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Example 1 with MergedDataInfo

use of cbit.vcell.simdata.MergedDataInfo 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();
    }
}
Also used : ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) DataIdentifier(cbit.vcell.simdata.DataIdentifier) ArrayList(java.util.ArrayList) MergedDataInfo(cbit.vcell.simdata.MergedDataInfo) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) FRAPStudy(cbit.vcell.microscopy.FRAPStudy) SimulationWorkspaceModelInfo(cbit.vcell.client.data.SimulationWorkspaceModelInfo) SimulationJob(cbit.vcell.solver.SimulationJob) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) DataIdentifierFilter(cbit.vcell.client.data.DataIdentifierFilter) SimulationModelInfo(cbit.vcell.solver.SimulationModelInfo) FieldFunctionArguments(cbit.vcell.field.FieldFunctionArguments) SimulationSymbolTable(cbit.vcell.solver.SimulationSymbolTable) Point(java.awt.Point) OutputContext(cbit.vcell.simdata.OutputContext) Simulation(cbit.vcell.solver.Simulation) PDEDataManager(cbit.vcell.simdata.PDEDataManager) Expression(cbit.vcell.parser.Expression) FieldDataIdentifierSpec(cbit.vcell.field.FieldDataIdentifierSpec) ClientPDEDataContext(cbit.vcell.simdata.ClientPDEDataContext) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) PDEDataViewer(cbit.vcell.client.data.PDEDataViewer)

Example 2 with MergedDataInfo

use of cbit.vcell.simdata.MergedDataInfo in project vcell by virtualcell.

the class FRAPStudyPanel method showMovie.

