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

Example 16 with VariableType

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

the class SimulationSymbolTable method createAnnotatedFunctionsList.

public Vector<AnnotatedFunction> createAnnotatedFunctionsList(MathDescription mathDescription) throws InconsistentDomainException {
    // Get the list of (volVariables) in the simulation. Needed to determine 'type' of  functions
    boolean bSpatial = getSimulation().isSpatial();
    String[] variableNames = null;
    VariableType[] variableTypes = null;
    if (bSpatial) {
        Variable[] allVariables = getVariables();
        Vector<Variable> varVector = new Vector<Variable>();
        for (int i = 0; i < allVariables.length; i++) {
            if ((allVariables[i] instanceof VolVariable) || (allVariables[i] instanceof VolumeRegionVariable) || (allVariables[i] instanceof MemVariable) || (allVariables[i] instanceof MembraneRegionVariable) || (allVariables[i] instanceof FilamentVariable) || (allVariables[i] instanceof FilamentRegionVariable) || (allVariables[i] instanceof PointVariable) || (allVariables[i] instanceof ParticleVariable) || (allVariables[i] instanceof InsideVariable) || (allVariables[i] instanceof OutsideVariable)) {
                varVector.addElement(allVariables[i]);
            } else if (allVariables[i] instanceof Constant || (allVariables[i] instanceof Function)) {
            } else {
                System.err.println("SimulationSymbolTable.createAnnotatedFunctionsList() found unexpected variable type " + allVariables[i].getClass().getSimpleName() + " in spatial simulation");
            }
        }
        variableNames = new String[varVector.size()];
        for (int i = 0; i < variableNames.length; i++) {
            variableNames[i] = varVector.get(i).getName();
        }
        // Lookup table for variableType for each variable in 'variables' array.
        variableTypes = new VariableType[variableNames.length];
        for (int i = 0; i < variableNames.length; i++) {
            variableTypes[i] = VariableType.getVariableType(varVector.get(i));
        }
    }
    // 
    // Bind and substitute functions to simulation before storing them in the '.functions' file
    // 
    Function[] functions = getFunctions();
    Vector<AnnotatedFunction> annotatedFunctionVector = new Vector<AnnotatedFunction>();
    for (int i = 0; i < functions.length; i++) {
        if (isFunctionSaved(functions[i])) {
            String errString = "";
            VariableType funcType = null;
            try {
                Expression substitutedExp = substituteFunctions(functions[i].getExpression());
                substitutedExp.bindExpression(this);
                functions[i].setExpression(substitutedExp.flatten());
            } catch (MathException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                errString = errString + ", " + e.getMessage();
            // throw new RuntimeException(e.getMessage());
            }
            // 
            // get function's data type from the types of it's identifiers
            // 
            funcType = bSpatial ? getFunctionVariableType(functions[i], mathDescription, variableNames, variableTypes, bSpatial) : VariableType.NONSPATIAL;
            AnnotatedFunction annotatedFunc = new AnnotatedFunction(functions[i].getName(), functions[i].getExpression(), functions[i].getDomain(), errString, funcType, FunctionCategory.PREDEFINED);
            annotatedFunctionVector.addElement(annotatedFunc);
        }
    }
    return annotatedFunctionVector;
}

