Examples with VCDataManager cbit.vcell.simdata.VCDataManager used on opensource projects

Example 1 with VCDataManager

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

the class ClientSimManager method showSimulationResults0.

private AsynchClientTask[] showSimulationResults0(final boolean isLocal, final ViewerType viewerType) {
    // Create the AsynchClientTasks
    ArrayList<AsynchClientTask> taskList = new ArrayList<AsynchClientTask>();
    taskList.add(new AsynchClientTaskFunction(h -> {
        h.put(H_LOCAL_SIM, isLocal);
        h.put(H_VIEWER_TYPE, viewerType);
    }, "setLocal", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING));
    final DocumentWindowManager documentWindowManager = getDocumentWindowManager();
    AsynchClientTask retrieveResultsTask = new AsynchClientTask("Retrieving results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @SuppressWarnings("unchecked")
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Simulation[] simsToShow = (Simulation[]) hashTable.get("simsArray");
            for (int i = 0; i < simsToShow.length; i++) {
                final Simulation sim = simsToShow[i];
                final VCSimulationIdentifier vcSimulationIdentifier = sim.getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
                final SimulationWindow simWindow = documentWindowManager.haveSimulationWindow(vcSimulationIdentifier);
                OutputContext outputContext = (OutputContext) hashTable.get("outputContext");
                if (simWindow == null && (viewerType == ViewerType.NativeViewer_only)) {
                    try {
                        // make the manager and wire it up
                        DataViewerController dataViewerController = null;
                        if (!isLocal) {
                            dataViewerController = documentWindowManager.getRequestManager().getDataViewerController(outputContext, sim, 0);
                            // For changes in time or variable
                            documentWindowManager.addDataListener(dataViewerController);
                        } else {
                            // ---- preliminary : construct the localDatasetControllerProvider
                            File primaryDir = ResourceUtil.getLocalRootDir();
                            User usr = sim.getVersion().getOwner();
                            DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
                            ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
                            LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(usr, dataSetControllerImpl, localExportServiceImpl);
                            VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
                            File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
                            LocalVCDataIdentifier vcDataId = new LocalVCSimulationDataIdentifier(vcSimulationIdentifier, 0, localSimDir);
                            DataManager dataManager = null;
                            if (sim.isSpatial()) {
                                dataManager = new PDEDataManager(outputContext, vcDataManager, vcDataId);
                            } else {
                                dataManager = new ODEDataManager(outputContext, vcDataManager, vcDataId);
                            }
                            dataViewerController = new SimResultsViewerController(dataManager, sim);
                            dataSetControllerImpl.addDataJobListener(documentWindowManager);
                        }
                        // make the viewer
                        Hashtable<VCSimulationIdentifier, DataViewerController> dataViewerControllers = (Hashtable<VCSimulationIdentifier, DataViewerController>) hashTable.get(H_DATA_VIEWER_CONTROLLERS);
                        if (dataViewerControllers == null) {
                            dataViewerControllers = new Hashtable<VCSimulationIdentifier, DataViewerController>();
                            hashTable.put(H_DATA_VIEWER_CONTROLLERS, dataViewerControllers);
                        }
                        dataViewerControllers.put(vcSimulationIdentifier, dataViewerController);
                    } catch (Throwable exc) {
                        exc.printStackTrace(System.out);
                        saveFailure(hashTable, sim, exc);
                    }
                }
            }
        }
    };
    taskList.add(retrieveResultsTask);
    AsynchClientTask displayResultsTask = new AsynchClientTask("Showing results", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @SuppressWarnings("unchecked")
