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Example 1 with DataSetController

use of cbit.vcell.server.DataSetController 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;
}
Also used : VtuVarInfo(org.vcell.vis.io.VtuVarInfo) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) DataIdentifier(cbit.vcell.simdata.DataIdentifier) TimeSeriesJobSpec(org.vcell.util.document.TimeSeriesJobSpec) ExportSpecs(cbit.vcell.export.server.ExportSpecs) FieldDataFileOperationSpec(cbit.vcell.field.io.FieldDataFileOperationSpec) DataProcessingOutputInfo(cbit.vcell.simdata.DataOperationResults.DataProcessingOutputInfo) ArrayList(java.util.ArrayList) DataProcessingOutputInfoOP(cbit.vcell.simdata.DataOperation.DataProcessingOutputInfoOP) PDEDataInfo(cbit.vcell.simdata.PDEDataInfo) DataSetControllerProvider(cbit.vcell.server.DataSetControllerProvider) SimDataBlock(cbit.vcell.simdata.SimDataBlock) SpatialSelection(cbit.vcell.simdata.SpatialSelection) VCDataManager(cbit.vcell.simdata.VCDataManager) DataAccessException(org.vcell.util.DataAccessException) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) DataOperation(cbit.vcell.simdata.DataOperation) DataSetController(cbit.vcell.server.DataSetController) OutputContext(cbit.vcell.simdata.OutputContext) PDEDataManager(cbit.vcell.simdata.PDEDataManager) DataProcessingOutputInfo(cbit.vcell.simdata.DataOperationResults.DataProcessingOutputInfo) DataOperationResults(cbit.vcell.simdata.DataOperationResults) ClientPDEDataContext(cbit.vcell.simdata.ClientPDEDataContext) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier)

Example 2 with DataSetController

use of cbit.vcell.server.DataSetController in project vcell by virtualcell.

the class DisplayTimeSeriesOp method getDataSetControllerProvider.

private DataSetControllerProvider getDataSetControllerProvider(final ImageTimeSeries<? extends Image> imageTimeSeries, final PDEDataViewer pdeDataViewer) 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 {
            pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_START, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
            if (!timeSeriesJobSpec.isCalcSpaceStats() && !timeSeriesJobSpec.isCalcTimeStats()) {
                int[][] indices = timeSeriesJobSpec.getIndices();
                double[] timeStamps = imageTimeSeries.getImageTimeStamps();
                // [var][dataindex+1][timeindex]
                double[][][] dataValues = new double[1][indices[0].length + 1][timeStamps.length];
                for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
                    // index 0 is time
                    dataValues[0][0][timeIndex] = timeStamps[timeIndex];
                }
                for (int timeIndex = 0; timeIndex < timeStamps.length; timeIndex++) {
                    float[] pixelValues = imageTimeSeries.getAllImages()[timeIndex].getFloatPixels();
                    for (int samplePointIndex = 0; samplePointIndex < indices[0].length; samplePointIndex++) {
                        int pixelIndex = indices[0][samplePointIndex];
                        dataValues[0][samplePointIndex + 1][timeIndex] = pixelValues[pixelIndex];
                    }
                }
                TSJobResultsNoStats timeSeriesJobResults = new TSJobResultsNoStats(new String[] { "var" }, indices, timeStamps, dataValues);
                pdeDataViewer.dataJobMessage(new DataJobEvent(timeSeriesJobSpec.getVcDataJobID(), MessageEvent.DATA_COMPLETE, vcdataID.getDataKey(), vcdataID.getID(), new Double(0)));
                return timeSeriesJobResults;
            }
            return null;
        }

