Examples with VCDataIdentifier org.vcell.util.document.VCDataIdentifier used on opensource projects

Example 41 with VCDataIdentifier

use of org.vcell.util.document.VCDataIdentifier in project vcell by virtualcell.

the class PDEExportDataPanel method startExport.

/**
 * Comment
 */
private void startExport() {
    if (getExportSettings1().getSelectedFormat() == ExportFormat.QUICKTIME && getJSlider1().getValue() == getJSlider2().getValue()) {
        DialogUtils.showWarningDialog(this, "User selected 'begin' and 'end' export times are the same.  'Movie' export format 'begin' and 'end' times must be different");
        return;
    }
    DisplayPreferences[] displayPreferences = null;
    @SuppressWarnings("deprecation") Object[] variableSelections = getJListVariables().getSelectedValues();
    boolean selectionHasVolumeVariables = false;
    boolean selectionHasMembraneVariables = false;
    switch(getExportSettings1().getSelectedFormat()) {
        case PLY:
        case QUICKTIME:
        case GIF:
        case FORMAT_JPEG:
        case ANIMATED_GIF:
            {
                displayPreferences = new DisplayPreferences[variableSelections.length];
                StringBuffer noScaleInfoNames = new StringBuffer();
                for (int i = 0; i < displayPreferences.length; i++) {
                    BitSet domainValid = null;
                    try {
                        if (dataInfoProvider != null) {
                            DataIdentifier varSelectionDataIdnetDataIdentifier = null;
                            for (int j = 0; j < dataInfoProvider.getPDEDataContext().getDataIdentifiers().length; j++) {
                                if (dataInfoProvider.getPDEDataContext().getDataIdentifiers()[j].getName().equals(variableSelections[i])) {
                                    varSelectionDataIdnetDataIdentifier = dataInfoProvider.getPDEDataContext().getDataIdentifiers()[j];
                                }
                            }
                            if (varSelectionDataIdnetDataIdentifier != null) {
                                selectionHasVolumeVariables = selectionHasVolumeVariables || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.VOLUME) || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.POSTPROCESSING) || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.VOLUME_REGION);
                                selectionHasMembraneVariables = selectionHasMembraneVariables || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.MEMBRANE) || varSelectionDataIdnetDataIdentifier.getVariableType().equals(VariableType.MEMBRANE_REGION);
                                CartesianMesh cartesianMesh = dataInfoProvider.getPDEDataContext().getCartesianMesh();
                                int dataLength = cartesianMesh.getDataLength(varSelectionDataIdnetDataIdentifier.getVariableType());
                                domainValid = new BitSet(dataLength);
                                domainValid.clear();
                                for (int j = 0; j < dataLength; j++) {
                                    if (dataInfoProvider.isDefined(varSelectionDataIdnetDataIdentifier, j)) {
                                        domainValid.set(j);
                                    }
                                }
                            } else {
                                throw new Exception("No DataIdentifer found for variable name '" + variableSelections[i] + "'");
                            }
                        }
                    } catch (Exception e) {
                        e.printStackTrace();
                        DialogUtils.showErrorDialog(this, "Error during domain evaluation:\n" + e.getMessage());
                        return;
                    }
                    displayPreferences[i] = new DisplayPreferences(getDisplayAdapterService().getDisplayPreferences((String) variableSelections[i]), domainValid);
                    if (!getDisplayAdapterService().hasStateID((String) variableSelections[i])) {
                        noScaleInfoNames.append("--- " + (String) variableSelections[i] + "\n");
                    }
                }
                break;
            }
        case CSV:
            {
                // check for membrane variables... warn for 3D geometry...
                // one gets the whole nine yards by index, not generally useful... except for a few people like Boris :)
                boolean mbVars = false;
                DataIdentifier[] dataIDs = getPdeDataContext().getDataIdentifiers();
                for (int i = 0; i < variableSelections.length; i++) {
                    String varName = (String) variableSelections[i];
                    for (int j = 0; j < dataIDs.length; j++) {
                        if (dataIDs[j].getName().equals(varName) && dataIDs[j].getVariableType().equals(VariableType.MEMBRANE)) {
                            mbVars = true;
                            break;
                        }
                    }
                }
                if (mbVars && getPdeDataContext().getCartesianMesh().getGeometryDimension() == 3 && getJRadioButtonSlice().isSelected()) {
                    String choice = PopupGenerator.showWarningDialog(this, getDataViewerManager().getUserPreferences(), UserMessage.warn_exportMembraneData3D, null);
                    if (choice.equals(UserMessage.OPTION_CANCEL)) {
                        // user canceled
                        return;
                    }
                }
                getExportSettings1().setSimulationSelector(createSimulationSelector());
                getExportSettings1().setIsCSVExport(true);
                break;
            }
        case NRRD:
        case IMAGEJ:
        case UCD:
        case VTK_IMAGE:
        case VTK_UNSTRUCT:
            break;
        default:
            break;
    }
    ;
    if (getJRadioButtonROI().isSelected() && getROISelections().getSelectedIndex() == -1) {
        PopupGenerator.showErrorDialog(this, "To export selections, you must select at least one item from the ROI selection list");
    }
    getExportSettings1().setTimeSpecs(new TimeSpecs(getJSlider1().getValue(), getJSlider2().getValue(), getPdeDataContext().getTimePoints(), ExportConstants.TIME_RANGE));
