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

Example 11 with FunctionColumnDescription

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

the class EstParams_ReactionOffRatePanel method displayResults.

private void displayResults(FRAPData frapData, int startIndexRecovery) throws ExpressionException, DivideByZeroException {
    Parameter[] currentParams = offRateParamPanel.getCurrentParameters();
    if (frapData == null || currentParams == null) {
        multisourcePlotPane.setDataSources(null);
    } else {
        double[] frapDataTimeStamps = frapData.getImageDataset().getImageTimeStamps();
        // Experiment - Cell ROI Average
        double[] temp_background = frapData.getAvgBackGroundIntensity();
        double[] preBleachAvgXYZ = FrapDataUtils.calculatePreBleachAverageXYZ(frapData, startIndexRecovery);
        /*double[] cellRegionData = FRAPDataAnalysis.getAverageROIIntensity(frapData, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()),preBleachAvgXYZ,temp_background);
			ReferenceData expCellAvgData = new SimpleReferenceData(new String[] { ReservedSymbol.TIME.getName(), "CellROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] {frapDataTimeStamps, cellRegionData });
			DataSource expCellAvgDataSource = new DataSource.DataSourceReferenceData("exp", expCellAvgData);
			//Analytic - Cell ROI Average with Bleach while monitor
			ODESolverResultSet bleachWhileMonitorOdeSolverResultSet = new ODESolverResultSet();
			bleachWhileMonitorOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(ReservedSymbol.TIME.getName()));
			Expression cellAvgExp = new Expression(FRAPOptFunctions.FUNC_CELL_INTENSITY);
			// substitute parameter values 
			cellAvgExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_I_inicell), new Expression(cellRegionData[startIndexRecovery]));
			cellAvgExp.substituteInPlace(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(currentParams[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getInitialGuess()));
			// time shift
			cellAvgExp.substituteInPlace(new Expression(ReservedSymbol.TIME.getName()), new Expression(ReservedSymbol.TIME.getName()+"-"+frapDataTimeStamps[startIndexRecovery]));
			try {
				bleachWhileMonitorOdeSolverResultSet.addFunctionColumn(
					new FunctionColumnDescription(
						cellAvgExp,
						"CellROIAvg",
						null,"bleachWhileMonitorFit",true));
			} catch (ExpressionException e) {
				e.printStackTrace();
			}
			for (int i = startIndexRecovery; i < frapDataTimeStamps.length; i++) 
			{
				bleachWhileMonitorOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
			}
			DataSource bleachWhileMonitorDataSource = new DataSource.DataSourceOdeSolverResultSet("fit", bleachWhileMonitorOdeSolverResultSet);*/
        // experimental bleach region average intensity curve
        double[] bleachRegionData = FRAPDataAnalysis.getAverageROIIntensity(frapData, frapData.getRoi(FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name()), preBleachAvgXYZ, temp_background);
        ;
        ReferenceData expRefData = new SimpleReferenceData(new String[] { ReservedVariable.TIME.getName(), "BleachROIAvg" }, new double[] { 1.0, 1.0 }, new double[][] { frapDataTimeStamps, bleachRegionData });
        DataSource expBleachDataSource = new DataSource.DataSourceReferenceData("exp", expRefData);
        // Analytic - bleach region average intensity with bleach while monitoring rate
        ODESolverResultSet koffFitOdeSolverResultSet = new ODESolverResultSet();
        koffFitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(ReservedVariable.TIME.getName()));
        Expression bleachedAvgExp = frapWorkspace.getWorkingFrapStudy().getFrapOptFunc().getRecoveryExpressionWithCurrentParameters(currentParams);
        try {
            koffFitOdeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(bleachedAvgExp, "BleachROIAvg", null, "recoveryFit", true));
        } catch (ExpressionException e) {
            e.printStackTrace();
        }
        double[] truncatedTimes = new double[frapDataTimeStamps.length - startIndexRecovery];
        for (int i = startIndexRecovery; i < frapDataTimeStamps.length; i++) {
            koffFitOdeSolverResultSet.addRow(new double[] { frapDataTimeStamps[i] });
            truncatedTimes[i - startIndexRecovery] = frapDataTimeStamps[i];
        }
        setCurrentEstimationResults(frapWorkspace.getWorkingFrapStudy().getFrapOptFunc().createData(bleachedAvgExp.flatten(), truncatedTimes));
        DataSource koffFitDataSource = new DataSource.DataSourceRowColumnResultSet("fit", koffFitOdeSolverResultSet);
        multisourcePlotPane.setDataSources(new DataSource[] { expBleachDataSource, koffFitDataSource /*, expCellAvgDataSource , bleachWhileMonitorDataSource*/
        });
        multisourcePlotPane.selectAll();
    }
}

