Examples with OptRunResultSet cbit.vcell.opt.OptSolverResultSet.OptRunResultSet used on opensource projects

Example 1 with OptRunResultSet

use of cbit.vcell.opt.OptSolverResultSet.OptRunResultSet in project vcell by virtualcell.

the class OptXmlReader method getOptRunResultSet.

private static OptRunResultSet getOptRunResultSet(Element optRunElement) throws DataConversionException {
    double bestObjectFuncValue = optRunElement.getAttribute(OptXmlTags.OptSolverResultSetBestObjectiveFunction_Attr).getDoubleValue();
    long numObjectFuncEvals = optRunElement.getAttribute(OptXmlTags.OptSolverResultSetNumObjectiveFunctionEvaluations_Attr).getLongValue();
    String status = optRunElement.getAttributeValue(OptXmlTags.OptSolverResultSetStatus_Attr);
    Attribute statusMessageAttr = optRunElement.getAttribute(OptXmlTags.OptSolverResultSetStatusMessage_Attr);
    List<Element> paramElementList = optRunElement.getChildren(OptXmlTags.Parameter_Tag);
    String[] parameterNames = new String[paramElementList.size()];
    double[] parameterValues = new double[paramElementList.size()];
    int count = 0;
    for (Element parameterElement : paramElementList) {
        parameterNames[count] = parameterElement.getAttributeValue(OptXmlTags.ParameterName_Attr);
        parameterValues[count] = Double.parseDouble(parameterElement.getAttributeValue(OptXmlTags.ParameterBestValue_Attr));
        count++;
    }
    int statusID = OptimizationStatus.statusFromXMLName(status);
    String statusMessage = null;
    if (statusMessageAttr != null) {
        statusMessage = statusMessageAttr.getValue();
    }
    OptimizationStatus optimizationStatus = new OptimizationStatus(statusID, statusMessage);
    OptRunResultSet optRun = new OptRunResultSet(parameterValues, new Double(bestObjectFuncValue), numObjectFuncEvals, optimizationStatus);
    return optRun;
}

Example 2 with OptRunResultSet

use of cbit.vcell.opt.OptSolverResultSet.OptRunResultSet in project vcell by virtualcell.

the class ReactionDominantTest method outputProfileLikelihood.

private void outputProfileLikelihood(ProfileDistribution pd, int paramIdx, String fixedParamName, File outputDir) {
    try {
        System.out.println("Writing profile likelihood...");
        // output results
        String outFileName = outputDir.getAbsolutePath() + "\\" + fixedParamName + "_profileLikelihood" + ".txt";
        File outFile = new File(outFileName);
        FileWriter fstream = new FileWriter(outFile);
        BufferedWriter out = new BufferedWriter(fstream);
        // output profile
        out.write("Log base 10 param value" + "\t" + "error");
        ArrayList<OptRunResultSet> orrs = pd.getOptRunResultSetList();
        for (int i = 0; i < orrs.size(); i++) {
            out.newLine();
            String rowStr = Math.log10(orrs.get(i).getParameterValues()[paramIdx]) + "\t" + orrs.get(i).getObjectiveFunctionValue();
            out.write(rowStr);
        }
        out.close();
        System.out.println("Output is done. Restults saved to " + outFileName);
    } catch (IOException e) {
        e.printStackTrace(System.out);
    }
}

Example 3 with OptRunResultSet

use of cbit.vcell.opt.OptSolverResultSet.OptRunResultSet in project vcell by virtualcell.

the class ParameterEstimationTaskXMLPersistence method getParameterEstimationTask.

