Examples with ChomboVtkFileWriter org.vcell.vis.mapping.chombo.ChomboVtkFileWriter used on opensource projects

Example 1 with ChomboVtkFileWriter

use of org.vcell.vis.mapping.chombo.ChomboVtkFileWriter in project vcell by virtualcell.

the class DataSetControllerImpl method getVtuMeshData.

public double[] getVtuMeshData(ChomboFiles chomboFiles, OutputContext outputContext, VCDataIdentifier vcdataID, VtuVarInfo var, double time) throws DataAccessException {
    try {
        double[] times = getDataSetTimes(vcdataID);
        int timeIndex = -1;
        for (int i = 0; i < times.length; i++) {
            if (times[i] == time) {
                timeIndex = i;
                break;
            }
        }
        if (timeIndex < 0) {
            throw new DataAccessException("data for dataset " + vcdataID + " not found at time " + time);
        }
        ChomboVtkFileWriter chomboVTKFileWriter = new ChomboVtkFileWriter();
        double[] vtuData = chomboVTKFileWriter.getVtuMeshData(chomboFiles, outputContext, getUserDataDirectory(vcdataID), time, var, timeIndex);
        return vtuData;
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("failed to retrieve VTK files: " + e.getMessage(), e);
    }
}

Example 2 with ChomboVtkFileWriter

use of org.vcell.vis.mapping.chombo.ChomboVtkFileWriter in project vcell by virtualcell.

the class DataSetControllerImpl method getEmptyVtuMeshFiles.

public VtuFileContainer getEmptyVtuMeshFiles(ChomboFiles chomboFiles, VCDataIdentifier vcdataID, int timeIndex) throws DataAccessException {
    try {
        if (timeIndex > 0) {
            throw new RuntimeException("only time index 0 supported for chombo vtk mesh files");
        }
        ChomboVtkFileWriter chomboVTKFileWriter = new ChomboVtkFileWriter();
        File primaryDirectory = getPrimaryUserDir(vcdataID.getOwner(), false);
        VtuFileContainer vtuFiles = chomboVTKFileWriter.getEmptyVtuMeshFiles(chomboFiles, primaryDirectory);
        return vtuFiles;
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("failed to retrieve VTK files: " + e.getMessage(), e);
    }
}

Example 3 with ChomboVtkFileWriter

use of org.vcell.vis.mapping.chombo.ChomboVtkFileWriter in project vcell by virtualcell.

the class RasterExporter method makeVTKUnstructuredData_Chombo.

public ExportOutput[] makeVTKUnstructuredData_Chombo(OutputContext outputContext, final JobRequest jobRequest, User user, DataServerImpl dataServerImpl, ExportSpecs exportSpecs, File tmpDir, FileDataContainerManager fileDataContainerManager) throws Exception {
    String simID = exportSpecs.getVCDataIdentifier().getID();
    final VCDataIdentifier vcdID = exportSpecs.getVCDataIdentifier();
    VariableSpecs variableSpecs = exportSpecs.getVariableSpecs();
    TimeSpecs timeSpecs = exportSpecs.getTimeSpecs();
    ChomboFiles chomboFiles = dataServerImpl.getChomboFiles(user, vcdID);
    ChomboVtkFileWriter chomboVTKFileWriter = new ChomboVtkFileWriter();
    File[] vtkFiles = chomboVTKFileWriter.writeVtuExportFiles(chomboFiles, tmpDir, new ChomboVtkFileWriter.ProgressListener() {

        public void progress(double percentDone) {
            exportServiceImpl.fireExportProgress(jobRequest.getJobID(), vcdID, "VTKUNSTR", percentDone);
        }
    });
    Vector<ExportOutput> exportOutV = new Vector<ExportOutput>();
    for (File file : vtkFiles) {
        String dataID = file.getName().replace(simID.toString(), "");
        ExportOutput exportOut = new ExportOutput(true, ".vtu", simID.toString(), dataID, fileDataContainerManager);
        fileDataContainerManager.manageExistingTempFile(exportOut.getFileDataContainerID(), file);
        exportOutV.add(exportOut);
    }
    ExportOutput[] exportOutputArr = exportOutV.toArray(new ExportOutput[0]);
    return exportOutputArr;
}

Example 4 with ChomboVtkFileWriter

use of org.vcell.vis.mapping.chombo.ChomboVtkFileWriter in project vcell by virtualcell.

the class DataSetControllerImpl method getVtuVarInfos.

public VtuVarInfo[] getVtuVarInfos(ChomboFiles chomboFiles, OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException {
    try {
        ChomboVtkFileWriter chomboVTKFileWriter = new ChomboVtkFileWriter();
        VtuVarInfo[] vtuVarInfos = chomboVTKFileWriter.getVtuVarInfos(chomboFiles, outputContext, getVCData(vcdataID));
        return vtuVarInfos;
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("failed to retrieve VTK variable list: " + e.getMessage(), e);
    }
}