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

Example 6 with DataIdentifier

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

the class PDEPlotControlPanel method initConnections.

/**
 * Initializes connections
 * @exception java.lang.Exception The exception description.
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void initConnections() throws java.lang.Exception {
    // user code begin {1}
    // user code end
    getJTextField1().addActionListener(ivjEventHandler);
    getJTextField1().addFocusListener(ivjEventHandler);
    getDefaultListModelCivilized1().addListDataListener(ivjEventHandler);
    getViewFunctionButton().addActionListener(ivjEventHandler);
    getPlotVariableJList().setModel(getDefaultListModelCivilized1());
    getJSliderTime().getModel().addChangeListener(ivjEventHandler);
    getPlotVariableJList().addListSelectionListener(ivjEventHandler);
    getPlotVariableJList().setCellRenderer(new DefaultListCellRenderer() {

        public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
            JLabel c = (JLabel) super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
            if (dataInfoProvider == null) {
                if (value instanceof DataIdentifier) {
                    DataIdentifier var = (DataIdentifier) value;
                    if (var.getVariableType() == VariableType.POSTPROCESSING) {
                        setToolTipText(getText());
                        setText(var.getName());
                    }
                }
                return this;
            }
            // System.out.println("rendering object "+value+" of type "+value.getClass());
            DataIdentifier var = (DataIdentifier) value;
            c.setText(var.getName());
            c.setToolTipText("dataInfoProvier not found");
            DataSymbolMetadataResolver dataSymbolMetadataResolver = dataInfoProvider.getSimulationModelInfo().getDataSymbolMetadataResolver();
            if (dataSymbolMetadataResolver != null && dataSymbolMetadataResolver.getDataSymbolMetadata(var.getName()) != null) {
                DataSymbolMetadata dsm = dataSymbolMetadataResolver.getDataSymbolMetadata(var.getName());
                String tooltipString = "dataInfoProvider found, but identifier " + var.getName() + " not found";
                if (dsm == null) {
                    tooltipString = "did not find info on variable " + var.getDisplayName();
                } else {
                    c.setText(var.getName() + " [" + dsm.unit + "]");
                    tooltipString = dsm.tooltipString;
                }
                c.setToolTipText(tooltipString);
            }
            return this;
        }
    });
}

Example 7 with DataIdentifier

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

the class PDEPlotControlPanel method getFilterVarNamesTasks.

private AsynchClientTask[] getFilterVarNamesTasks() {
    final Object oldselection = getPlotVariableJList().getSelectedValue();
    final ArrayList<DataIdentifier> displayDataIdentifiers = new ArrayList<DataIdentifier>();
    AsynchClientTask task2 = new AsynchClientTask("filter variables", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (PDEPlotControlPanel.this.getName().equals("PostProcessPDEPCP")) {
                System.out.println("PostProcessPDEPCP");
            }
            getViewFunctionButton().setVisible(bHasOldUserDefinedFunctions);
            if (myDataIdentifiers != null && myDataIdentifiers.length > 0) {
                DataIdentifier[] dataIdentifierArr = new DataIdentifier[myDataIdentifiers.length];
                System.arraycopy(myDataIdentifiers, 0, dataIdentifierArr, 0, myDataIdentifiers.length);
                Arrays.sort(dataIdentifierArr, new Comparator<DataIdentifier>() {

