Examples with ReferenceDataMappingSpec cbit.vcell.modelopt.ReferenceDataMappingSpec used on opensource projects

Example 1 with ReferenceDataMappingSpec

use of cbit.vcell.modelopt.ReferenceDataMappingSpec in project vcell by virtualcell.

the class ParameterEstimationRunTaskPanel method plot.

private void plot() {
    try {
        java.util.Vector<DataSource> dataSourceList = new java.util.Vector<DataSource>();
        java.util.Vector<String> nameVector = new java.util.Vector<String>();
        ModelOptimizationSpec modelOptimizationSpec = parameterEstimationTask.getModelOptimizationSpec();
        final ReferenceDataMappingSpec[] mappingSpecs = modelOptimizationSpec.getReferenceDataMappingSpecs();
        int timeIndex = modelOptimizationSpec.getReferenceDataTimeColumnIndex();
        ReferenceData referenceData = modelOptimizationSpec.getReferenceData();
        if (referenceData != null) {
            dataSourceList.add(new DataSource.DataSourceReferenceData("EXPT", timeIndex, referenceData));
            String[] refColumnNames = referenceData.getColumnNames();
            for (int i = 0; i < refColumnNames.length; i++) {
                if (i == timeIndex) {
                    continue;
                }
                nameVector.add(refColumnNames[i]);
                break;
            }
        }
        ParameterEstimationTaskSimulatorIDA parestSimulator = new ParameterEstimationTaskSimulatorIDA();
        ODESolverResultSet odeSolverResultSet = parestSimulator.getOdeSolverResultSet(parameterEstimationTask);
        if (odeSolverResultSet != null) {
            dataSourceList.add(new DataSource.DataSourceRowColumnResultSet("EST", odeSolverResultSet));
            if (mappingSpecs != null) {
                for (int i = 0; i < mappingSpecs.length; i++) {
                    if (i == timeIndex) {
                        continue;
                    }
                    Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(mappingSpecs[i].getModelObject());
                    nameVector.add(var.getName());
                    break;
                }
            }
        }
        DataSource[] dataSources = (DataSource[]) BeanUtils.getArray(dataSourceList, DataSource.class);
        MultisourcePlotPane multisourcePlotPane = new MultisourcePlotPane();
        multisourcePlotPane.setGroupingListSorter(new Comparator<SortDataReferenceHelper>() {

            @Override
            public int compare(SortDataReferenceHelper o1, SortDataReferenceHelper o2) {
                DataSource ds01 = o1.dataReference.getDataSource();
                DataSource ds02 = o2.dataReference.getDataSource();
                // System.out.println(ds01.getClass().getSimpleName()+" "+o1.dataReference.getIdentifier()+" "+ds02.getClass().getSimpleName()+" "+o2.dataReference.getIdentifier());
                if (ds01 instanceof DataSource.DataSourceReferenceData) {
                    if (ds02 instanceof DataSource.DataSourceReferenceData) {
                        // both reference data, sort names
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            // Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o1.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o2.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return o1.dataReference.getIdentifier().compareToIgnoreCase(o2.dataReference.getIdentifier());
                        } else if (mspec01 != null && mspec02 != null) {
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else {
                            return 1;
                        }
                    } else {
                        // compare ref to ode
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o1.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o2.dataReference.getIdentifier().equals(var.getName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return -1;
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else if (mspec02 != null && mspec01 == null) {
                            return 1;
                        } else {
                            // BeanUtils.forceStringSize(mspec02.getReferenceDataColumnName(), 25, " ", true));
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        }
                    }
                } else {
                    if (ds02 instanceof DataSource.DataSourceRowColumnResultSet) {
                        // both OdeSolverResultSet data, sort names
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o1.dataReference.getIdentifier().equals(var.getName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o2.dataReference.getIdentifier().equals(var.getName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return o1.dataReference.getIdentifier().compareToIgnoreCase(o2.dataReference.getIdentifier());
                        } else if (mspec01 != null && mspec02 != null) {
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else {
                            return 1;
                        }
                    } else {
                        // compare ode to ref
                        ReferenceDataMappingSpec mspec01 = null;
                        ReferenceDataMappingSpec mspec02 = null;
                        for (ReferenceDataMappingSpec rdMappingSpec : mappingSpecs) {
                            Variable var = parameterEstimationTask.getMathSymbolMapping().getVariable(rdMappingSpec.getModelObject());
                            if (rdMappingSpec.getModelObject() instanceof ReservedSymbol) {
                                continue;
                            }
                            if (o2.dataReference.getIdentifier().equals(rdMappingSpec.getReferenceDataColumnName())) {
                                mspec02 = rdMappingSpec;
                                o2.setReferenceDataMappingSpec(rdMappingSpec);
                            } else if (o1.dataReference.getIdentifier().equals(var.getName())) {
                                mspec01 = rdMappingSpec;
                                o1.setReferenceDataMappingSpec(rdMappingSpec);
                            }
                        }
                        if (mspec01 == null && mspec02 == null) {
                            return 1;
                        } else if (mspec01 != null && mspec02 == null) {
                            return -1;
                        } else if (mspec02 != null && mspec01 == null) {
                            return 1;
                        } else {
                            // BeanUtils.forceStringSize(mspec02.getReferenceDataColumnName(), 25, " ", true));
                            return mspec01.getReferenceDataColumnName().compareToIgnoreCase(mspec02.getReferenceDataColumnName());
                        }
                    }
                }
            }
        });
        multisourcePlotPane.setDataSources(dataSources);
        String[] nameArray = new String[nameVector.size()];
        nameArray = (String[]) BeanUtils.getArray(nameVector, String.class);
        multisourcePlotPane.select(nameArray);
        DialogUtils.showComponentCloseDialog(JOptionPane.getFrameForComponent(this), multisourcePlotPane, "Data Plot");
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 2 with ReferenceDataMappingSpec

