Examples with ExpressionException cbit.vcell.parser.ExpressionException used on opensource projects

Example 71 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class ODESimData method readIn.

/**
 * JMW : This really should be synchronized...
 */
public void readIn(DataInputStream input) throws IOException {
    formatID = input.readUTF();
    if (formatID.equals(SIMPLE_ODE_DATA_FORMAT_ID)) {
        this.mathName = input.readUTF();
        // read data from old format file
        double saveInterval = input.readDouble();
        int savedNumber = input.readInt();
        int variableNumber = input.readInt();
        String[] variableNames = new String[variableNumber];
        double[][] dataValues = new double[savedNumber][variableNumber];
        for (int i = 0; i < variableNumber; i++) {
            int flag = input.readInt();
            variableNames[i] = input.readUTF();
            for (int j = 0; j < savedNumber; j++) {
                dataValues[j][i] = input.readDouble();
            }
        }
        // now put data in new data structure
        int rowCount = savedNumber;
        int columnCount = variableNumber + 1;
        addDataColumn(new ODESolverResultSetColumnDescription("t", "t"));
        for (int c = 1; c < columnCount; c++) {
            addDataColumn(new ODESolverResultSetColumnDescription(variableNames[c - 1], variableNames[c - 1]));
        }
        double[] values = new double[columnCount];
        for (int c = 0; c < columnCount; c++) values[c] = 0.0;
        for (int r = 0; r < rowCount; r++) {
            values[0] = r * saveInterval / 1000.0;
            addRow(values);
        }
        for (int c = 1; c < columnCount; c++) {
            for (int r = 0; r < rowCount; r++) {
                setValue(r, c, dataValues[r][c - 1]);
            }
        }
    } else if (formatID.equals(GENERIC_ODE_DATA_FORMAT_ID)) {
        this.mathName = input.readUTF();
        int rowCount = input.readInt();
        int columnCount = input.readInt();
        for (int c = 0; c < columnCount; c++) {
            String columnName = input.readUTF();
            String columnDisplayName = input.readUTF();
            addDataColumn(new ODESolverResultSetColumnDescription(columnName, columnDisplayName));
        }
        double[] values = new double[columnCount];
        for (int r = 0; r < rowCount; r++) {
            for (int c = 0; c < columnCount; c++) {
                values[c] = input.readDouble();
            }
            addRow(values);
        }
    } else if (formatID.equals(COMPACT_ODE_DATA_FORMAT_ID)) {
        this.mathName = input.readUTF();
        int rowCount = input.readInt();
        int columnCount = input.readInt();
        for (int c = 0; c < columnCount; c++) {
            String columnName = input.readUTF();
            String columnDisplayName = input.readUTF();
            String columnParameterName = input.readUTF();
            if (columnParameterName.equals("null")) {
                columnParameterName = null;
            }
            addDataColumn(new ODESolverResultSetColumnDescription(columnName, columnParameterName, columnDisplayName));
        }
        double[] values = new double[columnCount];
        for (int r = 0; r < rowCount; r++) {
            for (int c = 0; c < columnCount; c++) {
                values[c] = input.readDouble();
            }
            addRow(values);
        }
        try {
            int functionCount = input.readInt();
            for (int c = 0; c < functionCount; c++) {
                String columnName = input.readUTF();
                String columnDisplayName = input.readUTF();
                String columnParameterName = input.readUTF();
                if (columnParameterName.equals("null")) {
                    columnParameterName = null;
                }
                String expressionString = input.readUTF();
                try {
                    Expression expression = new Expression(expressionString);
                    addFunctionColumn(new FunctionColumnDescription(expression, columnName, columnParameterName, columnDisplayName, false));
                } catch (ExpressionBindingException e) {
                    e.printStackTrace(System.out);
                    System.out.println("ODESimData.readIn(): unable to bind expression '" + expressionString + "'");
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    System.out.println("ODESimData.readIn(): unable to parse expression '" + expressionString + "'");
                }
            }
        } catch (EOFException e) {
        }
    } else {
        throw new IOException("DataInputStream is wrong format '" + formatID + "'");
    }
}

Example 72 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class ODESimData method readIDADataFile.

public static ODESimData readIDADataFile(VCDataIdentifier vcdId, File dataFile, int keepMost, File functionsFile) throws DataAccessException {
    // read ida file
    System.out.println("reading ida file : " + dataFile);
    ODESimData odeSimData = new ODESimData();
    odeSimData.formatID = IDA_DATA_FORMAT_ID;
    odeSimData.mathName = vcdId.getID();
    BufferedReader bufferedReader = null;
    try {
        bufferedReader = new BufferedReader(new InputStreamReader(new FileInputStream(dataFile)));
        // Read header
        String line = bufferedReader.readLine();
        if (line == null) {
            // throw exception
            return null;
        }
        StringTokenizer st = new StringTokenizer(line, ":");
        while (st.hasMoreTokens()) {
            odeSimData.addDataColumn(new ODESolverResultSetColumnDescription(st.nextToken()));
        }
        // Read data
        while ((line = bufferedReader.readLine()) != null) {
            st = new StringTokenizer(line);
            double[] values = new double[odeSimData.getDataColumnCount()];
            int count = 0;
            while (st.hasMoreTokens()) {
                values[count++] = Double.valueOf(st.nextToken()).doubleValue();
            }
            if (count == odeSimData.getDataColumnCount()) {
                odeSimData.addRow(values);
            } else {
                break;
            }
        }
    // 
    } catch (Exception e) {
        e.printStackTrace(System.out);
        return null;
    } finally {
        try {
            if (bufferedReader != null) {
                bufferedReader.close();
            }
        } catch (Exception ex) {
            ex.printStackTrace(System.out);
        }
    }
    if (!odeSimData.getColumnDescriptions(0).getName().equals(SimDataConstants.HISTOGRAM_INDEX_NAME)) {
        Vector<AnnotatedFunction> funcList;
        try {
            funcList = FunctionFileGenerator.readFunctionsFile(functionsFile, vcdId.getID());
            for (AnnotatedFunction func : funcList) {
                try {
                    Expression expression = new Expression(func.getExpression());
                    odeSimData.addFunctionColumn(new FunctionColumnDescription(expression, func.getName(), null, func.getName(), false));
                } catch (ExpressionException e) {
                    throw new RuntimeException("Could not add function " + func.getName() + " to annotatedFunctionList");
                }
            }
        } catch (FileNotFoundException e1) {
            e1.printStackTrace(System.out);
            throw new DataAccessException(e1.getMessage());
        } catch (IOException e1) {
            e1.printStackTrace(System.out);
            throw new DataAccessException(e1.getMessage());
        }
    }
    if (keepMost > 0) {
        odeSimData.trimRows(keepMost);
    }
    return odeSimData;
}