Example 12 with FunctionColumnDescription

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

the class CopasiOptimizationSolver method getOdeSolverResultSet.

private static ODESolverResultSet getOdeSolverResultSet(RowColumnResultSet rcResultSet, SimulationSymbolTable simSymbolTable, String[] parameterNames, double[] parameterValues) {
    // 
    // get simulation results - copy from RowColumnResultSet into OdeSolverResultSet
    // 
    ODESolverResultSet odeSolverResultSet = new ODESolverResultSet();
    for (int i = 0; i < rcResultSet.getDataColumnCount(); i++) {
        odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(rcResultSet.getColumnDescriptions(i).getName()));
    }
    for (int i = 0; i < rcResultSet.getRowCount(); i++) {
        odeSolverResultSet.addRow(rcResultSet.getRow(i));
    }
    // 
    // add appropriate Function columns to result set
    // 
    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).flatten();
                // 
                for (int j = 0; parameterNames != null && j < parameterNames.length; j++) {
                    exp1.substituteInPlace(new Expression(parameterNames[j]), new Expression(parameterValues[j]));
                }
            } 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);
            }
        }
    }
    return odeSolverResultSet;
}

Example 13 with FunctionColumnDescription

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

the class GibsonSolver method getStochSolverResultSet.

/**
 * Get data columns and function columns to be ready for plot.
 * Creation date: (8/15/2006 11:36:43 AM)
 * @return cbit.vcell.solver.stoch.StochSolverResultSet
 */
public ODESolverResultSet getStochSolverResultSet() {
    // read .stoch file, this funciton here equals to getODESolverRestultSet()+getStateVariableResultSet()  in ODE.
    ODESolverResultSet stSolverResultSet = new ODESolverResultSet();
    FileInputStream inputStream = null;
    try {
        inputStream = new FileInputStream(getBaseName() + IDA_DATA_EXTENSION);
        InputStreamReader inputStreamReader = new InputStreamReader(inputStream);
        BufferedReader bufferedReader = new BufferedReader(inputStreamReader);
        // Read header
        String line = bufferedReader.readLine();
        if (line == null) {
            // throw exception
            System.out.println("There is no data in output file!");
            return null;
        }
        while (line.indexOf(':') > 0) {
            String name = line.substring(0, line.indexOf(':'));
            stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name));
            line = line.substring(line.indexOf(':') + 1);
        }
        // Read data
        while ((line = bufferedReader.readLine()) != null) {
            line = line + "\t";
            double[] values = new double[stSolverResultSet.getDataColumnCount()];
            boolean bCompleteRow = true;
            for (int i = 0; i < stSolverResultSet.getDataColumnCount(); i++) {
                if (line.indexOf('\t') == -1) {
                    bCompleteRow = false;
                    break;
                } else {
                    String value = line.substring(0, line.indexOf('\t')).trim();
                    values[i] = Double.valueOf(value).doubleValue();
                    line = line.substring(line.indexOf('\t') + 1);
                }
            }
            if (bCompleteRow) {
                stSolverResultSet.addRow(values);
            } else {
                break;
            }
        }
    // 
    } catch (Exception e) {
        e.printStackTrace(System.out);
        return null;
    } finally {
        try {
            if (inputStream != null) {
                inputStream.close();
            }
        } catch (Exception ex) {
            lg.error(ex.getMessage(), ex);
        }
    }
    /*
	Add appropriate Function columns to result set if the stochastic simulation is to display the trajectory.
	No function columns for the results of multiple stochastic trials
	*/
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    if (simSymbolTable.getSimulation().getSolverTaskDescription().getStochOpt().getNumOfTrials() == 1) {
        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);
                    stSolverResultSet.addFunctionColumn(cd);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                }
            }
        }
    }
    return stSolverResultSet;
}

Example 14 with FunctionColumnDescription

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

the class HybridSolver method getHybridSolverResultSet.

