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

Example 6 with ODESolverResultSet

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

the class NonGUIFRAPTest method dumpSpatialResults.

public static void dumpSpatialResults(SpatialAnalysisResults spatialAnalysisResults, double[] frapDataTimeStamps, File outputFile) throws Exception {
    FileWriter fw = new FileWriter(outputFile);
    // FileOutputStream fos = new FileOutputStream(outputFile);
    // BufferedOutputStream bos = new BufferedOutputStream(fos);
    ReferenceData[] referenceDataArr = spatialAnalysisResults.createReferenceDataForAllDiffusionRates(frapDataTimeStamps);
    ODESolverResultSet[] odeSolverResultSetArr = spatialAnalysisResults.createODESolverResultSetForAllDiffusionRates();
    for (int i = 0; i < spatialAnalysisResults.analysisParameters.length; i++) {
        DataSource expDataSource = new DataSource.DataSourceReferenceData("experiment", referenceDataArr[i]);
        DataSource fitDataSource = new DataSource.DataSourceRowColumnResultSet("fit", odeSolverResultSetArr[i]);
    // MultisourcePlotListModel multisourcePlotListModel =
    // new MultisourcePlotListModel();
    // multisourcePlotListModel.setDataSources(new DataSource[] {expDataSource,fitDataSource});
    // System.out.println("AnalysisParameters = "+spatialAnalysisResults.analysisParameters[i]);
    // for (int j = 0; j < multisourcePlotListModel.getSize(); j++) {
    // DataReference dataReference = (DataReference)multisourcePlotListModel.getElementAt(j);
    // DataSource dataSource = dataReference.getDataSource();
    // for (int k = 0; k < dataSource.getNumRows(); k++) {
    // for (int k2 = 0; k2 < dataSource.getNumColumns(); k2++) {
    // System.out.print(dataSource.getRowData(k)[k2]+" ");
    // fw.write(dataSource.getRowData(k)[k2]+" ");
    // }
    // System.out.println();
    // fw.write("\n");
    // }
    // if(dataReference.getDataSource().getSource() instanceof ReferenceData){
    // ReferenceData refData = (ReferenceData)dataReference.getDataSource().getSource();
    // for (int k = 0; k < refData.getNumRows(); k++) {
    // for (int k2 = 0; k2 < refData.getNumColumns(); k2++) {
    // System.out.print(refData.getRowData(k)[k2]+" ");
    // fw.write(refData.getRowData(k)[k2]+" ");
    // }
    // System.out.println();
    // fw.write("\n");
    // }
    // }else{
    // ODESolverResultSet odeRS = (ODESolverResultSet)dataReference.getDataSource().getSource();
    // for (int k = 0; k < odeRS.getRowCount(); k++) {
    // for (int k2 = 0; k2 < odeRS.getDataColumnCount(); k2++) {
    // System.out.print(odeRS.getRow(k)[k2]+" ");
    // fw.write(odeRS.getRow(k)[k2]+" ");
    // }
    // System.out.println();
    // fw.write("\n");
    // }
    // }
    // }
    }
    fw.close();
}

Example 7 with ODESolverResultSet

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

the class SpatialAnalysisResults method createODESolverResultSet.

public ODESolverResultSet createODESolverResultSet(AnalysisParameters argAnalysisParameters, String argROIName, String description) {
    if (argROIName != null) {
        if (!isROITypeOK(argROIName)) {
            throw new IllegalArgumentException("couldn't find ROIType " + argROIName);
        }
    }
    int analysisParametersIndex = -1;
    for (int i = 0; i < analysisParameters.length; i++) {
        if (analysisParameters[i].equals(argAnalysisParameters)) {
            analysisParametersIndex = i;
            break;
        }
    }
    if (analysisParametersIndex == -1) {
        throw new IllegalArgumentException("couldn't find AnalysisParameteers " + analysisParametersIndex);
    }
    int numROITypes = (argROIName == null ? SpatialAnalysisResults.ORDERED_ROINAMES.length : 1);
    ODESolverResultSet fitOdeSolverResultSet = new ODESolverResultSet();
    fitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
    for (int j = 0; j < numROITypes; j++) {
        String currentROIName = (argROIName == null ? SpatialAnalysisResults.ORDERED_ROINAMES[j] : argROIName);
        String name = (description == null ? /*"sim D="+diffusionRates[diffusionRateIndex]+"::"*/
        "" : description) + currentROIName;
        fitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name));
    }
    // 
    for (int j = 0; j < shiftedSimTimes.length; j++) {
        double[] row = new double[numROITypes + 1];
        row[0] = shiftedSimTimes[j];
        fitOdeSolverResultSet.addRow(row);
    }
    // 
    for (int j = 0; j < numROITypes; j++) {
        String currentROIName = (argROIName == null ? SpatialAnalysisResults.ORDERED_ROINAMES[j] : argROIName);
        // get simulated data for this ROI
        double[] values = curveHash.get(new CurveInfo(analysisParameters[analysisParametersIndex], currentROIName));
        for (int k = 0; k < values.length; k++) {
            fitOdeSolverResultSet.setValue(k, j + 1, values[k]);
        }
    }
    return fitOdeSolverResultSet;
}

