Examples with DataIdentifierFilter cbit.vcell.client.data.DataIdentifierFilter used on opensource projects

Example 1 with DataIdentifierFilter

use of cbit.vcell.client.data.DataIdentifierFilter in project vcell by virtualcell.

the class FRAPStudyPanel method refreshPDEDisplay.

protected void refreshPDEDisplay(DisplayChoice choice) throws Exception {
    Simulation sim = null;
    FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
    if (fStudy == null || fStudy.getBioModel() == null || fStudy.getBioModel().getSimulations() == null || fStudy.getBioModel().getSimulations().length < 1) {
        return;
    }
    sim = fStudy.getBioModel().getSimulations()[0];
    FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
    FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFunctionArgs.length];
    for (int i = 0; i < fieldDataIdentifierSpecs.length; i++) {
        fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier());
    }
    PDEDataViewer flourViewer = getFlourDataViewer();
    PDEDataManager dataManager = null;
    if (choice == DisplayChoice.EXTTIMEDATA) {
        flourViewer.setSimulation(null);
        flourViewer.setPdeDataContext(null);
        flourViewer.setDataIdentifierFilter(new DataIdentifierFilter() {

            private String ALL_DATAIDENTIFIERS = "All";

            private String EXP_NORM_FLUOR = "Exp. Norm. Fluor";

            private String SIM_NORM_FLUOR = "Sim. Norm. Fluor";

            private String DEFAULT_VIEW = "Default View (more...)";

            private String[] filterSetNames = new String[] { ALL_DATAIDENTIFIERS, EXP_NORM_FLUOR, SIM_NORM_FLUOR, DEFAULT_VIEW };

            public boolean accept(String filterSetName, List<AnnotatedFunction> myFunctionList, DataIdentifier dataidentifier) {
                if (filterSetName.equals(ALL_DATAIDENTIFIERS)) {
                    return true;
                } else if (filterSetName.equals(EXP_NORM_FLUOR)) {
                    return dataidentifier.getName().indexOf(NORM_FLUOR_VAR) != -1;
                } else if (filterSetName.equals(SIM_NORM_FLUOR)) {
                    boolean a = (dataidentifier.getName().indexOf(REACTION_RATE_PREFIX) == -1) && ((dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_COMBINED) != -1) || (dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_IMMOBILE) != -1) || (dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_MOBILE) != -1) || (dataidentifier.getName().indexOf(FRAPStudy.SPECIES_NAME_PREFIX_SLOW_MOBILE) != -1));
                    return a;
                } else if (filterSetName.equals(DEFAULT_VIEW)) {
                    boolean a = (dataidentifier.getName().indexOf(REACTION_RATE_PREFIX) == -1) && ((dataidentifier.getName().indexOf(NORM_FLUOR_VAR) != -1) || (dataidentifier.getName().indexOf(NORM_SIM_VAR) != -1));
                    return a;
                }
                throw new IllegalArgumentException("DataIdentifierFilter: Unknown filterSetName " + filterSetName);
            }

            public String getDefaultFilterName() {
                return DEFAULT_VIEW;
            }

            public String[] getFilterSetNames() {
                return filterSetNames;
            }

            public boolean isAcceptAll(String filterSetName) {
                return filterSetName.equals(ALL_DATAIDENTIFIERS);
            }

            @Override
            public void setPostProcessingMode(boolean bPostProcessingMode) {
            // TODO Auto-generated method stub
            }

            @Override
            public boolean isPostProcessingMode() {
                // TODO Auto-generated method stub
                return false;
            }

            @Override
            public ArrayList<DataIdentifier> accept(String filterSetName, List<AnnotatedFunction> myFunctionList, DataIdentifier[] dataidentifiers) {
                if (filterSetName.equals(DEFAULT_VIEW)) {
                    ArrayList<DataIdentifier> dataIds = new ArrayList<>();
                    if (dataidentifiers != null) {
                        for (int i = 0; i < dataidentifiers.length; i++) {
                            dataIds.add(dataidentifiers[i]);
                        }
                    }
                    return dataIds;
                }
                throw new RuntimeException("Not Implemented for FRAP");
            }
        });
        ExternalDataIdentifier timeSeriesExtDataID = fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier();
        ExternalDataIdentifier maskExtDataID = fStudy.getRoiExternalDataInfo().getExternalDataIdentifier();
        // add sim
        int jobIndex = 0;
        SimulationJob simJob = new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs);
        // add function to display normalized fluorence data
        Norm_Exp_Fluor = new Expression(Norm_Exp_Fluor_Str);
        SimulationSymbolTable simSymbolTable = simJob.getSimulationSymbolTable();
        if (// one diffusing component
        simSymbolTable.getVariable(FRAPStudy.SPECIES_NAME_PREFIX_SLOW_MOBILE) == null) {
            Norm_Sim = new Expression(Norm_Sim_One_Diff_Str);
        } else // two diffusing components
        {
            Norm_Sim = new Expression(Norm_Sim_Two_Diff_Str);
        }
        AnnotatedFunction[] func = { new AnnotatedFunction(NORM_FLUOR_VAR, Norm_Exp_Fluor, null, null, VariableType.VOLUME, FunctionCategory.OLDUSERDEFINED), new AnnotatedFunction(NORM_SIM_VAR, Norm_Sim, null, null, VariableType.VOLUME, FunctionCategory.OLDUSERDEFINED) };
        VCDataIdentifier[] dataIDs = new VCDataIdentifier[] { timeSeriesExtDataID, maskExtDataID, simJob.getVCDataIdentifier() };
        VCDataIdentifier vcDataId = new MergedDataInfo(LocalWorkspace.getDefaultOwner(), dataIDs, FRAPStudy.VFRAP_DS_PREFIX);
        outputContext = new OutputContext(func);
        dataManager = new PDEDataManager(outputContext, getLocalWorkspace().getVCDataManager(), vcDataId);
        ClientPDEDataContext pdeDataContext = new ClientPDEDataContext(dataManager);
        pdeDataContext.refreshIdentifiers();
        flourViewer.setSimulation(sim);
        flourViewer.setPdeDataContext(pdeDataContext);
        SimulationModelInfo simModelInfo = new SimulationWorkspaceModelInfo(fStudy.getBioModel().getSimulationContext(sim), sim.getName());
        flourViewer.setSimulationModelInfo(simModelInfo);
        getLocalWorkspace().getDataSetControllerImpl().addDataJobListener(flourViewer);
        ((VirtualFrapWindowManager) flourViewer.getDataViewerManager()).setLocalWorkSpace(getLocalWorkspace());
        // do now show post data processing for VFRAP
        flourViewer.setPostProcessingPanelVisible(false);
        flourViewer.repaint();
    }
}