Example 17 with VariableType

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

the class SimulationData method getSimDataBlock.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.DataBlock
 * @param user cbit.vcell.server.User
 * @param simID java.lang.String
 */
public synchronized SimDataBlock getSimDataBlock(OutputContext outputContext, String varName, double time) throws DataAccessException, IOException {
    refreshLogFile();
    try {
        getFunctionDataIdentifiers(outputContext);
    } catch (Exception ex) {
        ex.printStackTrace(System.out);
    }
    try {
        if (isPostProcessing(outputContext, varName)) {
            PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(), vcDataId.getID(), varName, time, lastDataProcessingOutputInfoTime);
            DataProcessingOutputDataValuesOP dataProcessingOutputDataValuesOP = new DataProcessingOutputDataValuesOP(vcDataId, varName, TimePointHelper.createSingleTimeTimePointHelper(extractClosestPostProcessTime(time)), DataIndexHelper.createAllDataIndexesDataIndexHelper(), outputContext, null);
            DataProcessingOutputDataValues dataProcessingOutputDataValues = (DataProcessingOutputDataValues) DataSetControllerImpl.getDataProcessingOutput(dataProcessingOutputDataValuesOP, getDataProcessingOutputSourceFileHDF5());
            return new SimDataBlock(pdeDataInfo, dataProcessingOutputDataValues.getDataValues()[0], /*1 time only*/
            VariableType.POSTPROCESSING);
        }
    } catch (Exception e) {
        // ignore
        e.printStackTrace();
    }
    File pdeFile = getPDEDataFile(time);
    if (pdeFile == null) {
        return null;
    }
    DataSet dataSet = getPDEDataSet(pdeFile, time);
    File zipFile = null;
    try {
        zipFile = getPDEDataZipFile(time);
    } catch (DataAccessException ex) {
        zipFile = null;
    }
    long lastModified = getLastModified(pdeFile, zipFile);
    DataSetIdentifier dsi = getDataSetIdentifier(varName);
    if (dsi == null) {
        throw new DataAccessException("data not found for variable " + varName);
    }
    final String varNameInDataSet = dsi.getQualifiedName();
    double[] data = dataSet.getData(varNameInDataSet, zipFile, time, amplistorHelper.solverDataType);
    int varTypeInt = dataSet.getVariableTypeInteger(varNameInDataSet);
    VariableType variableType = null;
    try {
        variableType = VariableType.getVariableTypeFromInteger(varTypeInt);
    } catch (IllegalArgumentException e) {
        e.printStackTrace(System.out);
        System.out.println("invalid varTypeInt = " + varTypeInt + " for variable " + varName + " at time " + time);
        try {
            variableType = SimulationData.getVariableTypeFromLength(getMesh(), data.length);
        } catch (MathException ex) {
            ex.printStackTrace(System.out);
            throw new DataAccessException(ex.getMessage());
        }
    }
    PDEDataInfo pdeDataInfo = new PDEDataInfo(vcDataId.getOwner(), vcDataId.getID(), varName, time, lastModified);
    if (data != null) {
        return new SimDataBlock(pdeDataInfo, data, variableType);
    } else {
        return null;
    }
}

Example 18 with VariableType

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

the class SimulationData method getVarAndFunctionDataIdentifiers.

