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

Example 1 with PDEDataViewer

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

the class DisplayTimeSeriesOp method displayImageTimeSeries.

public void displayImageTimeSeries(final ImageTimeSeries<? extends Image> imageTimeSeries, final String title, final WindowListener windowListener) throws ImageException, IOException {
    try {
        System.out.println("starting to prepare data for time series viewing");
        final PDEDataViewer pdeDataViewer = new PDEDataViewer();
        DataSetControllerProvider dataSetControllerProvider;
        try {
            dataSetControllerProvider = getDataSetControllerProvider(imageTimeSeries, pdeDataViewer);
        } catch (ImageException | IOException e1) {
            e1.printStackTrace();
            throw new RuntimeException(e1.getMessage(), e1);
        }
        VCDataManager vcDataManager = new VCDataManager(dataSetControllerProvider);
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        final VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

            public User getOwner() {
                return new User("nouser", null);
            }

            public KeyValue getDataKey() {
                return null;
            }

            public String getID() {
                return "mydata";
            }
        };
        PDEDataManager pdeDataManager = new PDEDataManager(outputContext, vcDataManager, vcDataIdentifier);
        final ClientPDEDataContext myPdeDataContext = new ClientPDEDataContext(pdeDataManager);
        final RequestManager requestManager = new RequestManagerAdapter() {
        };
        final DataViewerManager dataViewerManager = new DataViewerManager() {

            public void dataJobMessage(DataJobEvent event) {
            }

            public void exportMessage(ExportEvent event) {
            }

            public void addDataListener(DataListener newListener) {
            }

            public UserPreferences getUserPreferences() {
                // getRequestManager().getUserPreferences();
                return null;
            }

            public void removeDataListener(DataListener newListener) {
            }

            public void startExport(Component requester, OutputContext outputContext, ExportSpecs exportSpecs) {
            // getLocalRequestManager().startExport(outputContext, FieldDataWindowManager.this, exportSpecs);
            }

            public void simStatusChanged(SimStatusEvent simStatusEvent) {
            }

            public User getUser() {
                return new User("dummy", new KeyValue("123"));
            // return getRequestManager().getDocumentManager().getUser();
            }

            public RequestManager getRequestManager() {
                return requestManager;
            }
        };
        System.out.println("ready to display time series");
        SwingUtilities.invokeAndWait(new Runnable() {

            @Override
            public void run() {
                JFrame jframe = new TopLevelFrame();
                jframe.setTitle(title);
                jframe.getContentPane().add(pdeDataViewer);
                jframe.setSize(1000, 600);
                jframe.setVisible(true);
                if (windowListener != null) {
                    jframe.addWindowListener(windowListener);
                }
                try {
                    pdeDataViewer.setDataViewerManager(dataViewerManager);
                } catch (PropertyVetoException e) {
                    e.printStackTrace();
                }
                pdeDataViewer.setPdeDataContext(myPdeDataContext);
            }
        });
    } catch (InvocationTargetException | InterruptedException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 2 with PDEDataViewer

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

the class FieldDataWindowManager method viewData.

public void viewData(final ExternalDataIdentifier eDI) {
    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(getComponent());
    if (eDI != null && eDI.equals(currentlyViewedEDI) && childWindowManager != null && childWindowManager.getChildWindowFromContext(eDI) != null) {
        childWindowManager.getChildWindowFromContext(eDI).show();
    } else {
        if (currentlyViewedOutputFunctionViewer != null) {
            if (getLocalRequestManager() != null && getLocalRequestManager().getAsynchMessageManager() != null) {
                getLocalRequestManager().getAsynchMessageManager().removeDataJobListener(currentlyViewedOutputFunctionViewer.getPDEDataViewer());
            }
            if (currentlyViewedOutputFunctionViewer != null) {
                currentlyViewedOutputFunctionViewer.getPDEDataViewer().getPdeDataContext().removePropertyChangeListener(this);
            }
        }
        if (currentlyViewedOutputFunctionViewer != null) {
            ChildWindow childWindow = childWindowManager.getChildWindowFromContext(eDI);
            if (childWindow != null) {
                childWindow.close();
            }
        }
        currentlyViewedEDI = null;
        currentlyViewedOutputFunctionViewer = null;
        if (eDI == null) {
            return;
        }
        AsynchClientTask task1 = new AsynchClientTask("retrieve data", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                ClientPDEDataContext newPDEDataContext = getPDEDataContext(eDI, new OutputContext(new AnnotatedFunction[0]));
                hashTable.put("newPDEDataContext", newPDEDataContext);
            }
        };
        AsynchClientTask task2 = new AsynchClientTask("show data", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                try {
                    PDEDataViewer currentlyViewedPDEDV = new PDEDataViewer();
                    ClientPDEDataContext newPDEDataContext = (ClientPDEDataContext) hashTable.get("newPDEDataContext");
                    currentlyViewedPDEDV.setPdeDataContext(newPDEDataContext);
                    newPDEDataContext.addPropertyChangeListener(FieldDataWindowManager.this);
                    getLocalRequestManager().getAsynchMessageManager().addDataJobListener(currentlyViewedPDEDV);
                    currentlyViewedOutputFunctionViewer = new OutputFunctionViewer(currentlyViewedPDEDV, FieldDataWindowManager.this, eDI);
                    DataViewerManager dvm = new DataViewerManager() {

                        public void dataJobMessage(DataJobEvent event) {
                        }

                        public void exportMessage(ExportEvent event) {
                        }

                        public void addDataListener(DataListener newListener) {
                        }

                        public UserPreferences getUserPreferences() {
                            return getRequestManager().getUserPreferences();
                        }