Example 8 with ODESolverResultSet

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

the class EstParams_CompareResultsDescriptor method aboutToDisplayPanel.

public void aboutToDisplayPanel() {
    FRAPStudy fStudy = frapWorkspace.getWorkingFrapStudy();
    // create Mean square error for different models under different ROIs
    // if(fStudy.getAnalysisMSESummaryData() == null)
    // {
    fStudy.createAnalysisMSESummaryData();
    // }
    // auto find best model for user if best model is not selected.
    double[][] mseSummaryData = fStudy.getAnalysisMSESummaryData();
    // for(int i =0; i<10; i++)
    // System.out.print(mseSummaryData[0][i]+"  ");
    // find best model with significance and has least error
    int bestModel = FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT;
    if (// best model is saved and there is no model selection change
    fStudy.getBestModelIndex() != null) {
        bestModel = fStudy.getBestModelIndex().intValue();
    } else // need to find the best model
    {
        // check model significance if more than one model
        if (fStudy.getSelectedModels().size() > 1) {
            if (getFrapWorkspace().getWorkingFrapStudy().getFrapOptData() != null || getFrapWorkspace().getWorkingFrapStudy().getFrapOptFunc() != null) {
                ProfileSummaryData[][] allProfileSumData = FRAPOptimizationUtils.getAllProfileSummaryData(fStudy);
                FRAPModel[] frapModels = frapWorkspace.getWorkingFrapStudy().getModels();
                int confidenceIdx = ((EstParams_CompareResultsPanel) this.getPanelComponent()).getSelectedConfidenceIndex();
                boolean[] modelSignificance = new boolean[FRAPModel.NUM_MODEL_TYPES];
                Arrays.fill(modelSignificance, true);
                if (frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] != null && frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters() != null && allProfileSumData != null && allProfileSumData[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] != null) {
                    for (int i = 0; i < FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF; i++) {
                        ConfidenceInterval[] intervals = allProfileSumData[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT][i].getConfidenceIntervals();
                        if (intervals[confidenceIdx].getUpperBound() == frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters()[i].getUpperBound() && intervals[confidenceIdx].getLowerBound() == frapModels[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters()[i].getLowerBound()) {
                            modelSignificance[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] = false;
                            break;
                        }
                    }
                }
                if (frapModels[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] != null && frapModels[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters() != null && allProfileSumData != null && allProfileSumData[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] != null) {
                    for (int i = 0; i < FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF; i++) {
                        ConfidenceInterval[] intervals = allProfileSumData[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS][i].getConfidenceIntervals();
                        if (intervals[confidenceIdx].getUpperBound() == frapModels[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters()[i].getUpperBound() && intervals[confidenceIdx].getLowerBound() == frapModels[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters()[i].getLowerBound()) {
                            modelSignificance[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] = false;
                            break;
                        }
                    }
                }
