Examples with Parameter cbit.vcell.opt.Parameter used on opensource projects

Example 51 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class MicroscopyXmlproducer method getXML.

private static Element getXML(ProfileDataElement profileDataElement) {
    Element profileDataElementNode = new Element(MicroscopyXMLTags.ProfieDataElementTag);
    profileDataElementNode.setAttribute(MicroscopyXMLTags.profileDataElementParameterNameAttrTag, profileDataElement.getParamName());
    profileDataElementNode.setAttribute(MicroscopyXMLTags.profileDataElementParameterValueAttrTag, profileDataElement.getParameterValue() + "");
    profileDataElementNode.setAttribute(MicroscopyXMLTags.profileDataElementLikelihoodAttrTag, profileDataElement.getLikelihood() + "");
    Parameter[] parameters = profileDataElement.getBestParameters();
    for (int i = 0; i < parameters.length; i++) {
        if (// some of parameters in reaction off rate model are null.
        parameters[i] != null) {
            profileDataElementNode.addContent(getXML(parameters[i]));
        }
    }
    return profileDataElementNode;
}

Example 52 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class NonGUIFRAPTest method runSolver.

/**
 * @param args
 */
public static void runSolver(String[] args) throws Exception {
    String startingIndexForRecovery = args[0];
    String freeDiffusionRateStr = args[1];
    String freeMobileFractionStr = args[2];
    String complexDiffusionRateStr = args[3];
    String complexMobileFractionStr = args[4];
    String bleachWhileMonitoringRateString = args[5];
    String immobileFractionStr = args[6];
    String bindingSiteConcentrationStr = args[7];
    String reacOnRateStr = args[8];
    String reacOffRateStr = args[9];
    String workingDirectoryPath = args[10];
    String inputFRAPDataFileName = args[11];
    String inputCellROIFileName = args[12];
    String inputBleachROIFileName = args[13];
    String inputBackgroundROIFileName = args[14];
    String outputXMLFileName = args[15];
    String commaSepTimeStamps = args[16];
    String commaSepExtentXYZ = args[17];
    LocalWorkspace localWorkspace = new LocalWorkspace(new File(workingDirectoryPath));
    ExternalDataFileContents extDataFileContents = readExternalDataContents(inputFRAPDataFileName, inputCellROIFileName, inputBleachROIFileName, inputBackgroundROIFileName);
    ROI cellROI = new ROI(extDataFileContents.cellROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name());
    ROI bleachROI = new ROI(extDataFileContents.bleachROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BLEACHED.name());
    ROI backgroundROI = new ROI(extDataFileContents.backgroundROIData.getImage(0, 0, 0), FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name());
    // Insert Time information
    double[] timeStamps = new double[extDataFileContents.imageData.getAllImages().length];
    StringTokenizer commaStringTokenizer = new StringTokenizer(commaSepTimeStamps, ",");
    int timeCount = 0;
    while (commaStringTokenizer.hasMoreTokens()) {
        timeStamps[timeCount] = Double.parseDouble(commaStringTokenizer.nextToken());
        timeCount++;
    }
    ImageDataset frapDataImageDataSet = new ImageDataset(extDataFileContents.imageData.getAllImages(), timeStamps, 1);
    // Insert Extent information
    commaStringTokenizer = new StringTokenizer(commaSepExtentXYZ, ",");
    Extent extent = new Extent(Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()), Double.parseDouble(commaStringTokenizer.nextToken()));
    frapDataImageDataSet.setExtent(extent);
    bleachROI.getRoiImages()[0].setExtent(extent);
    cellROI.getRoiImages()[0].setExtent(extent);
    backgroundROI.getRoiImages()[0].setExtent(extent);
    FRAPData frapData = FrapDataUtils.importFRAPDataFromImageDataSet(frapDataImageDataSet);
    frapData.addReplaceRoi(bleachROI);
    frapData.addReplaceRoi(cellROI);
    frapData.addReplaceRoi(backgroundROI);
    FRAPStudy frapStudy = new FRAPStudy();
    frapStudy.setFrapData(frapData);