private void showMovie() {
    AsynchClientTask createMovieTask = new AsynchClientTask("Buffering movie data...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            if (fStudy == null) {
                return;
            }
            if (fStudy.getMovieURLString() != null && fStudy.getMovieFileString() != null) {
                hashTable.put("FrapStudy", fStudy);
                return;
            }
            // create export specs
            Simulation sim = null;
            if (fStudy.getBioModel() == null || fStudy.getBioModel().getSimulations() == null || fStudy.getBioModel().getSimulations().length < 1) {
                return;
            } else {
                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());
            }
            ExternalDataIdentifier timeSeriesExtDataID = fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier();
            ExternalDataIdentifier maskExtDataID = fStudy.getRoiExternalDataInfo().getExternalDataIdentifier();
            // add sim
            int jobIndex = 0;
            SimulationJob simJob = new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs);
            VCDataIdentifier[] dataIDs = new VCDataIdentifier[] { timeSeriesExtDataID, maskExtDataID, simJob.getVCDataIdentifier() };
            VCDataIdentifier vcDataId = new MergedDataInfo(LocalWorkspace.getDefaultOwner(), dataIDs, FRAPStudy.VFRAP_DS_PREFIX);
            PDEDataManager dataManager = new PDEDataManager(null, getLocalWorkspace().getVCDataManager(), vcDataId);
            PDEDataContext pdeDataContext = new ClientPDEDataContext(dataManager);
            ExportFormat format = ExportFormat.QUICKTIME;
            String[] variableNames = new String[] { NORM_FLUOR_VAR, NORM_SIM_VAR };
            VariableSpecs variableSpecs = new VariableSpecs(variableNames, ExportConstants.VARIABLE_MULTI);
            // int endTimeIndex = (int)Math.round(sim.getSolverTaskDescription().getTimeBounds().getEndingTime()/((UniformOutputTimeSpec)sim.getSolverTaskDescription().getOutputTimeSpec()).getOutputTimeStep());
            int endTimeIndex = getFRAPSimDataViewerPanel().getOriginalDataViewer().getPdeDataContext().getTimePoints().length - 1;
            TimeSpecs timeSpecs = new TimeSpecs(0, endTimeIndex, pdeDataContext.getTimePoints(), ExportConstants.TIME_RANGE);
            int geoMode = ExportConstants.GEOMETRY_SLICE;
            GeometrySpecs geometrySpecs = new GeometrySpecs(null, Coordinate.Z_AXIS, 0, geoMode);
            // 10s
            double duration = 10000;
            DisplayPreferences pref1 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences pref2 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences[] displayPref = new DisplayPreferences[] { pref1, pref2 };
            int imageScale = 1;
            int membraneScale = 1;
            int scaleMode = ImagePaneModel.MESH_MODE;
            // the default setting in MediaSettingsPanel.
            int volVarMemOutlineThickness = 1;
            MovieSpecs mSpec = new MovieSpecs(duration, true, displayPref, ExportFormat.QUICKTIME, ExportConstants.NO_MIRRORING, volVarMemOutlineThickness, imageScale, membraneScale, scaleMode, FormatSpecificSpecs.CODEC_JPEG, 1.0f, /*lossless*/
            false, FormatSpecificSpecs.PARTICLE_NONE);
            // mSpec.setViewZoom(1);
            ExportSpecs exSpecs = new ExportSpecs(vcDataId, format, variableSpecs, timeSpecs, geometrySpecs, mSpec, fStudy.getName(), null);
            // pass the request
            ExportEvent exportEvt = ((VirtualFrapWindowManager) getFlourDataViewer().getDataViewerManager()).startExportMovie(exSpecs, outputContext, this.getClientTaskStatusSupport());
            hashTable.put("ExportEvt", exportEvt);
            hashTable.put("FrapStudy", fStudy);
        }
    };
    AsynchClientTask showMovieTask = new AsynchClientTask("Showing movie ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExportEvent exportEvt = (ExportEvent) hashTable.get("ExportEvt");
            FRAPStudy fStudy = (FRAPStudy) hashTable.get("FrapStudy");
            // show movie if successfully exported
            if (exportEvt != null) {
                final String fileURLString = System.getProperty(PropertyLoader.exportBaseURLProperty) + exportEvt.getJobID() + ".mov";
                final String fileString = System.getProperty(PropertyLoader.exportBaseDirInternalProperty) + exportEvt.getJobID() + ".mov";
                fStudy.setMovieURLString(fileURLString);
                fStudy.setMovieFileString(fileString);
            }
            showMovieInDialog(fStudy.getMovieURLString(), fStudy.getMovieFileString());
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { createMovieTask, showMovieTask }, true, true, null, true);
}
Also used : ClientPDEDataContext(cbit.vcell.simdata.ClientPDEDataContext) PDEDataContext(cbit.vcell.simdata.PDEDataContext) AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) ExportSpecs(cbit.vcell.export.server.ExportSpecs) ExportEvent(cbit.rmi.event.ExportEvent) GeometrySpecs(cbit.vcell.export.server.GeometrySpecs) MergedDataInfo(cbit.vcell.simdata.MergedDataInfo) DisplayPreferences(cbit.image.DisplayPreferences) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) FRAPStudy(cbit.vcell.microscopy.FRAPStudy) TimeSpecs(cbit.vcell.export.server.TimeSpecs) SimulationJob(cbit.vcell.solver.SimulationJob) FieldFunctionArguments(cbit.vcell.field.FieldFunctionArguments) Hashtable(java.util.Hashtable) ExportFormat(cbit.vcell.export.server.ExportFormat) Range(org.vcell.util.Range) Point(java.awt.Point) VariableSpecs(cbit.vcell.export.server.VariableSpecs) MovieSpecs(cbit.vcell.export.server.MovieSpecs) Simulation(cbit.vcell.solver.Simulation) PDEDataManager(cbit.vcell.simdata.PDEDataManager) FieldDataIdentifierSpec(cbit.vcell.field.FieldDataIdentifierSpec) ClientPDEDataContext(cbit.vcell.simdata.ClientPDEDataContext) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier)

Example 3 with MergedDataInfo

use of cbit.vcell.simdata.MergedDataInfo in project vcell by virtualcell.

the class TestingFrameworkWindowManager method compare.