    getExportSettings1().setDisplayPreferences(displayPreferences, Arrays.asList(variableSelections).toArray(new String[0]), viewZoom);
    getExportSettings1().setSliceCount(FormatSpecificSpecs.getSliceCount(getJRadioButtonFull().isSelected(), getNormalAxis(), getPdeDataContext().getCartesianMesh()));
    getExportSettings1().setImageSizeCalculationInfo(getPdeDataContext().getCartesianMesh(), getNormalAxis());
    getExportSettings1().setIsSmoldyn(isSmoldyn);
    ExportFormat format = getSelectedFormat();
    if (format.equals(ExportFormat.PLY)) {
        getExportSettings1().setFormatSpecificSpecs(new PLYSpecs(true, displayPreferences));
    }
    if (format.requiresFollowOn()) {
        Frame theFrame = JOptionPane.getFrameForComponent(this);
        boolean okToExport = getExportSettings1().showFormatSpecificDialog(theFrame, selectionHasVolumeVariables, selectionHasMembraneVariables);
        if (!okToExport) {
            return;
        }
    }
    if (format.equals(ExportFormat.IMAGEJ)) {
        // export nrrd for imagej direct, the we'll send to imagej from vcell client
        getExportSettings1().setFormatSpecificSpecs(new RasterSpecs(ExportConstants.NRRD_SINGLE, false));
    }
    // determine of sim result is from local (quick) run or on server.
    final OutputContext outputContext = ((ClientPDEDataContext) getPdeDataContext()).getDataManager().getOutputContext();
    final ExportSpecs exportSpecs = getExportSpecs();
    boolean isLocalSimResult = false;
    VCDataIdentifier vcId = exportSpecs.getVCDataIdentifier();
    if (vcId instanceof LocalVCDataIdentifier) {
        isLocalSimResult = true;
    }
    // find out if smoldyn export choice is 'particle' - not available at this time
    boolean isParticle = false;
    if (getExportSettings1().getFormatSpecificSpecs() instanceof ImageSpecs) {
        isParticle = ((ImageSpecs) getExportSettings1().getFormatSpecificSpecs()).getParticleMode() == FormatSpecificSpecs.PARTICLE_SELECT;
    } else if (getExportSettings1().getFormatSpecificSpecs() instanceof MovieSpecs) {
        isParticle = ((MovieSpecs) getExportSettings1().getFormatSpecificSpecs()).getParticleMode() == FormatSpecificSpecs.PARTICLE_SELECT;
    }
    if (isLocalSimResult && isParticle) {
        DialogUtils.showErrorDialog(this, "Particle export for Smoldyn particles unavailable in local data at this time.");
        return;
    }
    // pass the export request down the line; non-blocking call
    if (!isLocalSimResult) {
        // for sims that ran on server, do as before.
        getDataViewerManager().startExport(this, outputContext, exportSpecs);
    } else {
        final String SOURCE_FILE_KEY = "SOURCE_FILE_KEY";
        final String DESTINATION_FILE_KEY = "DEESTINATION_FILE_KEY";
        AsynchClientTask localExportTast = new AsynchClientTask("Start Local Export", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                try {
                    File primaryDir = ResourceUtil.getLocalRootDir();
                    User usr = User.tempUser;
                    File usrDir = new File(primaryDir.getAbsolutePath(), usr.getName());
                    System.setProperty(PropertyLoader.exportBaseDirInternalProperty, usrDir.getAbsolutePath() + File.separator);
                    System.setProperty(PropertyLoader.exportBaseURLProperty, usrDir.toURI().toURL().toString());
                    DataSetControllerImpl dataSetControllerImpl = new DataSetControllerImpl(null, primaryDir, null);
                    ExportServiceImpl localExportServiceImpl = new ExportServiceImpl();
                    DataServerImpl dataServerImpl = new DataServerImpl(dataSetControllerImpl, localExportServiceImpl);
                    ExportEvent localExportEvent = dataServerImpl.makeRemoteFile(outputContext, usr, exportSpecs);
                    File sourceFile = new File(usrDir, new File((new URL(localExportEvent.getLocation()).getPath())).getName());
                    hashTable.put(SOURCE_FILE_KEY, sourceFile);
                } catch (Exception e) {
                    throw new Exception("Unable to export local sim results data : " + e.getMessage(), e);
                }
            }
        };
        AsynchClientTask localSaveTask = new AsynchClientTask("Start Local Export", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                File sourceFile = (File) hashTable.get(SOURCE_FILE_KEY);
                JFileChooser jFileChooser = new JFileChooser();
                jFileChooser.setSelectedFile(new File(sourceFile.getName()));
                if (jFileChooser.showSaveDialog(PDEExportDataPanel.this) == JFileChooser.APPROVE_OPTION) {
                    File destinationFile = jFileChooser.getSelectedFile();
                    if (destinationFile.exists()) {
                        final String OVERWRITE = "Overwrite";
                        final String CANCEL = "Cancel";
                        String response = DialogUtils.showWarningDialog(PDEExportDataPanel.this, "OK to Overwrite " + destinationFile.getAbsolutePath() + "?", new String[] { OVERWRITE, CANCEL }, OVERWRITE);
                        if (response == null || !response.equals(OVERWRITE)) {
                            return;
                        }
                    }
                    hashTable.put(DESTINATION_FILE_KEY, destinationFile);
                }
            }
        };
        AsynchClientTask localDeleteTempTask = new AsynchClientTask("Start Local Export", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                File sourceFile = (File) hashTable.get(SOURCE_FILE_KEY);
                File destinationFile = (File) hashTable.get(DESTINATION_FILE_KEY);
                if (sourceFile != null && sourceFile.exists()) {
                    try {
                        if (destinationFile != null) {
                            copyFile(sourceFile, destinationFile);
                        }
                    } finally {
                        sourceFile.delete();
                    }
                }
            }
        };
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { localExportTast, localSaveTask, localDeleteTempTask }, false, true, null);
    }
}