                if (frapModels[FRAPModel.IDX_MODEL_REACTION_OFF_RATE] != null && frapModels[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters() != null && allProfileSumData != null && allProfileSumData[FRAPModel.IDX_MODEL_REACTION_OFF_RATE] != null) {
                    for (int i = 0; i < FRAPModel.NUM_MODEL_PARAMETERS_REACTION_OFF_RATE; i++) {
                        if (i == FRAPModel.INDEX_BLEACH_MONITOR_RATE) {
                            ConfidenceInterval[] intervals = allProfileSumData[FRAPModel.IDX_MODEL_REACTION_OFF_RATE][FRAPModel.INDEX_BLEACH_MONITOR_RATE].getConfidenceIntervals();
                            if (intervals[confidenceIdx].getUpperBound() == frapModels[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters()[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getUpperBound() && intervals[confidenceIdx].getLowerBound() == frapModels[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters()[FRAPModel.INDEX_BLEACH_MONITOR_RATE].getLowerBound()) {
                                modelSignificance[FRAPModel.IDX_MODEL_REACTION_OFF_RATE] = false;
                                break;
                            }
                        } else if (i == FRAPModel.INDEX_OFF_RATE) {
                            ConfidenceInterval[] intervals = allProfileSumData[FRAPModel.IDX_MODEL_REACTION_OFF_RATE][FRAPModel.INDEX_OFF_RATE].getConfidenceIntervals();
                            if (intervals[confidenceIdx].getUpperBound() == frapModels[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters()[FRAPModel.INDEX_OFF_RATE].getUpperBound() && intervals[confidenceIdx].getLowerBound() == frapModels[FRAPModel.IDX_MODEL_REACTION_OFF_RATE].getModelParameters()[FRAPModel.INDEX_OFF_RATE].getLowerBound()) {
                                modelSignificance[FRAPModel.IDX_MODEL_REACTION_OFF_RATE] = false;
                                break;
                            }
                        }
                    }
                }
                // check least error model with significance
                double minError = 1E8;
                if (mseSummaryData != null) {
                    // exclude cell and bkground ROIs, include sum of error
                    int secDimLen = FRAPData.VFRAP_ROI_ENUM.values().length - 2 + 1;
                    if (modelSignificance[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] == modelSignificance[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] && modelSignificance[FRAPModel.IDX_MODEL_REACTION_OFF_RATE] == modelSignificance[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS]) {
                        // if all models' significance are the same, find the least error
                        for (int i = 0; i < FRAPModel.NUM_MODEL_TYPES; i++) {
                            if ((minError > mseSummaryData[i][secDimLen - 1])) {
                                minError = mseSummaryData[i][secDimLen - 1];
                                bestModel = i;
                            }
                        }
                    } else {
                        // if models' significance are different, find the least error with significance
                        for (int i = 0; i < FRAPModel.NUM_MODEL_TYPES; i++) {
                            if (modelSignificance[i] && (minError > mseSummaryData[i][secDimLen - 1])) {
                                minError = mseSummaryData[i][secDimLen - 1];
                                bestModel = i;
                            }
                        }
                    }
                }
            }
        } else // only one model is selected and the selected model should be the best model
        {
            for (int i = 0; i < fStudy.getModels().length; i++) {
                if (fStudy.getModels()[i] != null) {
                    bestModel = i;
                    break;
                }
            }
        }
    }
    ((EstParams_CompareResultsPanel) this.getPanelComponent()).setBestModelRadioButton(bestModel);