use of cbit.vcell.modelopt.ReferenceDataMappingSpec in project vcell by virtualcell.

the class OptXmlWriter method getCopasiDataXML.

public static Element getCopasiDataXML(ParameterEstimationTask parameterEstimationTask) throws IOException {
    ReferenceData refData = parameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    Element refDataElement = null;
    if (refData instanceof SimpleReferenceData) {
        refDataElement = new Element(OptXmlTags.SimpleReferenceData_Tag);
    } else if (refData instanceof SpatialReferenceData) {
        refDataElement = new Element(OptXmlTags.SpatialReferenceData_Tag);
    }
    if (refDataElement != null) {
        // write variable declarations
        // independent variable is t and dimension is 1, these are fixed.
        Element timeVarElement = new Element(OptXmlTags.Variable_Tag);
        timeVarElement.setAttribute(OptXmlTags.VariableType_Attr, OptXmlTags.VariableType_Attr_Independent);
        timeVarElement.setAttribute(OptXmlTags.VariableName_Attr, ReservedVariable.TIME.getName());
        refDataElement.addContent(timeVarElement);
        // check if t is at the first column
        int timeIndex = refData.findColumn(ReservedVariable.TIME.getName());
        if (timeIndex != 0) {
            throw new RuntimeException("t must be the first column");
        }
        // add all other dependent variables, recall that the dependent variables start from 2nd column onward in reference data
        File expDataFile = File.createTempFile("expData", ".txt", ResourceUtil.getVcellHome());
        PrintWriter pw = new PrintWriter(expDataFile);
        pw.print("# Time\t");
        for (int i = 1; i < refData.getNumDataColumns(); i++) {
            ReferenceDataMappingSpec rdms = parameterEstimationTask.getModelOptimizationSpec().getReferenceDataMappingSpec(refData.getColumnNames()[i]);
            Element variableElement = new Element(OptXmlTags.Variable_Tag);
            variableElement.setAttribute(OptXmlTags.VariableType_Attr, OptXmlTags.VariableType_Attr_Dependent);
            variableElement.setAttribute(OptXmlTags.VariableName_Attr, rdms.getModelObject().getName());
            refDataElement.addContent(variableElement);
            pw.print(refData.getColumnNames()[i] + "\t");
        }
        pw.println();
        // write data
        for (int i = 0; i < refData.getNumDataRows(); i++) {
            double[] data = refData.getDataByRow(i);
            for (int j = 0; j < data.length; j++) {
                pw.print(data[j] + "\t");
            }
            pw.println();
        }
        pw.close();
        Element dataFileElement = new Element(OptXmlTags.ExperimentalDataFile_Tag);
        dataFileElement.setAttribute(OptXmlTags.ExperimentalDataFile_Attr_LastRow, (refData.getNumDataRows() + 1) + "");
        dataFileElement.addContent(expDataFile.getAbsolutePath());
        refDataElement.addContent(dataFileElement);
    }
    return refDataElement;
}

Example 3 with ReferenceDataMappingSpec

use of cbit.vcell.modelopt.ReferenceDataMappingSpec in project vcell by virtualcell.

the class ReferenceDataMappingSpecTableModel method setModelOptimizationSpec.