Example 42 with VCDataIdentifier

use of org.vcell.util.document.VCDataIdentifier in project vcell by virtualcell.

the class RestDatabaseService method getDataSetTimeSeries.

public DataSetTimeSeries getDataSetTimeSeries(SimDataValuesServerResource resource, User vcellUser) throws DataAccessException, ObjectNotFoundException, SQLException {
    if (vcellUser == null) {
        vcellUser = VCellApiApplication.DUMMY_USER;
    }
    UserLoginInfo userLoginInfo = new UserLoginInfo(vcellUser.getName(), null);
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String simId = resource.getAttribute(VCellApiApplication.SIMDATAID);
    // resource.getRequestAttributes().get(VCellApiApplication.SIMDATAID);
    String jobIndexString = resource.getAttribute(VCellApiApplication.JOBINDEX);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    int jobIndex = Integer.parseInt(jobIndexString);
    // TODO: pass in variables names from the query parameters.
    String[] variableNames = null;
    User owner = simRep.getOwner();
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        RpcDataServerProxy rpcDataServerProxy = new RpcDataServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        VCDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
        DataSetTimeSeries dataSetTimeSeries = rpcDataServerProxy.getDataSetTimeSeries(vcdID, variableNames);
        return dataSetTimeSeries;
    } finally {
        rpcSession.close();
    }
}