        @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;
        }
    };
    return dataSetControllerProvider;
}
Also used : Origin(org.vcell.util.Origin) VtuVarInfo(org.vcell.vis.io.VtuVarInfo) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) DataIdentifier(cbit.vcell.simdata.DataIdentifier) TimeSeriesJobSpec(org.vcell.util.document.TimeSeriesJobSpec) Extent(org.vcell.util.Extent) ISize(org.vcell.util.ISize) ExportSpecs(cbit.vcell.export.server.ExportSpecs) FieldDataFileOperationSpec(cbit.vcell.field.io.FieldDataFileOperationSpec) VCImage(cbit.image.VCImage) PDEDataInfo(cbit.vcell.simdata.PDEDataInfo) DataSetControllerProvider(cbit.vcell.server.DataSetControllerProvider) SimDataBlock(cbit.vcell.simdata.SimDataBlock) SpatialSelection(cbit.vcell.simdata.SpatialSelection) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) DataOperation(cbit.vcell.simdata.DataOperation) VariableType(cbit.vcell.math.VariableType) DataSetController(cbit.vcell.server.DataSetController) VCImageUncompressed(cbit.image.VCImageUncompressed) OutputContext(cbit.vcell.simdata.OutputContext) DataJobEvent(cbit.rmi.event.DataJobEvent) CartesianMesh(cbit.vcell.solvers.CartesianMesh) RegionImage(cbit.vcell.geometry.RegionImage) Domain(cbit.vcell.math.Variable.Domain) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) TSJobResultsNoStats(org.vcell.util.document.TSJobResultsNoStats)

Example 3 with DataSetController

use of cbit.vcell.server.DataSetController in project vcell by virtualcell.

the class ClientSimManager method importBatchSimulation.

private ODESimData importBatchSimulation(OutputContext outputContext, Simulation sim) throws DataAccessException, RemoteProxyException, ExpressionException {
    boolean success = false;
    ODESimData simData = null;
    if (sim.getVersion() == null) {
        throw new RuntimeException("Missing Version.");
    }
    SimulationInfo simInfo = sim.getSimulationInfo();
    if (simInfo == null) {
        throw new RuntimeException("Missing Simulation Info.");
    }
    User usr = sim.getVersion().getOwner();
    VCSimulationIdentifier asi = simInfo.getAuthoritativeVCSimulationIdentifier();
    // sim.getScanCount()  number of jobs must be one, so job index is 0
    VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(asi, 0);
    ClientServerManager csm = VCellClientTest.getVCellClient().getClientServerManager();
    DataSetController dsc = csm.getDataSetController();
    simData = dsc.getODEData(vcSimulationDataIdentifier);
    System.out.println(sim.getName() + ": simulation results recovered");
    return simData;
/*
	
	final VCSimulationIdentifier vcSimulationIdentifier = simInfo.getAuthoritativeVCSimulationIdentifier();
	DataManager dataManager = null;

	try {
//		DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null,localBatchDir,null);
		ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
	
//		LocalDataSetControllerProvider localDSCProvider = new LocalDataSetControllerProvider(usr, dataSetControllerImpl, localExportServiceImpl);
//		VCDataManager vcDataManager = new VCDataManager(localDSCProvider);
//		LocalVCDataIdentifier vcDataId = new LocalVCSimulationDataIdentifier(vcSimulationIdentifier, 0, localSimDir);
//		if (sim.isSpatial()) {
//			dataManager = new PDEDataManager(outputContext,vcDataManager, vcDataId);
//		} else {
//			dataManager = new ODEDataManager(outputContext,vcDataManager, vcDataId);
//		}	
		System.out.println("start!");
		DataViewerController dataViewerController = documentWindowManager.getRequestManager().getDataViewerController(outputContext,sim, 0);
		
//		if(!(dataViewerController instanceof SimResultsViewerController)) {
//			throw new RuntimeException("Unable to initialize the SimResultsViewerController");
//		}
//		SimResultsViewerController rvc = (SimResultsViewerController)dataViewerController;
		DataViewer dw = dataViewerController.createViewer();
//		DataViewerManager dwm = dw.getDataViewerManager();
		if(!(dw instanceof SimResultsViewer)) {
			throw new RuntimeException("Wrong data viewer type, must be SimResultsViewer.");
		}
		SimResultsViewer srw = (SimResultsViewer)dw;

		// I need DataViewer.ODEDataManager.ODESimData (Ode Solver Result Set !!!!)
		