/**
 * Sets the modelOptimizationSpec property (cbit.vcell.modelopt.ModelOptimizationSpec) value.
 * @param modelOptimizationSpec The new value for the property.
 * @see #getModelOptimizationSpec
 */
public void setModelOptimizationSpec(ModelOptimizationSpec newValue) {
    ModelOptimizationSpec oldValue = fieldModelOptimizationSpec;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(this);
        ReferenceDataMappingSpec[] refDataMappingSpecs = oldValue.getReferenceDataMappingSpecs();
        for (int i = 0; refDataMappingSpecs != null && i < refDataMappingSpecs.length; i++) {
            refDataMappingSpecs[i].removePropertyChangeListener(this);
        }
    }
    fieldModelOptimizationSpec = newValue;
    if (newValue != null) {
        newValue.addPropertyChangeListener(this);
        ReferenceDataMappingSpec[] refDataMappingSpecs = newValue.getReferenceDataMappingSpecs();
        for (int i = 0; refDataMappingSpecs != null && i < refDataMappingSpecs.length; i++) {
            refDataMappingSpecs[i].addPropertyChangeListener(this);
        }
    }
    fireTableDataChanged();
}

Example 4 with ReferenceDataMappingSpec

use of cbit.vcell.modelopt.ReferenceDataMappingSpec in project vcell by virtualcell.

the class ReferenceDataPanel method setParameterEstimationTask.

public void setParameterEstimationTask(ParameterEstimationTask newValue) {
    ParameterEstimationTask oldValue = fieldParameterEstimationTask;
    fieldParameterEstimationTask = newValue;
    if (oldValue != null) {
        oldValue.getModelOptimizationSpec().removePropertyChangeListener(ivjEventHandler);
        ReferenceDataMappingSpec[] refDataMappingSpecs = oldValue.getModelOptimizationSpec().getReferenceDataMappingSpecs();
        if (refDataMappingSpecs != null) {
            for (ReferenceDataMappingSpec refDataMappingSpec : refDataMappingSpecs) {
                refDataMappingSpec.removePropertyChangeListener(ivjEventHandler);
            }
        }
    }
    if (fieldParameterEstimationTask != null) {
        newValue.getModelOptimizationSpec().addPropertyChangeListener(ivjEventHandler);
        ReferenceDataMappingSpec[] refDataMappingSpecs = fieldParameterEstimationTask.getModelOptimizationSpec().getReferenceDataMappingSpecs();
        if (refDataMappingSpecs != null) {
            for (ReferenceDataMappingSpec refDataMappingSpec : refDataMappingSpecs) {
                refDataMappingSpec.addPropertyChangeListener(ivjEventHandler);
            }
        }
        timeIndex = fieldParameterEstimationTask.getModelOptimizationSpec().getReferenceDataTimeColumnIndex();
    } else {
        // fieldParameterEstimationTask is null, so referenceData cannot have any data, should be null too?
        timeIndex = 0;
    }
    updatePlot();
}

Example 5 with ReferenceDataMappingSpec

use of cbit.vcell.modelopt.ReferenceDataMappingSpec in project vcell by virtualcell.

the class CopasiServicePython method makeOptProblem.

public static OptProblem makeOptProblem(ParameterEstimationTask parameterEstimationTask) throws IOException, ExpressionException, SBMLException, XMLStreamException {
    OptimizationSpec optimizationSpec = parameterEstimationTask.getModelOptimizationMapping().getOptimizationSpec();
    SimulationContext simulationContext = parameterEstimationTask.getSimulationContext();
    MathMappingCallback callback = new MathMappingCallback() {

        @Override
        public void setProgressFraction(float fractionDone) {
            Thread.dumpStack();
            System.out.println("---> stdout mathMapping: progress = " + (fractionDone * 100.0) + "% done");
        }

        @Override
        public void setMessage(String message) {
            Thread.dumpStack();
            System.out.println("---> stdout mathMapping: message = " + message);
        }

