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

Example 1 with SimDataBlock

use of cbit.vcell.simdata.SimDataBlock 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 SimDataBlock

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

the class SmoldynFileWriter method writeDataProcessor.

private void writeDataProcessor() throws DataAccessException, IOException, MathException, DivideByZeroException, ExpressionException {
    Simulation simulation = simTask.getSimulation();
    DataProcessingInstructions dpi = simulation.getDataProcessingInstructions();
    if (dpi == null) {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " begin " + DataProcessingInstructions.ROI_TIME_SERIES);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " end");
    } else {
        FieldDataIdentifierSpec fdis = dpi.getSampleImageFieldData(simulation.getVersion().getOwner());
        if (fdis == null) {
            throw new DataAccessException("Can't find sample image in data processing instructions");
        }
        File userDirectory = outputFile.getParentFile();
        String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, null);
        DataSetControllerImpl dsci = new DataSetControllerImpl(null, userDirectory.getParentFile(), secondarySimDataDir == null ? null : new File(secondarySimDataDir));
        CartesianMesh origMesh = dsci.getMesh(fdis.getExternalDataIdentifier());
        SimDataBlock simDataBlock = dsci.getSimDataBlock(null, fdis.getExternalDataIdentifier(), fdis.getFieldFuncArgs().getVariableName(), fdis.getFieldFuncArgs().getTime().evaluateConstant());
        VariableType varType = fdis.getFieldFuncArgs().getVariableType();
        VariableType dataVarType = simDataBlock.getVariableType();
        if (!varType.equals(VariableType.UNKNOWN) && !varType.equals(dataVarType)) {
            throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
        }
        double[] origData = simDataBlock.getData();
        String filename = SimulationJob.createSimulationJobID(Simulation.createSimulationID(simulation.getKey()), simTask.getSimulationJob().getJobIndex()) + SimulationData.getDefaultFieldDataFileNameForSimulation(fdis.getFieldFuncArgs());
        File fdatFile = new File(userDirectory, filename);
        DataSet.writeNew(fdatFile, new String[] { fdis.getFieldFuncArgs().getVariableName() }, new VariableType[] { simDataBlock.getVariableType() }, new ISize(origMesh.getSizeX(), origMesh.getSizeY(), origMesh.getSizeZ()), new double[][] { origData });
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " begin " + dpi.getScriptName());
        StringTokenizer st = new StringTokenizer(dpi.getScriptInput(), "\n\r");
        while (st.hasMoreTokens()) {
            String str = st.nextToken();
            if (str.trim().length() > 0) {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " " + str);
            }
        }
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " SampleImageFile " + fdis.getFieldFuncArgs().getVariableName() + " " + fdis.getFieldFuncArgs().getTime().infix() + " " + fdatFile);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " end");
    }
}

Example 3 with SimDataBlock

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

the class RasterExporter method makeUCDData.

