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

Example 16 with FunctionColumnDescription

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

the class MergedData method getODEDataBlock.

/**
 * Insert the method's description here.
 * Creation date: (1/14/00 2:28:47 PM)
 * @return cbit.vcell.simdata.ODEDataBlock
 */
public ODEDataBlock getODEDataBlock() throws DataAccessException {
    ODESolverResultSet combinedODESolverRSet = new ODESolverResultSet();
    ODEDataBlock refDataBlock = dataSetControllerImpl.getODEDataBlock(datasetsIDList[0]);
    ODESimData refSimData = refDataBlock.getODESimData();
    // Can use dataTimes field later (for genuine SimulationData), but for now, obtain it on the fly
    double[] times = null;
    try {
        int independentVarIndex = refSimData.findColumn("t");
        if (independentVarIndex < 0) {
            independentVarIndex = refSimData.findColumn(HISTOGRAM_INDEX_NAME);
        }
        times = refSimData.extractColumn(independentVarIndex);
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
    }
    // Adding data/function columns to new resultSet
    ODESolverResultSet[] resultSetList = new ODESolverResultSet[datasetsIDList.length];
    for (int i = 0; i < datasetsIDList.length; i++) {
        ODEDataBlock dataBlock = dataSetControllerImpl.getODEDataBlock(datasetsIDList[i]);
        ODESimData simData = dataBlock.getODESimData();
        ODESolverResultSet newODErset = new ODESolverResultSet();
        // First resultSet is reference resultSet. From the second onwards, resample the resultSet wrt the reference.
        if (i > 0) {
            try {
                newODErset = resampleODEData(refSimData, simData);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException("\n >>>> Could not resample data! <<<<\n");
            }
        } else {
            newODErset = simData;
        }
        resultSetList[i] = newODErset;
        // Add data columns
        String[] newVarNames = new String[newODErset.getDataColumnCount()];
        for (int j = 0; j < newODErset.getDataColumnCount(); j++) {
            // If 'time' column is present in combinedResultSet, continue with next data column
            if ((combinedODESolverRSet.findColumn("t") > -1) && (newODErset.getDataColumnDescriptions()[j].getName().equals("t"))) {
                newVarNames[j] = newODErset.getDataColumnDescriptions()[j].getName();
                continue;
            }
            // Retain 'time' column as 't', without using datasetID as prefix to avoid multiple time columns in combinedODEResultSet.
            // Adding the time column from the first dataset to combinedResultSet, since it is treated as the reference dataset.
            String newColName = null;
            if (j == 0 && newODErset.getDataColumnDescriptions()[j].getName().equals("t")) {
                newColName = newODErset.getDataColumnDescriptions()[j].getName();
            } else {
                newColName = dataSetPrefix[i] + "." + newODErset.getDataColumnDescriptions()[j].getName();
            }
            newVarNames[j] = newColName;
            ColumnDescription cd = newODErset.getDataColumnDescriptions()[j];
            if (cd instanceof ODESolverResultSetColumnDescription) {
                ODESolverResultSetColumnDescription newCD = new ODESolverResultSetColumnDescription(newColName, cd.getParameterName(), newColName);
                combinedODESolverRSet.addDataColumn(newCD);
            }
        }
        // Add function columns
        for (int j = 0; j < newODErset.getFunctionColumnCount(); j++) {
            try {
                String newColName = dataSetPrefix[i] + "." + newODErset.getFunctionColumnDescriptions()[j].getName();
                FunctionColumnDescription fcd = newODErset.getFunctionColumnDescriptions()[j];
                Expression newExp = new Expression(fcd.getExpression());
                String[] symbols = newExp.getSymbols();
                if (symbols != null && (symbols.length > 0)) {
                    for (int jj = 0; jj < symbols.length; jj++) {
                        for (int kk = 0; kk < newVarNames.length; kk++) {
                            if (newVarNames[kk].equals(dataSetPrefix[i] + "." + symbols[jj])) {
                                newExp.substituteInPlace(new Expression(symbols[jj]), new Expression(newVarNames[kk]));
                                break;
                            }
                        }
                    }
                }
                FunctionColumnDescription newFcd = new FunctionColumnDescription(newExp, newColName, fcd.getParameterName(), newColName, fcd.getIsUserDefined());
                combinedODESolverRSet.addFunctionColumn(newFcd);
            } catch (ExpressionException e) {
                e.printStackTrace(System.out);
            }
        }
    }
    // Populating new dataset
    for (int i = 0; i < times.length; i++) {
        double[] newRow = new double[combinedODESolverRSet.getDataColumnCount()];
        int indx = 0;
        for (int j = 0; j < resultSetList.length; j++) {
            ODESolverResultSet resultSet = resultSetList[j];
            double[] tempRow = resultSet.getRow(i);
            int startIndx = 0;
            int arrayLen = tempRow.length;
            if (j > 0) {
                // From the second dataset onwards, we do not want to copy the time column, hence skip to
                // the next element/col in dataset, that reduces the # of elements in the row by 1.
                startIndx = 1;
                arrayLen = tempRow.length - 1;
            }
            System.arraycopy(tempRow, startIndx, newRow, indx, arrayLen);
            indx += tempRow.length;
        }
        combinedODESolverRSet.addRow(newRow);
    }
    ODEDataInfo odeDataInfo = new ODEDataInfo(getResultsInfoObject().getOwner(), getResultsInfoObject().getID(), 0);
    ODESimData odeSimData = new ODESimData(getResultsInfoObject(), combinedODESolverRSet);
    return new ODEDataBlock(odeDataInfo, odeSimData);
}

