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

Example 1 with ODESolverResultSetColumnDescription

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

the class ReferenceDataPanel method subsample.

/**
 * Comment
 */
private ReferenceData subsample() {
    ReferenceData refData = fieldParameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    if (refData == null) {
        return refData;
    }
    RowColumnResultSet rc = new RowColumnResultSet();
    String[] columnNames = refData.getColumnNames();
    for (int i = 0; i < columnNames.length; i++) {
        rc.addDataColumn(new ODESolverResultSetColumnDescription(i == timeIndex ? ReservedVariable.TIME.getName() : columnNames[i]));
    }
    for (int i = 0; i < refData.getNumDataRows(); i++) {
        rc.addRow((double[]) refData.getDataByRow(i).clone());
    }
    int desiredNumRows = refData.getNumDataRows() / 2;
    if (desiredNumRows < 3) {
        return refData;
    }
    try {
        rc.trimRows(desiredNumRows);
        double[] weights = null;
        if (refData.getColumnWeights() != null) {
            weights = (double[]) refData.getColumnWeights().clone();
        } else {
            weights = new double[refData.getColumnNames().length];
            java.util.Arrays.fill(weights, 1.0);
        }
        SimpleReferenceData srd = new SimpleReferenceData(rc, weights);
        return srd;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        DialogUtils.showErrorDialog(this, e.getMessage(), e);
        return refData;
    }
}

Example 2 with ODESolverResultSetColumnDescription

use of cbit.vcell.math.ODESolverResultSetColumnDescription 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 3 with ODESolverResultSetColumnDescription

use of cbit.vcell.math.ODESolverResultSetColumnDescription 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());
    }
}

Example 4 with ODESolverResultSetColumnDescription

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

the class ModelOptimizationMapping method getRemappedReferenceData.

/**
 * Gets the constraintData property (cbit.vcell.opt.ConstraintData) value.
 * @return The constraintData property value.
 * @see #setConstraintData
 */
private ReferenceData getRemappedReferenceData(MathMapping mathMapping) throws MappingException {
    if (modelOptimizationSpec.getReferenceData() == null) {
        return null;
    }
    // 
    // make sure time is mapped
    // 
    ReferenceData refData = modelOptimizationSpec.getReferenceData();
    ReferenceDataMappingSpec[] refDataMappingSpecs = modelOptimizationSpec.getReferenceDataMappingSpecs();
    RowColumnResultSet rowColResultSet = new RowColumnResultSet();
    Vector<SymbolTableEntry> modelObjectList = new Vector<SymbolTableEntry>();
    Vector<double[]> dataList = new Vector<double[]>();
    // 
    // find bound columns, (time is always mapped to the first column)
    // 
    int mappedColumnCount = 0;
    for (int i = 0; i < refDataMappingSpecs.length; i++) {
        SymbolTableEntry modelObject = refDataMappingSpecs[i].getModelObject();
        if (modelObject != null) {
            int mappedColumnIndex = mappedColumnCount;
            if (modelObject instanceof Model.ReservedSymbol && ((ReservedSymbol) modelObject).isTime()) {
                mappedColumnIndex = 0;
            }
            String origRefDataColumnName = refDataMappingSpecs[i].getReferenceDataColumnName();
            int origRefDataColumnIndex = refData.findColumn(origRefDataColumnName);
            if (origRefDataColumnIndex < 0) {
                throw new RuntimeException("reference data column named '" + origRefDataColumnName + "' not found");
            }
            double[] columnData = refData.getDataByColumn(origRefDataColumnIndex);
            if (modelObjectList.contains(modelObject)) {
                throw new RuntimeException("multiple reference data columns mapped to same model object '" + modelObject.getName() + "'");
            }
            modelObjectList.insertElementAt(modelObject, mappedColumnIndex);
            dataList.insertElementAt(columnData, mappedColumnIndex);
            mappedColumnCount++;
        }
    }
    // 
    if (modelObjectList.size() == 0) {
        throw new RuntimeException("reference data was not associated with model");
    }
    if (modelObjectList.size() == 1) {
        throw new RuntimeException("reference data was not associated with model, must map time and at least one other column");
    }
    boolean bFoundTimeVar = false;
    for (SymbolTableEntry ste : modelObjectList) {
        if (ste instanceof Model.ReservedSymbol && ((ReservedSymbol) ste).isTime()) {
            bFoundTimeVar = true;
            break;
        }
    }
    if (!bFoundTimeVar) {
        throw new RuntimeException("must map time column of reference data to model");
    }
    // 
    for (int i = 0; i < modelObjectList.size(); i++) {
        SymbolTableEntry modelObject = (SymbolTableEntry) modelObjectList.elementAt(i);
        try {
            // Find by name because MathSybolMapping has different 'objects' than refDataMapping 'objects'
            Variable variable = mathMapping.getMathSymbolMapping().findVariableByName(modelObject.getName());
            if (variable != null) {
                String symbol = variable.getName();
                rowColResultSet.addDataColumn(new ODESolverResultSetColumnDescription(symbol));
            } else if (modelObject instanceof Model.ReservedSymbol && ((Model.ReservedSymbol) modelObject).isTime()) {
                Model.ReservedSymbol time = (Model.ReservedSymbol) modelObject;
                String symbol = time.getName();
                rowColResultSet.addDataColumn(new ODESolverResultSetColumnDescription(symbol));
            }
        } catch (MathException | MatrixException | ExpressionException | ModelException e) {
            e.printStackTrace();
            throw new MappingException(e.getMessage(), e);
        }
    }
    // 
    // populate data columns (time and rest)
    // 
    double[] weights = new double[rowColResultSet.getColumnDescriptionsCount()];
    weights[0] = 1.0;
    int numRows = ((double[]) dataList.elementAt(0)).length;
    int numColumns = modelObjectList.size();
    for (int j = 0; j < numRows; j++) {
        double[] row = new double[numColumns];
        for (int i = 0; i < numColumns; i++) {
            row[i] = ((double[]) dataList.elementAt(i))[j];
            if (i > 0) {
                weights[i] += row[i] * row[i];
            }
        }
        rowColResultSet.addRow(row);
    }
    for (int i = 0; i < numColumns; i++) {
        if (weights[i] == 0) {
            weights[i] = 1;
        } else {
            weights[i] = 1 / weights[i];
        }
    }
    SimpleReferenceData remappedRefData = new SimpleReferenceData(rowColResultSet, weights);
    return remappedRefData;
}