/**
 * Insert the method's description here.
 * Creation date: (1/20/2003 11:52:18 AM)
 * @return boolean
 * @param mathDesc cbit.vcell.math.MathDescription
 */
public void compare(final TestCriteriaNew testCriteria, final SimulationInfo userDefinedRegrSimInfo) {
    final String KEY_MERGEDDATAINFO = "KEY_MERGEDDATAINFO";
    final String KEY_MERGEDDATASETVIEWERCNTRLR = "KEY_MERGEDDATASETVIEWERCNTRLR";
    AsynchClientTask gatherDataTask = new AsynchClientTask("Gathering compare Dta...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // create the merged data for the simulationInfo in testCriteria and the regression simInfo
            SimulationInfo simInfo = testCriteria.getSimInfo();
            SimulationInfo regrSimInfo = null;
            if (userDefinedRegrSimInfo != null) {
                regrSimInfo = userDefinedRegrSimInfo;
            } else {
                regrSimInfo = testCriteria.getRegressionSimInfo();
            }
            if (regrSimInfo == null) {
                return;
            }
            VCDataIdentifier vcSimId1 = new VCSimulationDataIdentifier(simInfo.getAuthoritativeVCSimulationIdentifier(), 0);
            VCDataIdentifier vcSimId2 = new VCSimulationDataIdentifier(regrSimInfo.getAuthoritativeVCSimulationIdentifier(), 0);
            User user = simInfo.getOwner();
            VCDataIdentifier[] vcIdentifierArray = new VCDataIdentifier[] { vcSimId2, vcSimId1 };
            MergedDataInfo mergedDataInfo = new MergedDataInfo(user, vcIdentifierArray, MergedDataInfo.createDefaultPrefixNames(vcIdentifierArray.length));
            hashTable.put(KEY_MERGEDDATAINFO, mergedDataInfo);
            // get the data manager and wire it up
            // 
            // get all "Data1.XXX" data identifiers ... and remove those which are functions
            // add functions of the form DIFF_XXX = (Data1.XXX - Data2.XXX) for convenience in comparing results.
            // 
            Simulation sim1 = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(simInfo);
            Simulation sim2 = ((ClientDocumentManager) getRequestManager().getDocumentManager()).getSimulation(regrSimInfo);
            boolean isSpatial = sim1.isSpatial();
            if (sim2.isSpatial() != isSpatial) {
                throw new RuntimeException("Cannot compare spatial and non-spatial data sets : " + simInfo + "& " + regrSimInfo);
            }
            DataManager mergedDataManager = getRequestManager().getDataManager(null, mergedDataInfo, isSpatial);
            DataManager data1Manager = getRequestManager().getDataManager(null, vcSimId1, isSpatial);
            DataManager data2Manager = getRequestManager().getDataManager(null, vcSimId2, isSpatial);
            Vector<AnnotatedFunction> functionList = new Vector<AnnotatedFunction>();
            AnnotatedFunction[] data1Functions = data1Manager.getFunctions();
            AnnotatedFunction[] existingFunctions = mergedDataManager.getFunctions();
            DataIdentifier[] data1Identifiers = data1Manager.getDataIdentifiers();
            DataIdentifier[] data2Identifiers = data2Manager.getDataIdentifiers();
            for (int i = 0; i < data1Identifiers.length; i++) {
                // 
                // make sure dataIdentifier is not already a function
                // 
                boolean bIsFunction = false;
                for (int j = 0; j < data1Functions.length; j++) {
                    if (data1Identifiers[i].getName().equals(data1Functions[j].getName())) {
                        bIsFunction = true;
                    }
                }
                if (bIsFunction) {
                    continue;
                }
                // 
                // make sure corresponding identifier exists in "Data2"
                // 
                boolean bIsInData2 = false;
                for (int j = 0; j < data2Identifiers.length; j++) {
                    if (data2Identifiers[j].getName().equals(data1Identifiers[i].getName())) {
                        bIsInData2 = true;
                    }
                }
                if (!bIsInData2) {
                    continue;