    // old model parameters, need to rewrite
    // FRAPStudy.FRAPModelParameters frapModelParameters = new FRAPStudy.FRAPModelParameters(
    // new FRAPStudy.InitialModelParameters(freeDiffusionRateStr, freeMobileFractionStr, bleachWhileMonitoringRateString, startingIndexForRecovery),
    // null,
    // null);
    // frapStudy.setFrapModelParameters(frapModelParameters);
    frapStudy.refreshDependentROIs();
    ExternalDataInfo imageDatasetExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.IMAGE_EXTDATA_NAME);
    ExternalDataInfo roiExternalDataInfo = FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_EXTDATA_NAME);
    frapStudy.setFrapDataExternalDataInfo(imageDatasetExternalDataInfo);
    frapStudy.setRoiExternalDataInfo(roiExternalDataInfo);
    frapStudy.saveImageDatasetAsExternalData(localWorkspace, frapStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    frapStudy.saveROIsAsExternalData(localWorkspace, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
    // Double bleachWhileMonitoringRate =
    // (!bleachWhileMonitoringRateString.equals("-")
    // ?Double.parseDouble(bleachWhileMonitoringRateString)
    // :null);
    double fd, ff, bwmr, cd, cf, imf, bs, on, off;
    try {
        fd = Double.parseDouble(freeDiffusionRateStr);
        ff = Double.parseDouble(freeMobileFractionStr);
        bwmr = Double.parseDouble(bleachWhileMonitoringRateString);
        cd = Double.parseDouble(complexDiffusionRateStr);
        cf = Double.parseDouble(complexMobileFractionStr);
        imf = Double.parseDouble(immobileFractionStr);
        bs = Double.parseDouble(bindingSiteConcentrationStr);
        on = Double.parseDouble(reacOnRateStr);
        off = Double.parseDouble(reacOffRateStr);
    } catch (NumberFormatException e) {
        throw new Exception("Input parameters are not all valid. Check if they are empty or in illegal forms.");
    }
    BioModel bioModel = FRAPStudy.createNewSimBioModel(frapStudy, createParameterArray(fd, ff, bwmr, cd, cf, imf, bs, on, off), null, LocalWorkspace.createNewKeyValue(), LocalWorkspace.getDefaultOwner(), new Integer(frapStudy.getStartingIndexForRecovery()));
    frapStudy.setBioModel(bioModel);
    // no progress listener, need to change
    MicroscopyXmlproducer.writeXMLFile(frapStudy, new File(outputXMLFileName), true, null, false);
    FRAPStudy.runFVSolverStandalone(new File(localWorkspace.getDefaultSimDataDirectory()), bioModel.getSimulation(0), imageDatasetExternalDataInfo.getExternalDataIdentifier(), roiExternalDataInfo.getExternalDataIdentifier(), null);
    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(bioModel.getSimulations()[0].getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), FieldDataFileOperationSpec.JOBINDEX_DEFAULT);
    PDEDataManager simulationDataManager = new PDEDataManager(null, localWorkspace.getVCDataManager(), vcSimulationDataIdentifier);
    double[] frapDataTimeStamps = frapData.getImageDataset().getImageTimeStamps();
    VCDataManager testVCDataManager = localWorkspace.getVCDataManager();
    double[] prebleachAverage = testVCDataManager.getSimDataBlock(null, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), "prebleach_avg", 0).getData();
    // TODO: need to create parameters here.
    Parameter[] parameters = null;
    SpatialAnalysisResults spatialAnalysisResults = FRAPStudy.spatialAnalysis(simulationDataManager, new Integer(frapStudy.getStartingIndexForRecovery()), frapDataTimeStamps[new Integer(frapStudy.getStartingIndexForRecovery())], parameters, frapData, prebleachAverage);
    dumpSummaryReport(spatialAnalysisResults, frapDataTimeStamps, new Integer(startingIndexForRecovery).intValue(), new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
    dumpSpatialResults(spatialAnalysisResults, frapDataTimeStamps, new File(workingDirectoryPath, "nonguiSpatialResults.txt"));
}

Example 53 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class NonGUIFRAPTest method createParameterArray.