public ExportOutput[] makeUCDData(OutputContext outputContext, JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
    String simID = exportSpecs.getVCDataIdentifier().getID();
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    VariableSpecs variableSpecs = exportSpecs.getVariableSpecs();
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    cbit.vcell.solvers.CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    CartesianMesh.UCDInfo ucdInfo = mesh.getUCDInfo();
    CartesianMesh.UCDInfo ucdInfoReduced = ucdInfo.removeNonMembraneGridNodes();
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    // for (int i = 0; i < variableSpecs.getVariableNames().length; i++){
    for (int j = timeSpecs.getBeginTimeIndex(); j <= timeSpecs.getEndTimeIndex(); j++) {
        exportServiceImpl.fireExportProgress(jobRequest.getJobID(), vcdID, "UCD", (double) (j - timeSpecs.getBeginTimeIndex()) / (double) (timeSpecs.getEndTimeIndex() - timeSpecs.getBeginTimeIndex() + 1));
        // String fileID = simID + "_Full_" + formatTime(timeSpecs.getAllTimes()[j]) + "time_" + variableSpecs.getVariableNames().length + "vars";
        // File datafile = new File(tempDir, fileID + "_data.ucd");
        // FileWriter fileWriter = new FileWriter(datafile);
        Vector<double[]> volumeDataV = new Vector<double[]>();
        Vector<String> volumeDataNameV = new Vector<String>();
        Vector<String> volumeDataUnitV = new Vector<String>();
        Vector<double[]> membraneDataV = new Vector<double[]>();
        Vector<String> membraneDataNameV = new Vector<String>();
        Vector<String> membraneDataUnitV = new Vector<String>();
        for (int k = 0; k < variableSpecs.getVariableNames().length; k++) {
            SimDataBlock simDataBlock = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[k], timeSpecs.getAllTimes()[j]);
            if (simDataBlock.getVariableType().equals(VariableType.VOLUME)) {
                volumeDataNameV.add(variableSpecs.getVariableNames()[k]);
                volumeDataUnitV.add("unknown");
                volumeDataV.add(simDataBlock.getData());
            } else {
                membraneDataNameV.add(variableSpecs.getVariableNames()[k]);
                membraneDataUnitV.add("unknown");
                membraneDataV.add(simDataBlock.getData());
            }
        }
        if (volumeDataV.size() > 0) {
            StringWriter stringWriter = new StringWriter();
            AVS_UCD_Exporter.writeUCDVolGeomAndData(ucdInfo, volumeDataNameV.toArray(new String[0]), volumeDataUnitV.toArray(new String[0]), volumeDataV.toArray(new double[0][]), stringWriter);
            ExportOutput exportOut = new ExportOutput(true, ".ucd", simID.toString(), "_vol_" + j, fileDataContainerManager);
            fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
            exportOutV.add(exportOut);
        }
        if (membraneDataV.size() > 0) {
            StringWriter stringWriter = new StringWriter();
            AVS_UCD_Exporter.writeUCDMembGeomAndData(ucdInfoReduced, /*ucdInfo*/
            membraneDataNameV.toArray(new String[0]), membraneDataUnitV.toArray(new String[0]), membraneDataV.toArray(new double[0][]), stringWriter);
            ExportOutput exportOut = new ExportOutput(true, ".ucd", simID.toString(), "_memb_" + j, fileDataContainerManager);
            fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
            exportOutV.add(exportOut);
        }
    // AVS_UCD_Exporter.writeUCD(mesh,
    // (volumeDataNameV.size() == 0?null:volumeDataNameV.toArray(new String[0])),
    // (volumeDataUnitV.size() == 0?null:volumeDataUnitV.toArray(new String[0])),
    // (volumeDataV.size() == 0?null:volumeDataV.toArray(new double[0][])),
    // 
    // (membraneDataNameV.size() == 0?null:membraneDataNameV.toArray(new String[0])),
    // (membraneDataUnitV.size() == 0?null:membraneDataUnitV.toArray(new String[0])),
    // (membraneDataV.size() == 0?null:membraneDataV.toArray(new double[0][])),
    // stringWriter);
    // ExportOutput exportOut = new ExportOutput(true,".ucd",simID.toString(),fileID,stringWriter.toString().getBytes());
    // exportOutV.add(exportOut);
    }
    // }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
// String fileID = simID + "_Full_" + NUM_TIMES + "times_" + variableSpecs.getVariableNames().length + "vars";
// File datafile = new File(tempDir, fileID + "_data.nrrd");
// nrrdInfo.setDatafile(datafile.getName());
// DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(datafile)));
// try {
// for (int i = 0; i < variableSpecs.getVariableNames().length; i++){
// for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++){
// double[] data = dataServerImpl.getSimDataBlock(user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
// for (int k = 0; k < data.length; k++){
// out.writeDouble(data[k]);
// }
// }
// }
// } catch (IOException exc) {
// throw new DataAccessException(exc.toString());
// } finally {
// out.close();
// }
}

Example 4 with SimDataBlock

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

the class RasterExporter method makeVTKUnstructuredData.