/**
 * Get data columns and function columns to be ready for plot.
 * Creation date: (8/15/2006 11:36:43 AM)
 * @return cbit.vcell.solver.stoch.StochSolverResultSet
 */
private ODESolverResultSet getHybridSolverResultSet() {
    // read .stoch file, this funciton here equals to getODESolverRestultSet()+getStateVariableResultSet()  in ODE.
    ODESolverResultSet stSolverResultSet = new ODESolverResultSet();
    try {
        String filename = getBaseName() + NETCDF_DATA_EXTENSION;
        NetCDFEvaluator ncEva = new NetCDFEvaluator();
        NetCDFReader ncReader = null;
        try {
            ncEva.setNetCDFTarget(filename);
            ncReader = ncEva.getNetCDFReader();
        } catch (Exception e) {
            e.printStackTrace(System.err);
            throw new RuntimeException("Cannot open simulation result file: " + filename + "!");
        }
        // Read result according to trial number
        if (ncReader.getNumTrials() == 1) {
            // Read header
            String[] varNames = ncReader.getSpeciesNames_val();
            // first column will be time t.
            stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
            // following columns are stoch variables
            for (int i = 0; i < varNames.length; i++) {
                stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(varNames[i]));
            }
            // Read data
            // data only, no time points
            ArrayDouble data = (ArrayDouble) ncEva.getTimeSeriesData(1);
            double[] timePoints = ncReader.getTimePoints();
            System.out.println("time points length is " + timePoints.length);
            // shape[0]:num of timepoints, shape[1]: num of species
            int[] shape = data.getShape();
            if (// one species
            shape.length == 1) {
                ArrayDouble.D1 temData = (ArrayDouble.D1) data;
                System.out.println("one species in time series data and size is " + temData.getSize());
                for (// rows
                int k = 0; // rows
                k < timePoints.length; // rows
                k++) {
                    double[] values = new double[stSolverResultSet.getDataColumnCount()];
                    values[0] = timePoints[k];
                    for (int i = 1; i < stSolverResultSet.getDataColumnCount(); i++) {
                        values[i] = temData.get(k);
                    }
                    stSolverResultSet.addRow(values);
                }
            }
            if (// more than one species
            shape.length == 2) {
                ArrayDouble.D2 temData = (ArrayDouble.D2) data;
                System.out.println("multiple species in time series, the length of time series is :" + data.getShape()[0] + ", and the total number of speceis is: " + data.getShape()[1]);
                for (// rows
                int k = 0; // rows
                k < timePoints.length; // rows
                k++) {
                    double[] values = new double[stSolverResultSet.getDataColumnCount()];
                    values[0] = timePoints[k];
                    for (int i = 1; i < stSolverResultSet.getDataColumnCount(); i++) {
                        values[i] = temData.get(k, i - 1);
                    }
                    stSolverResultSet.addRow(values);
                }
            }
        } else if (ncReader.getNumTrials() > 1) {
            // Read header
            String[] varNames = ncReader.getSpeciesNames_val();
            // first column will be time t.
            stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("TrialNo"));
            // following columns are stoch variables
            for (int i = 0; i < varNames.length; i++) {
                stSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(varNames[i]));
            }
            // Read data
            // data only, no trial numbers
            ArrayDouble data = (ArrayDouble) ncEva.getDataOverTrials(ncReader.getTimePoints().length - 1);
            int[] trialNum = ncEva.getNetCDFReader().getTrialNumbers();
            // System.out.println("total trials are "+trialNum.length);
            // shape[0]:number of trials, shape[1]: num of species
            int[] shape = data.getShape();
            if (// one species
            shape.length == 1) {
                ArrayDouble.D1 temData = (ArrayDouble.D1) data;
                // System.out.println("one species over trials, size is: "+temData.getSize());
                for (// rows
                int k = 0; // rows
                k < trialNum.length; // rows
                k++) {
                    double[] values = new double[stSolverResultSet.getDataColumnCount()];
                    values[0] = trialNum[k];
                    for (int i = 1; i < stSolverResultSet.getDataColumnCount(); i++) {
                        values[i] = temData.get(k);
                    }
                    stSolverResultSet.addRow(values);
                }
            }
            if (// more than one species
            shape.length == 2) {
                ArrayDouble.D2 temData = (ArrayDouble.D2) data;
                // System.out.println("multiple species in multiple trials, the length of trials is :"+data.getShape()[0]+", and the total number of speceis is: "+data.getShape()[1]);
                for (// rows
                int k = 0; // rows
                k < trialNum.length; // rows
                k++) {
                    double[] values = new double[stSolverResultSet.getDataColumnCount()];
                    values[0] = trialNum[k];
                    for (int i = 1; i < stSolverResultSet.getDataColumnCount(); i++) {
                        values[i] = temData.get(k, i - 1);
                    }
                    stSolverResultSet.addRow(values);
                }
            }
        } else {
            throw new RuntimeException("Number of trials should be a countable positive value, from 1 to N.");
        }
    } catch (Exception e) {
        e.printStackTrace(System.err);
        throw new RuntimeException("Problem encountered in parsing hybrid simulation results.\n" + e.getMessage());
    }
    /*
	 *Add appropriate Function columns to result set if the stochastic simulation is to display the trajectory.
	 *No function columns for the results of multiple stochastic trials.
	 *In stochastic simulation the functions include probability functions and clamped variable.
	 */
    SimulationSymbolTable simSymbolTable = simTask.getSimulationJob().getSimulationSymbolTable();
    if (simSymbolTable.getSimulation().getSolverTaskDescription().getStochOpt().getNumOfTrials() == 1) {
        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);
                    stSolverResultSet.addFunctionColumn(cd);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                }
            }
        }
    }
    return stSolverResultSet;
}