Example 17 with FunctionColumnDescription

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

the class MergedData method resampleODEData.

/**
 * Insert the method's description here.
 * Creation date: (10/11/00 1:28:51 PM)
 * @param function cbit.vcell.math.Function
 */
private ODESolverResultSet resampleODEData(ODESimData refSimdata, ODESimData simData) throws ExpressionException {
    // If simData and refSimdata times are equal, return simData without resampling.
    // Else resampling is necessary.
    double[] refTimeArray = refSimdata.extractColumn(Math.max(refSimdata.findColumn(HISTOGRAM_INDEX_NAME), refSimdata.findColumn("t")));
    double[] timeArray = simData.extractColumn(Math.max(simData.findColumn(HISTOGRAM_INDEX_NAME), simData.findColumn("t")));
    if (refTimeArray.length == timeArray.length) {
        boolean bEqual = true;
        for (int i = 0; i < refTimeArray.length; i++) {
            if (refTimeArray[i] == timeArray[i]) {
                bEqual = bEqual && true;
            } else {
                bEqual = bEqual && false;
            }
        }
        if (bEqual) {
            return simData;
        }
    }
    ODESolverResultSet newODEresultSet = new ODESolverResultSet();
    for (int i = 0; i < simData.getDataColumnCount(); i++) {
        if (simData.getDataColumnDescriptions()[i] instanceof ODESolverResultSetColumnDescription) {
            ODESolverResultSetColumnDescription colDesc = ((ODESolverResultSetColumnDescription) simData.getDataColumnDescriptions()[i]);
            newODEresultSet.addDataColumn(colDesc);
        }
    }
    for (int i = 0; i < simData.getFunctionColumnCount(); i++) {
        FunctionColumnDescription colDesc = simData.getFunctionColumnDescriptions()[i];
        newODEresultSet.addFunctionColumn(colDesc);
    }
    double[][] resampledData = new double[refTimeArray.length][simData.getDataColumnCount()];
    for (int i = 0; i < simData.getDataColumnCount(); i++) {
        ColumnDescription colDesc = simData.getDataColumnDescriptions()[i];
        // If it is the first column (time), set value in new SimData to the timeArray values in refSimData.
        if (i == 0 && colDesc.getName().equals("t")) {
            for (int j = 0; j < refTimeArray.length; j++) {
                resampledData[j][i] = refTimeArray[j];
            }
            continue;
        }
        double[] data = simData.extractColumn(i);
        int k = 0;
        for (int j = 0; j < refTimeArray.length; j++) {
            // CHECK IF refTimeArray or timeArry has to be used here,
            while ((k < timeArray.length - 2) && (refTimeArray[j] > timeArray[k + 1])) {
                k++;
            }
            // apply first order linear basis for reference data interpolation.
            resampledData[j][i] = data[k] + (data[k + 1] - data[k]) * (refTimeArray[j] - timeArray[k]) / (timeArray[k + 1] - timeArray[k]);
        }
    }
    for (int i = 0; i < refTimeArray.length; i++) {
        newODEresultSet.addRow(resampledData[i]);
    }
    return newODEresultSet;
}