                    public int compare(DataIdentifier o1, DataIdentifier o2) {
                        int bEqualIgnoreCase = o1.getDisplayName().compareToIgnoreCase(o2.getDisplayName());
                        if (bEqualIgnoreCase == 0) {
                            return o1.getDisplayName().compareTo(o2.getDisplayName());
                        }
                        return bEqualIgnoreCase;
                    }
                });
                if (dataIdentifierFilter == null) {
                    displayDataIdentifiers.addAll(Arrays.asList(dataIdentifierArr));
                } else {
                    ArrayList<DataIdentifier> acceptedDataIdentifiers = dataIdentifierFilter.accept((String) filterComboBox.getSelectedItem(), Arrays.asList(myAnnotFunctions), dataIdentifierArr);
                    if (acceptedDataIdentifiers != null) {
                        displayDataIdentifiers.addAll(acceptedDataIdentifiers);
                    }
                }
            }
        }
    };
    AsynchClientTask task3 = new AsynchClientTask("Update filtered variables", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (PDEPlotControlPanel.this.getName().equals("PostProcessPDEPCP")) {
                System.out.println("PostProcessPDEPCP");
            }
            getDefaultListModelCivilized1().removeListDataListener(ivjEventHandler);
            getDefaultListModelCivilized1().setContents(displayDataIdentifiers.size() == 0 ? null : displayDataIdentifiers.toArray(new DataIdentifier[0]));
            getPlotVariableJList().clearSelection();
            getDefaultListModelCivilized1().addListDataListener(ivjEventHandler);
            if (getPlotVariableJList().getModel().getSize() > 0) {
                if (oldselection == null) {
                    getPlotVariableJList().setSelectedIndex(0);
                } else {
                    boolean bFound = false;
                    for (int i = 0; i < getPlotVariableJList().getModel().getSize(); i++) {
                        if (oldselection.equals(getPlotVariableJList().getModel().getElementAt(i))) {
                            getPlotVariableJList().setSelectedIndex(i);
                            bFound = true;
                            break;
                        }
                    }
                    if (!bFound) {
                        getPlotVariableJList().setSelectedIndex(0);
                    }
                }
            }
        }
    };
    return new AsynchClientTask[] { task2, task3 };
}

Example 8 with DataIdentifier

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

the class SingleFileDescriptor method preNextProcess.