                }
                // 
                // create "Diff" function
                // 
                String data1Name = "Data1." + data1Identifiers[i].getName();
                String data2Name = "Data2." + data1Identifiers[i].getName();
                String functionName = "DIFF_" + data1Identifiers[i].getName();
                VariableType varType = data1Identifiers[i].getVariableType();
                Expression exp = new Expression(data1Name + "-" + data2Name);
                AnnotatedFunction newFunction = new AnnotatedFunction(functionName, exp, data1Identifiers[i].getDomain(), "", varType, FunctionCategory.OUTPUTFUNCTION);
                // 
                // make sure new "Diff" function isn't already in existing function list.
                // 
                boolean bDiffFunctionAlreadyHere = false;
                for (int j = 0; j < existingFunctions.length; j++) {
                    if (newFunction.getName().equals(existingFunctions[j].getName())) {
                        bDiffFunctionAlreadyHere = true;
                    }
                }
                if (bDiffFunctionAlreadyHere) {
                    continue;
                }
                functionList.add(newFunction);
            }
            OutputContext outputContext = null;
            if (functionList.size() > 0) {
                AnnotatedFunction[] newDiffFunctions = (AnnotatedFunction[]) BeanUtils.getArray(functionList, AnnotatedFunction.class);
                outputContext = new OutputContext(newDiffFunctions);
            }
            MergedDatasetViewerController mergedDatasetViewerCtr = getRequestManager().getMergedDatasetViewerController(outputContext, mergedDataInfo, !isSpatial);
            hashTable.put(KEY_MERGEDDATASETVIEWERCNTRLR, mergedDatasetViewerCtr);
        }
    };
    AsynchClientTask showResultsTask = new AsynchClientTask("Showing Compare Results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            // make the viewer
            MergedDatasetViewerController mergedDatasetViewerCtr = (MergedDatasetViewerController) hashTable.get(KEY_MERGEDDATASETVIEWERCNTRLR);
            addDataListener(mergedDatasetViewerCtr);
            DataViewer viewer = mergedDatasetViewerCtr.createViewer();
            viewer.setDataViewerManager(TestingFrameworkWindowManager.this);
            addExportListener(viewer);
            VCDataIdentifier vcDataIdentifier = (MergedDataInfo) hashTable.get(KEY_MERGEDDATAINFO);
            ChildWindowManager childWindowManager = TFWFinder.findChildWindowManager(getComponent());
            ChildWindow childWindow = childWindowManager.addChildWindow(viewer, vcDataIdentifier, "Comparing ... " + vcDataIdentifier.getID());
            childWindow.pack();
            // childWindow.setSize(450, 450);
            childWindow.setIsCenteredOnParent();
            childWindow.show();
        }
    };
    ClientTaskDispatcher.dispatch(getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { gatherDataTask, showResultsTask }, false);
}
Also used : AsynchClientTask(cbit.vcell.client.task.AsynchClientTask) User(org.vcell.util.document.User) VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) DataIdentifier(cbit.vcell.simdata.DataIdentifier) ClientDocumentManager(cbit.vcell.clientdb.ClientDocumentManager) MergedDataInfo(cbit.vcell.simdata.MergedDataInfo) DataViewer(cbit.vcell.client.data.DataViewer) Vector(java.util.Vector) MergedDatasetViewerController(cbit.vcell.client.data.MergedDatasetViewerController) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) VariableType(cbit.vcell.math.VariableType) Hashtable(java.util.Hashtable) PDEDataManager(cbit.vcell.simdata.PDEDataManager) ODEDataManager(cbit.vcell.simdata.ODEDataManager) DataManager(cbit.vcell.simdata.DataManager) VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier) ChildWindow(cbit.vcell.client.ChildWindowManager.ChildWindow) OutputContext(cbit.vcell.simdata.OutputContext) Simulation(cbit.vcell.solver.Simulation) Expression(cbit.vcell.parser.Expression) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) SimulationInfo(cbit.vcell.solver.SimulationInfo)

