Examples with FileDataContainerID cbit.vcell.export.server.FileDataContainerManager.FileDataContainerID used on opensource projects

Example 1 with FileDataContainerID

use of cbit.vcell.export.server.FileDataContainerManager.FileDataContainerID in project vcell by virtualcell.

the class ASCIIExporter method getPointsTimeSeries.

/**
 * This method was created in VisualAge.
 * @return java.lang.String
 * @throws IOException
 */
private FileDataContainerID getPointsTimeSeries(OutputContext outputContext, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, String variableName, GeometrySpecs geometrySpecs, double[] allTimes, int beginIndex, int endIndex, boolean switchRowsColumns, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    org.vcell.util.document.TimeSeriesJobSpec timeSeriesJobSpec = new org.vcell.util.document.TimeSeriesJobSpec(new String[] { variableName }, new int[][] { geometrySpecs.getPointIndexes() }, null, allTimes[beginIndex], 1, allTimes[endIndex], VCDataJobID.createVCDataJobID(user, false));
    org.vcell.util.document.TSJobResultsNoStats timeSeriesJobResults = (org.vcell.util.document.TSJobResultsNoStats) dataServerImpl.getTimeSeriesValues(outputContext, user, vcdID, timeSeriesJobSpec);
    // variableValues[0] is time array
    // variableValues[1] is values for 1st spatial point.
    // variableValues[2] is values for 2nd spatial point.
    // variableValues[n] (n>=1) is values for nth spatial point.
    // the length of variableValues should always be 1 + pointIndexes.length
    // the length of variableValues[n] is allTimes.length
    final double[][] variableValues = timeSeriesJobResults.getTimesAndValuesForVariable(variableName);
    // 
    // put data in csv format
    // 
    SpatialSelection[] pointSpatialSelections = geometrySpecs.getPointSpatialSelections();
    FileDataContainerID fileDataContainerID = fileDataContainerManager.getNewFileDataContainerID();
    // FileDataContainer container = fileDataContainerManager.getFileDataContainer(fileDataContainerID);
    // buffer.append(
    // "\"Time Series for variable '" + variableName + "'\" over the range " + allTimes[beginIndex] + " to " + allTimes[endIndex] + "\n");
    fileDataContainerManager.append(fileDataContainerID, "\"variable ('" + variableName + "') times (" + allTimes[beginIndex] + " " + allTimes[endIndex] + ") " + /*+getSpatialSelectionDescription(curve)*/
    "\"\n");
    if (switchRowsColumns) {
        fileDataContainerManager.append(fileDataContainerID, ",Coordinates\n");
        fileDataContainerManager.append(fileDataContainerID, "Time,");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int k = 0; k < pointSpatialSelections.length; k++) {
            fileDataContainerManager.append(fileDataContainerID, "," + getSpatialSelectionDescription(pointSpatialSelections[k]));
            for (int i = beginIndex; i <= endIndex; i++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[k + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    } else {
        fileDataContainerManager.append(fileDataContainerID, ",Time\n");
        fileDataContainerManager.append(fileDataContainerID, "Coordinates,");
        for (int k = 0; k < pointSpatialSelections.length; k++) {
            fileDataContainerManager.append(fileDataContainerID, "," + getSpatialSelectionDescription(pointSpatialSelections[k]));
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
            for (int k = 0; k < pointSpatialSelections.length; k++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[k + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    }
    return fileDataContainerID;
}

Example 2 with FileDataContainerID

use of cbit.vcell.export.server.FileDataContainerManager.FileDataContainerID in project vcell by virtualcell.

the class ASCIIExporter method getCurveTimeSeries.