		
		System.out.println("done!");
//	} catch (FileNotFoundException e) {
//		e.printStackTrace();
	} catch (DataAccessException e) {
		e.printStackTrace();
	}
	
	*/
}
Also used : VCSimulationIdentifier(cbit.vcell.solver.VCSimulationIdentifier) ClientServerManager(cbit.vcell.client.server.ClientServerManager) User(org.vcell.util.document.User) DataSetController(cbit.vcell.server.DataSetController) ODESimData(cbit.vcell.solver.ode.ODESimData) VCSimulationDataIdentifier(cbit.vcell.solver.VCSimulationDataIdentifier) SimulationInfo(cbit.vcell.solver.SimulationInfo)

Example 4 with DataSetController

use of cbit.vcell.server.DataSetController 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);
}
Also used : Origin(org.vcell.util.Origin) VtuVarInfo(org.vcell.vis.io.VtuVarInfo) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) DataIdentifier(cbit.vcell.simdata.DataIdentifier) User(org.vcell.util.document.User) TimeSeriesJobSpec(org.vcell.util.document.TimeSeriesJobSpec) Extent(org.vcell.util.Extent) ISize(org.vcell.util.ISize) ExportSpecs(cbit.vcell.export.server.ExportSpecs) FieldDataFileOperationSpec(cbit.vcell.field.io.FieldDataFileOperationSpec) VCImage(cbit.image.VCImage) PDEDataInfo(cbit.vcell.simdata.PDEDataInfo) DataSetControllerProvider(cbit.vcell.server.DataSetControllerProvider) SimDataBlock(cbit.vcell.simdata.SimDataBlock) SpatialSelection(cbit.vcell.simdata.SpatialSelection) JFrame(javax.swing.JFrame) VCDataManager(cbit.vcell.simdata.VCDataManager) AnnotatedFunction(cbit.vcell.solver.AnnotatedFunction) DataOperation(cbit.vcell.simdata.DataOperation) VariableType(cbit.vcell.math.VariableType) DataSetController(cbit.vcell.server.DataSetController) VCImageUncompressed(cbit.image.VCImageUncompressed) OutputContext(cbit.vcell.simdata.OutputContext) CartesianMesh(cbit.vcell.solvers.CartesianMesh) PDEDataManager(cbit.vcell.simdata.PDEDataManager) RegionImage(cbit.vcell.geometry.RegionImage) ClientPDEDataContext(cbit.vcell.simdata.ClientPDEDataContext) Domain(cbit.vcell.math.Variable.Domain) VCDataIdentifier(org.vcell.util.document.VCDataIdentifier) PDEDataViewer(cbit.vcell.client.data.PDEDataViewer)

Aggregations

DataSetController (cbit.vcell.server.DataSetController)4 ExportSpecs (cbit.vcell.export.server.ExportSpecs)3 FieldDataFileOperationSpec (cbit.vcell.field.io.FieldDataFileOperationSpec)3 DataSetControllerProvider (cbit.vcell.server.DataSetControllerProvider)3 DataIdentifier (cbit.vcell.simdata.DataIdentifier)3 DataOperation (cbit.vcell.simdata.DataOperation)3 OutputContext (cbit.vcell.simdata.OutputContext)3 PDEDataInfo (cbit.vcell.simdata.PDEDataInfo)3 SimDataBlock (cbit.vcell.simdata.SimDataBlock)3 SpatialSelection (cbit.vcell.simdata.SpatialSelection)3 AnnotatedFunction (cbit.vcell.solver.AnnotatedFunction)3 TimeSeriesJobSpec (org.vcell.util.document.TimeSeriesJobSpec)3 VCDataIdentifier (org.vcell.util.document.VCDataIdentifier)3 VtuVarInfo (org.vcell.vis.io.VtuVarInfo)3 VCImage (cbit.image.VCImage)2 VCImageUncompressed (cbit.image.VCImageUncompressed)2 RegionImage (cbit.vcell.geometry.RegionImage)2 Domain (cbit.vcell.math.Variable.Domain)2 VariableType (cbit.vcell.math.VariableType)2 ClientPDEDataContext (cbit.vcell.simdata.ClientPDEDataContext)2