/**
 * This method was created in VisualAge.
 * @return java.lang.String[]
 */
public synchronized DataIdentifier[] getVarAndFunctionDataIdentifiers(OutputContext outputContext) throws IOException, DataAccessException {
    // Is this zip format?
    boolean bIsChombo = false;
    try {
        bIsChombo = isChombo();
    } catch (FileNotFoundException e) {
        e.printStackTrace(System.out);
    }
    File zipFile1 = getZipFile(bIsChombo, null);
    File zipFile2 = getZipFile(bIsChombo, 0);
    bZipFormat1 = false;
    bZipFormat2 = false;
    if (zipFile1.exists()) {
        bZipFormat1 = true;
    } else if (zipFile2.exists()) {
        bZipFormat2 = true;
    }
    refreshLogFile();
    if (!isComsol()) {
        try {
            refreshMeshFile();
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new DataAccessException(e.getMessage());
        }
    }
    if (!isRulesData && !getIsODEData() && !isComsol() && dataFilenames != null) {
        // read variables only when I have never read the file since variables don't change
        if (dataSetIdentifierList.size() == 0) {
            File file = getPDEDataFile(0.0);
            DataSet dataSet = getPDEDataSet(file, 0.0);
            String[] varNames = dataSet.getDataNames();
            int[] varTypeInts = dataSet.getVariableTypeIntegers();
            if (varNames == null) {
                return null;
            }
            dataSetIdentifierList.clear();
            for (int i = 0; i < varNames.length; i++) {
                VariableType varType = null;
                try {
                    varType = VariableType.getVariableTypeFromInteger(varTypeInts[i]);
                } catch (IllegalArgumentException e) {
                    if (LG.isEnabledFor(Level.WARN)) {
                        LG.warn("Exception typing " + varNames[i] + " has unsupported type " + varTypeInts[i] + ": " + e.getMessage());
                    }
                    varType = SimulationData.getVariableTypeFromLength(mesh, dataSet.getDataLength(varNames[i]));
                }
                Domain domain = Variable.getDomainFromCombinedIdentifier(varNames[i]);
                String varName = Variable.getNameFromCombinedIdentifier(varNames[i]);
                dataSetIdentifierList.addElement(new DataSetIdentifier(varName, varType, domain));
            }
            refreshDataProcessingOutputInfo(outputContext);
            if (dataProcessingOutputInfo != null) {
                for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                    if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(DataProcessingOutputInfo.PostProcessDataType.image)) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null));
                    }
                }
            }
        }
        // always read functions file since functions might change
        getFunctionDataIdentifiers(outputContext);
    }
    if ((isRulesData || getIsODEData()) && dataSetIdentifierList.size() == 0) {
        ODEDataBlock odeDataBlock = getODEDataBlock();
        if (odeDataBlock == null) {
            throw new DataAccessException("Results are not availabe yet. Please try again later.");
        }
        ODESimData odeSimData = odeDataBlock.getODESimData();
        int colCount = odeSimData.getColumnDescriptionsCount();
        // assume index=0 is time "t"
        int DATA_OFFSET = 1;
        dataSetIdentifierList.clear();
        for (int i = 0; i < (colCount - DATA_OFFSET); i++) {
            String varName = odeSimData.getColumnDescriptions(i + DATA_OFFSET).getDisplayName();
            // TODO domain
            Domain domain = null;
            dataSetIdentifierList.addElement(new DataSetIdentifier(varName, VariableType.NONSPATIAL, domain));
        }
    }
    if (isComsol() && dataSetIdentifierList.size() == 0) {
        ComsolSimFiles comsolSimFiles = getComsolSimFiles();
        if (comsolSimFiles.simTaskXMLFile != null) {
            try {
                String xmlString = FileUtils.readFileToString(comsolSimFiles.simTaskXMLFile);
                SimulationTask simTask = XmlHelper.XMLToSimTask(xmlString);
                Enumeration<Variable> variablesEnum = simTask.getSimulation().getMathDescription().getVariables();
                while (variablesEnum.hasMoreElements()) {
                    Variable var = variablesEnum.nextElement();
                    if (var instanceof VolVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.VOLUME, var.getDomain()));
                    } else if (var instanceof MemVariable) {
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), VariableType.MEMBRANE, var.getDomain()));
                    } else if (var instanceof Function) {
                        VariableType varType = VariableType.UNKNOWN;
                        if (var.getDomain() != null && var.getDomain().getName() != null) {
                            SubDomain subDomain = simTask.getSimulation().getMathDescription().getSubDomain(var.getDomain().getName());
                            if (subDomain instanceof CompartmentSubDomain) {
                                varType = VariableType.VOLUME;
                            } else if (subDomain instanceof MembraneSubDomain) {
                                varType = VariableType.MEMBRANE;
                            } else if (subDomain instanceof FilamentSubDomain) {
                                throw new RuntimeException("filament subdomains not supported");
                            } else if (subDomain instanceof PointSubDomain) {
                                varType = VariableType.POINT_VARIABLE;
                            }
                        }
                        dataSetIdentifierList.addElement(new DataSetIdentifier(var.getName(), varType, var.getDomain()));
                    } else if (var instanceof Constant) {
                        System.out.println("ignoring Constant " + var.getName());
                    } else if (var instanceof InsideVariable) {
                        System.out.println("ignoring InsideVariable " + var.getName());
                    } else if (var instanceof OutsideVariable) {
                        System.out.println("ignoring OutsideVariable " + var.getName());
                    } else {
                        throw new RuntimeException("unexpected variable " + var.getName() + " of type " + var.getClass().getName());
                    }
                }
            } catch (XmlParseException | ExpressionException e) {
                e.printStackTrace();
                throw new RuntimeException("failed to read sim task file, msg: " + e.getMessage(), e);
            }
        }
    }
    DataIdentifier[] dis = new DataIdentifier[dataSetIdentifierList.size()];
    for (int i = 0; i < dataSetIdentifierList.size(); i++) {
        DataSetIdentifier dsi = (DataSetIdentifier) dataSetIdentifierList.elementAt(i);
        String displayName = dsi.getName();
        if (dsi.isFunction()) {
            AnnotatedFunction f = null;
            for (int j = 0; j < annotatedFunctionList.size(); j++) {
                AnnotatedFunction function = (AnnotatedFunction) annotatedFunctionList.elementAt(j);
                if (function.getName().equals(dsi.getName())) {
                    f = function;
                    break;
                }
            }
            if (f != null) {
                displayName = f.getDisplayName();
            }
        }
        dis[i] = new DataIdentifier(dsi.getName(), dsi.getVariableType(), dsi.getDomain(), dsi.isFunction(), displayName);
    }
    return dis;
}

Example 19 with VariableType

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

the class OutputFunctionContext method computeFunctionTypeWRTExpression.