/**
 * This method was created in VisualAge.
 * @return java.lang.String
 * @throws IOException
 */
private FileDataContainerID getCurveTimeSeries(OutputContext outputContext, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, String variableName, SpatialSelection curve, double[] allTimes, int beginIndex, int endIndex, boolean switchRowsColumns, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    int[] pointIndexes = null;
    double[] distances = null;
    int[] crossingMembraneIndexes = null;
    if (curve instanceof SpatialSelectionVolume) {
        SpatialSelection.SSHelper ssh = ((SpatialSelectionVolume) curve).getIndexSamples(0.0, 1.0);
        pointIndexes = ssh.getSampledIndexes();
        distances = ssh.getWorldCoordinateLengths();
        crossingMembraneIndexes = ssh.getMembraneIndexesInOut();
    } else if (curve instanceof SpatialSelectionMembrane) {
        SpatialSelection.SSHelper ssh = ((SpatialSelectionMembrane) curve).getIndexSamples();
        if (((SpatialSelectionMembrane) curve).getSelectionSource() instanceof SinglePoint) {
            pointIndexes = new int[] { ssh.getSampledIndexes()[0] };
            distances = new double[] { 0 };
        } else {
            pointIndexes = ssh.getSampledIndexes();
            distances = ssh.getWorldCoordinateLengths();
        }
    }
    org.vcell.util.document.TimeSeriesJobSpec timeSeriesJobSpec = new org.vcell.util.document.TimeSeriesJobSpec(new String[] { variableName }, new int[][] { pointIndexes }, new int[][] { crossingMembraneIndexes }, allTimes[beginIndex], 1, allTimes[endIndex], VCDataJobID.createVCDataJobID(user, false));
    org.vcell.util.document.TSJobResultsNoStats timeSeriesJobResults = (org.vcell.util.document.TSJobResultsNoStats) dataServerImpl.getTimeSeriesValues(outputContext, user, vcdID, timeSeriesJobSpec);
    // variableValues[0] is time array
    // variableValues[1] is values for 1st spatial point.
    // variableValues[2] is values for 2nd spatial point.
    // variableValues[n] (n>=1) is values for nth spatial point.
    // the length of variableValues should always be 1 + pointIndexes.length
    // the length of variableValues[n] is allTimes.length
    final double[][] variableValues = timeSeriesJobResults.getTimesAndValuesForVariable(variableName);
    // 
    // put data in csv format
    // 
    FileDataContainerID fileDataContainerID = fileDataContainerManager.getNewFileDataContainerID();
    fileDataContainerManager.append(fileDataContainerID, "\"variable ('" + variableName + "') times (" + allTimes[beginIndex] + " " + allTimes[endIndex] + ") " + getSpatialSelectionDescription(curve) + "\"\n");
    if (switchRowsColumns) {
        fileDataContainerManager.append(fileDataContainerID, ",Distances\n");
        fileDataContainerManager.append(fileDataContainerID, "Times,");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int j = 0; j < distances.length; j++) {
            fileDataContainerManager.append(fileDataContainerID, "," + distances[j]);
            for (int i = beginIndex; i <= endIndex; i++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[j + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    } else {
        fileDataContainerManager.append(fileDataContainerID, ",Times\n");
        fileDataContainerManager.append(fileDataContainerID, "Distances,");
        for (int i = 0; i < distances.length; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + distances[i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
            for (int j = 0; j < distances.length; j++) {
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[j + 1][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    }
    return fileDataContainerID;
}

Example 3 with FileDataContainerID

use of cbit.vcell.export.server.FileDataContainerManager.FileDataContainerID in project vcell by virtualcell.

the class ASCIIExporter method getODEDataValues.