private static Parameter[] createParameterArray(double freeDiffRate, double freeFraction, double monitorBleachRate, double complexDifffRate, double complexFraction, double immFraction, double bsConc, double onRate, double offRate) {
    Parameter[] params = null;
    Parameter freeDiff = new cbit.vcell.opt.Parameter(STR_FREE_DIFF_RATE, FRAPModel.REF_DIFFUSION_RATE_PARAM.getLowerBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getUpperBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getScale(), freeDiffRate);
    Parameter freeFrac = new cbit.vcell.opt.Parameter(STR_FREE_FRACTION, FRAPModel.REF_MOBILE_FRACTION_PARAM.getLowerBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getUpperBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getScale(), freeFraction);
    Parameter bleachWhileMonitoringRate = new cbit.vcell.opt.Parameter(STR_BLEACH_MONITOR_RATE, FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getLowerBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getUpperBound(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getScale(), monitorBleachRate);
    Parameter complexdiff = new Parameter(STR_COMPLEX_DIFF_RATE, FRAPModel.REF_DIFFUSION_RATE_PARAM.getLowerBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getUpperBound(), FRAPModel.REF_DIFFUSION_RATE_PARAM.getScale(), complexDifffRate);
    Parameter complexFrac = new Parameter(STR_COMPLEX_FRACTION, FRAPModel.REF_MOBILE_FRACTION_PARAM.getLowerBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getUpperBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getScale(), complexFraction);
    Parameter immFrac = new Parameter(STR_IMMOBILE_FRACTION, FRAPModel.REF_MOBILE_FRACTION_PARAM.getLowerBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getUpperBound(), FRAPModel.REF_MOBILE_FRACTION_PARAM.getScale(), immFraction);
    Parameter bsConcentration = new Parameter(STR_BINDING_SITE_CONCENTRATION, 0, 1, 1, bsConc);
    Parameter onReacRate = new Parameter(STR_ON_RATE, 0, 1e6, 1, onRate);
    Parameter offReacRate = new Parameter(STR_OFF_RATE, 0, 1e6, 1, offRate);
    params = new Parameter[] { freeDiff, freeFrac, bleachWhileMonitoringRate, complexdiff, complexFrac, immFrac, bsConcentration, onReacRate, offReacRate };
    return params;
}

Example 54 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class ModelOptimizationMapping method computeOptimizationSpec.