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            boolean isLocal = fetch(hashTable, H_LOCAL_SIM, Boolean.class, true);
            SimulationWindow.LocalState localState = isLocal ? LocalState.LOCAL : LocalState.SERVER;
            Hashtable<Simulation, Throwable> failures = (Hashtable<Simulation, Throwable>) hashTable.get(H_FAILURES);
            Simulation[] simsToShow = (Simulation[]) hashTable.get("simsArray");
            for (int i = 0; i < simsToShow.length; i++) {
                final Simulation sim = simsToShow[i];
                if (failures != null && failures.containsKey(sim)) {
                    continue;
                }
                final VCSimulationIdentifier vcSimulationIdentifier = simsToShow[i].getSimulationInfo().getAuthoritativeVCSimulationIdentifier();
                final SimulationWindow simWindow = documentWindowManager.haveSimulationWindow(vcSimulationIdentifier);
                if (simWindow != null) {
                    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(documentWindowManager.getComponent());
                    ChildWindow childWindow = childWindowManager.getChildWindowFromContext(simWindow);
                    if (childWindow == null) {
                        childWindow = childWindowManager.addChildWindow(simWindow.getDataViewer(), simWindow);
                        childWindow.pack();
                        childWindow.setIsCenteredOnParent();
                        childWindow.show();
                    }
                    setFinalWindow(hashTable, childWindow);
                    simWindow.setLocalState(localState);
                } else {
                    // wire it up the viewer
                    Hashtable<VCSimulationIdentifier, DataViewerController> dataViewerControllers = (Hashtable<VCSimulationIdentifier, DataViewerController>) hashTable.get(H_DATA_VIEWER_CONTROLLERS);
                    DataViewerController viewerController = dataViewerControllers.get(vcSimulationIdentifier);
                    Throwable ex = (failures == null ? null : failures.get(sim));
                    if (viewerController != null && ex == null) {
                        // no failure
                        DataViewer viewer = viewerController.createViewer();
                        getSimWorkspace().getSimulationOwner().getOutputFunctionContext().addPropertyChangeListener(viewerController);
                        documentWindowManager.addExportListener(viewer);
                        // For data related activities such as calculating statistics
                        documentWindowManager.addDataJobListener(viewer);
                        viewer.setSimulationModelInfo(new SimulationWorkspaceModelInfo(getSimWorkspace().getSimulationOwner(), sim.getName()));
                        viewer.setDataViewerManager(documentWindowManager);
                        SimulationWindow newWindow = new SimulationWindow(vcSimulationIdentifier, sim, getSimWorkspace().getSimulationOwner(), viewer);
                        BeanUtils.addCloseWindowKeyboardAction(newWindow.getDataViewer());
                        documentWindowManager.addResultsFrame(newWindow);
                        setFinalWindow(hashTable, viewer);
                        newWindow.setLocalState(localState);
                    }
                }
            }
            StringBuffer failMessage = new StringBuffer();
            if (failures != null) {
                if (!failures.isEmpty()) {
                    failMessage.append("Error, " + failures.size() + " of " + simsToShow.length + " sim results failed to display:\n");
                    Enumeration<Simulation> en = failures.keys();
                    while (en.hasMoreElements()) {
                        Simulation sim = en.nextElement();
                        Throwable exc = (Throwable) failures.get(sim);
                        failMessage.append("'" + sim.getName() + "' - " + exc.getMessage());
                    }
                }
            }
            if (failMessage.length() > 0) {
                PopupGenerator.showErrorDialog(ClientSimManager.this.getDocumentWindowManager(), failMessage.toString());
            }
        }
    };
    if (viewerType == ViewerType.NativeViewer_only) {
        taskList.add(displayResultsTask);
    }
    // Dispatch the tasks using the ClientTaskDispatcher.
    AsynchClientTask[] taskArray = new AsynchClientTask[taskList.size()];
    taskList.toArray(taskArray);
    return taskArray;
}