/**
 * Insert the method's description here.
 * Creation date: (1/17/00 6:02:37 PM)
 * @return java.lang.String
 * @param odeSimData cbit.vcell.simdata.ODESimData
 * @param variableNames java.lang.String[]
 * @param beginIndex int
 * @param endIndex int
 * @param switchRowsColumns boolean
 * @exception org.vcell.util.DataAccessException The exception description.
 * @throws IOException
 */
private FileDataContainerID getODEDataValues(long jobID, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, String[] variableNames, int beginIndex, int endIndex, boolean switchRowsColumns, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    ODESimData odeSimData = dataServerImpl.getODEData(user, vcdID);
    double progress = 0.0;
    boolean isTimeSeries = (odeSimData.findColumn("t") > -1) ? true : false;
    boolean isMultiTrial = (odeSimData.findColumn("TrialNo") > -1) ? true : false;
    // get arrays
    double[] allTimes = null;
    try {
        if (isTimeSeries)
            allTimes = odeSimData.extractColumn(odeSimData.findColumn("t"));
        else if (isMultiTrial)
            allTimes = odeSimData.extractColumn(odeSimData.findColumn("TrialNo"));
    } catch (cbit.vcell.parser.ExpressionException e) {
        e.printStackTrace(System.out);
    }
    double[][] variableValues = new double[variableNames.length][endIndex - beginIndex + 1];
    for (int k = 0; k < variableNames.length; k++) {
        for (int i = beginIndex; i <= endIndex; i++) {
            progress = (double) (i + k * (endIndex - beginIndex + 1)) / (2 * variableNames.length * (endIndex - beginIndex + 1));
            exportServiceImpl.fireExportProgress(jobID, vcdID, "CSV", progress);
            try {
                variableValues[k][i - beginIndex] = odeSimData.extractColumn(odeSimData.findColumn(variableNames[k]))[i];
            } catch (cbit.vcell.parser.ExpressionException e) {
                e.printStackTrace(System.out);
                throw new DataAccessException("error evaluating function in dataset: " + e.getMessage());
            }
        }
    }
    // put data in csv format
    FileDataContainerID fileDataContainerID = fileDataContainerManager.getNewFileDataContainerID();
    if (isTimeSeries) {
        fileDataContainerManager.append(fileDataContainerID, "Variable values over the time range " + allTimes[beginIndex] + " to " + allTimes[endIndex] + "\n\n");
    } else if (isMultiTrial) {
        fileDataContainerManager.append(fileDataContainerID, "Variable values over the Trials " + allTimes[beginIndex] + " to " + allTimes[endIndex] + "\n\n");
    }
    if (switchRowsColumns) {
        fileDataContainerManager.append(fileDataContainerID, ",Variable\n");
        if (isTimeSeries)
            fileDataContainerManager.append(fileDataContainerID, "Time,");
        else if (isMultiTrial)
            fileDataContainerManager.append(fileDataContainerID, "Trial No,");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int k = 0; k < variableNames.length; k++) {
            fileDataContainerManager.append(fileDataContainerID, "," + variableNames[k]);
            for (int i = beginIndex; i <= endIndex; i++) {
                progress = 0.5 + (double) (i + k * (endIndex - beginIndex + 1)) / (2 * variableNames.length * (endIndex - beginIndex + 1));
                exportServiceImpl.fireExportProgress(jobID, vcdID, "CSV", progress);
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[k][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    } else {
        if (isTimeSeries)
            fileDataContainerManager.append(fileDataContainerID, ",Time\n");
        else if (isMultiTrial)
            fileDataContainerManager.append(fileDataContainerID, ",Trial No\n");
        fileDataContainerManager.append(fileDataContainerID, "Variable,");
        for (int k = 0; k < variableNames.length; k++) {
            fileDataContainerManager.append(fileDataContainerID, "," + variableNames[k]);
        }
        fileDataContainerManager.append(fileDataContainerID, "\n");
        for (int i = beginIndex; i <= endIndex; i++) {
            fileDataContainerManager.append(fileDataContainerID, "," + allTimes[i]);
            for (int k = 0; k < variableNames.length; k++) {
                progress = 0.5 + (double) (i + k * (endIndex - beginIndex + 1)) / (2 * variableNames.length * (endIndex - beginIndex + 1));
                exportServiceImpl.fireExportProgress(jobID, vcdID, "CSV", progress);
                fileDataContainerManager.append(fileDataContainerID, "," + variableValues[k][i - beginIndex]);
            }
            fileDataContainerManager.append(fileDataContainerID, "\n");
        }
    }
    return fileDataContainerID;
}

Example 4 with FileDataContainerID

use of cbit.vcell.export.server.FileDataContainerManager.FileDataContainerID in project vcell by virtualcell.

the class ASCIIExporter method getSlice.