    // set data source to multiSourcePlotPane
    // length should be fStudy.getSelectedModels().size()+1, however, reaction binding may not have data
    ArrayList<DataSource> comparableDataSource = new ArrayList<DataSource>();
    // add exp data
    ReferenceData expReferenceData = FRAPOptimizationUtils.doubleArrayToSimpleRefData(fStudy.getDimensionReducedExpData(), fStudy.getFrapData().getImageDataset().getImageTimeStamps(), fStudy.getStartingIndexForRecovery(), fStudy.getSelectedROIsForErrorCalculation());
    final DataSource expDataSource = new DataSource.DataSourceReferenceData("exp", expReferenceData);
    comparableDataSource.add(expDataSource);
    // add opt/sim data
    // using the same loop, disable the radio button if the model is not included
    // adjust radio buttons
    ((EstParams_CompareResultsPanel) this.getPanelComponent()).disableAllRadioButtons();
    ArrayList<Integer> selectedModelIndexes = fStudy.getSelectedModels();
    for (int i = 0; i < selectedModelIndexes.size(); i++) {
        DataSource newDataSource = null;
        double[] timePoints = fStudy.getFrapData().getImageDataset().getImageTimeStamps();
        int startingIndex = fStudy.getStartingIndexForRecovery();
        double[] truncatedTimes = new double[timePoints.length - startingIndex];
        System.arraycopy(timePoints, startingIndex, truncatedTimes, 0, truncatedTimes.length);
        if (selectedModelIndexes.get(i).equals(FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT)) {
            // adjust radio button
            ((EstParams_CompareResultsPanel) this.getPanelComponent()).enableRadioButton(FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT);
            FRAPModel temModel = fStudy.getFrapModel(FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT);
            ODESolverResultSet temSolverResultSet = FRAPOptimizationUtils.doubleArrayToSolverResultSet(temModel.getData(), truncatedTimes, 0, fStudy.getSelectedROIsForErrorCalculation());
            newDataSource = new DataSource.DataSourceRowColumnResultSet("opt_DF1", temSolverResultSet);
        } else if (selectedModelIndexes.get(i).equals(FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS)) {
            // adjust radio button
            ((EstParams_CompareResultsPanel) this.getPanelComponent()).enableRadioButton(FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS);
            FRAPModel temModel = fStudy.getFrapModel(FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS);
            ODESolverResultSet temSolverResultSet = FRAPOptimizationUtils.doubleArrayToSolverResultSet(temModel.getData(), truncatedTimes, 0, fStudy.getSelectedROIsForErrorCalculation());
            newDataSource = new DataSource.DataSourceRowColumnResultSet("opt_DF2", temSolverResultSet);
        } else if (selectedModelIndexes.get(i).equals(FRAPModel.IDX_MODEL_REACTION_OFF_RATE)) {
            // adjust radio button
            ((EstParams_CompareResultsPanel) this.getPanelComponent()).enableRadioButton(FRAPModel.IDX_MODEL_REACTION_OFF_RATE);
            FRAPModel temModel = fStudy.getFrapModel(FRAPModel.IDX_MODEL_REACTION_OFF_RATE);
            if (temModel.getData() != null) {
                ODESolverResultSet temSolverResultSet = FRAPOptimizationUtils.doubleArrayToSolverResultSet(temModel.getData(), truncatedTimes, 0, // for reaction off model, display curve under bleached region only
                FRAPStudy.createSelectedROIsForReactionOffRateModel());
                newDataSource = new DataSource.DataSourceRowColumnResultSet("sim_Koff", temSolverResultSet);
            }
        }
        if (newDataSource != null) {
            comparableDataSource.add(newDataSource);
        }
    }
    // set data to multiSourcePlotPane
    ((EstParams_CompareResultsPanel) this.getPanelComponent()).setPlotData(comparableDataSource.toArray(new DataSource[comparableDataSource.size()]));
}