/**
 * Insert the method's description here.
 * Creation date: (5/5/2006 4:50:36 PM)
 * @return cbit.vcell.modelopt.ParameterEstimationTask
 * @param element org.jdom.Element
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
public static ParameterEstimationTask getParameterEstimationTask(Element parameterEstimationTaskElement, SimulationContext simContext) throws ExpressionException, MappingException, MathException, java.beans.PropertyVetoException {
    Namespace ns = parameterEstimationTaskElement.getNamespace();
    ParameterEstimationTask parameterEstimationTask = new ParameterEstimationTask(simContext);
    String name = parameterEstimationTaskElement.getAttributeValue(NameAttribute);
    parameterEstimationTask.setName(name);
    Element annotationElement = parameterEstimationTaskElement.getChild(AnnotationTag, ns);
    if (annotationElement != null) {
        String annotationText = annotationElement.getText();
        parameterEstimationTask.setAnnotation(annotationText);
    }
    // 
    // read ParameterMappingSpecs
    // 
    Element parameterMappingSpecListElement = parameterEstimationTaskElement.getChild(ParameterMappingSpecListTag, ns);
    if (parameterMappingSpecListElement != null) {
        List<Element> parameterMappingSpecElementList = parameterMappingSpecListElement.getChildren(ParameterMappingSpecTag, ns);
        for (Element parameterMappingSpecElement : parameterMappingSpecElementList) {
            String parameterName = parameterMappingSpecElement.getAttributeValue(ParameterReferenceAttribute);
            SymbolTableEntry ste = getSymbolTableEntry(simContext, parameterName);
            if (ste instanceof Parameter) {
                Parameter parameter = (Parameter) ste;
                ParameterMappingSpec parameterMappingSpec = parameterEstimationTask.getModelOptimizationSpec().getParameterMappingSpec(parameter);
                if (parameterMappingSpec != null) {
                    String lowLimitString = parameterMappingSpecElement.getAttributeValue(LowLimitAttribute);
                    if (lowLimitString != null) {
                        parameterMappingSpec.setLow(parseDouble(lowLimitString));
                    }
                    String highLimitString = parameterMappingSpecElement.getAttributeValue(HighLimitAttribute);
                    if (highLimitString != null) {
                        parameterMappingSpec.setHigh(parseDouble(highLimitString));
                    }
                    String currentValueString = parameterMappingSpecElement.getAttributeValue(CurrentValueAttribute);
                    if (currentValueString != null) {
                        parameterMappingSpec.setCurrent(Double.parseDouble(currentValueString));
                    }
                    String selectedString = parameterMappingSpecElement.getAttributeValue(SelectedAttribute);
                    if (selectedString != null) {
                        parameterMappingSpec.setSelected(Boolean.valueOf(selectedString).booleanValue());
                    }
                }
            } else {
                System.out.println("couldn't read parameterMappingSpec '" + parameterName + "', ste=" + ste);
            }
        }
    }
    // 
    // read ReferenceData
    // 
    Element referenceDataElement = parameterEstimationTaskElement.getChild(ReferenceDataTag, ns);
    if (referenceDataElement != null) {
        String numRowsText = referenceDataElement.getAttributeValue(NumRowsAttribute);
        String numColsText = referenceDataElement.getAttributeValue(NumColumnsAttribute);
        // int numRows = Integer.parseInt(numRowsText);
        int numCols = Integer.parseInt(numColsText);
        // 
        // read columns
        // 
        String[] columnNames = new String[numCols];
        double[] columnWeights = new double[numCols];
        int columnCounter = 0;
        Element dataColumnListElement = referenceDataElement.getChild(DataColumnListTag, ns);
        List<Element> dataColumnList = dataColumnListElement.getChildren(DataColumnTag, ns);
        for (Element dataColumnElement : dataColumnList) {
            columnNames[columnCounter] = dataColumnElement.getAttributeValue(NameAttribute);
            columnWeights[columnCounter] = Double.parseDouble(dataColumnElement.getAttributeValue(WeightAttribute));
            columnCounter++;
        }
        // 
        // read rows
        // 
        Vector<double[]> rowDataVector = new Vector<double[]>();
        Element dataRowListElement = referenceDataElement.getChild(DataRowListTag, ns);
        List<Element> dataRowList = dataRowListElement.getChildren(DataRowTag, ns);
        for (Element dataRowElement : dataRowList) {
            String rowText = dataRowElement.getText();
            CommentStringTokenizer tokens = new CommentStringTokenizer(rowText);
            double[] rowData = new double[numCols];
            for (int j = 0; j < numCols; j++) {
                if (tokens.hasMoreTokens()) {
                    String token = tokens.nextToken();
                    rowData[j] = Double.parseDouble(token);
                } else {
                    throw new RuntimeException("failed to read row data for ReferenceData");
                }
            }
            rowDataVector.add(rowData);
        }
        ReferenceData referenceData = new SimpleReferenceData(columnNames, columnWeights, rowDataVector);
        parameterEstimationTask.getModelOptimizationSpec().setReferenceData(referenceData);
    }
    // 
    // read ReferenceDataMappingSpecs
    // 
    Element referenceDataMappingSpecListElement = parameterEstimationTaskElement.getChild(ReferenceDataMappingSpecListTag, ns);
    if (referenceDataMappingSpecListElement != null) {
        List<Element> referenceDataMappingSpecList = referenceDataMappingSpecListElement.getChildren(ReferenceDataMappingSpecTag, ns);
        for (Element referenceDataMappingSpecElement : referenceDataMappingSpecList) {
            String referenceDataColumnName = referenceDataMappingSpecElement.getAttributeValue(ReferenceDataColumnNameAttribute);
            String referenceDataModelSymbolName = referenceDataMappingSpecElement.getAttributeValue(ReferenceDataModelSymbolAttribute);
            ReferenceDataMappingSpec referenceDataMappingSpec = parameterEstimationTask.getModelOptimizationSpec().getReferenceDataMappingSpec(referenceDataColumnName);