/**
 * This method was created in VisualAge.
 * @return java.io.File
 * @param variable java.lang.String
 * @param time double
 * @throws IOException
 */
private FileDataContainerID getSlice(OutputContext outputContext, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, String variable, int timeIndex, String slicePlane, int sliceNumber, boolean switchRowsColumns, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    double[] allTimes = dataServerImpl.getDataSetTimes(user, vcdID);
    double timepoint = allTimes[timeIndex];
    SimDataBlock simDataBlock = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variable, timepoint);
    double[] data = simDataBlock.getData();
    cbit.vcell.solvers.CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    int[] sizeXYZ = { mesh.getSizeX(), mesh.getSizeY(), mesh.getSizeZ() };
    FileDataContainerID fileDataContainerID = fileDataContainerManager.getNewFileDataContainerID();
    if (simDataBlock.getVariableType().equals(VariableType.VOLUME) || simDataBlock.getVariableType().equals(VariableType.POSTPROCESSING)) {
        // 
        // put data in csv format
        // 
        fileDataContainerManager.append(fileDataContainerID, "2D Slice for variable " + variable + " at time " + timepoint);
        if (slicePlane.equals(Coordinate.getNormalAxisPlaneName(Coordinate.Z_AXIS))) {
            fileDataContainerManager.append(fileDataContainerID, " in plane XY at Z = " + sliceNumber + "\n\n");
            int start = sliceNumber * sizeXYZ[0] * sizeXYZ[1];
            if (switchRowsColumns) {
                fileDataContainerManager.append(fileDataContainerID, "X in rows, Y in columns\n");
                for (int j = 0; j < sizeXYZ[0]; j++) {
                    for (int i = 0; i < sizeXYZ[1]; i++) {
                        fileDataContainerManager.append(fileDataContainerID, data[start + i * sizeXYZ[0] + j] + ",");
                    }
                    fileDataContainerManager.append(fileDataContainerID, "\n");
                }
            } else {
                fileDataContainerManager.append(fileDataContainerID, "X in columns, Y in rows\n");
                for (int i = 0; i < sizeXYZ[1]; i++) {
                    for (int j = 0; j < sizeXYZ[0]; j++) {
                        fileDataContainerManager.append(fileDataContainerID, data[start + i * sizeXYZ[0] + j] + ",");
                    }
                    fileDataContainerManager.append(fileDataContainerID, "\n");
                }
            }
        }
        if (slicePlane.equals(Coordinate.getNormalAxisPlaneName(Coordinate.Y_AXIS))) {
            fileDataContainerManager.append(fileDataContainerID, " in plane XZ at Y = " + sliceNumber + "\n\n");
            int start = sliceNumber * sizeXYZ[0];
            if (switchRowsColumns) {
                fileDataContainerManager.append(fileDataContainerID, "X in rows, Z in columns\n");
                for (int i = 0; i < sizeXYZ[0]; i++) {
                    for (int j = 0; j < sizeXYZ[2]; j++) {
                        fileDataContainerManager.append(fileDataContainerID, data[start + j * sizeXYZ[0] * sizeXYZ[1] + i] + ",");
                    }
                    fileDataContainerManager.append(fileDataContainerID, "\n");
                }
            } else {
                fileDataContainerManager.append(fileDataContainerID, "X in columns, Z in rows\n");
                for (int j = 0; j < sizeXYZ[2]; j++) {
                    for (int i = 0; i < sizeXYZ[0]; i++) {
                        fileDataContainerManager.append(fileDataContainerID, data[start + j * sizeXYZ[0] * sizeXYZ[1] + i] + ",");
                    }
                    fileDataContainerManager.append(fileDataContainerID, "\n");
                }
            }
        }
        if (slicePlane.equals(Coordinate.getNormalAxisPlaneName(Coordinate.X_AXIS))) {
            fileDataContainerManager.append(fileDataContainerID, " in plane YZ at X = " + sliceNumber + "\n\n");
            int start = sliceNumber;
            if (switchRowsColumns) {
                fileDataContainerManager.append(fileDataContainerID, "Y in rows, Z in columns\n");
                for (int j = 0; j < sizeXYZ[1]; j++) {
                    for (int i = 0; i < sizeXYZ[2]; i++) {
                        fileDataContainerManager.append(fileDataContainerID, data[start + i * sizeXYZ[0] * sizeXYZ[1] + j * sizeXYZ[0]] + ",");
                    }
                    fileDataContainerManager.append(fileDataContainerID, "\n");
                }
            } else {
                fileDataContainerManager.append(fileDataContainerID, "Y in columns, Z in rows\n");
                for (int i = 0; i < sizeXYZ[2]; i++) {
                    for (int j = 0; j < sizeXYZ[1]; j++) {
                        fileDataContainerManager.append(fileDataContainerID, data[start + i * sizeXYZ[0] * sizeXYZ[1] + j * sizeXYZ[0]] + ",");
                    }
                    fileDataContainerManager.append(fileDataContainerID, "\n");
                }
            }
        }
    // } else if (mesh.getGeometryDimension() < 3) {
    } else {
        // membrane variable; we export the data by index
        // for 3D one gets the whole dataset for now... warning at the client level... will get more sophisticated later...
        fileDataContainerManager.append(fileDataContainerID, "Data for membrane variable " + variable + " at time " + timepoint + "\nEntire datablock by index\n\n");
        for (int i = 0; i < data.length; i++) {
            fileDataContainerManager.append(fileDataContainerID, data[i] + "\n");
        }
    // buffer.append("\n");
    // } else {
    // throw new RuntimeException("3D export for membrane or region variables not supported yet");
    }
    return fileDataContainerID;
}