Example 9 with ODESolverResultSet

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

the class EstParams_OneDiffComponentPanel method plotDerivedSimulationResults.

private void plotDerivedSimulationResults(AnalysisParameters[] anaParams) {
    try {
        String description = null;
        int totalROIlen = FRAPData.VFRAP_ROI_ENUM.values().length;
        boolean[] wantsROITypes = new boolean[totalROIlen];
        System.arraycopy(frapWorkspace.getWorkingFrapStudy().getSelectedROIsForErrorCalculation(), 0, wantsROITypes, 0, totalROIlen);
        ODESolverResultSet fitOdeSolverResultSet = new ODESolverResultSet();
        fitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
        for (int j = 0; j < totalROIlen; j++) {
            if (!wantsROITypes[j]) {
                continue;
            }
            String currentROIName = FRAPData.VFRAP_ROI_ENUM.values()[j].name();
            String name = (description == null ? /*"sim D="+diffusionRates[diffusionRateIndex]+"::"*/
            "" : description) + currentROIName;
            fitOdeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name));
        }
        int totalWantedROIlen = 0;
        for (int i = 0; i < wantsROITypes.length; i++) {
            if (wantsROITypes[i]) {
                totalWantedROIlen++;
            }
        }
        // 
        // populate time
        // 
        double[] shiftedSimTimes = frapOptData.getReducedExpTimePoints();
        int startIndexRecovery = frapOptData.getExpFrapStudy().getStartingIndexForRecovery();
        for (int j = 0; j < shiftedSimTimes.length; j++) {
            double[] row = new double[totalWantedROIlen + 1];
            row[0] = shiftedSimTimes[j] + frapOptData.getExpFrapStudy().getFrapData().getImageDataset().getImageTimeStamps()[startIndexRecovery];
            fitOdeSolverResultSet.addRow(row);
        }
        // populate values
        double[][] currentOptFitData = getPureDiffusionPanel().getCurrentFitData();
        // store results
        setCurrentEstimationResults(currentOptFitData);
        if (allDataHash != null && currentOptFitData != null) {
            // populate optimization data
            int columncounter = 0;
            for (int j = 0; j < totalROIlen; j++) {
                if (!wantsROITypes[j]) {
                    continue;
                }
                // if(!isSimData) //opt data
                // {
                double[] values = currentOptFitData[j];
                for (int k = 0; k < values.length; k++) {
                    fitOdeSolverResultSet.setValue(k, columncounter + 1, values[k]);
                }
                // }
                columncounter++;
            }
            // boolean hasSimData = false;
            // anaParams[0] is the key in allDataHash to get the dataSource[]:exp & sim
            DataSource[] selectedRowDataSourceArr = allDataHash.get(anaParams[0]);
            if (selectedRowDataSourceArr != null) {
                // referenceData is the exp data
                // ReferenceData referenceData = (ReferenceData)selectedRowDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE];
                // new DataSource.DataSourceReferenceData("exp", referenceData);
                final DataSource expDataSource = selectedRowDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE];
                DataSource optDataSource = new DataSource.DataSourceRowColumnResultSet("opt", fitOdeSolverResultSet);
                DataSource[] newDataSourceArr = new DataSource[2];
                newDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE] = expDataSource;
                newDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_SIMDATASOURCE] = optDataSource;
                if (currentOptFitData == null) {
                    multisourcePlotPane.setDataSources(null);
                } else {
                    // the following paragraph of code is just to get selected color for selected ROIs
                    // and make them the same as we show on ChooseModel_RoiForErrorPanel/RoiForErrorPanel
                    // double valid ROI colors (not include cell and background)
                    int validROISize = FRAPData.VFRAP_ROI_ENUM.values().length - 2;
                    Color[] fullColors = ColorUtil.generateAutoColor(validROISize * 2, getBackground(), new Integer(0));
                    boolean[] selectedROIs = frapWorkspace.getWorkingFrapStudy().getSelectedROIsForErrorCalculation();
                    int selectedROICounter = 0;
                    for (int i = 0; i < selectedROIs.length; i++) {
                        if (selectedROIs[i]) {
                            selectedROICounter++;
                        }
                    }
                    // double the size, each ROI is a comparison of exp and sim
                    Color[] selectedColors = new Color[selectedROICounter * 2];
                    int selectedColorIdx = 0;
                    for (int i = 0; i < selectedROIs.length; i++) {
                        if (selectedROIs[i] && i == 0) {
                            selectedColors[selectedColorIdx] = fullColors[i];
                            selectedColors[selectedColorIdx + selectedROICounter] = fullColors[i + validROISize];
                            selectedColorIdx++;
                        }
                        if (// skip cell and background ROIs
                        selectedROIs[i] && i > 2) {
                            selectedColors[selectedColorIdx] = fullColors[i - 2];
                            selectedColors[selectedColorIdx + selectedROICounter] = fullColors[i - 2 + validROISize];
                            selectedColorIdx++;
                        }
                    }
                    int[] selectedIndices = multisourcePlotPane.getUnsortedSelectedIndices();
                    multisourcePlotPane.setDataSources(newDataSourceArr, selectedColors);
                    if (selectedIndices.length == 0) {
                        multisourcePlotPane.selectAll();
                    } else {
                        multisourcePlotPane.setUnsortedSelectedIndices(selectedIndices);
                    }
                }
            }
        }
    } catch (Exception e2) {
        e2.printStackTrace();
        DialogUtils.showErrorDialog(this, "Error graphing Optimizer data " + e2.getMessage());
    }
}

Example 10 with ODESolverResultSet

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

the class EstParams_ReacBindingPanel method plotDerivedSimulationResults.