Example 43 with VCDataIdentifier

use of org.vcell.util.document.VCDataIdentifier in project vcell by virtualcell.

the class DataSetControllerImpl method getVCData.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.simdata.SimResults
 * @param user User
 * @param simID java.lang.String
 */
public VCData getVCData(VCDataIdentifier vcdID) throws DataAccessException, IOException {
    VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") ... <<ENTER>>");
    VCData vcData = (cacheTable0 != null ? cacheTable0.get(vcdID) : null);
    // 
    if (vcData == null) {
        // System.out.println("getVCData " + vcdID);
        if (vcdID instanceof MergedDataInfo) {
            try {
                User user = vcdID.getOwner();
                VCDataIdentifier[] vcdIdentifiers = ((MergedDataInfo) vcdID).getDataIDs();
                VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : creating new MergedData : <<BEGIN>>");
                vcData = new MergedData(user, getPrimaryUserDir(vcdID.getOwner(), false), getSecondaryUserDir(vcdID.getOwner()), this, vcdIdentifiers, ((MergedDataInfo) vcdID).getDataSetPrefix());
                VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : creating new MergedData : <<END>>");
            } catch (IOException e) {
                e.printStackTrace(System.out);
                throw new RuntimeException(e.getMessage());
            }
        } else {
            // assume vcdID instanceof cbit.vcell.solver.SimulationInfo or a test adapter
            VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : creating new SimulationData : <<BEGIN>>");
            SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
            vcData = new SimulationData(vcdID, getPrimaryUserDir(vcdID.getOwner(), false), getSecondaryUserDir(vcdID.getOwner()), simDataAmplistorInfo);
            VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : creating new SimulationData : <<END>>");
        }
        if (cacheTable0 != null) {
            try {
                VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : caching vcData : <<BEGIN>>");
                cacheTable0.put(vcdID, vcData);
                VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") : caching vcData : <<END>>");
            } catch (CacheException e) {
                // if  can't cache the data, it is ok
                e.printStackTrace();
            }
        }
    }
    VCMongoMessage.sendTrace("DataSetControllerImpl.getVCData(" + vcdID.getID() + ") ... <<EXIT>>");
    return vcData;
}

Example 44 with VCDataIdentifier

use of org.vcell.util.document.VCDataIdentifier in project vcell by virtualcell.

the class DataSetControllerImpl method calcSpatialStatsInfo.