// check if the new expression is valid for outputFunction of functionType
public VariableType computeFunctionTypeWRTExpression(AnnotatedFunction outputFunction, Expression exp) throws ExpressionException, InconsistentDomainException {
    MathDescription mathDescription = getSimulationOwner().getMathDescription();
    boolean bSpatial = getSimulationOwner().getGeometry().getDimension() > 0;
    if (!bSpatial) {
        return VariableType.NONSPATIAL;
    }
    Expression newexp = new Expression(exp);
    // making sure that output function is not direct function of constant.
    newexp.bindExpression(this);
    // here use math description as symbol table because we allow
    // new expression itself to be function of constant.
    newexp = MathUtilities.substituteFunctions(newexp, this).flatten();
    String[] symbols = newexp.getSymbols();
    VariableType functionType = outputFunction.getFunctionType();
    String funcName = outputFunction.getName();
    Domain funcDomain = outputFunction.getDomain();
    VariableType[] varTypes = null;
    if (symbols != null && symbols.length > 0) {
        // making sure that new expression is defined in the same domain
        varTypes = new VariableType[symbols.length];
        for (int i = 0; i < symbols.length; i++) {
            if (ReservedMathSymbolEntries.getReservedVariableEntry(symbols[i]) != null) {
                varTypes[i] = functionType;
            } else {
                Variable var = mathDescription.getVariable(symbols[i]);
                if (var == null) {
                    var = mathDescription.getPostProcessingBlock().getDataGenerator(symbols[i]);
                }
                varTypes[i] = VariableType.getVariableType(var);
                if (funcDomain != null) {
                    if (var.getDomain() == null) {
                        // OK
                        continue;
                    }
                    GeometryClass funcGeoClass = simulationOwner.getGeometry().getGeometryClass(funcDomain.getName());
                    GeometryClass varGeoClass = simulationOwner.getGeometry().getGeometryClass(var.getDomain().getName());
                    if (varGeoClass instanceof SubVolume && funcGeoClass instanceof SurfaceClass) {
                        // seems ok if membrane refereces volume
                        if (!((SurfaceClass) funcGeoClass).isAdjacentTo((SubVolume) varGeoClass)) {
                            // but has to be adjacent
                            String errMsg = "'" + funcName + "' defined on Membrane '" + funcDomain.getName() + "' directly or indirectly references " + " variable '" + symbols[i] + "' defined on Volume '" + var.getDomain().getName() + " which is not adjacent to Membrane '" + funcDomain.getName() + "'.";
                            throw new ExpressionException(errMsg);
                        }
                    } else if (!var.getDomain().compareEqual(funcDomain)) {
                        String errMsg = "'" + funcName + "' defined on '" + funcDomain.getName() + "' directly or indirectly references " + " variable '" + symbols[i] + "' defined on '" + var.getDomain().getName() + ".";
                        throw new ExpressionException(errMsg);
                    }
                }
            }
        }
    }
    // if there are no variables (like built in function, vcRegionArea), check with flattened expression to find out the variable type of the new expression
    VariableDomain functionVariableDomain = functionType.getVariableDomain();
    Function flattenedFunction = new Function(funcName, newexp, funcDomain);
    flattenedFunction.bind(this);
    VariableType newVarType = SimulationSymbolTable.getFunctionVariableType(flattenedFunction, getSimulationOwner().getMathDescription(), symbols, varTypes, bSpatial);
    if (!newVarType.getVariableDomain().equals(functionVariableDomain)) {
        String errMsg = "The expression for '" + funcName + "' includes at least one " + newVarType.getVariableDomain().getName() + " variable. Please make sure that only " + functionVariableDomain.getName() + " variables are " + "referenced in " + functionVariableDomain.getName() + " output functions.";
        throw new ExpressionException(errMsg);
    }
    return newVarType;
}

Example 20 with VariableType

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

the class RunRefSimulationFastOp method saveROIsAsExternalData.

private void saveROIsAsExternalData(ROI[] rois, LocalWorkspace localWorkspace, ExternalDataIdentifier newROIExtDataID) throws ObjectNotFoundException, ImageException, IOException {
    ISize isize = rois[0].getISize();
    Origin origin = rois[0].getRoiImages()[0].getOrigin();
    Extent extent = rois[0].getRoiImages()[0].getExtent();
    VCImage vcImage = new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ());
    RegionImage regionImage = new RegionImage(vcImage, 0, null, null, RegionImage.NO_SMOOTHING);
    CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, regionImage);
    int NumTimePoints = 1;
    int NumChannels = rois.length;
    // dimensions: time points, channels, whole image ordered by z slices.
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    int index = 0;
    for (ROI roi : rois) {
        pixData[0][index++] = createDoubleArray(roi.getBinaryPixelsXYZ(1));
    }
    // Origin origin = new Origin(0,0,0);
    FieldDataFileOperationSpec fdos = new FieldDataFileOperationSpec();
    fdos.opType = FieldDataFileOperationSpec.FDOS_ADD;
    fdos.cartesianMesh = cartesianMesh;
    fdos.doubleSpecData = pixData;
    fdos.specEDI = newROIExtDataID;
    ArrayList<String> varNames = new ArrayList<String>();
    ArrayList<VariableType> varTypes = new ArrayList<VariableType>();
    for (ROI roi : rois) {
        varNames.add(ROI_MASK_NAME_PREFIX + roi.getROIName());
        varTypes.add(VariableType.VOLUME);
    }
    fdos.varNames = varNames.toArray(new String[0]);
    fdos.owner = LocalWorkspace.getDefaultOwner();
    fdos.times = new double[] { 0.0 };
    fdos.variableTypes = varTypes.toArray(new VariableType[0]);
    fdos.origin = origin;
    fdos.extent = extent;
    fdos.isize = isize;
    localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
}