private void plotDerivedSimulationResults(AnalysisParameters[] anaParams) {
    try {
        if (getCurrentSimResults() == null || getCurrentRawSimTimePoints() == null || allDataHash == null || allDataHash.get(anaParams[0]) == null || (allDataHash.get(anaParams[0])[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE]) == null) {
            multisourcePlotPane.setDataSources(null);
            return;
        }
        String description = null;
        int totalROIlen = FRAPData.VFRAP_ROI_ENUM.values().length;
        boolean[] wantsROITypes = new boolean[totalROIlen];
        System.arraycopy(frapWorkspace.getWorkingFrapStudy().getSelectedROIsForErrorCalculation(), 0, wantsROITypes, 0, totalROIlen);
        ODESolverResultSet simSolverResultSet = new ODESolverResultSet();
        simSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
        for (int j = 0; j < totalROIlen; j++) {
            if (!wantsROITypes[j]) {
                continue;
            }
            String currentROIName = FRAPData.VFRAP_ROI_ENUM.values()[j].name();
            String name = (description == null ? /*"sim D="+diffusionRates[diffusionRateIndex]+"::"*/
            "" : description) + currentROIName;
            simSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(name));
        }
        int totalWantedROIlen = 0;
        for (int i = 0; i < wantsROITypes.length; i++) {
            if (wantsROITypes[i]) {
                totalWantedROIlen++;
            }
        }
        FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
        // 
        // populate time
        // 
        double[] shiftedSimTimes = getCurrentRawSimTimePoints();
        int startIndexRecovery = fStudy.getStartingIndexForRecovery();
        for (int j = 0; j < shiftedSimTimes.length; j++) {
            double[] row = new double[totalWantedROIlen + 1];
            row[0] = shiftedSimTimes[j] + fStudy.getFrapData().getImageDataset().getImageTimeStamps()[startIndexRecovery];
            simSolverResultSet.addRow(row);
        }
        // 
        // populate values
        // 
        double[][] currentSimData = getCurrentSimResults();
        // populate sim data
        int columncounter = 0;
        for (int j = 0; j < totalROIlen; j++) {
            if (!wantsROITypes[j]) {
                continue;
            }
            double[] values = currentSimData[j];
            for (int k = 0; k < values.length; k++) {
                simSolverResultSet.setValue(k, columncounter + 1, values[k]);
            }
            columncounter++;
        }
        // get exp data and generate datasource to display
        // anaParams[0] is the key in allDataHash to get the dataSource[]:exp & sim
        DataSource[] selectedRowDataSourceArr = allDataHash.get(anaParams[0]);
        if (selectedRowDataSourceArr != null) {
            // referenceData is the exp data
            // ReferenceData referenceData = (ReferenceData)selectedRowDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE].getSource();
            final DataSource expDataSource = /*new DataSource(referenceData,"exp")*/
            selectedRowDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE];
            // from simulation
            final DataSource simDataSource = new DataSource.DataSourceRowColumnResultSet("sim", simSolverResultSet);
            DataSource[] newDataSourceArr = new DataSource[2];
            newDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_EXPDATASOURCE] = expDataSource;
            newDataSourceArr[SpatialAnalysisResults.ARRAY_INDEX_SIMDATASOURCE] = simDataSource;
            // the following paragraph of code is just to get selected color for selected ROIs
            // and make them the same as we show on ChooseModel_RoiForErrorPanel/RoiForErrorPanel
            // double valid ROI colors (not include cell and background)
            int validROISize = FRAPData.VFRAP_ROI_ENUM.values().length - 2;
            Color[] fullColors = ColorUtil.generateAutoColor(validROISize * 2, getBackground(), new Integer(0));
            boolean[] selectedROIs = frapWorkspace.getWorkingFrapStudy().getSelectedROIsForErrorCalculation();
            int selectedROICounter = 0;
            for (int i = 0; i < selectedROIs.length; i++) {
                if (selectedROIs[i]) {
                    selectedROICounter++;
                }
            }
            // double the size, each ROI is a comparison of exp and sim
            Color[] selectedColors = new Color[selectedROICounter * 2];
            int selectedColorIdx = 0;
            for (int i = 0; i < selectedROIs.length; i++) {
                if (selectedROIs[i] && i == 0) {
                    selectedColors[selectedColorIdx] = fullColors[i];
                    selectedColors[selectedColorIdx + selectedROICounter] = fullColors[i + validROISize];
                    selectedColorIdx++;
                }
                if (// skip cell and background ROIs
                selectedROIs[i] && i > 2) {
                    selectedColors[selectedColorIdx] = fullColors[i - 2];
                    selectedColors[selectedColorIdx + selectedROICounter] = fullColors[i - 2 + validROISize];
                    selectedColorIdx++;
                }
            }
            multisourcePlotPane.setDataSources(newDataSourceArr, selectedColors);
            multisourcePlotPane.selectAll();
        }
    } catch (Exception e2) {
        e2.printStackTrace();
        DialogUtils.showErrorDialog(this, "Error graphing Optimizer data " + e2.getMessage());
    }
}