// load the data before the panel disappears
public ArrayList<AsynchClientTask> preNextProcess() {
    // create AsynchClientTask arraylist
    ArrayList<AsynchClientTask> taskArrayList = new ArrayList<AsynchClientTask>();
    if (singleFilePanel.getFileName().length() > 0) {
        final String fileStr = singleFilePanel.getFileName();
        final String LOADING_MESSAGE = "Loading " + fileStr + "...";
        AsynchClientTask updateUIBeforeLoadTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                VirtualFrapBatchRunFrame.updateStatus(LOADING_MESSAGE);
            }
        };
        AsynchClientTask loadTask = new AsynchClientTask(LOADING_MESSAGE, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                FRAPStudy newFRAPStudy = null;
                File inFile = new File(fileStr);
                if (// .log (vcell log file)
                inFile.getName().endsWith(SimDataConstants.LOGFILE_EXTENSION)) {
                    DataIdentifier[] dataIdentifiers = FrapDataUtils.getDataIdentiferListFromVCellSimulationData(inFile, 0);
                    String[][] rowData = new String[dataIdentifiers.length][1];
                    for (int i = 0; i < dataIdentifiers.length; i++) {
                        if (dataIdentifiers[i].getVariableType().equals(VariableType.VOLUME)) {
                            rowData[i][0] = dataIdentifiers[i].getName();
                        }
                    }
                    int[] selectedIndexArr = DialogUtils.showComponentOKCancelTableList(SingleFileDescriptor.this.getPanelComponent(), "Select Volume Variable", new String[] { "Volume Variable Name" }, rowData, ListSelectionModel.SINGLE_SELECTION);
                    if (selectedIndexArr != null && selectedIndexArr.length > 0) {
                        // newFRAPStudy = getFrapWorkspace().loadFRAPDataFromVcellLogFile(inFile, dataIdentifiers[selectedIndexArr[0]].getName(), this.getClientTaskStatusSupport());
                        isFileLoaded = true;
                    } else {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                } else if (// .vfrap
                inFile.getName().endsWith(VirtualFrapLoader.VFRAP_EXTENSION)) {
                    String xmlString = XmlUtil.getXMLString(inFile.getAbsolutePath());
                    MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
                    newFRAPStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), this.getClientTaskStatusSupport());
                    newFRAPStudy.setXmlFilename(inFile.getAbsolutePath());
                    if (!FRAPWorkspace.areExternalDataOK(localWorkspace, newFRAPStudy.getFrapDataExternalDataInfo(), newFRAPStudy.getRoiExternalDataInfo())) {
                        newFRAPStudy.setFrapDataExternalDataInfo(null);
                        newFRAPStudy.setRoiExternalDataInfo(null);
                    }
                } else // .lsm or other image formatss
                {
                    newFRAPStudy = FRAPWorkspace.loadFRAPDataFromImageFile(inFile, this.getClientTaskStatusSupport());
                    isFileLoaded = true;
                }
                // otherwise, popup a dialog saying the result will be invalid.
                if (!batchRunWorkspace.isBatchRunResultsAvailable()) {
                    hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
                } else if ((batchRunWorkspace.isBatchRunResultsAvailable() && inFile.getName().endsWith(VirtualFrapLoader.VFRAP_EXTENSION)) && ((newFRAPStudy.getFrapModel(batchRunWorkspace.getSelectedModel()) != null) && (newFRAPStudy.getFrapModel(batchRunWorkspace.getSelectedModel()).getModelParameters() != null))) {
                    // put newfrapstudy into hashtable to be used for next task
                    hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
                } else {
                    String continueStr = "Remove results and continue";
                    String cancelStr = "Cancel loading data";
                    String msg = "Loading a new data file,\n or a vfrap file with no model data,\n or a vfrap file with different selected model type, \n will INVALID the existing resuls.";
                    String choice = DialogUtils.showWarningDialog(singleFilePanel, msg, new String[] { continueStr, cancelStr }, continueStr);
                    if (choice == continueStr) {
                        hashTable.put(CLEAR_RESULT_KEY, new Boolean(true));
                        hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
                    } else // cancel
                    {
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                }
            }
        };
        AsynchClientTask afterLoadingSwingTask = new AsynchClientTask(LOADING_MESSAGE, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                // check to see if results need to be cleared
                Boolean needClear = (Boolean) hashTable.get(CLEAR_RESULT_KEY);
                if (needClear != null && needClear.booleanValue()) {
                    double[][] oldAnalysisData = batchRunWorkspace.getAnalysisMSESummaryData();
                    double[][] newAnalysisData = null;
                    batchRunWorkspace.firePropertyChange(FRAPBatchRunWorkspace.PROPERTY_CHANGE_BATCHRUN_CLEAR_RESULTS, oldAnalysisData, newAnalysisData);
                }
                FRAPStudy newFRAPStudy = (FRAPStudy) hashTable.get(FRAPStudyPanel.NEW_FRAPSTUDY_KEY);
                // setFrapStudy fires property change, so we have to put it in Swing thread.
                getBatchRunWorkspace().getWorkingSingleWorkspace().setFrapStudy(newFRAPStudy, true);
                VirtualFrapBatchRunFrame.updateProgress(0);
                if (isFileLoaded) {
                    VirtualFrapBatchRunFrame.updateStatus("Loaded " + fileStr);
                } else {
                    VirtualFrapBatchRunFrame.updateStatus("Failed loading " + fileStr + ".");
                }
            }
        };
        taskArrayList.add(updateUIBeforeLoadTask);
        taskArrayList.add(loadTask);
        taskArrayList.add(afterLoadingSwingTask);
    } else {
        DialogUtils.showErrorDialog(singleFilePanel, "Load File name is empty. Please input a file name to continue.");
        throw new RuntimeException("Load File name is empty. Please input a file name to continue.");
    }
    return taskArrayList;
}

Example 9 with DataIdentifier

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

the class LoadFRAPData_SingleFileDescriptor method preNextProcess.

