BLOCK_END);
        printWriter.println();
        return;
    }
    if (bChomboSolver && postProcessingBlock.getDataGeneratorList().size() > 0) {
        throw new Exception("Data generators are not supported by " + simTask.getSimulation().getSolverTaskDescription().getSolverDescription().getDisplayLabel());
    }
    printWriter.println(" # Post Processing Block");
    printWriter.println(FVInputFileKeyword.POST_PROCESSING_BLOCK_BEGIN);
    for (DataGenerator dataGenerator : postProcessingBlock.getDataGeneratorList()) {
        String varName = dataGenerator.getName();
        Domain domain = dataGenerator.getDomain();
        String domainName = domain == null ? null : domain.getName();
        if (dataGenerator instanceof ProjectionDataGenerator) {
            ProjectionDataGenerator pdg = (ProjectionDataGenerator) dataGenerator;
            Expression function = subsituteExpression(pdg.getFunction(), VariableDomain.VARIABLEDOMAIN_VOLUME);
            printWriter.println(FVInputFileKeyword.PROJECTION_DATA_GENERATOR + " " + varName + " " + domainName + " " + pdg.getAxis() + " " + pdg.getOperation() + " " + function.infix() + ";");
        } else if (dataGenerator instanceof ConvolutionDataGenerator) {
            ConvolutionDataGenerator convolutionDataGenerator = (ConvolutionDataGenerator) dataGenerator;
            ConvolutionDataGeneratorKernel kernel = convolutionDataGenerator.getKernel();
            if (kernel instanceof GaussianConvolutionDataGeneratorKernel) {
                GaussianConvolutionDataGeneratorKernel gck = (GaussianConvolutionDataGeneratorKernel) kernel;
                Expression volFunction = subsituteExpression(convolutionDataGenerator.getVolFunction(), VariableDomain.VARIABLEDOMAIN_VOLUME);
                Expression memFunction = subsituteExpression(convolutionDataGenerator.getMemFunction(), VariableDomain.VARIABLEDOMAIN_MEMBRANE);
                Expression sigmaXY = subsituteExpression(gck.getSigmaXY_um(), VariableDomain.VARIABLEDOMAIN_VOLUME);
                Expression sigmaZ = subsituteExpression(gck.getSigmaZ_um(), VariableDomain.VARIABLEDOMAIN_VOLUME);
                String volFuncStr = volFunction.infix();
                String memFuncStr = memFunction.infix();
                printWriter.println(FVInputFileKeyword.GAUSSIAN_CONVOLUTION_DATA_GENERATOR + " " + varName + " " + domainName + " " + sigmaXY.infix() + " " + sigmaZ.infix() + " " + FVInputFileKeyword.GAUSSIAN_CONVOLUTION_VOL_FUNCTION + " " + volFuncStr + "; " + FVInputFileKeyword.GAUSSIAN_CONVOLUTION_MEM_FUNCTION + " " + memFuncStr + ";");
            }
        } else if (dataGenerator instanceof cbit.vcell.microscopy.ROIDataGenerator) {
            /*
			ROI_DATA_GENERATOR_BEGIN roidata
			VolumePoints 20
			2667 2676 2679 2771 2969 2877 3067 3277 3185 3283 3473 3580 3690 3687 3878 4086 3990 4182 4193 1077 (all points in one line)
			SampleImage 9 0 1341426862190 vcField('sumROIData','roiSumDataVar',0.0,'Volume')
			StoreEnabled false

			SampleImageFile roiSumDataVar 0.0 C:\Users\abcde\VirtualMicroscopy\SimulationData\SimID_1341426862125_0_sumROIData_roiSumDataVar_0_0_Volume.fdat
			DATA_PROCESSOR_END
			*/
            cbit.vcell.microscopy.ROIDataGenerator roiDataGenerator = (cbit.vcell.microscopy.ROIDataGenerator) dataGenerator;
            printWriter.println(roiDataGenerator.getROIDataGeneratorDescription(workingDirectory, simTask.getSimulationJob()));
        } else if (dataGenerator instanceof org.vcell.vmicro.workflow.data.ROIDataGenerator) {
            /*
			ROI_DATA_GENERATOR_BEGIN roidata
			VolumePoints 20
			2667 2676 2679 2771 2969 2877 3067 3277 3185 3283 3473 3580 3690 3687 3878 4086 3990 4182 4193 1077 (all points in one line)
			SampleImage 9 0 1341426862190 vcField('sumROIData','roiSumDataVar',0.0,'Volume')
			StoreEnabled false

			SampleImageFile roiSumDataVar 0.0 C:\Users\abcde\VirtualMicroscopy\SimulationData\SimID_1341426862125_0_sumROIData_roiSumDataVar_0_0_Volume.fdat
			DATA_PROCESSOR_END
			*/
            org.vcell.vmicro.workflow.data.ROIDataGenerator roiDataGenerator = (org.vcell.vmicro.workflow.data.ROIDataGenerator) dataGenerator;
            printWriter.println(roiDataGenerator.getROIDataGeneratorDescription(workingDirectory, simTask.getSimulationJob()));
        } else {
            throw new SolverException(dataGenerator.getClass() + " : data generator not supported yet.");
        }
    }
    printWriter.println(FVInputFileKeyword.POST_PROCESSING_BLOCK_END);
    printWriter.println();
}

Example 47 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class FunctionFileGenerator method readFunctionsFile.