Example 73 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class ODESimData method readNFSIMDataFile.

public static ODESimData readNFSIMDataFile(VCDataIdentifier vcdId, File dataFile, File functionsFile) throws DataAccessException, IOException {
    System.out.println("reading NetCDF file : " + dataFile);
    ODESimData odeSimData = new ODESimData();
    odeSimData.formatID = NETCDF_DATA_FORMAT_ID;
    odeSimData.mathName = vcdId.getID();
    String file = dataFile.getPath();
    BufferedReader reader = new BufferedReader(new FileReader(file));
    String firstLine = reader.readLine();
    StringTokenizer st = new StringTokenizer(firstLine);
    // #
    st.nextToken();
    // time
    st.nextToken();
    // first column will be time t.
    odeSimData.addDataColumn(new ODESolverResultSetColumnDescription("t"));
    int count = st.countTokens();
    String varName = new String();
    for (int i = 0; i < count; i++) {
        varName = st.nextToken();
        odeSimData.addDataColumn(new ODESolverResultSetColumnDescription(varName));
    }
    // Read data
    // String         ls = System.getProperty("line.separator");
    // StringBuilder  stringBuilder = new StringBuilder();
    String line = null;
    while ((line = reader.readLine()) != null) {
        double[] values = new double[odeSimData.getDataColumnCount()];
        st = new StringTokenizer(line);
        count = st.countTokens();
        String sData = new String();
        for (int i = 0; i < count; i++) {
            sData = st.nextToken();
            double dData = Double.parseDouble(sData);
            values[i] = dData;
        }
        odeSimData.addRow(values);
    }
    if (!odeSimData.getColumnDescriptions(0).getName().equals(SimDataConstants.HISTOGRAM_INDEX_NAME)) {
        Vector<AnnotatedFunction> funcList;
        try {
            funcList = FunctionFileGenerator.readFunctionsFile(functionsFile, vcdId.getID());
            for (AnnotatedFunction func : funcList) {
                try {
                    Expression expression = new Expression(func.getExpression());
                    odeSimData.addFunctionColumn(new FunctionColumnDescription(expression, func.getName(), null, func.getName(), false));
                } catch (ExpressionException e) {
                    throw new RuntimeException("Could not add function " + func.getName() + " to annotatedFunctionList");
                }
            }
        } catch (FileNotFoundException e1) {
            e1.printStackTrace(System.out);
            throw new DataAccessException(e1.getMessage());
        } catch (IOException e1) {
            e1.printStackTrace(System.out);
            throw new DataAccessException(e1.getMessage());
        }
    }
    return odeSimData;
}

Example 74 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class RungeKuttaFehlbergSolver method step.

/**
 * Integrate over time step using the forward Euler method (1st order explicit)
 * results must be stored in NumVectors-1 = vector(4);
 *  t is the current time
 *  h is the time step
 */
protected void step(double t, double h) throws SolverException {
    try {
        double[] oldValues = getValueVector(0);
        double[] newValues = getValueVector(1);
        // 
        // update time
        oldValues[getTimeIndex()] = t;
        // 
        for (int i = 0; i < 6; i++) {
            newValues[getTimeIndex()] = t + a[i] * h;
            for (int j = 0; j < getStateVariableCount(); j++) {
                int J = getVariableIndex(j);
                newValues[J] = oldValues[J];
                for (int m = 0; m < i; m++) {
                    newValues[J] += b[i][m] * k[m][J];
                }
            }
            for (int j = 0; j < getStateVariableCount(); j++) {
                k[i][getVariableIndex(j)] = h * evaluate(newValues, j);
            }
        }
        for (int i = 0; i < getStateVariableCount(); i++) {
            int I = getVariableIndex(i);
            newValues[I] = oldValues[I];
            for (int j = 0; j < 6; j++) {
                newValues[I] += c[j] * k[j][I];
            }
        }
    } catch (ExpressionException expressionException) {
        throw new SolverException(expressionException.getMessage());
    }
}

Example 75 with ExpressionException

use of cbit.vcell.parser.ExpressionException in project vcell by virtualcell.

the class XmlBase method unMangleExpression.

public static Expression unMangleExpression(String expStr) {
    Expression tempExp = null;
    // 
    try {
        tempExp = new Expression(unMangle(expStr));
        tempExp = MathFunctionDefinitions.fixFunctionSyntax(tempExp);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException(e.getMessage());
    }
    return tempExp;
}