public ExportOutput[] makeVTKUnstructuredData(OutputContext outputContext, JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
    String simID = exportSpecs.getVCDataIdentifier().getID();
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    VariableSpecs variableSpecs = exportSpecs.getVariableSpecs();
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    cbit.vcell.solvers.CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    CartesianMesh.UCDInfo ucdInfo = mesh.getUCDInfo();
    CartesianMesh.UCDInfo ucdInfoReduced = ucdInfo.removeNonMembraneGridNodes();
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    // for (int i = 0; i < variableSpecs.getVariableNames().length; i++){
    for (int j = timeSpecs.getBeginTimeIndex(); j <= timeSpecs.getEndTimeIndex(); j++) {
        exportServiceImpl.fireExportProgress(jobRequest.getJobID(), vcdID, "VTKUNSTR", (double) (j - timeSpecs.getBeginTimeIndex()) / (double) (timeSpecs.getEndTimeIndex() - timeSpecs.getBeginTimeIndex() + 1));
        // String fileID = simID + "_Full_" + formatTime(timeSpecs.getAllTimes()[j]) + "time_" + variableSpecs.getVariableNames().length + "vars";
        // File datafile = new File(tempDir, fileID + "_data.ucd");
        // FileWriter fileWriter = new FileWriter(datafile);
        Vector<double[]> volumeDataV = new Vector<double[]>();
        Vector<String> volumeDataNameV = new Vector<String>();
        Vector<String> volumeDataUnitV = new Vector<String>();
        Vector<double[]> membraneDataV = new Vector<double[]>();
        Vector<String> membraneDataNameV = new Vector<String>();
        Vector<String> membraneDataUnitV = new Vector<String>();
        for (int k = 0; k < variableSpecs.getVariableNames().length; k++) {
            SimDataBlock simDataBlock = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[k], timeSpecs.getAllTimes()[j]);
            if (simDataBlock.getVariableType().equals(VariableType.VOLUME)) {
                volumeDataNameV.add(variableSpecs.getVariableNames()[k]);
                volumeDataUnitV.add("unknown");
                volumeDataV.add(simDataBlock.getData());
            } else {
                membraneDataNameV.add(variableSpecs.getVariableNames()[k]);
                membraneDataUnitV.add("unknown");
                membraneDataV.add(simDataBlock.getData());
            }
        }
        if (volumeDataV.size() > 0) {
            int[] regionIDs = new int[mesh.getNumVolumeElements()];
            for (int i = 0; i < regionIDs.length; i++) {
                regionIDs[i] = mesh.getVolumeRegionIndex(i);
            }
            StringWriter stringWriter = new StringWriter();
            writeVTKUnstructuredHeader(ucdInfo, vcdID, stringWriter);
            int CELL_INFO_COUNT = 1 + 4 + (ucdInfo.getNumVolumeNodesZ() > 1 ? 4 : 0);
            stringWriter.write("CELLS " + ucdInfo.getNumVolumeCells() + " " + (ucdInfo.getNumVolumeCells() * CELL_INFO_COUNT) + "\n");
            stringWriter.write(ucdInfo.getVolumeCellsString(true));
            writeVTKCellTypes(ucdInfo, ucdInfo.getNumVolumeCells(), (ucdInfo.getNumVolumeNodesZ() > 1 ? VTK_HEXAHEDRON : VTK_QUAD), stringWriter);
            writeVTKCellData(volumeDataV.toArray(new double[0][]), regionIDs, volumeDataNameV.toArray(new String[0]), stringWriter);
            // AVS_UCD_Exporter.writeUCDVolume(
            // ucdInfo,
            // volumeDataNameV.toArray(new String[0]),