Example 15 with FunctionColumnDescription

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

the class VCellSBMLSolver method getODESolverResultSet.

public static ODESolverResultSet getODESolverResultSet(SimulationJob argSimJob, String idaFileName) {
    // read .ida file
    ODESolverResultSet odeSolverResultSet = new ODESolverResultSet();
    FileInputStream inputStream = null;
    try {
        inputStream = new FileInputStream(idaFileName);
        InputStreamReader inputStreamReader = new InputStreamReader(inputStream);
        BufferedReader bufferedReader = new BufferedReader(inputStreamReader);
        // Read header
        String line = bufferedReader.readLine();
        if (line == null) {
        // throw exception
        }
        while (line.indexOf(':') > 0) {
            String name = line.substring(0, line.indexOf(':'));
            odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name));
            line = line.substring(line.indexOf(':') + 1);
        }
        // Read data
        while ((line = bufferedReader.readLine()) != null) {
            line = line + "\t";
            double[] values = new double[odeSolverResultSet.getDataColumnCount()];
            boolean bCompleteRow = true;
            for (int i = 0; i < odeSolverResultSet.getDataColumnCount(); i++) {
                if (line.indexOf('\t') == -1) {
                    bCompleteRow = false;
                    break;
                } else {
                    String value = line.substring(0, line.indexOf('\t')).trim();
                    values[i] = Double.valueOf(value).doubleValue();
                    line = line.substring(line.indexOf('\t') + 1);
                }
            }
            if (bCompleteRow) {
                odeSolverResultSet.addRow(values);
            } else {
                break;
            }
        }
    // 
    } catch (Exception e) {
        e.printStackTrace(System.out);
    } finally {
        try {
            if (inputStream != null) {
                inputStream.close();
            }
        } catch (Exception ex) {
            ex.printStackTrace(System.out);
        }
    }
    // add appropriate Function columns to result set
    cbit.vcell.math.Function[] functions = argSimJob.getSimulationSymbolTable().getFunctions();
    for (int i = 0; i < functions.length; i++) {
        if (SimulationSymbolTable.isFunctionSaved(functions[i])) {
            Expression exp1 = new Expression(functions[i].getExpression());
            try {
                exp1 = argSimJob.getSimulationSymbolTable().substituteFunctions(exp1);
            } catch (cbit.vcell.math.MathException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("Substitute function failed on function " + functions[i].getName() + " " + e.getMessage());
            } catch (cbit.vcell.parser.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 (cbit.vcell.parser.ExpressionException e) {
                e.printStackTrace(System.out);
            }
        }
    }
    return odeSolverResultSet;
}