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

Example 6 with FunctionColumnDescription

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

the class SundialsSolver method getODESolverResultSet.

/**
 * This method was created in VisualAge.
 * @return double[]
 * @param vectorIndex int
 */
public ODESolverResultSet getODESolverResultSet() {
    // 
    // read .ida file
    // 
    ODESolverResultSet odeSolverResultSet = getStateVariableResultSet();
    if (odeSolverResultSet == null) {
        return null;
    }
    // 
    // add appropriate Function columns to result set
    // 
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    Function[] functions = simSymbolTable.getFunctions();
    for (int i = 0; i < functions.length; i++) {
        if (SimulationSymbolTable.isFunctionSaved(functions[i])) {
            Expression exp1 = new Expression(functions[i].getExpression());
            try {
                exp1 = simSymbolTable.substituteFunctions(exp1);
            } catch (MathException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
            }
            try {
                FunctionColumnDescription cd = new FunctionColumnDescription(exp1.flatten(), functions[i].getName(), null, functions[i].getName(), false);
                odeSolverResultSet.addFunctionColumn(cd);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
            }
        }
    }
    if (getSensitivityParameter() != null) {
        try {
            if (odeSolverResultSet.findColumn(getSensitivityParameter().getName()) == -1) {
                FunctionColumnDescription fcd = new FunctionColumnDescription(new Expression(getSensitivityParameter().getConstantValue()), getSensitivityParameter().getName(), null, getSensitivityParameter().getName(), false);
                odeSolverResultSet.addFunctionColumn(fcd);
            }
            Variable[] variables = simSymbolTable.getVariables();
            StateVariable[] stateVars = createStateVariables();
            for (int i = 0; i < variables.length; i++) {
                if (variables[i] instanceof Function && SimulationSymbolTable.isFunctionSaved((Function) variables[i])) {
                    Function depSensFunction = (Function) variables[i];
                    Expression depSensFnExpr = new Expression(depSensFunction.getExpression());
                    depSensFnExpr = simSymbolTable.substituteFunctions(depSensFnExpr);
                    depSensFnExpr = getFunctionSensitivity(depSensFnExpr, getSensitivityParameter(), stateVars);
                    // depSensFnExpr = depSensFnExpr.flatten(); 	// already bound and flattened in getFunctionSensitivity, no need here.....
                    String depSensFnName = new String("sens_" + depSensFunction.getName() + "_wrt_" + getSensitivityParameter().getName());
                    if (depSensFunction != null) {
                        FunctionColumnDescription cd = new FunctionColumnDescription(depSensFnExpr.flatten(), depSensFnName, getSensitivityParameter().getName(), depSensFnName, false);
                        odeSolverResultSet.addFunctionColumn(cd);
                    }
                }
            }
        } catch (MathException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Error adding function to resultSet: " + e.getMessage());
        }
    }
    return odeSolverResultSet;
}

Example 7 with FunctionColumnDescription

use of cbit.vcell.math.FunctionColumnDescription 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 8 with FunctionColumnDescription

use of cbit.vcell.math.FunctionColumnDescription 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 9 with FunctionColumnDescription

use of cbit.vcell.math.FunctionColumnDescription 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 10 with FunctionColumnDescription

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

the class FRAPEstimationPanel_NotUsed method displayFit.