/**
 * Insert the method's description here.
 * Creation date: (3/20/2006 3:37:39 PM)
 */
private SpatialStatsInfo calcSpatialStatsInfo(OutputContext outputContext, TimeSeriesJobSpec timeSeriesJobSpec, VCDataIdentifier vcdID) throws Exception {
    if (getVCData(vcdID) instanceof SimulationData && ((SimulationData) getVCData(vcdID)).isPostProcessing(outputContext, timeSeriesJobSpec.getVariableNames()[0])) {
        return new SpatialStatsInfo();
    }
    SpatialStatsInfo ssi = new SpatialStatsInfo();
    // Determine weights for indices of each variable if we are going to be calculating spatial statistics
    ssi.bWeightsValid = true;
    // if(timeSeriesJobSpec.isCalcSpaceStats()){
    CartesianMesh myMesh = getMesh(vcdID);
    DataIdentifier[] dataIDs = getDataIdentifiers(outputContext, vcdID);
    ssi.spaceWeight = new double[timeSeriesJobSpec.getVariableNames().length][];
    ssi.totalSpace = new double[timeSeriesJobSpec.getVariableNames().length];
    for (int i = 0; i < timeSeriesJobSpec.getVariableNames().length; i += 1) {
        ssi.spaceWeight[i] = new double[timeSeriesJobSpec.getIndices()[i].length];
        Boolean isVolume = null;
        for (int j = 0; j < dataIDs.length; j += 1) {
            if (dataIDs[j].getName().equals(timeSeriesJobSpec.getVariableNames()[i])) {
                isVolume = new Boolean(dataIDs[j].getVariableType().equals(VariableType.VOLUME) || dataIDs[j].getVariableType().equals(VariableType.VOLUME_REGION));
                break;
            }
        }
        if (isVolume == null) {
            throw new RuntimeException("Couldn't find variable type for varname=" + timeSeriesJobSpec.getVariableNames()[i] + " during TimeSeries calc spatial stats");
        } else {
            for (int j = 0; j < timeSeriesJobSpec.getIndices()[i].length; j += 1) {
                if (isVolume.booleanValue()) {
                    ssi.spaceWeight[i][j] = myMesh.calculateMeshElementVolumeFromVolumeIndex(timeSeriesJobSpec.getIndices()[i][j]);
                } else {
                    // assume membrane
                    double area = myMesh.getMembraneElements()[timeSeriesJobSpec.getIndices()[i][j]].getArea();
                    if (area == MembraneElement.AREA_UNDEFINED) {
                        ssi.bWeightsValid = false;
                        break;
                    }
                    ssi.spaceWeight[i][j] = area;
                }
                ssi.totalSpace[i] += ssi.spaceWeight[i][j];
            }
        }
        if (!ssi.bWeightsValid) {
            break;
        }
    }
    // if(ssi.bWeightsValid){
    return ssi;
// }else{
// return null;
// }
}

Example 45 with VCDataIdentifier

use of org.vcell.util.document.VCDataIdentifier in project vcell by virtualcell.

the class DataSetControllerImpl method getVtuVarInfos.

public VtuVarInfo[] getVtuVarInfos(MovingBoundarySimFiles movingBoundaryFiles, OutputContext outputContext, VCDataIdentifier vcdataID) throws DataAccessException {
    try {
        DataIdentifier[] dataIdentifiers = getDataIdentifiers(outputContext, vcdataID);
        if (dataIdentifiers == null) {
            return null;
        }
        ArrayList<VtuVarInfo> vtuVarInfos = new ArrayList<VtuVarInfo>();
        for (DataIdentifier di : dataIdentifiers) {
            String name = di.getName();
            String displayName = di.getDisplayName();
            if (di.getDomain() != null) {
                System.err.println("DataSetControllerImpl.getVtuVarInfos(movingboundary): need to support proper domain names now");
            }
            String domainName = MovingBoundaryReader.getFakeInsideDomainName();
            VariableDomain variableDomain = null;
            VariableType variableType = di.getVariableType();
            if (variableType.equals(VariableType.VOLUME) || variableType.equals(VariableType.VOLUME_REGION)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_VOLUME;
            } else if (variableType.equals(VariableType.MEMBRANE) || variableType.equals(VariableType.MEMBRANE_REGION)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_MEMBRANE;
            } else if (variableType.equals(VariableType.POINT_VARIABLE)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_POINT;
            } else if (variableType.equals(VariableType.CONTOUR) || variableType.equals(VariableType.CONTOUR_REGION)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_CONTOUR;
            } else if (variableType.equals(VariableType.NONSPATIAL)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_UNKNOWN;
            } else if (variableType.equals(VariableType.POSTPROCESSING)) {
                variableDomain = VariableDomain.VARIABLEDOMAIN_POSTPROCESSING;
            } else {
                System.err.print("skipping var " + di + ", unsupported data type");
            }
            String functionExpression = null;
            boolean bMeshVariable = false;
            if (name.toUpperCase().contains("SIZE")) {
                System.err.println("Skipping Moving Boundary variable '" + name + "' because it is a size ... change later");
                continue;
            }
            vtuVarInfos.add(new VtuVarInfo(name, displayName, domainName, variableDomain, functionExpression, DataType.CellData, bMeshVariable));
        }
        return vtuVarInfos.toArray(new VtuVarInfo[0]);
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException("failed to retrieve VTK variable list: " + e.getMessage(), e);
    }
}