/**
 * Insert the method's description here.
 * Creation date: (8/22/2005 9:26:52 AM)
 * @return cbit.vcell.opt.OptimizationSpec
 * @param modelOptimizationSpec cbit.vcell.modelopt.ModelOptimizationSpec
 */
MathSymbolMapping computeOptimizationSpec() throws MathException, MappingException {
    if (getModelOptimizationSpec().getReferenceData() == null) {
        System.out.println("no referenced data defined");
        return null;
    }
    OptimizationSpec optSpec = new OptimizationSpec();
    optSpec.setComputeProfileDistributions(modelOptimizationSpec.isComputeProfileDistributions());
    parameterMappings = null;
    // 
    // get original MathDescription (later to be substituted for local/global parameters).
    // 
    SimulationContext simContext = modelOptimizationSpec.getSimulationContext();
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathDescription origMathDesc = null;
    mathSymbolMapping = null;
    try {
        origMathDesc = mathMapping.getMathDescription();
        mathSymbolMapping = mathMapping.getMathSymbolMapping();
    } catch (MatrixException e) {
        e.printStackTrace(System.out);
        throw new MappingException(e.getMessage());
    } catch (ModelException e) {
        e.printStackTrace(System.out);
        throw new MappingException(e.getMessage());
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new MathException(e.getMessage());
    }
    // 
    // create objective function (mathDesc and data)
    // 
    ReferenceData referenceData = getRemappedReferenceData(mathMapping);
    if (referenceData == null) {
        throw new RuntimeException("no referenced data defined");
    }
    // 
    // get parameter mappings
    // 
    ParameterMappingSpec[] parameterMappingSpecs = modelOptimizationSpec.getParameterMappingSpecs();
    Vector<ParameterMapping> parameterMappingList = new Vector<ParameterMapping>();
    Variable[] allVars = (Variable[]) BeanUtils.getArray(origMathDesc.getVariables(), Variable.class);
    for (int i = 0; i < parameterMappingSpecs.length; i++) {
        cbit.vcell.model.Parameter modelParameter = parameterMappingSpecs[i].getModelParameter();
        String mathSymbol = null;
        Variable mathVariable = null;
        if (mathSymbolMapping != null) {
            Variable variable = mathSymbolMapping.getVariable(modelParameter);
            if (variable != null) {
                mathSymbol = variable.getName();
            }
            if (mathSymbol != null) {
                mathVariable = origMathDesc.getVariable(mathSymbol);
            }
        }
        if (mathVariable != null) {
            if (parameterMappingSpecs[i].isSelected()) {
                if (parameterMappingSpecs[i].getHigh() < parameterMappingSpecs[i].getLow()) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is greater than its upper bound.");
                }
                if (parameterMappingSpecs[i].getCurrent() < parameterMappingSpecs[i].getLow()) {
                    throw new MathException("The initial guess of '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is smaller than its lower bound.");
                }
                if (parameterMappingSpecs[i].getCurrent() > parameterMappingSpecs[i].getHigh()) {
                    throw new MathException("The initial guess of '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is greater than its upper bound.");
                }
                if (parameterMappingSpecs[i].getLow() < 0) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is negative. All lower bounds must not be negative.");
                }
                if (Double.isInfinite(parameterMappingSpecs[i].getLow())) {
                    throw new MathException("The lower bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is infinity. Lower bounds must not be infinity.");
                }
                if (parameterMappingSpecs[i].getHigh() <= 0) {
                    throw new MathException("The upper bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is negative. All upper bounds must be positive.");
                }
                if (Double.isInfinite(parameterMappingSpecs[i].getHigh())) {
                    throw new MathException("The upper bound for Parameter '" + parameterMappingSpecs[i].getModelParameter().getName() + "' is infinity. Upper bounds must not be infinity.");
                }
            }
            double low = parameterMappingSpecs[i].isSelected() && parameterMappingSpecs[i].getLow() == 0 ? 1e-8 : parameterMappingSpecs[i].getLow();
            double high = parameterMappingSpecs[i].getHigh();
            double scale = Math.abs(parameterMappingSpecs[i].getCurrent()) < 1.0E-10 ? 1.0 : Math.abs(parameterMappingSpecs[i].getCurrent());
            double current = parameterMappingSpecs[i].getCurrent();
            low = Math.min(low, current);
            high = Math.max(high, current);
            Parameter optParameter = new Parameter(mathSymbol, low, high, scale, current);
            ParameterMapping parameterMapping = new ParameterMapping(modelParameter, optParameter, mathVariable);
            // 
            if (mathVariable instanceof Constant) {
                Constant origConstant = (Constant) mathVariable;
                for (int j = 0; j < allVars.length; j++) {
                    if (allVars[j].equals(origConstant)) {
                        if (parameterMappingSpecs[i].isSelected()) {
                            allVars[j] = new ParameterVariable(origConstant.getName());
                        } else {
                            allVars[j] = new Constant(origConstant.getName(), new Expression(optParameter.getInitialGuess()));
                        }
                        break;
                    }
                }
            }
            // 
            if (parameterMappingSpecs[i].isSelected()) {
                parameterMappingList.add(parameterMapping);
            }
        }
    }
    parameterMappings = (ParameterMapping[]) BeanUtils.getArray(parameterMappingList, ParameterMapping.class);
    try {
        origMathDesc.setAllVariables(allVars);
    } catch (ExpressionBindingException e) {
        e.printStackTrace(System.out);
        throw new MathException(e.getMessage());
    }
    // 
    for (int i = 0; i < parameterMappings.length; i++) {
        optSpec.addParameter(parameterMappings[i].getOptParameter());
    }
    Vector<Issue> issueList = new Vector<Issue>();
    IssueContext issueContext = new IssueContext();
    optSpec.gatherIssues(issueContext, issueList);
    for (int i = 0; i < issueList.size(); i++) {
        Issue issue = issueList.elementAt(i);
        if (issue.getSeverity() == Issue.SEVERITY_ERROR) {
            throw new RuntimeException(issue.getMessage());
        }
    }
    // 
    // 
    // 
    optimizationSpec = optSpec;
    return mathSymbolMapping;
}

Example 55 with Parameter

use of cbit.vcell.opt.Parameter in project vcell by virtualcell.

the class OptUtils method getAugmentedObjectiveFunction.

