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

Example 6 with RowColumnResultSet

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

the class Generate2DOptContext method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws ExpressionException {
    // get inputs
    RowColumnResultSet normExpDataset = context.getData(normExpData);
    RowColumnResultSet measurementErrorDataset = context.getData(normalizedMeasurementErrors);
    OptModel optmodel = context.getData(optModel);
    // do op
    Generate2DOptContextOp op = new Generate2DOptContextOp();
    ErrorFunction errorFunction = context.getData(this.errorFunction);
    OptContext optcontext = op.generate2DOptContext(optmodel, normExpDataset, measurementErrorDataset, errorFunction);
    // set output
    context.setData(optContext, optcontext);
}

Example 7 with RowColumnResultSet

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

the class GenerateReducedData method compute0.

@Override
protected void compute0(TaskContext context, final ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    // get input
    ROI[] rois = context.getData(imageDataROIs);
    ImageTimeSeries<? extends Image> simData = (ImageTimeSeries<? extends Image>) context.getData(imageTimeSeries);
    // do op
    GenerateReducedDataOp op = new GenerateReducedDataOp();
    RowColumnResultSet reducedData = op.generateReducedData(simData, rois);
    // set output
    context.setData(reducedROIData, reducedData);
}

Example 8 with RowColumnResultSet

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

the class ComputeMeasurementErrorOp method computeNormalizedMeasurementError.

public RowColumnResultSet computeNormalizedMeasurementError(NormalizedSampleFunction[] rois, int indexPostbleach, ImageTimeSeries<UShortImage> rawImageDataset, FloatImage prebleachAvgImage, final ClientTaskStatusSupport clientTaskStatusSupport) throws ImageException {
    UShortImage[] rawImages = rawImageDataset.getAllImages();
    double[] timeStamps = rawImageDataset.getImageTimeStamps();
    double[][] sigma = refreshNormalizedMeasurementError(rawImages, timeStamps, prebleachAvgImage, rois, indexPostbleach);
    String[] columnNames = new String[rois.length + 1];
    columnNames[0] = "t";
    for (int i = 0; i < rois.length; i++) {
        columnNames[i + 1] = rois[i].getName();
    }
    RowColumnResultSet rowColumnResultSet = new RowColumnResultSet(columnNames);
    double[] allTimePoints = timeStamps;
    for (int time = 0; time < (allTimePoints.length - indexPostbleach); time++) {
        double[] rowValues = new double[rois.length + 1];
        rowValues[0] = allTimePoints[time + indexPostbleach];
        for (int col = 0; col < rois.length; col++) {
            rowValues[col + 1] = sigma[col][time];
        }
        rowColumnResultSet.addRow(rowValues);
    }
    return rowColumnResultSet;
}

Example 9 with RowColumnResultSet

use of cbit.vcell.math.RowColumnResultSet 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 10 with RowColumnResultSet

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

the class ParameterEstimationTaskSimulatorIDA method getOdeSolverResultSet.

private ODESolverResultSet getOdeSolverResultSet(ParameterEstimationTask parameterEstimationTask, OptimizationSpec optSpec, OptimizationResultSet optResultSet) throws Exception {
    if (optResultSet == null) {
        return null;
    }
    String[] parameterNames = optResultSet.getOptSolverResultSet().getParameterNames();
    double[] bestEstimates = optResultSet.getOptSolverResultSet().getBestEstimates();
    // if we don't have parameter names or best estimates, return null. if we have them, we can run a simulation and generate a solution
    if (parameterNames == null || parameterNames.length == 0 || bestEstimates == null || bestEstimates.length == 0) {
        return null;
    }
    // check if we have solution or not, if not, generate a solution since we have the best estimates
    if (optResultSet.getSolutionNames() == null) {
        RowColumnResultSet rcResultSet = getRowColumnRestultSetByBestEstimations(parameterEstimationTask, parameterNames, bestEstimates);
        optResultSet.setSolutionFromRowColumnResultSet(rcResultSet);
    }
    String[] solutionNames = optResultSet.getSolutionNames();
    if (solutionNames != null && solutionNames.length > 0) {
        ODESolverResultSet odeSolverResultSet = new ODESolverResultSet();
        // add data column descriptions
        for (int i = 0; i < solutionNames.length; i++) {
            odeSolverResultSet.addDataColumn(new ODESolverResultSetColumnDescription(solutionNames[i]));
        }
        // 
        // add row data
        // 
        int numRows = optResultSet.getSolutionValues(0).length;
        for (int i = 0; i < numRows; i++) {
            odeSolverResultSet.addRow(optResultSet.getSolutionRow(i));
        }
        // 
        // make temporary simulation (with overrides for parameter values)
        // 
        MathDescription mathDesc = parameterEstimationTask.getSimulationContext().getMathDescription();
        Simulation simulation = new Simulation(mathDesc);
        SimulationSymbolTable simSymbolTable = new SimulationSymbolTable(simulation, 0);
        // 
        for (int i = 0; i < optSpec.getParameters().length; i++) {
            cbit.vcell.opt.Parameter parameter = optSpec.getParameters()[i];
            simulation.getMathOverrides().putConstant(new Constant(parameter.getName(), new Expression(parameter.getInitialGuess())));
        }
        // 
        for (int i = 0; i < parameterNames.length; i++) {
            simulation.getMathOverrides().putConstant(new Constant(parameterNames[i], new Expression(optResultSet.getOptSolverResultSet().getBestEstimates()[i])));
        }
        // 
        // add functions (evaluating them at optimal parameter)
        // 
        Vector<AnnotatedFunction> annotatedFunctions = simSymbolTable.createAnnotatedFunctionsList(mathDesc);
        for (AnnotatedFunction f : annotatedFunctions) {
            Expression funcExp = f.getExpression();
            for (int j = 0; j < parameterNames.length; j++) {
                funcExp.substituteInPlace(new Expression(parameterNames[j]), new Expression(optResultSet.getOptSolverResultSet().getBestEstimates()[j]));
            }
            odeSolverResultSet.addFunctionColumn(new FunctionColumnDescription(funcExp, f.getName(), null, f.getName(), false));
        }
        return odeSolverResultSet;
    } else {
        return null;
    }
}