Example 5 with FileDataContainerID

use of cbit.vcell.export.server.FileDataContainerManager.FileDataContainerID in project vcell by virtualcell.

the class ASCIIExporter method exportPDEData.

/**
 * This method was created in VisualAge.
 * @throws IOException
 */
private List<ExportOutput> exportPDEData(OutputContext outputContext, long jobID, User user, DataServerImpl dataServerImpl, final VCDataIdentifier orig_vcdID, VariableSpecs variableSpecs, TimeSpecs timeSpecs, GeometrySpecs geometrySpecs, ASCIISpecs asciiSpecs, String contextName, FileDataContainerManager fileDataContainerManager) throws DataAccessException, IOException {
    ExportSpecs.SimNameSimDataID[] simNameSimDataIDs = asciiSpecs.getSimNameSimDataIDs();
    Vector<ExportOutput[]> exportOutputV = new Vector<ExportOutput[]>();
    double progressCounter = 0;
    final int SIM_COUNT = simNameSimDataIDs.length;
    final int PARAMSCAN_COUNT = (asciiSpecs.getExportMultipleParamScans() != null ? asciiSpecs.getExportMultipleParamScans().length : 1);
    final int endTimeIndex = timeSpecs.getEndTimeIndex();
    final int beginTimeIndex = timeSpecs.getBeginTimeIndex();
    final int TIME_COUNT = endTimeIndex - beginTimeIndex + 1;
    double TOTAL_EXPORTS_OPS = 0;
    switch(geometrySpecs.getModeID()) {
        case GEOMETRY_SELECTIONS:
            TOTAL_EXPORTS_OPS = SIM_COUNT * PARAMSCAN_COUNT * variableSpecs.getVariableNames().length * (geometrySpecs.getCurves().length + (geometrySpecs.getPointCount() > 0 ? 1 : 0));
            break;
        case GEOMETRY_SLICE:
            TOTAL_EXPORTS_OPS = SIM_COUNT * PARAMSCAN_COUNT * variableSpecs.getVariableNames().length * TIME_COUNT;
            break;
    }
    if (asciiSpecs.getCSVRoiLayout() == ASCIISpecs.csvRoiLayout.time_sim_var) {
        exportOutputV.add(new ExportOutput[] { sofyaFormat(outputContext, jobID, user, dataServerImpl, orig_vcdID, variableSpecs, timeSpecs, geometrySpecs, asciiSpecs, contextName, fileDataContainerManager) });
    } else {
        for (int v = 0; v < SIM_COUNT; v++) {
            int simJobIndex = simNameSimDataIDs[v].getDefaultJobIndex();
            VCDataIdentifier vcdID = simNameSimDataIDs[v].getVCDataIdentifier(simJobIndex);
            // 3. simNameSimDataIDs[v].getExportParamScanInfo() != null and asciiSpecs.getExportMultipleParamScans() != null, parameter scan use simNameSimDataIDs[v].getExportParamScanInfo().getParamScanJobIndexes() loop through
            for (int ps = 0; ps < PARAMSCAN_COUNT; ps++) {
                if (asciiSpecs.getExportMultipleParamScans() != null) {
                    simJobIndex = simNameSimDataIDs[v].getExportParamScanInfo().getParamScanJobIndexes()[asciiSpecs.getExportMultipleParamScans()[ps]];
                    vcdID = simNameSimDataIDs[v].getVCDataIdentifier(simJobIndex);
                }
                // Get times for each sim{paramscan} because they may be different
                final double[] allTimes = dataServerImpl.getDataSetTimes(user, vcdID);
                if (allTimes.length <= beginTimeIndex || allTimes.length <= endTimeIndex) {
                    throw new DataAccessException("Sim '" + simNameSimDataIDs[v].getSimulationName() + "' id=" + vcdID.getID() + " simJob=" + simJobIndex + ", time array length=" + allTimes.length + " has no endTimeIndex=" + endTimeIndex);
                }
                String paramScanInfo = "";
                if (simNameSimDataIDs[v].getExportParamScanInfo() != null) {
                    for (int i = 0; i < simNameSimDataIDs[v].getExportParamScanInfo().getParamScanConstantNames().length; i++) {
                        String psName = simNameSimDataIDs[v].getExportParamScanInfo().getParamScanConstantNames()[i];
                        paramScanInfo = paramScanInfo + " '" + psName + "'=" + simNameSimDataIDs[v].getExportParamScanInfo().getParamScanConstantValues()[simJobIndex][i];
                    }
                }
                String simID = vcdID.getID();
                String dataType = ".csv";
                FileDataContainerID fileDataContainerID_header = fileDataContainerManager.getNewFileDataContainerID();
                SimulationDescription simulationDescription = new SimulationDescription(outputContext, user, dataServerImpl, vcdID, false, null);