// load the data before the panel disappears
public ArrayList<AsynchClientTask> preNextProcess() {
    // create AsynchClientTask arraylist
    ArrayList<AsynchClientTask> taskArrayList = new ArrayList<AsynchClientTask>();
    if (singleFilePanel.getFileName().length() > 0) {
        final String fileStr = singleFilePanel.getFileName();
        final String LOADING_MESSAGE = "Loading " + fileStr + "...";
        AsynchClientTask updateUIBeforeLoadTask = new AsynchClientTask("", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                VirtualFrapMainFrame.updateStatus(LOADING_MESSAGE);
            }
        };
        AsynchClientTask loadTask = new AsynchClientTask(LOADING_MESSAGE, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                FRAPStudy newFRAPStudy = null;
                File inFile = new File(fileStr);
                if (inFile != null) {
                    if (// .log (vcell log file)
                    inFile.getName().endsWith(SimDataConstants.LOGFILE_EXTENSION)) {
                        DataIdentifier[] dataIdentifiers = FrapDataUtils.getDataIdentiferListFromVCellSimulationData(inFile, 0);
                        ArrayList<String> selectedIdentifiers = new ArrayList<String>();
                        for (int i = 0; i < dataIdentifiers.length; i++) {
                            if (dataIdentifiers[i].getVariableType().equals(VariableType.VOLUME)) {
                                selectedIdentifiers.add(dataIdentifiers[i].getName());
                            }
                        }
                        String[][] rowData = new String[selectedIdentifiers.size()][1];
                        for (int i = 0; i < selectedIdentifiers.size(); i++) {
                            rowData[i][0] = selectedIdentifiers.get(i);
                        }
                        int[] selectedIndexArr = DialogUtils.showComponentOKCancelTableList(LoadFRAPData_SingleFileDescriptor.this.getPanelComponent(), "Select Volume Variable", new String[] { "Volume Variable Name" }, rowData, ListSelectionModel.SINGLE_SELECTION);
                        if (selectedIndexArr != null && selectedIndexArr.length > 0) {
                            scalePanel = getScalePanelForLoadingLogFile();
                            int choice = DialogUtils.showComponentOKCancelDialog(LoadFRAPData_SingleFileDescriptor.this.getPanelComponent(), scalePanel, "Input image maximum intensity (max: 65535)");
                            if (choice == JOptionPane.OK_OPTION) {
                                Double maxIntensity = null;
                                if (scalePanel.getInputScaleString() != null) {
                                    maxIntensity = new Double(scalePanel.getInputScaleString());
                                }
                                newFRAPStudy = FRAPWorkspace.loadFRAPDataFromVcellLogFile(inFile, selectedIdentifiers.get(selectedIndexArr[0]), null, maxIntensity, true, this.getClientTaskStatusSupport());
                                isFileLoaded = true;
                            } else {
                                throw UserCancelException.CANCEL_GENERIC;
                            }
                        } else {
                            throw UserCancelException.CANCEL_GENERIC;
                        }
                    } else if (inFile.getName().endsWith(SimDataConstants.DATA_PROCESSING_OUTPUT_EXTENSION_HDF5)) {
                        scalePanel = getScalePanelForLoadingLogFile();
                        int choice = DialogUtils.showComponentOKCancelDialog(LoadFRAPData_SingleFileDescriptor.this.getPanelComponent(), scalePanel, "Input data maximum value (max: 65535) which is used to avoid losing double precision when casting it to short.");
                        if (choice == JOptionPane.OK_OPTION) {
                            Double maxIntensity = null;
                            if (scalePanel.getInputScaleString() != null) {
                                maxIntensity = new Double(scalePanel.getInputScaleString());
                            }
                            newFRAPStudy = FRAPWorkspace.loadFRAPDataFromHDF5File(inFile, maxIntensity, this.getClientTaskStatusSupport());
                            isFileLoaded = true;
                        } else {
                            throw UserCancelException.CANCEL_GENERIC;
                        }
                    } else // .lsm or other image formatss
                    {
                        newFRAPStudy = FRAPWorkspace.loadFRAPDataFromImageFile(inFile, this.getClientTaskStatusSupport());
                        isFileLoaded = true;
                    }
                } else {
                    throw new RuntimeException("Input file is null.");
                }
                // for all loaded file
                hashTable.put(FRAPStudyPanel.NEW_FRAPSTUDY_KEY, newFRAPStudy);
            }
        };
        AsynchClientTask afterLoadingSwingTask = new AsynchClientTask(LOADING_MESSAGE, AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            public void run(Hashtable<String, Object> hashTable) throws Exception {
                FRAPStudy newFRAPStudy = (FRAPStudy) hashTable.get(FRAPStudyPanel.NEW_FRAPSTUDY_KEY);
                // setFrapStudy fires property change, so we have to put it in Swing thread.
                getFrapWorkspace().setFrapStudy(newFRAPStudy, true);
                VirtualFrapLoader.mf.setMainFrameTitle("");
                VirtualFrapMainFrame.updateProgress(0);
                if (isFileLoaded) {
                    VirtualFrapMainFrame.updateStatus("Loaded " + fileStr);
                } else {
                    VirtualFrapMainFrame.updateStatus("Failed loading " + fileStr + ".");
                }
            }
        };
        taskArrayList.add(updateUIBeforeLoadTask);
        taskArrayList.add(loadTask);
        taskArrayList.add(afterLoadingSwingTask);
    } else {
        DialogUtils.showErrorDialog(singleFilePanel, "Load File name is empty. Please input a file name to continue.");
        throw new RuntimeException("Load File name is empty. Please input a file name to continue.");
    }
    return taskArrayList;
}