            // volumeDataUnitV.toArray(new String[0]),
            // volumeDataV.toArray(new double[0][]),
            // stringWriter);
            ExportOutput exportOut = new ExportOutput(true, ".vtk", simID.toString(), "vol_" + j, fileDataContainerManager);
            fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
            exportOutV.add(exportOut);
        }
        if (membraneDataV.size() > 0) {
            int[] regionIDs = new int[mesh.getNumMembraneElements()];
            for (int i = 0; i < regionIDs.length; i++) {
                regionIDs[i] = mesh.getMembraneRegionIndex(i);
            }
            StringWriter stringWriter = new StringWriter();
            writeVTKUnstructuredHeader(ucdInfoReduced, /*ucdInfo*/
            vcdID, stringWriter);
            int MEMBR_INFO_COUNT = 1 + 2 + (ucdInfo.getNumVolumeNodesZ() > 1 ? 2 : 0);
            stringWriter.write("CELLS " + ucdInfoReduced.getNumMembraneCells() + " " + (ucdInfoReduced.getNumMembraneCells() * MEMBR_INFO_COUNT) + "\n");
            stringWriter.write(ucdInfoReduced.getMembraneCellsString(0, true));
            writeVTKCellTypes(ucdInfoReduced, /*ucdInfo*/
            ucdInfoReduced.getNumMembraneCells(), (ucdInfo.getNumVolumeNodesZ() > 1 ? VTK_QUAD : VTK_LINE), stringWriter);
            writeVTKCellData(membraneDataV.toArray(new double[0][]), regionIDs, membraneDataNameV.toArray(new String[0]), stringWriter);
            // AVS_UCD_Exporter.writeUCDMembrane(
            // ucdInfo,
            // membraneDataNameV.toArray(new String[0]),
            // membraneDataUnitV.toArray(new String[0]),
            // membraneDataV.toArray(new double[0][]),
            // stringWriter);
            ExportOutput exportOut = new ExportOutput(true, ".vtk", simID.toString(), "memb_" + j, fileDataContainerManager);
            fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
            exportOutV.add(exportOut);
        }
    // AVS_UCD_Exporter.writeUCD(mesh,
    // (volumeDataNameV.size() == 0?null:volumeDataNameV.toArray(new String[0])),
    // (volumeDataUnitV.size() == 0?null:volumeDataUnitV.toArray(new String[0])),
    // (volumeDataV.size() == 0?null:volumeDataV.toArray(new double[0][])),
    // 
    // (membraneDataNameV.size() == 0?null:membraneDataNameV.toArray(new String[0])),
    // (membraneDataUnitV.size() == 0?null:membraneDataUnitV.toArray(new String[0])),
    // (membraneDataV.size() == 0?null:membraneDataV.toArray(new double[0][])),
    // stringWriter);
    // ExportOutput exportOut = new ExportOutput(true,".ucd",simID.toString(),fileID,stringWriter.toString().getBytes());
    // exportOutV.add(exportOut);
    }
    // }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
// String fileID = simID + "_Full_" + NUM_TIMES + "times_" + variableSpecs.getVariableNames().length + "vars";
// File datafile = new File(tempDir, fileID + "_data.nrrd");
// nrrdInfo.setDatafile(datafile.getName());
// DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(datafile)));
// try {
// for (int i = 0; i < variableSpecs.getVariableNames().length; i++){
// for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++){
// double[] data = dataServerImpl.getSimDataBlock(user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
// for (int k = 0; k < data.length; k++){
// out.writeDouble(data[k]);
// }
// }
// }
// } catch (IOException exc) {
// throw new DataAccessException(exc.toString());
// } finally {
// out.close();
// }
}

