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

Example 21 with ODESolverResultSetColumnDescription

use of cbit.vcell.math.ODESolverResultSetColumnDescription 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;
}

Example 22 with ODESolverResultSetColumnDescription

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

the class FRAPOptimizationUtils method doubleArrayToSolverResultSet.

// used by opt or sim data, no truncation of time/data. @param startingIndex is used to shift opt/sim times to compare with exp times
public static ODESolverResultSet doubleArrayToSolverResultSet(double[][] origData, double[] timePoints, double timePointOffset, boolean[] selectedROIs) /*throws Exception*/
{
    if (origData != null && timePoints != null && selectedROIs != null) {
        int numSelectedROITypes = 0;
        for (int i = 0; i < selectedROIs.length; i++) {
            if (selectedROIs[i]) {
                numSelectedROITypes++;
            }
        }
        ODESolverResultSet newOdeSolverResultSet = new ODESolverResultSet();
        newOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
        for (int j = 0; j < selectedROIs.length; j++) {
            if (!selectedROIs[j]) {
                continue;
            }
            String currentROIName = FRAPData.VFRAP_ROI_ENUM.values()[j].name();
            String name = currentROIName;
            newOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name));
        }
        // set time
        for (int j = 0; j < timePoints.length; j++) {
            double[] row = new double[numSelectedROITypes + 1];
            row[0] = timePoints[j] + timePointOffset;
            newOdeSolverResultSet.addRow(row);
        }
        // set data
        int columncounter = 0;
        for (int j = 0; j < selectedROIs.length; j++) {
            if (!selectedROIs[j]) {
                continue;
            }
            double[] values = origData[j];
            for (int k = 0; k < values.length; k++) {
                newOdeSolverResultSet.setValue(k, columncounter + 1, values[k]);
            }
            columncounter++;
        }
        return newOdeSolverResultSet;
    }
    return null;
}

Example 23 with ODESolverResultSetColumnDescription

use of cbit.vcell.math.ODESolverResultSetColumnDescription 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 24 with ODESolverResultSetColumnDescription

use of cbit.vcell.math.ODESolverResultSetColumnDescription 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 25 with ODESolverResultSetColumnDescription

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

the class SundialsSolver method getStateVariableResultSet.

/**
 * This method was created in VisualAge.
 * @return double[]
 * @param vectorIndex int
 */
private ODESolverResultSet getStateVariableResultSet() {
    ODESolverResultSet odeSolverResultSet = 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
            return null;
        }
        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);
        return null;
    } finally {
        try {
            if (inputStream != null) {
                inputStream.close();
            }
        } catch (Exception ex) {
            lg.error(ex.getMessage(), ex);
        }
    }
    return (odeSolverResultSet);
}