            SymbolTableEntry modelSymbolTableEntry = null;
            if (referenceDataModelSymbolName != null) {
                modelSymbolTableEntry = getSymbolTableEntry(simContext, referenceDataModelSymbolName);
                if (referenceDataMappingSpec != null && modelSymbolTableEntry != null) {
                    referenceDataMappingSpec.setModelObject(modelSymbolTableEntry);
                }
            }
        }
    }
    // 
    // read OptimizationSolverSpec
    // 
    Element optimizationSolverSpecElement = parameterEstimationTaskElement.getChild(OptimizationSolverSpecTag, ns);
    if (optimizationSolverSpecElement != null) {
        OptimizationSolverSpec optSolverSpec = null;
        String optimizationSolverTypeName = optimizationSolverSpecElement.getAttributeValue(OptimizationSolverTypeAttribute);
        // getting parameters
        Element optimizationSolverParameterList = optimizationSolverSpecElement.getChild(OptimizationListOfParametersTag, ns);
        if (optimizationSolverParameterList != null) {
            List<Element> listOfSolverParams = optimizationSolverParameterList.getChildren(OptimizationParameterTag, ns);
            CopasiOptimizationMethod copasiOptMethod = null;
            if (listOfSolverParams != null && listOfSolverParams.size() > 0) {
                List<CopasiOptimizationParameter> copasiSolverParams = new ArrayList<CopasiOptimizationParameter>();
                for (Element solverParam : listOfSolverParams) {
                    String paramName = solverParam.getAttributeValue(OptimizationParameterNameAttribute);
                    double paramValue = Double.parseDouble(solverParam.getAttributeValue(OptimizationParameterValueAttribute));
                    CopasiOptimizationParameter copasiParam = new CopasiOptimizationParameter(getCopasiOptimizationParameterTypeByName(paramName), paramValue);
                    copasiSolverParams.add(copasiParam);
                }
                copasiOptMethod = new CopasiOptimizationMethod(getCopasiOptimizationMethodTypeByName(optimizationSolverTypeName), copasiSolverParams.toArray(new CopasiOptimizationParameter[copasiSolverParams.size()]));
            } else // no parameters
            {
                copasiOptMethod = new CopasiOptimizationMethod(getCopasiOptimizationMethodTypeByName(optimizationSolverTypeName), new CopasiOptimizationParameter[0]);
            }
            optSolverSpec = new OptimizationSolverSpec(copasiOptMethod);
            // add number of runs attribute
            String numOfRunsStr = optimizationSolverSpecElement.getAttributeValue(OptimizationSolverNumOfRunsAttribute);
            if (numOfRunsStr != null) {
                int numOfRuns = Integer.parseInt(numOfRunsStr);
                optSolverSpec.setNumOfRuns(numOfRuns);
            }
        }
        parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
    }
    if (// optimization solver spec is null create a default copasi evolutionary programming
    optimizationSolverSpecElement == null || parameterEstimationTask.getOptimizationSolverSpec() == null) {
        OptimizationSolverSpec optSolverSpec = new OptimizationSolverSpec(new CopasiOptimizationMethod(CopasiOptimizationMethodType.EvolutionaryProgram));
        parameterEstimationTask.setOptimizationSolverSpec(optSolverSpec);
    }
    // read optimization solver result set
    Element optimizationResultSetElement = parameterEstimationTaskElement.getChild(OptXmlTags.OptimizationResultSet_Tag, ns);
    if (optimizationResultSetElement != null) {
        OptimizationResultSet optResultSet = null;
        // read optsolverResultSet
        if (optimizationResultSetElement.getChild(OptXmlTags.bestOptRunResultSet_Tag, ns) != null) {
            Element optSolverResultSetElement = optimizationResultSetElement.getChild(OptXmlTags.bestOptRunResultSet_Tag, ns);
            OptSolverResultSet optSolverResultSet = null;
            // get best parameters, best func value, number of evaluations and construct an optRunResultSet
            Element paramListElement = optSolverResultSetElement.getChild(OptimizationListOfParametersTag, ns);
            OptRunResultSet optRunResultSet = null;
            List<String> paramNames = new ArrayList<String>();
            List<Double> paramValues = new ArrayList<Double>();
            if (paramListElement != null && !paramListElement.getChildren().isEmpty()) {
                List<Element> paramElements = paramListElement.getChildren(OptimizationParameterTag, ns);
                if (paramElements != null) {
                    for (Element paramElement : paramElements) {
                        String paramName = paramElement.getAttributeValue(OptimizationParameterNameAttribute);
                        double paramValue = Double.parseDouble(paramElement.getAttributeValue(OptimizationParameterValueAttribute));
                        paramNames.add(paramName);
                        paramValues.add(paramValue);
                    }
                }
            }
            Element bestFuncValueElement = optSolverResultSetElement.getChild(OptXmlTags.ObjectiveFunction_Tag, ns);
            double bestFuncValue = Double.parseDouble(bestFuncValueElement.getAttributeValue(OptimizationParameterValueAttribute));
            Element numEvaluationsElement = optSolverResultSetElement.getChild(OptXmlTags.OptSolverResultSetFunctionEvaluations_Tag, ns);
            long numEvaluations = Long.parseLong(numEvaluationsElement.getAttributeValue(OptimizationParameterValueAttribute));
            // change List<Double> to double[]
            double[] values = new double[paramValues.size()];
            int index = 0;
            for (Double value : paramValues) {
                values[index++] = value;
            }
            optRunResultSet = new OptRunResultSet(values, bestFuncValue, numEvaluations, null);
            // create optSolverResultSet
            optSolverResultSet = new OptSolverResultSet(paramNames.toArray(new String[paramNames.size()]), optRunResultSet);
            // create optimization result set
            optResultSet = new OptimizationResultSet(optSolverResultSet, null);
        }
        parameterEstimationTask.setOptimizationResultSet(optResultSet);
    }
    return parameterEstimationTask;
}