Example 4 with MergedDataInfo

use of cbit.vcell.simdata.MergedDataInfo in project vcell by virtualcell.

the class PDEDataViewer method calcAutoAllTimes.

private void calcAutoAllTimes() throws Exception {
    HashSet<String> stateVarNames = null;
    Variable theVariable = null;
    boolean bStateVar = true;
    boolean isFieldData = getPdeDataContext().getVCDataIdentifier() instanceof ExternalDataIdentifier || getPdeDataContext().getVCDataIdentifier() instanceof MergedDataInfo;
    if (isFieldData) {
        // fielddata
        DataIdentifier[] dataids = getPdeDataContext().getDataIdentifiers();
        stateVarNames = new HashSet<>();
        for (int i = 0; i < dataids.length; i++) {
            if (!dataids[i].isFunction()) {
                stateVarNames.add(dataids[i].getName());
            }
        // System.out.println("name:'"+dataids[i].getName()+"' type:"+dataids[i].getVariableType()+" func:"+dataids[i].isFunction());
        }
        bStateVar = !getPdeDataContext().getDataIdentifier().isFunction();
        if (bStateVar) {
            theVariable = new VolVariable(getPdeDataContext().getDataIdentifier().getName(), getPdeDataContext().getDataIdentifier().getDomain());
        } else {
            AnnotatedFunction[] funcs = getPdeDataContext().getFunctions();
            for (int i = 0; i < funcs.length; i++) {
                if (funcs[i].getName().equals(getPdeDataContext().getDataIdentifier().getName())) {
                    theVariable = funcs[i];
                    break;
                }
            }
        }
    } else {
        stateVarNames = getSimulation().getMathDescription().getStateVariableNames();
        theVariable = getSimulation().getMathDescription().getVariable(getPdeDataContext().getVariableName());
        if (theVariable == null) {
            theVariable = ((ClientPDEDataContext) getPdeDataContext()).getDataManager().getOutputContext().getOutputFunction(getPdeDataContext().getVariableName());
        }
        if (theVariable == null) {
            DataProcessingOutputInfo dataProcessingOutputInfo = DataProcessingResultsPanel.getDataProcessingOutputInfo(getPdeDataContext());
            if (dataProcessingOutputInfo != null && Arrays.asList(dataProcessingOutputInfo.getVariableNames()).contains(getPdeDataContext().getVariableName())) {
                // PostProcess Variable
                return;
            }
        }
        bStateVar = stateVarNames.contains(getPdeDataContext().getVariableName());
    }
    if (theVariable == null) {
        throw new Exception("Unexpected Alltimes... selected variable '" + getPdeDataContext().getVariableName() + "' is not stateVariable or OutputFunction");
    }
    if (getPDEDataContextPanel1().getdisplayAdapterService1().getAllTimes()) {
        // min-max over all timepoints (allTimes)
        if (theVariable.isConstant()) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__STATE_TEXT);
            double constVal = theVariable.getExpression().evaluateConstant();
            getPDEDataContextPanel1().setFunctionStatisticsRange(new Range(constVal, constVal));
        } else if (bStateVar) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__STATE_TEXT);
            ArrayList<VarStatistics> varStatsArr = calcVarStat(getPdeDataContext(), new String[] { theVariable.getName() });
            if (errorAutoAllTimes(varStatsArr != null, (varStatsArr == null ? null : varStatsArr.size() > 0), isFieldData)) {
                // no postprocessinfo
                return;
            }
            FunctionStatistics functionStatistics = new FunctionStatistics(varStatsArr.get(0).minValuesOverTime, varStatsArr.get(0).maxValuesOverTime);
            getPDEDataContextPanel1().setFunctionStatisticsRange(new Range(functionStatistics.getMinOverTime(), functionStatistics.getMaxOverTime()));
        } else if (theVariable instanceof Function) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__APPROX_TEXT);
            Function flattened = MathDescription.getFlattenedFunctions(SimulationSymbolTable.createMathSymbolTableFactory(), getSimulation().getMathDescription(), new String[] { theVariable.getName() })[0];
            if (flattened == null) {
                flattened = (Function) theVariable;
            }
            ArrayList<VarStatistics> varStatsArr = calcVarStat(getPdeDataContext(), stateVarNames.toArray(new String[0]));
            if (errorAutoAllTimes(varStatsArr != null, (varStatsArr == null ? null : varStatsArr.size() > 0), isFieldData)) {
                // check for no postprocessinfo
                return;
            }
            if (varStatsArr.size() == stateVarNames.size()) {
                if (getSimulation().getMeshSpecification().getGeometry().getGeometrySurfaceDescription().getRegionImage() == null) {
                    getSimulation().getMeshSpecification().getGeometry().getGeometrySurfaceDescription().updateAll();
                }
                FunctionStatistics functionStatistics = FunctionRangeGenerator.getFunctionStatistics(flattened.getExpression(), varStatsArr.toArray(new VarStatistics[0]), getPdeDataContext().getTimePoints(), getPdeDataContext().getCartesianMesh(), calcInDomainBitSet(), getPdeDataContext().getDataIdentifier().getVariableType());
                getPDEDataContextPanel1().setFunctionStatisticsRange(new Range(functionStatistics.getMinOverTime(), functionStatistics.getMaxOverTime()));
            } else {
                throw new Exception("Unexpectede AllTimes... calculated state var stats size != mathdescr state var size");
            }
        } else {
            throw new Exception("Unexpected AllTimes... not constant, stateVar or function");
        }
    } else {
        // min-max at each timepoint (currTime)
        if (!(theVariable instanceof Function)) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__STATE_TEXT);
        } else {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__APPROX_TEXT);
        }
        getPDEDataContextPanel1().setFunctionStatisticsRange(null);
    }
}
Also used : VolVariable(cbit.vcell.math.VolVariable) ReservedVariable(cbit.vcell.math.ReservedVariable) Variable(cbit.vcell.math.Variable) VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier) LocalVCSimulationDataIdentifier(cbit.vcell.client.ClientSimManager.LocalVCSimulationDataIdentifier) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) DataIdentifier(cbit.vcell.simdata.DataIdentifier) VolVariable(cbit.vcell.math.VolVariable) ArrayList(java.util.ArrayList) Range(org.vcell.util.Range) Point(java.awt.Point) SinglePoint(cbit.vcell.geometry.SinglePoint) DataAccessException(org.vcell.util.DataAccessException) PropertyVetoException(java.beans.PropertyVetoException) ImageException(cbit.image.ImageException) UserCancelException(org.vcell.util.UserCancelException) MergedDataInfo(cbit.vcell.simdata.MergedDataInfo) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) Function(cbit.vcell.math.Function) VarStatistics(cbit.vcell.util.FunctionRangeGenerator.VarStatistics) DataProcessingOutputInfo(cbit.vcell.simdata.DataOperationResults.DataProcessingOutputInfo) ExternalDataIdentifier(org.vcell.util.document.ExternalDataIdentifier) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) FunctionStatistics(cbit.vcell.util.FunctionRangeGenerator.FunctionStatistics)