                        public void removeDataListener(DataListener newListener) {
                        }

                        public void startExport(Component requester, OutputContext outputContext, ExportSpecs exportSpecs) {
                            getLocalRequestManager().startExport(outputContext, requester, exportSpecs);
                        }

                        public void simStatusChanged(SimStatusEvent simStatusEvent) {
                        }

                        public User getUser() {
                            return getRequestManager().getDocumentManager().getUser();
                        }

                        public RequestManager getRequestManager() {
                            return FieldDataWindowManager.this.getRequestManager();
                        }
                    };
                    try {
                        currentlyViewedPDEDV.setDataViewerManager(dvm);
                    } catch (PropertyVetoException e) {
                        e.printStackTrace();
                    }
                    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(getComponent());
                    currentlyViewedEDI = eDI;
                    ChildWindow childWindow = childWindowManager.addChildWindow(currentlyViewedOutputFunctionViewer, currentlyViewedEDI, "Field Data Viewer (" + eDI.getName() + ")");
                    childWindow.setSize(600, 500);
                    childWindow.setIsCenteredOnParent();
                    childWindow.show();
                } catch (Exception e) {
                    if (currentlyViewedOutputFunctionViewer != null) {
                        if (getLocalRequestManager() != null && getLocalRequestManager().getAsynchMessageManager() != null) {
                            getLocalRequestManager().getAsynchMessageManager().removeDataJobListener(currentlyViewedOutputFunctionViewer.getPDEDataViewer());
                        }
                        if (currentlyViewedOutputFunctionViewer != null) {
                            currentlyViewedOutputFunctionViewer.getPDEDataViewer().getPdeDataContext().removePropertyChangeListener(FieldDataWindowManager.this);
                        }
                    }
                    throw e;
                }
            }
        };
        ClientTaskDispatcher.dispatch(this.getComponent(), new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 }, false);
    }
}

Example 3 with PDEDataViewer

use of cbit.vcell.client.data.PDEDataViewer 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();
    }
}

Example 4 with PDEDataViewer

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

the class DisplayTimeSeries method displayImageTimeSeries.

public static void displayImageTimeSeries(final ImageTimeSeries<Image> imageTimeSeries, String title, WindowListener windowListener) throws ImageException, IOException {
    ISize size = imageTimeSeries.getISize();
    int dimension = (size.getZ() > 0) ? (3) : (2);
    Extent extent = imageTimeSeries.getExtent();
    Origin origin = imageTimeSeries.getAllImages()[0].getOrigin();
    // don't care ... no surfaces
    double filterCutoffFrequency = 0.5;
    VCImage vcImage = new VCImageUncompressed(null, new byte[size.getXYZ()], extent, size.getX(), size.getY(), size.getZ());
    RegionImage regionImage = new RegionImage(vcImage, dimension, extent, origin, filterCutoffFrequency);
    final CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, size, regionImage);
    final DataIdentifier dataIdentifier = new DataIdentifier("var", VariableType.VOLUME, new Domain("domain"), false, "var");
    final DataSetController dataSetController = new DataSetController() {

        @Override
        public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
            double timePoint = time;
            double[] timePoints = getDataSetTimes(vcdataID);
            int index = -1;
            for (int i = 0; i < timePoints.length; i++) {
                if (timePoint == timePoints[i]) {
                    index = i;
                    break;
                }
            }
            double[] data = imageTimeSeries.getAllImages()[index].getDoublePixels();
            PDEDataInfo pdeDataInfo = new PDEDataInfo(null, null, varName, time, 0);
            VariableType varType = VariableType.VOLUME;
            return new SimDataBlock(pdeDataInfo, data, varType);
        }

        @Override
        public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return false;
        }

        @Override
        public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return null;
        }

        @Override
        public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return mesh;
        }

        @Override
        public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public AnnotatedFunction[] getFunctions(OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            return new AnnotatedFunction[0];
        }

        @Override
        public double[] getDataSetTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return imageTimeSeries.getImageTimeStamps();
        }

        @Override
        public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            return new DataIdentifier[] { dataIdentifier };
        }

        @Override
        public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            throw new RuntimeException("not yet implemented");
        }

        @Override
        public double[] getVtuMeshData(OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public VtuVarInfo[] getVtuVarInfos(OutputContext outputContext, VCDataIdentifier vcDataIdentifier) throws DataAccessException, RemoteProxyException {
            // TODO Auto-generated method stub
            return null;
        }

        @Override
        public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
            // TODO Auto-generated method stub
            return null;
        }
    };
    DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {

        @Override
        public DataSetController getDataSetController() throws DataAccessException {
            return dataSetController;
        }
    };
    VCDataManager vcDataManager = new VCDataManager(dataSetControllerProvider);
    OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
    VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

        public User getOwner() {
            return new User("nouser", null);
        }

        public KeyValue getDataKey() {
            return null;
        }

        public String getID() {
            return "mydata";
        }
    };
    PDEDataManager pdeDataManager = new PDEDataManager(outputContext, vcDataManager, vcDataIdentifier);
    ClientPDEDataContext myPdeDataContext = new ClientPDEDataContext(pdeDataManager);
    PDEDataViewer pdeDataViewer = new PDEDataViewer();
    JFrame jframe = new JFrame();
    jframe.setTitle(title);
    jframe.getContentPane().add(pdeDataViewer);
    jframe.setSize(1000, 600);
    jframe.setVisible(true);
    if (windowListener != null) {
        jframe.addWindowListener(windowListener);
    }
    pdeDataViewer.setPdeDataContext(myPdeDataContext);
}