Example 4 with OptRunResultSet

use of cbit.vcell.opt.OptSolverResultSet.OptRunResultSet in project vcell by virtualcell.

the class CopasiOptimizationSolver method solveRemoteApi.

public static OptimizationResultSet solveRemoteApi(ParameterEstimationTaskSimulatorIDA parestSimulator, ParameterEstimationTask parameterEstimationTask, CopasiOptSolverCallbacks optSolverCallbacks, MathMappingCallback mathMappingCallback) throws IOException, ExpressionException, OptimizationException {
    try {
        OptProblem optProblem = CopasiServicePython.makeOptProblem(parameterEstimationTask);
        boolean bIgnoreCertProblems = true;
        boolean bIgnoreHostMismatch = true;
        // e.g. vcell.serverhost=vcellapi.cam.uchc.edu:8080
        String serverHost = PropertyLoader.getRequiredProperty(PropertyLoader.vcellServerHost);
        String[] parts = serverHost.split(":");
        String host = parts[0];
        int port = Integer.parseInt(parts[1]);
        VCellApiClient apiClient = new VCellApiClient(host, port, bIgnoreCertProblems, bIgnoreHostMismatch);
        TSerializer serializer = new TSerializer(new TJSONProtocol.Factory());
        String optProblemJson = serializer.toString(optProblem);
        String optimizationId = apiClient.submitOptimization(optProblemJson);
        // 20 second minute timeout
        final long TIMEOUT_MS = 1000 * 20;
        long startTime = System.currentTimeMillis();
        OptRun optRun = null;
        while ((System.currentTimeMillis() - startTime) < TIMEOUT_MS) {
            if (optSolverCallbacks.getStopRequested()) {
                throw new RuntimeException(STOP_REQUESTED);
            }
            String optRunJson = apiClient.getOptRunJson(optimizationId);
            TDeserializer deserializer = new TDeserializer(new TJSONProtocol.Factory());
            optRun = new OptRun();
            deserializer.deserialize(optRun, optRunJson.getBytes());
            OptRunStatus status = optRun.status;
            if (status == OptRunStatus.Complete) {
                System.out.println("job " + optimizationId + ": status " + status + " " + optRun.getOptResultSet().toString());
                break;
            }
            if (status == OptRunStatus.Failed) {
                throw new RuntimeException("optimization failed, message=" + optRun.statusMessage);
            }
            System.out.println("job " + optimizationId + ": status " + status);
            try {
                Thread.sleep(1000);
            } catch (InterruptedException e) {
            }
        }
        System.out.println("done with optimization");
        OptResultSet optResultSet = optRun.getOptResultSet();
        int numFittedParameters = optResultSet.getOptParameterValues().size();
        String[] paramNames = new String[numFittedParameters];
        double[] paramValues = new double[numFittedParameters];
        for (int pIndex = 0; pIndex < numFittedParameters; pIndex++) {
            OptParameterValue optParamValue = optResultSet.getOptParameterValues().get(pIndex);
            paramNames[pIndex] = optParamValue.parameterName;
            paramValues[pIndex] = optParamValue.bestValue;
        }
        OptimizationStatus status = new OptimizationStatus(OptimizationStatus.NORMAL_TERMINATION, optRun.statusMessage);
        OptRunResultSet optRunResultSet = new OptRunResultSet(paramValues, optResultSet.objectiveFunction, optResultSet.numFunctionEvaluations, status);
        OptSolverResultSet copasiOptSolverResultSet = new OptSolverResultSet(paramNames, optRunResultSet);
        RowColumnResultSet copasiRcResultSet = parestSimulator.getRowColumnRestultSetByBestEstimations(parameterEstimationTask, paramNames, paramValues);
        OptimizationResultSet copasiOptimizationResultSet = new OptimizationResultSet(copasiOptSolverResultSet, copasiRcResultSet);
        System.out.println("-----------SOLUTION FROM VCellAPI---------------\n" + optResultSet.toString());
        return copasiOptimizationResultSet;
    } catch (Exception e) {
        e.printStackTrace(System.out);
        if (e.getMessage() != null && e.getMessage().equals(STOP_REQUESTED)) {
            throw UserCancelException.CANCEL_GENERIC;
        }
        throw new OptimizationException(e.getCause() != null ? e.getCause().getMessage() : e.getMessage());
    }
}