private void displayFit(FrapDataAnalysisResults.DiffusionOnlyAnalysisRestults diffAnalysisResults, double[] frapDataTimeStamps, int startIndexForRecovery) {
    if (diffAnalysisResults == null) {
        FRAPParameterEstimateEnum.DIFFUSION_RATE.value = null;
        FRAPParameterEstimateEnum.MOBILE_FRACTION.value = null;
        FRAPParameterEstimateEnum.IMMOBILE_FRATION.value = null;
        FRAPParameterEstimateEnum.START_TIME_RECOVERY.value = null;
        FRAPParameterEstimateEnum.BLEACH_RATE_MONITOR.value = null;
        multisourcePlotPane.setDataSources(null);
    } else {
        FRAPParameterEstimateEnum.DIFFUSION_RATE.value = (diffAnalysisResults.getRecoveryDiffusionRate() == null ? null : diffAnalysisResults.getRecoveryDiffusionRate());
        FRAPParameterEstimateEnum.MOBILE_FRACTION.value = (diffAnalysisResults.getMobilefraction() == null ? null : diffAnalysisResults.getMobilefraction());
        FRAPParameterEstimateEnum.IMMOBILE_FRATION.value = (FRAPParameterEstimateEnum.MOBILE_FRACTION.value == null ? null : 1.0 - FRAPParameterEstimateEnum.MOBILE_FRACTION.value);
        FRAPParameterEstimateEnum.BLEACH_RATE_MONITOR.value = (diffAnalysisResults.getBleachWhileMonitoringTau() == null ? null : diffAnalysisResults.getBleachWhileMonitoringTau());
        // int startIndexForRecovery = FRAPDataAnalysis.getRecoveryIndex(initFRAPData);
        // 
        // Experiment - Cell ROI Average
        // 
        double[] temp_background = initFRAPData.getAvgBackGroundIntensity();
        double[] preBleachAvgXYZ = FrapDataUtils.calculatePreBleachAverageXYZ(initFRAPData, startIndexForRecovery);
        double[] cellRegionData = FRAPDataAnalysis.getAverageROIIntensity(initFRAPData, initFRAPData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()), preBleachAvgXYZ, temp_background);
        ReferenceData expCellAvgData = new SimpleReferenceData(new String[] { "t", "CellROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] { frapDataTimeStamps, cellRegionData });
        DataSource expCellAvgDataSource = new DataSource.DataSourceReferenceData("expCellAvg", expCellAvgData);
        // 
        // Analytic - Cell ROI Average with Bleach while monitor
        // 
        ODESolverResultSet bleachWhileMonitorOdeSolverResultSet = new ODESolverResultSet();
        bleachWhileMonitorOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
        try {
            bleachWhileMonitorOdeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(diffAnalysisResults.getFitBleachWhileMonitorExpression(), "CellROI_BleachWhileMonitor", null, "bleachWhileMonitorFit", true));
        } catch (ExpressionException e) {
            e.printStackTrace();
        }
        for (int i = startIndexForRecovery; i < frapDataTimeStamps.length; i++) {
            bleachWhileMonitorOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
        }
        // 
        // extend if necessary to plot theoretical curve to 4*tau
        // 
        {
            double T = frapDataTimeStamps[frapDataTimeStamps.length - 1];
            double deltaT = frapDataTimeStamps[frapDataTimeStamps.length - 1] - frapDataTimeStamps[frapDataTimeStamps.length - 2];
            while (T + deltaT < 6 * diffAnalysisResults.getRecoveryTau()) {
                bleachWhileMonitorOdeSolverResultSet.addRow(new double[] { T });
                T += deltaT;
            }
        }
        DataSource bleachWhileMonitorDataSource = new DataSource.DataSourceRowColumnResultSet("bleachwm", bleachWhileMonitorOdeSolverResultSet);
        // Recovery curve
        double[] bleachRegionData = FRAPDataAnalysis.getAverageROIIntensity(initFRAPData, initFRAPData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()), preBleachAvgXYZ, temp_background);
        ;
        ReferenceData expRefData = new SimpleReferenceData(new String[] { "t", "BleachROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] { frapDataTimeStamps, bleachRegionData });
        DataSource expDataSource = new DataSource.DataSourceReferenceData("experiment", expRefData);
        ODESolverResultSet fitOdeSolverResultSet = new ODESolverResultSet();
        fitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
        try {
            fitOdeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(diffAnalysisResults.getDiffFitExpression(), // "('"+FrapDataAnalysisResults.BLEACH_TYPE_NAMES[bleachEstimationComboBox.getSelectedIndex()]+"')",
            "BleachROI_Recovery", null, "recoveryFit", true));
        } catch (ExpressionException e) {
            e.printStackTrace();
        }
        for (int i = startIndexForRecovery; i < frapDataTimeStamps.length; i++) {
            fitOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
        }
        // 
        // extend if necessary to plot theoretical curve to 4*tau
        // 
        double T = frapDataTimeStamps[frapDataTimeStamps.length - 1];
        double deltaT = frapDataTimeStamps[frapDataTimeStamps.length - 1] - frapDataTimeStamps[frapDataTimeStamps.length - 2];
        while (T + deltaT < 6 * diffAnalysisResults.getRecoveryTau()) {
            fitOdeSolverResultSet.addRow(new double[] { T });
            T += deltaT;
        }
        DataSource fitDataSource = new DataSource.DataSourceRowColumnResultSet("fit", fitOdeSolverResultSet);
        multisourcePlotPane.setDataSources(new DataSource[] { expDataSource, fitDataSource, expCellAvgDataSource, bleachWhileMonitorDataSource });
        multisourcePlotPane.selectAll();
    }
    table.repaint();
}