/**
 * This method was created in VisualAge.
 * @param logFile java.io.File
 */
public static synchronized Vector<AnnotatedFunction> readFunctionsFile(File functionsFile, String simJobID) throws java.io.FileNotFoundException, java.io.IOException {
    // Check if file exists
    if (!functionsFile.exists()) {
        throw new java.io.FileNotFoundException("functions file " + functionsFile.getPath() + " not found");
    }
    // 
    // Read characters from functionFile into character array and transfer into string buffer.
    // 
    Vector<AnnotatedFunction> annotatedFunctionsVector = new Vector<AnnotatedFunction>();
    long fnFileLength = functionsFile.length();
    StringBuffer stringBuffer = new StringBuffer();
    FileInputStream is = null;
    try {
        is = new FileInputStream(functionsFile);
        InputStreamReader reader = new InputStreamReader(is);
        BufferedReader br = new BufferedReader(reader);
        char[] charArray = new char[10000];
        while (true) {
            int numRead = br.read(charArray, 0, charArray.length);
            if (numRead > 0) {
                stringBuffer.append(charArray, 0, numRead);
            } else if (numRead == -1) {
                break;
            }
        }
    } finally {
        if (is != null) {
            is.close();
        }
    }
    if (stringBuffer.length() != fnFileLength) {
        System.out.println("<<<SYSOUT ALERT>>>SimulationData.readFunctionFile(), read " + stringBuffer.length() + " of " + fnFileLength + " bytes of input file");
    }
    String newLineDelimiters = "\n\r";
    StringTokenizer lineTokenizer = new StringTokenizer(stringBuffer.toString(), newLineDelimiters);
    String token1 = new String("");
    int j = 0;
    // 
    // Each token is a line representing a function name and function expression,
    // separated by a semicolon
    // 
    HashSet<String> allSymbols = new HashSet<String>();
    while (lineTokenizer.hasMoreTokens()) {
        token1 = lineTokenizer.nextToken();
        FunctionFileGenerator.FuncFileLineInfo funcFileLineInfo = readFunctionLine(token1);
        if (funcFileLineInfo != null && funcFileLineInfo.functionName != null && funcFileLineInfo.functionExpr != null && funcFileLineInfo.funcVarType != null) {
            Expression functionExpr = null;
            try {
                functionExpr = new Expression(funcFileLineInfo.functionExpr);
                functionExpr = MathFunctionDefinitions.fixFunctionSyntax(functionExpr);
            } catch (cbit.vcell.parser.ExpressionException e) {
                throw new RuntimeException("Error in reading expression '" + funcFileLineInfo.functionExpr + "' for function \"" + funcFileLineInfo.functionName + "\"");
            }
            Domain domain = Variable.getDomainFromCombinedIdentifier(funcFileLineInfo.functionName);
            String funcName = Variable.getNameFromCombinedIdentifier(funcFileLineInfo.functionName);
            AnnotatedFunction annotatedFunc = new AnnotatedFunction(funcName, functionExpr, domain, funcFileLineInfo.errorString, funcFileLineInfo.funcVarType, funcFileLineInfo.funcIsUserDefined ? FunctionCategory.OLDUSERDEFINED : FunctionCategory.PREDEFINED);
            allSymbols.add(annotatedFunc.getName());
            String[] symbols = annotatedFunc.getExpression().getSymbols();
            if (symbols != null) {
                allSymbols.addAll(Arrays.asList(symbols));
            }
            annotatedFunctionsVector.addElement(annotatedFunc);
        }
        j++;
    }
    if (simJobID != null && simJobID.trim().length() > 0) {
        SimpleSymbolTable simpleSymbolTable = new SimpleSymbolTable(allSymbols.toArray(new String[0]));
        // bind
        for (AnnotatedFunction func : annotatedFunctionsVector) {
            if (func.isOldUserDefined()) {
                try {
                    func.bind(simpleSymbolTable);
                } catch (ExpressionBindingException e) {
                    e.printStackTrace();
                }
            }
        }
        // rename symbol table entries
        for (int i = 0; i < annotatedFunctionsVector.size(); i++) {
            AnnotatedFunction func = annotatedFunctionsVector.get(i);
            if (func.isOldUserDefined()) {
                SimpleSymbolTableEntry ste = (SimpleSymbolTableEntry) simpleSymbolTable.getEntry(func.getName());
                ste.setName(simJobID + "_" + func.getName());
            }
        }
        // rename in the expressions
        for (int i = 0; i < annotatedFunctionsVector.size(); i++) {
            AnnotatedFunction func = annotatedFunctionsVector.get(i);
            if (func.isOldUserDefined()) {
                try {
                    Expression exp = func.getExpression().renameBoundSymbols(simpleSymbolTable.getNameScope());
                    AnnotatedFunction newfunc = new AnnotatedFunction(simJobID + "_" + func.getName(), exp, func.getDomain(), func.getName(), func.getErrorString(), func.getFunctionType(), FunctionCategory.OLDUSERDEFINED);
                    annotatedFunctionsVector.set(i, newfunc);
                } catch (ExpressionBindingException e) {
                    e.printStackTrace();
                }
            }
        }
    }
    return annotatedFunctionsVector;
}

