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

Example 1 with PDEDataInfo

use of cbit.vcell.simdata.PDEDataInfo 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 2 with PDEDataInfo

use of cbit.vcell.simdata.PDEDataInfo 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;
}

Example 3 with PDEDataInfo

use of cbit.vcell.simdata.PDEDataInfo 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);
}