/**
 * Insert the method's description here.
 * Creation date: (8/4/2005 3:26:14 PM)
 * @return function.AugmentedObjectiveFunction
 * @param optSpec cbit.vcell.opt.OptimizationSpec
 * @param power double
 * @param mu double
 */
public static AugmentedObjectiveFunction getAugmentedObjectiveFunction(OptimizationSpec optSpec, double power, double mu, OptSolverCallbacks optSolverCallbacks) throws cbit.vcell.parser.ExpressionException {
    Parameter[] parameters = optSpec.getParameters();
    // 
    // build symbol list
    // 
    String[] origSymbols = optSpec.getParameterNames();
    String[] scaledSymbols = optSpec.getScaledParameterNames();
    double[] scaleFactors = optSpec.getScaleFactors();
    ScalarFunction objFunction = null;
    if (optSpec.getObjectiveFunction() instanceof ExplicitObjectiveFunction) {
        ExplicitObjectiveFunction explicitObjectiveFunction = (ExplicitObjectiveFunction) optSpec.getObjectiveFunction();
        // 
        // build objective function
        // 
        objFunction = new DynamicScalarFunction(explicitObjectiveFunction.getScaledExpression(origSymbols, scaledSymbols, scaleFactors), scaledSymbols);
    } else if (optSpec.getObjectiveFunction() instanceof ImplicitObjectiveFunction) {
        ImplicitObjectiveFunction implicitObjectiveFunction = (ImplicitObjectiveFunction) optSpec.getObjectiveFunction();
        // 
        // build objective function
        // 
        objFunction = implicitObjectiveFunction.getObjectiveFunction();
    } else if (optSpec.getObjectiveFunction() instanceof ExplicitFitObjectiveFunction) {
        ExplicitFitObjectiveFunction explicitFitObjectiveFunction = (ExplicitFitObjectiveFunction) optSpec.getObjectiveFunction();
        objFunction = explicitFitObjectiveFunction.getScalarFunction();
    } else {
        throw new RuntimeException("unsupported objective function type : " + optSpec.getObjectiveFunction().getClass().getName());
    }
    // 
    // build equality and inequality constraints
    // 
    DynamicVectorFunction equalityConstraints = null;
    DynamicVectorFunction inequalityConstraints = null;
    Constraint[] constraints = optSpec.getConstraints();
    Vector equExpList = new Vector();
    Vector inequExpList = new Vector();
    // 
    for (int i = 0; i < constraints.length; i++) {
        ConstraintType type = constraints[i].getConstraintType();
        if (type.equals(ConstraintType.LinearEquality) || type.equals(ConstraintType.NonlinearEquality)) {
            equExpList.add(constraints[i].getExpression());
        } else {
            inequExpList.add(constraints[i].getExpression());
        }
    }
    // 
    for (int i = 0; i < parameters.length; i++) {
        if (!Double.isInfinite(parameters[i].getLowerBound())) {
            inequExpList.add(new Expression("(" + parameters[i].getLowerBound() + " - " + parameters[i].getName() + ")/" + scaleFactors[i]));
        }
        if (!Double.isInfinite(parameters[i].getUpperBound())) {
            inequExpList.add(new Expression("(" + parameters[i].getName() + " - " + parameters[i].getUpperBound() + ")/" + scaleFactors[i]));
        }
    }
    if (equExpList.size() > 0) {
        Expression[] exps = (Expression[]) org.vcell.util.BeanUtils.getArray(equExpList, Expression.class);
        equalityConstraints = new DynamicVectorFunction(exps, origSymbols);
    }
    if (inequExpList.size() > 0) {
        Expression[] exps = (Expression[]) org.vcell.util.BeanUtils.getArray(inequExpList, Expression.class);
        inequalityConstraints = new DynamicVectorFunction(exps, origSymbols);
    }
    AugmentedObjectiveFunction augmentedObjFunc = new AugmentedObjectiveFunction(objFunction, equalityConstraints, inequalityConstraints, power, mu, optSolverCallbacks);
    return augmentedObjFunc;
}