Example 5 with SimDataBlock

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

the class RasterExporter method makePLYWithTexData.

public ExportOutput[] makePLYWithTexData(OutputContext outputContext, JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, FileDataContainerManager fileDataContainerManager) throws Exception {
    String simID = exportSpecs.getVCDataIdentifier().getID();
    VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    cbit.vcell.solvers.CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    VariableSpecs variableSpecs = exportSpecs.getVariableSpecs();
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    RegionImage regionImage = MeshDisplayAdapter.generateRegionImage(mesh, null);
    PLYSpecs plySpecs = (PLYSpecs) exportSpecs.getFormatSpecificSpecs();
    DisplayPreferences[] displayPreferences = plySpecs.getDisplayPreferences();
    // BitSet bInDomain = null;
    // String variableName = variableSpecs.getVariableNames()[0];
    // Domain varDomain = null;
    // DataIdentifier[] dataIdentifiers = dataServerImpl.getDataIdentifiers(outputContext, user, vcdID);
    // for (int i = 0; i < dataIdentifiers.length; i++) {
    // //dataIdentifier.getDomain();
    // if(dataIdentifiers[i].getName().equals(variableName)){
    // varDomain = dataIdentifiers[i].getDomain();
    // break;
    // }
    // }
    // MembraneElement membraneElement = mesh.getMembraneElements()[faceIndex];
    // String memSubdomainName = (varDomain==null?null:mesh.getMembraneSubdomainNamefromMemIndex(faceIndex));
    // boolean bInDomain = (varDomain==null?true:varDomain.getName().equals(memSubdomainName));
    DisplayAdapterService das = new DisplayAdapterService();
    StringWriter stringWriter = new StringWriter();
    PolyTexHelper imgResults = writeStanfordPolygonTex(regionImage, stringWriter, /*,bInDomain*/
    mesh);
    // mesh
    ExportOutput exportOut = new ExportOutput(true, ".ply", simID.toString(), "_memb", fileDataContainerManager);
    fileDataContainerManager.append(exportOut.getFileDataContainerID(), stringWriter.toString());
    exportOutV.add(exportOut);
    // special neighbor annotation image
    ExportOutput textImagetOut0 = new ExportOutput(true, ".png", simID.toString(), "_membAnnot", fileDataContainerManager);
    fileDataContainerManager.append(textImagetOut0.getFileDataContainerID(), imgResults.specialNeighborImage);
    exportOutV.add(textImagetOut0);
    for (int varNameIndex = 0; varNameIndex < variableSpecs.getVariableNames().length; varNameIndex++) {
        if (das.fetchColorModel(displayPreferences[varNameIndex].getColorMode()) == null) {
            if (displayPreferences[varNameIndex].getColorMode().equals(DisplayAdapterService.GRAY)) {
                das.addColorModelForValues(DisplayAdapterService.createGrayColorModel(), DisplayAdapterService.createBlueRedSpecialColors(), displayPreferences[varNameIndex].getColorMode());
            } else {
                das.addColorModelForValues(DisplayAdapterService.createBlueRedColorModel(), DisplayAdapterService.createGraySpecialColors(), displayPreferences[varNameIndex].getColorMode());
            // das.setActiveColorModelID("Contrast");
            }
        }
        // BitSet domainValid = (displayPreferences[varNameIndex]==null?null:(displayPreferences[varNameIndex].getDomainValid()==null?null:displayPreferences[varNameIndex].getDomainValid()));
        ExportSpecs.setupDisplayAdapterService(displayPreferences[varNameIndex], das, displayPreferences[varNameIndex].getScaleSettings());
        for (int j = timeSpecs.getBeginTimeIndex(); j <= timeSpecs.getEndTimeIndex(); j++) {
            BufferedImage image = createTextureImage(imgResults.imageSideSize);
            int[] imgBuffer = ((DataBufferInt) (image.getRaster().getDataBuffer())).getData();
            Arrays.fill(imgBuffer, Integer.MAX_VALUE);
            SimDataBlock simDataBlock = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[varNameIndex], timeSpecs.getAllTimes()[j]);
            for (int k = 0; k < imgResults.dataIndexes.length; k++) {
                if (imgBuffer[k] != Integer.MAX_VALUE) {
                    System.out.println("texture pixel used twice");
                }
                double avgVal = 0;
                for (int l = 0; l < imgResults.dataIndexes[k].length; l++) {
                    avgVal += simDataBlock.getData()[imgResults.dataIndexes[k][l]];
                }
                imgBuffer[k] = das.getColorFromValue(avgVal / imgResults.dataIndexes[k].length);
            }
            byte[] pngImage = flipPNG(image);
            ExportOutput textImagetOut = new ExportOutput(true, ".png", simID.toString(), "_memb_" + variableSpecs.getVariableNames()[varNameIndex] + "_" + j, fileDataContainerManager);
            fileDataContainerManager.append(textImagetOut.getFileDataContainerID(), pngImage);
            exportOutV.add(textImagetOut);
        }
    }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
}