Examples with ODESolverResultSet cbit.vcell.solver.ode.ODESolverResultSet used on opensource projects

Example 31 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet 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 32 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class SpatialAnalysisResults method createSummaryReportSourceData.

// This function put exp data and sim data in a hashtable, the key is analysisParameters(right now only 1)
public Hashtable<AnalysisParameters, DataSource[]> createSummaryReportSourceData(final double[] frapDataTimeStamps, int startIndexForRecovery, boolean[] selecredROIs, boolean isSimData) throws Exception {
    Hashtable<AnalysisParameters, DataSource[]> allDataHash = new Hashtable<AnalysisParameters, DataSource[]>();
    Hashtable<CurveInfo, double[]> ROIInfoHash = curveHash;
    Set<CurveInfo> roiInfoSet = ROIInfoHash.keySet();
    Iterator<CurveInfo> roiInfoIter = roiInfoSet.iterator();
    // exp data are stored by ROI type.
    Hashtable<String, double[]> expROIData = new Hashtable<String, double[]>();
    // sim data are stored by AnalysisParameters and then by ROI type.
    Hashtable<AnalysisParameters, Hashtable<String, double[]>> simROIData = new Hashtable<AnalysisParameters, Hashtable<String, double[]>>();
    int roiCount = 0;
    // how many set of parameters are used for sim. 1 for now.
    int analysisParametersCount = 0;
    while (roiInfoIter.hasNext()) {
        CurveInfo roiCurveInfo = roiInfoIter.next();
        if (roiCurveInfo.isExperimentInfo()) {
            expROIData.put(roiCurveInfo.getROIName(), ROIInfoHash.get(roiCurveInfo));
            roiCount++;
        } else {
            Hashtable<String, double[]> simROIDataHash = simROIData.get(roiCurveInfo.getAnalysisParameters());
            if (simROIDataHash == null) {
                simROIDataHash = new Hashtable<String, double[]>();
                simROIData.put(roiCurveInfo.getAnalysisParameters(), simROIDataHash);
                analysisParametersCount++;
            }
            simROIDataHash.put(roiCurveInfo.getROIName(), ROIInfoHash.get(roiCurveInfo));
        }
    }
    // this is for exp data. each row of reference data contains time + intensities under 9 ROIs(bleached + ring1..8). totally 10 cols for each row.
    ReferenceData referenceData = createReferenceData(frapDataTimeStamps, startIndexForRecovery, "", selecredROIs);
    // loop only 1 time, right now the analysisParameters[]'s length is 1.
    for (int analysisParametersRow = 0; analysisParametersRow < analysisParametersCount; analysisParametersRow++) {
        AnalysisParameters currentAnalysisParameters = analysisParameters[analysisParametersRow];
        DataSource[] newDataSourceArr = new DataSource[2];
        // rows for time points and cols for t + roibleached + ring1--8 (10 cols)
        final DataSource expDataSource = new DataSource.DataSourceReferenceData("exp", referenceData);
        newDataSourceArr[ARRAY_INDEX_EXPDATASOURCE] = expDataSource;
        DataSource simDataSource = null;
        if (isSimData) {
            ODESolverResultSet odeSolverResultSet = createODESolverResultSet(currentAnalysisParameters, null, "");
            // rows for time points and cols for t + roibleached + ring1--8 (10 cols)
            simDataSource = new DataSource.DataSourceRowColumnResultSet("sim", odeSolverResultSet);
        }
        newDataSourceArr[ARRAY_INDEX_SIMDATASOURCE] = simDataSource;
        allDataHash.put(currentAnalysisParameters, newDataSourceArr);
    }
    return allDataHash;
}

Example 33 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet in project vcell by virtualcell.

the class SpatialAnalysisResults method createSummaryReportTableData.

public Object[][] createSummaryReportTableData(double[] frapDataTimeStamps, int startTimeIndex) {
    String[] summaryReportColumnNames = SpatialAnalysisResults.getSummaryReportColumnNames();
    final Object[][] tableData = new Object[analysisParameters.length][summaryReportColumnNames.length];
    for (int analysisParametersRow = 0; analysisParametersRow < analysisParameters.length; analysisParametersRow++) {
        AnalysisParameters currentAnalysisParameters = analysisParameters[analysisParametersRow];
        for (int roiColumn = 0; roiColumn < SpatialAnalysisResults.ORDERED_ROINAMES.length; roiColumn++) {
            ODESolverResultSet simDataSource = createODESolverResultSet(currentAnalysisParameters, SpatialAnalysisResults.ORDERED_ROINAMES[roiColumn], "");
            ReferenceData expDataSource = // TODO to remove null to put SpatialAnalysisResults.ORDERED_ROINAMES[roiColumn]
            createReferenceData(frapDataTimeStamps, startTimeIndex, "", null);
            int numSamples = expDataSource.getNumDataRows();
            double sumSquaredError = MathTestingUtilities.calcWeightedSquaredError(simDataSource, expDataSource);
            tableData[analysisParametersRow][roiColumn + ANALYSISPARAMETERS_COLUMNS_COUNT] = // unbiased estimator is numsamples-1
            Math.sqrt(sumSquaredError) / (numSamples - 1);
        }
    }
    return tableData;
}

Example 34 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet 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 35 with ODESolverResultSet

use of cbit.vcell.solver.ode.ODESolverResultSet 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;
}