Example 10 with DataIdentifier

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

the class RasterExporter method exportPDEData.

private NrrdInfo[] exportPDEData(OutputContext outputContext, long jobID, User user, DataServerImpl dataServerImpl, VCDataIdentifier vcdID, VariableSpecs variableSpecs, TimeSpecs timeSpecs2, GeometrySpecs geometrySpecs, RasterSpecs rasterSpecs, FileDataContainerManager fileDataContainerManager) throws RemoteException, DataAccessException, IOException {
    CartesianMesh mesh = dataServerImpl.getMesh(user, vcdID);
    DataProcessingOutputInfo dataProcessingOutputInfo = null;
    // check if any of export variables are PostProcess and if so try to get PostProcessOutputInfo
    exportServiceImpl.fireExportProgress(jobID, vcdID, "Check PostProcess", 0.0);
    DataIdentifier[] dataIdentifiers = dataServerImpl.getDataIdentifiers(outputContext, user, vcdID);
    for (int i = 0; i < dataIdentifiers.length; i++) {
        for (int j = 0; j < variableSpecs.getVariableNames().length; j++) {
            if (variableSpecs.getVariableNames()[j].equals(dataIdentifiers[i].getName()) && VariableType.POSTPROCESSING.equals(dataIdentifiers[i].getVariableType())) {
                try {
                    // we need PostProcessOutputInfo
                    exportServiceImpl.fireExportProgress(jobID, vcdID, "Read PostProcess", 0.0);
                    dataProcessingOutputInfo = (DataProcessingOutputInfo) dataServerImpl.doDataOperation(user, new DataOperation.DataProcessingOutputInfoOP(vcdID, false, outputContext));
                    break;
                } catch (Exception e) {
                    throw new DataAccessException("Export variable '" + variableSpecs.getVariableNames()[j] + "' is PostProcessing type.  Error reading PostProcessing data: " + e.getClass().getName() + " " + e.getMessage());
                }
            }
        }
    }
    long lastUpdateTime = 0;
    switch(rasterSpecs.getFormat()) {
        case NRRD_SINGLE:
            {
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_FULL:
                        {
                            NrrdInfo nrrdInfo = NRRDHelper.getSizeCheckedNrrdHelper(variableSpecs, mesh.getISize(), mesh.getExtent(), dataProcessingOutputInfo).createSingleFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, rasterSpecs, timeSpecs2);
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-snglfull", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    NRRDHelper.appendDoubleData(nrrdInfo, fileDataContainerManager, data, variableSpecs.getVariableNames()[i]);
                                }
                            }
                            nrrdInfo = NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
                            return new NrrdInfo[] { nrrdInfo };
                        }
                    case GEOMETRY_SLICE:
                        {
                            NrrdInfo sliceNrrdInfo = createSliceNrrdHelper(mesh, dataProcessingOutputInfo, vcdID, variableSpecs, timeSpecs2, geometrySpecs, rasterSpecs, fileDataContainerManager).createSingleFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, rasterSpecs, timeSpecs2);
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-snglslice", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    appendSlice(variableSpecs.getVariableNames()[i], data, sliceNrrdInfo, mesh, geometrySpecs, fileDataContainerManager);
                                }
                            }
                            sliceNrrdInfo = NrrdWriter.writeNRRD(sliceNrrdInfo, fileDataContainerManager);
                            return new NrrdInfo[] { sliceNrrdInfo };
                        }
                    default:
                        {
                            throw new DataAccessException("NRRD export from slice not yet supported");
                        }
                }
            }
        case NRRD_BY_TIME:
            {
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_FULL:
                        {
                            NRRDHelper nrrdHelper = NRRDHelper.getSizeCheckedNrrdHelper(variableSpecs, mesh.getISize(), mesh.getExtent(), dataProcessingOutputInfo);
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-timefull", jobID, vcdID, progressIndex, progressEnd);
                                progressIndex++;
                                NrrdInfo nrrdInfo = nrrdHelper.createTimeFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, timeSpecs2.getAllTimes()[j], rasterSpecs);
                                nrrdinfoV.add(nrrdInfo);
                                for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    NRRDHelper.appendDoubleData(nrrdInfo, fileDataContainerManager, data, variableSpecs.getVariableNames()[i]);