Example 2 with VCDataManager

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

the class PDEDataViewerPostProcess method createPostProcessPDEDataContext.

public static PostProcessDataPDEDataContext createPostProcessPDEDataContext(final ClientPDEDataContext parentPDEDataContext) throws Exception {
    final DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) parentPDEDataContext.doDataOperation(new DataOperation.DataProcessingOutputInfoOP(parentPDEDataContext.getVCDataIdentifier(), false, parentPDEDataContext.getDataManager().getOutputContext()));
    if (dataProcessingOutputInfo == null) {
        return null;
    }
    DataSetControllerProvider dataSetControllerProvider = new DataSetControllerProvider() {

        @Override
        public DataSetController getDataSetController() throws DataAccessException {
            return new DataSetController() {

                // DataIdentifier[] dataIdentifiers;
                @Override
                public ExportEvent makeRemoteFile(OutputContext outputContext, ExportSpecs exportSpecs) throws DataAccessException, RemoteProxyException {
                    throw new DataAccessException("Not implemented");
                }

                @Override
                public TimeSeriesJobResults getTimeSeriesValues(OutputContext outputContext, VCDataIdentifier vcdataID, TimeSeriesJobSpec timeSeriesJobSpec) throws RemoteProxyException, DataAccessException {
                    // return parentPDEDataContext.getDataManager().getTimeSeriesValues(timeSeriesJobSpec);
                    DataOperation.DataProcessingOutputTimeSeriesOP dataProcessingOutputTimeSeriesOP = new DataOperation.DataProcessingOutputTimeSeriesOP(vcdataID, timeSeriesJobSpec, outputContext, getDataSetTimes(vcdataID));
                    DataOperationResults.DataProcessingOutputTimeSeriesValues dataopDataProcessingOutputTimeSeriesValues = (DataOperationResults.DataProcessingOutputTimeSeriesValues) parentPDEDataContext.doDataOperation(dataProcessingOutputTimeSeriesOP);
                    return dataopDataProcessingOutputTimeSeriesValues.getTimeSeriesJobResults();
                }

                @Override
                public SimDataBlock getSimDataBlock(OutputContext outputContext, VCDataIdentifier vcdataID, String varName, double time) throws RemoteProxyException, DataAccessException {
                    // return parentPDEDataContext.getDataManager().getSimDataBlock(varName, time);
                    DataOperationResults.DataProcessingOutputDataValues dataProcessingOutputValues = (DataOperationResults.DataProcessingOutputDataValues) parentPDEDataContext.doDataOperation(new DataOperation.DataProcessingOutputDataValuesOP(vcdataID, varName, TimePointHelper.createSingleTimeTimePointHelper(time), DataIndexHelper.createAllDataIndexesDataIndexHelper(), outputContext, null));
                    PDEDataInfo pdeDataInfo = new PDEDataInfo(vcdataID.getOwner(), vcdataID.getID(), varName, time, Long.MIN_VALUE);
                    SimDataBlock simDataBlock = new SimDataBlock(pdeDataInfo, dataProcessingOutputValues.getDataValues()[0], VariableType.POSTPROCESSING);
                    return simDataBlock;
                }

                @Override
                public boolean getParticleDataExists(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return false;
                }

                @Override
                public ParticleDataBlock getParticleDataBlock(VCDataIdentifier vcdataID, double time) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public ODESimData getODEData(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public CartesianMesh getMesh(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // throw new DataAccessException("PostProcessData mesh not available at this level");
                    return null;
                }

                @Override
                public PlotData getLineScan(OutputContext outputContext, VCDataIdentifier vcdataID, String variable, double time, SpatialSelection spatialSelection) throws RemoteProxyException, DataAccessException {
                    throw new DataAccessException("Remote getLineScan method should not be called for PostProcess");
                }

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

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

                @Override
                public DataSetTimeSeries getDataSetTimeSeries(VCDataIdentifier vcdataID, String[] variableNames) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public DataSetMetadata getDataSetMetadata(VCDataIdentifier vcdataID) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public DataIdentifier[] getDataIdentifiers(OutputContext outputContext, VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // return parentPDEDataContext.getDataIdentifiers();
                    ArrayList<DataIdentifier> postProcessDataIDs = new ArrayList<DataIdentifier>();
                    if (outputContext != null && outputContext.getOutputFunctions() != null) {
                        for (int i = 0; i < outputContext.getOutputFunctions().length; i++) {
                            if (outputContext.getOutputFunctions()[i].isPostProcessFunction()) {
                                postProcessDataIDs.add(new DataIdentifier(outputContext.getOutputFunctions()[i].getName(), VariableType.POSTPROCESSING, null, false, outputContext.getOutputFunctions()[i].getDisplayName()));
                            }
                        }
                    }
                    // get 'state' variables
                    for (int i = 0; i < dataProcessingOutputInfo.getVariableNames().length; i++) {
                        if (dataProcessingOutputInfo.getPostProcessDataType(dataProcessingOutputInfo.getVariableNames()[i]).equals(PostProcessDataType.image)) {
                            DataIdentifier dataIdentifier = new DataIdentifier(dataProcessingOutputInfo.getVariableNames()[i], VariableType.POSTPROCESSING, null, false, dataProcessingOutputInfo.getVariableNames()[i]);
                            postProcessDataIDs.add(dataIdentifier);
                        }
                    }
                    if (postProcessDataIDs.size() > 0) {
                        return postProcessDataIDs.toArray(new DataIdentifier[0]);
                    }
                    return null;
                }