                fileDataContainerManager.append(fileDataContainerID_header, "\"" + "Model: '" + contextName + "'\"\n\"Simulation: '" + simNameSimDataIDs[v].getSimulationName() + "' (" + paramScanInfo + ")\"\n" + simulationDescription.getHeader(dataType));
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_SELECTIONS:
                        {
                            // Set mesh on SpatialSelection because mesh is transient field because it's too big for messaging
                            SpatialSelection[] spatialSelections = geometrySpecs.getSelections();
                            CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
                            for (int i = 0; i < spatialSelections.length; i++) {
                                if (spatialSelections[i].getMesh() == null) {
                                    spatialSelections[i].setMesh(mesh);
                                } else if (!spatialSelections[i].getMesh().getISize().compareEqual(mesh.getISize()) || spatialSelections[i].getMesh().getNumMembraneElements() != mesh.getNumMembraneElements()) {
                                    // check just sizes not areas,normals,etc...
                                    // This will throw fail message
                                    spatialSelections[i].setMesh(mesh);
                                }
                            }
                            Vector<ExportOutput> outputV = new Vector<ExportOutput>();
                            if (geometrySpecs.getPointCount() > 0) {
                                // assemble single point data together (uses more compact formatting)
                                String dataID = "_Points_vars(" + geometrySpecs.getPointCount() + ")_times(" + (endTimeIndex - beginTimeIndex + 1) + ")";
                                // StringBuilder data1 = new StringBuilder(data.toString());
                                ExportOutput exportOutput1 = new ExportOutput(true, dataType, simID, dataID, /* + variableSpecs.getVariableNames()[i]*/
                                fileDataContainerManager);
                                fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), fileDataContainerID_header);
                                for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                    fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), getPointsTimeSeries(outputContext, user, dataServerImpl, vcdID, variableSpecs.getVariableNames()[i], geometrySpecs, allTimes, beginTimeIndex, endTimeIndex, asciiSpecs.getSwitchRowsColumns(), fileDataContainerManager));
                                    fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), "\n");
                                    progressCounter++;
                                    exportServiceImpl.fireExportProgress(jobID, orig_vcdID, "CSV", progressCounter / TOTAL_EXPORTS_OPS);
                                }
                                outputV.add(exportOutput1);
                            }
                            if (geometrySpecs.getCurves().length != 0) {
                                // assemble curve (non-single point) data together
                                String dataID = "_Curves_vars(" + (geometrySpecs.getCurves().length) + ")_times(" + (endTimeIndex - beginTimeIndex + 1) + ")";
                                // StringBuilder data1 = new StringBuilder(data.toString());
                                ExportOutput exportOutput1 = new ExportOutput(true, dataType, simID, dataID, /* + variableSpecs.getVariableNames()[i]*/
                                fileDataContainerManager);
                                fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), fileDataContainerID_header);
                                for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                    for (int s = 0; s < geometrySpecs.getCurves().length; s++) {
                                        if (!GeometrySpecs.isSinglePoint(geometrySpecs.getCurves()[s])) {
                                            fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), getCurveTimeSeries(outputContext, user, dataServerImpl, vcdID, variableSpecs.getVariableNames()[i], geometrySpecs.getCurves()[s], allTimes, beginTimeIndex, endTimeIndex, asciiSpecs.getSwitchRowsColumns(), fileDataContainerManager));