                                }
                                NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    case GEOMETRY_SLICE:
                        {
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-timeslice", jobID, vcdID, progressIndex, progressEnd);
                                progressIndex++;
                                NrrdInfo sliceNrrdInfo = createSliceNrrdHelper(mesh, dataProcessingOutputInfo, vcdID, variableSpecs, timeSpecs2, geometrySpecs, rasterSpecs, fileDataContainerManager).createTimeFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs, timeSpecs2.getAllTimes()[j], rasterSpecs);
                                nrrdinfoV.add(sliceNrrdInfo);
                                for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    appendSlice(variableSpecs.getVariableNames()[i], data, sliceNrrdInfo, mesh, geometrySpecs, fileDataContainerManager);
                                }
                                NrrdWriter.writeNRRD(sliceNrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    default:
                        {
                            throw new DataAccessException("NRRD export from slice not yet supported");
                        }
                }
            }
        case NRRD_BY_VARIABLE:
            {
                switch(geometrySpecs.getModeID()) {
                    case GEOMETRY_FULL:
                        {
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                NRRDHelper nrrdhelHelper = new NRRDHelper(variableSpecs.getVariableNames()[i], mesh.getISize(), mesh.getExtent(), dataProcessingOutputInfo);
                                NrrdInfo nrrdInfo = nrrdhelHelper.createVariableFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2, rasterSpecs);
                                nrrdinfoV.add(nrrdInfo);
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-varsfull", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    NRRDHelper.appendDoubleData(nrrdInfo, fileDataContainerManager, data, variableSpecs.getVariableNames()[i]);
                                }
                                nrrdInfo = NrrdWriter.writeNRRD(nrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    case GEOMETRY_SLICE:
                        {
                            Vector<NrrdInfo> nrrdinfoV = new Vector<NrrdInfo>();
                            int progressIndex = 1;
                            int progressEnd = variableSpecs.getVariableNames().length * (timeSpecs2.getEndTimeIndex() - timeSpecs2.getBeginTimeIndex() + 1);
                            for (int i = 0; i < variableSpecs.getVariableNames().length; i++) {
                                NrrdInfo sliceNrrdInfo = createSliceNrrdHelper(mesh, dataProcessingOutputInfo, vcdID, variableSpecs, timeSpecs2, geometrySpecs, rasterSpecs, fileDataContainerManager).createVariableFullNrrdInfo(fileDataContainerManager, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2, rasterSpecs);
                                nrrdinfoV.add(sliceNrrdInfo);
                                for (int j = timeSpecs2.getBeginTimeIndex(); j <= timeSpecs2.getEndTimeIndex(); j++) {
                                    lastUpdateTime = fireThrottledProgress(exportServiceImpl, lastUpdateTime, "NRRD-varsfull", jobID, vcdID, progressIndex, progressEnd);
                                    progressIndex++;
                                    double[] data = dataServerImpl.getSimDataBlock(outputContext, user, vcdID, variableSpecs.getVariableNames()[i], timeSpecs2.getAllTimes()[j]).getData();
                                    appendSlice(variableSpecs.getVariableNames()[i], data, sliceNrrdInfo, mesh, geometrySpecs, fileDataContainerManager);
                                }
                                NrrdWriter.writeNRRD(sliceNrrdInfo, fileDataContainerManager);
                            }
                            if (nrrdinfoV.size() > 0) {
                                NrrdInfo[] nrrdinfoArr = new NrrdInfo[nrrdinfoV.size()];
                                nrrdinfoV.copyInto(nrrdinfoArr);
                                return nrrdinfoArr;
                            }
                            return null;
                        }
                    default:
                        {
                            throw new DataAccessException("NRRD export from slice not yet supported");
                        }
                }
            }
        default:
            {
                throw new DataAccessException("Multiple NRRD file export not yet supported");
            }
    }
}