                @Override
                public FieldDataFileOperationResults fieldDataFileOperation(FieldDataFileOperationSpec fieldDataFileOperationSpec) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public DataOperationResults doDataOperation(DataOperation dataOperation) throws DataAccessException, RemoteProxyException {
                    // TODO Auto-generated method stub
                    return parentPDEDataContext.doDataOperation(dataOperation);
                }

                @Override
                public VtuFileContainer getEmptyVtuMeshFiles(VCDataIdentifier vcdataID, int timeIndex) throws DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @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) {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public double[] getVtuTimes(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }

                @Override
                public NFSimMolecularConfigurations getNFSimMolecularConfigurations(VCDataIdentifier vcdataID) throws RemoteProxyException, DataAccessException {
                    // TODO Auto-generated method stub
                    return null;
                }
            };
        }
    };
    VCDataManager postProcessVCDataManager = new VCDataManager(dataSetControllerProvider);
    PDEDataManager postProcessPDEDataManager = new PDEDataManager(((ClientPDEDataContext) parentPDEDataContext).getDataManager().getOutputContext(), postProcessVCDataManager, parentPDEDataContext.getVCDataIdentifier());
    PostProcessDataPDEDataContext postProcessDataPDEDataContext = new PostProcessDataPDEDataContext(postProcessPDEDataManager);
    return postProcessDataPDEDataContext;
}

Example 3 with VCDataManager

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

the class VCellClientDataServiceImpl method getVtkManager.

@Override
public VtkManager getVtkManager(SimulationDataSetRef simulationDataSetRef) throws FileNotFoundException, DataAccessException {
    VCSimulationDataIdentifier vcSimulationDataIdentifier = getVCSimulationDataIdentifier(simulationDataSetRef);
    VtkManager vtkManager = null;
    if (!simulationDataSetRef.isLocal) {
        vtkManager = vcellClient.getRequestManager().getVtkManager(null, vcSimulationDataIdentifier);
    } else {
        // ---- preliminary : construct the localDatasetControllerProvider
        File primaryDir = ResourceUtil.getLocalRootDir();
        User usr = User.tempUser;
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
        ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
        LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(usr, dataSetControllerImpl, localExportServiceImpl);
        VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
        vtkManager = new VtkManager(null, vcDataManager, vcSimulationDataIdentifier);
    }
    return vtkManager;
}

Example 4 with VCDataManager

use of cbit.vcell.simdata.VCDataManager 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 5 with VCDataManager

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

the class VCellClientDataServiceImpl method getVCSimulationDataIdentifier.

public VCSimulationDataIdentifier getVCSimulationDataIdentifier(SimulationDataSetRef simulationDataSetRef) throws FileNotFoundException {
    User user = new User(simulationDataSetRef.getUsername(), new KeyValue(simulationDataSetRef.getUserkey()));
    KeyValue simKeyValue = new KeyValue(simulationDataSetRef.getSimId());
    VCSimulationIdentifier vcSimulationIdentifier = new VCSimulationIdentifier(simKeyValue, user);
    if (simulationDataSetRef.isIsLocal()) {
        File primaryDir = ResourceUtil.getLocalRootDir();
        DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
        ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
        LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(user, dataSetControllerImpl, localExportServiceImpl);
        VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
        File localSimDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
        VCSimulationDataIdentifier simulationDataIdentifier = new LocalVCSimulationDataIdentifier(vcSimulationIdentifier, 0, localSimDir);
        return simulationDataIdentifier;
    } else {
        VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(vcSimulationIdentifier, simulationDataSetRef.getJobIndex());
        return vcSimulationDataIdentifier;
    }
}