                                            fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), "\n");
                                            progressCounter++;
                                            exportServiceImpl.fireExportProgress(jobID, orig_vcdID, "CSV", progressCounter / TOTAL_EXPORTS_OPS);
                                        }
                                    }
                                }
                                outputV.add(exportOutput1);
                            }
                            exportOutputV.add(outputV.toArray(new ExportOutput[0]));
                            break;
                        }
                    case GEOMETRY_SLICE:
                        {
                            String dataID = "_Slice_" + Coordinate.getNormalAxisPlaneName(geometrySpecs.getAxis()) + "_" + geometrySpecs.getSliceNumber() + "_";
                            ExportOutput[] output = new ExportOutput[variableSpecs.getVariableNames().length * TIME_COUNT];
                            for (int j = 0; j < variableSpecs.getVariableNames().length; j++) {
                                for (int i = 0; i < TIME_COUNT; i++) {
                                    StringBuilder inset = new StringBuilder(Integer.toString(i + beginTimeIndex));
                                    inset.reverse();
                                    inset.append("000");
                                    inset.setLength(4);
                                    inset.reverse();
                                    String dataID1 = dataID + variableSpecs.getVariableNames()[j] + "_" + inset.toString();
                                    ExportOutput exportOutput1 = new ExportOutput(true, dataType, simID, dataID1, /* + variableSpecs.getVariableNames()[i]*/
                                    fileDataContainerManager);
                                    fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), fileDataContainerID_header);
                                    fileDataContainerManager.append(exportOutput1.getFileDataContainerID(), getSlice(outputContext, user, dataServerImpl, vcdID, variableSpecs.getVariableNames()[j], i + beginTimeIndex, Coordinate.getNormalAxisPlaneName(geometrySpecs.getAxis()), geometrySpecs.getSliceNumber(), asciiSpecs.getSwitchRowsColumns(), fileDataContainerManager));
                                    output[j * TIME_COUNT + i] = exportOutput1;
                                    progressCounter++;
                                    exportServiceImpl.fireExportProgress(jobID, orig_vcdID, "CSV", progressCounter / TOTAL_EXPORTS_OPS);
                                // data1.cleanup();
                                // data2.cleanup();
                                }
                            }
                            exportOutputV.add(output);
                            break;
                        }
                    default:
                        {
                            throw new DataAccessException("Unexpected geometry modeID");
                        }
                }
            }
        }
    }
    if (exportOutputV.size() == 1) {
        // geometry_slice
        return Arrays.asList(exportOutputV.elementAt(0));
    }
    // geometry_selections (all are same length as first element)
    ArrayList<ExportOutput> combinedExportOutput = new ArrayList<>();
    for (int i = 0; i < exportOutputV.elementAt(0).length; i++) {
        String DATATYPE = exportOutputV.elementAt(0)[i].getDataType();
        String DATAID = exportOutputV.elementAt(0)[i].getDataID();
        ExportOutput eo = new ExportOutput(true, DATATYPE, "MultiSimulation", DATAID, fileDataContainerManager);
        // FileDataContainer container = fileDataContainerManager.getFileDataContainer(combinedExportOutput[i].getFileDataContainerID());
        for (int j = 0; j < exportOutputV.size(); j++) {
            fileDataContainerManager.append(eo.getFileDataContainerID(), exportOutputV.elementAt(j)[i].getFileDataContainerID());
            fileDataContainerManager.append(eo.getFileDataContainerID(), "\n");
        }
        combinedExportOutput.add(eo);
    }
    return combinedExportOutput;
}