Aggregations

MergedDataInfo (cbit.vcell.simdata.MergedDataInfo)4 VCDataIdentifier (org.vcell.util.document.VCDataIdentifier)4 DataIdentifier (cbit.vcell.simdata.DataIdentifier)3 PDEDataManager (cbit.vcell.simdata.PDEDataManager)3 AnnotatedFunction (cbit.vcell.solver.AnnotatedFunction)3 Simulation (cbit.vcell.solver.Simulation)3 Point (java.awt.Point)3 ExternalDataIdentifier (org.vcell.util.document.ExternalDataIdentifier)3 AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)2 FieldDataIdentifierSpec (cbit.vcell.field.FieldDataIdentifierSpec)2 FieldFunctionArguments (cbit.vcell.field.FieldFunctionArguments)2 FRAPStudy (cbit.vcell.microscopy.FRAPStudy)2 Expression (cbit.vcell.parser.Expression)2 ClientPDEDataContext (cbit.vcell.simdata.ClientPDEDataContext)2 OutputContext (cbit.vcell.simdata.OutputContext)2 SimulationJob (cbit.vcell.solver.SimulationJob)2 VCSimulationDataIdentifier (cbit.vcell.solver.VCSimulationDataIdentifier)2 ArrayList (java.util.ArrayList)2 Hashtable (java.util.Hashtable)2 Range (org.vcell.util.Range)2