Example 48 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class XmlReader method getOutputFunction.

private AnnotatedFunction getOutputFunction(Element param) throws XmlParseException {
    // get attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String temp = param.getText();
    Expression exp = unMangleExpression(temp);
    String errStr = unMangle(param.getAttributeValue(XMLTags.ErrorStringTag));
    VariableType funcType = VariableType.UNKNOWN;
    String funcTypeAttr = param.getAttributeValue(XMLTags.FunctionTypeTag);
    if (funcTypeAttr != null) {
        String funcTypeStr = unMangle(funcTypeAttr);
        funcType = VariableType.getVariableTypeFromVariableTypeName(funcTypeStr);
    }
    // -- create new AnnotatedFunction --
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    AnnotatedFunction function = new AnnotatedFunction(name, exp, domain, errStr, funcType, FunctionCategory.OUTPUTFUNCTION);
    return function;
}

Example 49 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class XmlReader method getMembraneRegionVariable.

/**
 * This method returns a MembraneRegionVariable object from a XML Element.
 * Creation date: (5/16/2001 2:56:34 PM)
 * @return cbit.vcell.math.MembraneRegionVariable
 * @param param org.jdom.Element
 */
private MembraneRegionVariable getMembraneRegionVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // -- create new MembraneRegionVariable object
    MembraneRegionVariable memRegVariable = new MembraneRegionVariable(name, domain);
    transcribeComments(param, memRegVariable);
    return memRegVariable;
}

Example 50 with Domain

use of cbit.vcell.math.Variable.Domain in project vcell by virtualcell.

the class CellQuanVCTranslator method addCompartmentSubDomain.

/**
 * 	addCompartmentSubDomain : we pick the variable name by reading through the mathML.
 * 	Redundancy in variable name with the volume variable?
 */
protected void addCompartmentSubDomain() throws Exception {
    String csdName = sRoot.getAttributeValue(CELLMLTags.name, sAttNamespace);
    CompartmentSubDomain csd = new CompartmentSubDomain(csdName, CompartmentSubDomain.NON_SPATIAL_PRIORITY);
    Iterator<?> compElementIter = sRoot.getChildren(CELLMLTags.COMPONENT, sNamespace).iterator();
    // JDOMTreeWalker walker = new JDOMTreeWalker(sRoot, new ElementFilter(CELLMLTags.COMPONENT));
    Element comp, math;
    String compName, varName, mangledName;
    while (compElementIter.hasNext()) {
        comp = (Element) compElementIter.next();
        compName = comp.getAttributeValue(CELLMLTags.name, sAttNamespace);
        @SuppressWarnings("unchecked") Iterator<Element> mathIter = comp.getChildren(CELLMLTags.MATH, mathns).iterator();
        while (mathIter.hasNext()) {
            math = mathIter.next();
            Element apply, apply2, apply3, ci;
            // allow multiple 'apply' children.
            @SuppressWarnings("unchecked") Iterator<Element> applyIter = math.getChildren(MathMLTags.APPLY, mathns).iterator();
            while (applyIter.hasNext()) {
                apply = applyIter.next();
                @SuppressWarnings("unchecked") ArrayList<Element> list = new ArrayList<Element>(apply.getChildren());
                if (list.size() < 3)
                    continue;
                if (!(list.get(0)).getName().equals(MathMLTags.EQUAL))
                    continue;
                apply2 = list.get(1);
                if (!apply2.getName().equals(MathMLTags.APPLY))
                    continue;
                @SuppressWarnings("unchecked") ArrayList<Element> list2 = new ArrayList<Element>(apply2.getChildren());
                if (list2.size() < 3)
                    continue;
                if (!(list2.get(0)).getName().equals(MathMLTags.DIFFERENTIAL))
                    continue;
                // skip the time variable
                ci = list2.get(2);
                varName = ci.getTextTrim();
                // can be a constant
                apply3 = list.get(2);
                mangledName = nm.getMangledName(compName, varName);
                Element trimmedMath = new Element(CELLMLTags.MATH, mathns).addContent(apply3.detach());
                fixMathMLBug(trimmedMath);
                Expression rateExp = null;
                try {
                    rateExp = (new ExpressionMathMLParser(null)).fromMathML(trimmedMath);
                    rateExp = processMathExp(comp, rateExp);
                    rateExp = rateExp.flatten();
                    nl.mangleString(rateExp.infix());
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new RuntimeException(e.getMessage());
                }
                Expression initExp = new Expression(getInitial(comp, varName));
                Domain domain = null;
                OdeEquation ode = new OdeEquation(new VolVariable(mangledName, domain), initExp, rateExp);
                csd.addEquation(ode);
            }
        }
    }
    mathDescription.addSubDomain(csd);
}