        @Override
        public boolean isInterrupted() {
            return false;
        }
    };
    simulationContext.refreshMathDescription(callback, NetworkGenerationRequirements.ComputeFullStandardTimeout);
    MathModel vcellMathModel = new MathModel(null);
    vcellMathModel.setMathDescription(simulationContext.getMathDescription());
    // get math model string
    String sbmlString = MathModel_SBMLExporter.getSBMLString(vcellMathModel, 2, 4);
    OptProblem optProblem = new OptProblem();
    optProblem.setMathModelSbmlContents(sbmlString);
    optProblem.setNumberOfOptimizationRuns(parameterEstimationTask.getOptimizationSolverSpec().getNumOfRuns());
    for (Parameter p : optimizationSpec.getParameters()) {
        ParameterDescription pdesc = new ParameterDescription(p.getName(), p.getScale(), p.getLowerBound(), p.getUpperBound(), p.getInitialGuess());
        optProblem.addToParameterDescriptionList(pdesc);
    }
    SimpleReferenceData refData = (SimpleReferenceData) parameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    // check if t is at the first column
    int timeIndex = refData.findColumn(ReservedVariable.TIME.getName());
    if (timeIndex != 0) {
        throw new RuntimeException("t must be the first column");
    }
    DataSet dataset = new DataSet();
    for (int rowIndex = 0; rowIndex < refData.getNumDataRows(); rowIndex++) {
        DataRow dataRow = new DataRow();
        double[] array = refData.getDataByRow(rowIndex);
        for (double d : array) {
            dataRow.addToData(d);
        }
        dataset.addToRows(dataRow);
    }
    optProblem.setExperimentalDataSet(dataset);
    optProblem.addToReferenceVariableList(new ReferenceVariable(ReservedVariable.TIME.getName(), ReferenceVariableType.independent));
    // add all other dependent variables, recall that the dependent variables start from 2nd column onward in reference data
    for (int i = 1; i < refData.getNumDataColumns(); i++) {
        ReferenceDataMappingSpec rdms = parameterEstimationTask.getModelOptimizationSpec().getReferenceDataMappingSpec(refData.getColumnNames()[i]);
        optProblem.addToReferenceVariableList(new ReferenceVariable(rdms.getModelObject().getName(), ReferenceVariableType.dependent));
    }
    cbit.vcell.opt.CopasiOptimizationMethod vcellCopasiOptimizationMethod = parameterEstimationTask.getOptimizationSolverSpec().getCopasiOptimizationMethod();
    OptimizationMethodType optMethodType = OptimizationMethodType.valueOf(vcellCopasiOptimizationMethod.getType().name());
    CopasiOptimizationMethod thriftOptMethod = new CopasiOptimizationMethod();
    thriftOptMethod.setOptimizationMethodType(optMethodType);
    for (cbit.vcell.opt.CopasiOptimizationParameter optParam : vcellCopasiOptimizationMethod.getParameters()) {
        org.vcell.optimization.thrift.CopasiOptimizationParameter p = new org.vcell.optimization.thrift.CopasiOptimizationParameter();
        p.setValue(optParam.getValue());
        org.vcell.optimization.thrift.OptimizationParameterType optParmType = null;
        org.vcell.optimization.thrift.OptimizationParameterDataType optDataType = null;
        switch(optParam.getType()) {
            case Cooling_Factor:
                optParmType = OptimizationParameterType.Cooling_Factor;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case IterationLimit:
                optParmType = OptimizationParameterType.IterationLimit;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Number_of_Generations:
                optParmType = OptimizationParameterType.Number_of_Generations;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Number_of_Iterations:
                optParmType = OptimizationParameterType.Number_of_Iterations;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Pf:
                optParmType = OptimizationParameterType.Pf;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Population_Size:
                optParmType = OptimizationParameterType.Population_Size;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Random_Number_Generator:
                optParmType = OptimizationParameterType.Random_Number_Generator;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Rho:
                optParmType = OptimizationParameterType.Rho;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Scale:
                optParmType = OptimizationParameterType.Scale;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Seed:
                optParmType = OptimizationParameterType.Seed;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Start_Temperature:
                optParmType = OptimizationParameterType.Start_Temperature;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Std_Deviation:
                optParmType = OptimizationParameterType.Std_Deviation;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            case Swarm_Size:
                optParmType = OptimizationParameterType.Swarm_Size;
                optDataType = OptimizationParameterDataType.INT;
                break;
            case Tolerance:
                optParmType = OptimizationParameterType.Tolerance;
                optDataType = OptimizationParameterDataType.DOUBLE;
                break;
            default:
                throw new RuntimeException("unsupported parameter type :" + optParam.getType().name() + " in COPASI optimization solver");
        }
        p.setParamType(optParmType);
        p.setDataType(optDataType);
        thriftOptMethod.addToOptimizationParameterList(p);
    }
    optProblem.setOptimizationMethod(thriftOptMethod);
    return optProblem;
}