Example 18 with FunctionColumnDescription

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

the class ODEDataManager method addOutputFunction.

private void addOutputFunction(AnnotatedFunction function, ODESolverResultSet odeRS) {
    // Get the new name and expression for the function and create a new
    // functioncolumndescription, check is function is valid. If it is, add it to the list of columns
    // in the ODEResultSet. Else, pop-up an error dialog indicating that function cannot be added.
    FunctionColumnDescription fcd = null;
    String funcName = function.getName();
    Expression funcExp = function.getExpression();
    fcd = new FunctionColumnDescription(funcExp, funcName, null, function.getDisplayName(), true);
    try {
        odeRS.checkFunctionValidity(fcd);
    } catch (ExpressionException e) {
        javax.swing.JOptionPane.showMessageDialog(null, e.getMessage() + ". " + funcName + " not added.", "Error Adding Function ", javax.swing.JOptionPane.ERROR_MESSAGE);
        // e.printStackTrace(System.out);
        return;
    }
    try {
        odeRS.addFunctionColumn(fcd);
    } catch (ExpressionException e) {
        javax.swing.JOptionPane.showMessageDialog(null, e.getMessage() + ". " + funcName + " not added.", "Error Adding Function ", javax.swing.JOptionPane.ERROR_MESSAGE);
        e.printStackTrace(System.out);
    }
}

Example 19 with FunctionColumnDescription

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

the class ODESimData method readNCDataFile.

public static ODESimData readNCDataFile(VCDataIdentifier vcdId, File dataFile, File functionsFile) throws DataAccessException {
    // read ida file
    System.out.println("reading NetCDF file : " + dataFile);
    ODESimData odeSimData = new ODESimData();
    odeSimData.formatID = NETCDF_DATA_FORMAT_ID;
    odeSimData.mathName = vcdId.getID();
    // read .stoch file, this funciton here equals to getODESolverRestultSet()+getStateVariableResultSet()  in ODE.
    try {
        NetCDFEvaluator ncEva = new NetCDFEvaluator();
        NetCDFReader ncReader = null;
        try {
            ncEva.setNetCDFTarget(dataFile.getAbsolutePath());
            ncReader = ncEva.getNetCDFReader();
        } catch (Exception e) {
            e.printStackTrace(System.err);
            throw new RuntimeException("Cannot open simulation result file: " + dataFile.getAbsolutePath() + "!");
        }
        // Read result according to trial number
        if (ncReader.getNumTrials() == 1) {
            // Read header
            String[] varNames = ncReader.getSpeciesNames_val();
            // first column will be time t.
            odeSimData.addDataColumn(new ODESolverResultSetColumnDescription("t"));
            // following columns are stoch variables
            for (int i = 0; i < varNames.length; i++) {
                odeSimData.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[odeSimData.getDataColumnCount()];
                    values[0] = timePoints[k];
                    for (int i = 1; i < odeSimData.getDataColumnCount(); i++) {
                        values[i] = temData.get(k);
                    }
                    odeSimData.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[odeSimData.getDataColumnCount()];
                    values[0] = timePoints[k];
                    for (int i = 1; i < odeSimData.getDataColumnCount(); i++) {
                        values[i] = temData.get(k, i - 1);
                    }
                    odeSimData.addRow(values);
                }
            }
        } else if (ncReader.getNumTrials() > 1) {
            // Read header
            String[] varNames = ncReader.getSpeciesNames_val();
            // first column will be time t.
            odeSimData.addDataColumn(new ODESolverResultSetColumnDescription("TrialNo"));
            // following columns are stoch variables
            for (int i = 0; i < varNames.length; i++) {
                odeSimData.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[odeSimData.getDataColumnCount()];
                    values[0] = trialNum[k];
                    for (int i = 1; i < odeSimData.getDataColumnCount(); i++) {
                        values[i] = temData.get(k);
                    }
                    odeSimData.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[odeSimData.getDataColumnCount()];
                    values[0] = trialNum[k];
                    for (int i = 1; i < odeSimData.getDataColumnCount(); i++) {
                        values[i] = temData.get(k, i - 1);
                    }
                    odeSimData.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());
    }
    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;
}