Example 5 with ODESolverResultSetColumnDescription

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

the class MathTestingUtilities method getConstructedResultSet.

/**
 * Insert the method's description here.
 * Creation date: (1/17/2003 3:47:43 PM)
 * @return cbit.vcell.solver.ode.ODESolverResultSet
 * @param sim cbit.vcell.solver.Simulation
 */
public static ODESolverResultSet getConstructedResultSet(MathDescription mathDesc, double[] time) throws Exception {
    if (mathDesc.getGeometry().getDimension() != 0) {
        throw new RuntimeException("can only handle non-spatial simulations.");
    }
    Simulation sim = new Simulation(mathDesc);
    SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(sim, 0);
    ODESolverResultSet resultSet = new ODESolverResultSet();
    resultSet.addDataColumn(new ODESolverResultSetColumnDescription("t"));
    for (int i = 0; i < time.length; i++) {
        resultSet.addRow(new double[] { time[i] });
    }
    java.util.Enumeration<SubDomain> subDomainEnum = mathDesc.getSubDomains();
    String errorString = "Variable(s) : ";
    while (subDomainEnum.hasMoreElements()) {
        SubDomain subDomain = subDomainEnum.nextElement();
        java.util.Enumeration<Equation> enumEquations = subDomain.getEquations();
        while (enumEquations.hasMoreElements()) {
            Equation equation = enumEquations.nextElement();
            Expression constructedSolution = equation.getExactSolution();
            if (constructedSolution != null) {
                constructedSolution = new Expression(constructedSolution);
                constructedSolution.bindExpression(simSymbolTable);
                constructedSolution = simSymbolTable.substituteFunctions(constructedSolution);
                constructedSolution = constructedSolution.flatten();
                resultSet.addFunctionColumn(new FunctionColumnDescription(constructedSolution, equation.getVariable().getName(), null, equation.getVariable().getName(), false));
            } else {
                errorString = errorString + equation.getVariable().getName() + ", ";
            }
        }
    }
    if (!errorString.equals("Variable(s) : ")) {
        throw new RuntimeException(errorString + " don't have a constructed solution");
    }
    return resultSet;
}