Example 5 with OptRunResultSet

use of cbit.vcell.opt.OptSolverResultSet.OptRunResultSet in project vcell by virtualcell.

the class CopasiOptimizationSolver method solveLocalPython.

public static OptimizationResultSet solveLocalPython(ParameterEstimationTaskSimulatorIDA parestSimulator, ParameterEstimationTask parameterEstimationTask, CopasiOptSolverCallbacks optSolverCallbacks, MathMappingCallback mathMappingCallback) throws IOException, ExpressionException, OptimizationException {
    File dir = Files.createTempDirectory("parest", new FileAttribute<?>[] {}).toFile();
    try {
        String prefix = "testing_" + Math.abs(new Random().nextInt(10000));
        File optProblemThriftFile = new File(dir, prefix + ".optprob.bin");
        File optRunFile = new File(dir, prefix + ".optrun.bin");
        // 
        // Setup Python COPASI opt problem and write to disk
        // 
        OptProblem optProblem = CopasiServicePython.makeOptProblem(parameterEstimationTask);
        CopasiServicePython.writeOptProblem(optProblemThriftFile, optProblem);
        // 
        // run Python COPASI opt problem
        // 
        CopasiServicePython.runCopasiPython(optProblemThriftFile, optRunFile);
        if (!optRunFile.exists()) {
            throw new RuntimeException("COPASI optimization output file not found:\n" + optRunFile.getAbsolutePath());
        }
        OptRun optRun = CopasiServicePython.readOptRun(optRunFile);
        OptResultSet optResultSet = optRun.getOptResultSet();
        int numFittedParameters = optResultSet.getOptParameterValues().size();
        String[] paramNames = new String[numFittedParameters];
        double[] paramValues = new double[numFittedParameters];
        for (int pIndex = 0; pIndex < numFittedParameters; pIndex++) {
            OptParameterValue optParamValue = optResultSet.getOptParameterValues().get(pIndex);
            paramNames[pIndex] = optParamValue.parameterName;
            paramValues[pIndex] = optParamValue.bestValue;
        }
        OptimizationStatus status = new OptimizationStatus(OptimizationStatus.NORMAL_TERMINATION, optRun.statusMessage);
        OptRunResultSet optRunResultSet = new OptRunResultSet(paramValues, optResultSet.objectiveFunction, optResultSet.numFunctionEvaluations, status);
        OptSolverResultSet copasiOptSolverResultSet = new OptSolverResultSet(paramNames, optRunResultSet);
        RowColumnResultSet copasiRcResultSet = parestSimulator.getRowColumnRestultSetByBestEstimations(parameterEstimationTask, paramNames, paramValues);
        OptimizationResultSet copasiOptimizationResultSet = new OptimizationResultSet(copasiOptSolverResultSet, copasiRcResultSet);
        System.out.println("-----------SOLUTION FROM PYTHON---------------\n" + optResultSet.toString());
        return copasiOptimizationResultSet;
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        throw new OptimizationException(e.getCause() != null ? e.getCause().getMessage() : e.getMessage());
    } finally {
        if (dir != null && dir.exists()) {
            FileUtils.deleteDirectory(dir);
        }
    }
}