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

Example 26 with VCDataIdentifier

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

the class DisplayTimeSeriesOp method displayImageTimeSeries.

public void displayImageTimeSeries(final ImageTimeSeries<? extends Image> imageTimeSeries, final String title, final WindowListener windowListener) throws ImageException, IOException {
    try {
        System.out.println("starting to prepare data for time series viewing");
        final PDEDataViewer pdeDataViewer = new PDEDataViewer();
        DataSetControllerProvider dataSetControllerProvider;
        try {
            dataSetControllerProvider = getDataSetControllerProvider(imageTimeSeries, pdeDataViewer);
        } catch (ImageException | IOException e1) {
            e1.printStackTrace();
            throw new RuntimeException(e1.getMessage(), e1);
        }
        VCDataManager vcDataManager = new VCDataManager(dataSetControllerProvider);
        OutputContext outputContext = new OutputContext(new AnnotatedFunction[0]);
        final VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

            public User getOwner() {
                return new User("nouser", null);
            }

            public KeyValue getDataKey() {
                return null;
            }

            public String getID() {
                return "mydata";
            }
        };
        PDEDataManager pdeDataManager = new PDEDataManager(outputContext, vcDataManager, vcDataIdentifier);
        final ClientPDEDataContext myPdeDataContext = new ClientPDEDataContext(pdeDataManager);
        final RequestManager requestManager = new RequestManagerAdapter() {
        };
        final DataViewerManager dataViewerManager = new DataViewerManager() {

            public void dataJobMessage(DataJobEvent event) {
            }

            public void exportMessage(ExportEvent event) {
            }

            public void addDataListener(DataListener newListener) {
            }

            public UserPreferences getUserPreferences() {
                // getRequestManager().getUserPreferences();
                return null;
            }

            public void removeDataListener(DataListener newListener) {
            }

            public void startExport(Component requester, OutputContext outputContext, ExportSpecs exportSpecs) {
            // getLocalRequestManager().startExport(outputContext, FieldDataWindowManager.this, exportSpecs);
            }

            public void simStatusChanged(SimStatusEvent simStatusEvent) {
            }

            public User getUser() {
                return new User("dummy", new KeyValue("123"));
            // return getRequestManager().getDocumentManager().getUser();
            }

            public RequestManager getRequestManager() {
                return requestManager;
            }
        };
        System.out.println("ready to display time series");
        SwingUtilities.invokeAndWait(new Runnable() {

            @Override
            public void run() {
                JFrame jframe = new TopLevelFrame();
                jframe.setTitle(title);
                jframe.getContentPane().add(pdeDataViewer);
                jframe.setSize(1000, 600);
                jframe.setVisible(true);
                if (windowListener != null) {
                    jframe.addWindowListener(windowListener);
                }
                try {
                    pdeDataViewer.setDataViewerManager(dataViewerManager);
                } catch (PropertyVetoException e) {
                    e.printStackTrace();
                }
                pdeDataViewer.setPdeDataContext(myPdeDataContext);
            }
        });
    } catch (InvocationTargetException | InterruptedException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 27 with VCDataIdentifier

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

the class RestDatabaseService method getDataSetMetadata.

public DataSetMetadata getDataSetMetadata(SimDataServerResource resource, User vcellUser) throws ObjectNotFoundException, DataAccessException, 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);
    KeyValue simKey = new KeyValue(simId);
    SimulationRep simRep = getSimulationRep(simKey);
    if (simRep == null) {
        throw new ObjectNotFoundException("Simulation with key " + simKey + " not found");
    }
    User owner = simRep.getOwner();
    int jobIndex = 0;
    VCMessageSession rpcSession = vcMessagingService.createProducerSession();
    try {
        RpcDataServerProxy rpcDataServerProxy = new RpcDataServerProxy(userLoginInfo, rpcSession);
        VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(simKey, owner);
        VCDataIdentifier vcdID = new VCSimulationDataIdentifier(vcSimID, jobIndex);
        DataSetMetadata dataSetMetadata = rpcDataServerProxy.getDataSetMetadata(vcdID);
        return dataSetMetadata;
    } finally {
        rpcSession.close();
    }
}

Example 28 with VCDataIdentifier

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

the class DataProcessingResultsPanel method onVariablesChange.

private void onVariablesChange() {
    try {
        // keep old indices
        lastSelectedIdxArray = varJList.getSelectedIndices();
        Object[] selectedObjects = varJList.getSelectedValues();
        int numSelectedVars = selectedObjects.length;
        int totalColumns = 1;
        for (int v = 0; v < numSelectedVars; v++) {
            totalColumns++;
        // String varName = (String)selectedObjects[v];
        // ucar.nc2.Variable volVar = ncfile.findVariable(varName);
        // int[] shape = volVar.getShape();
        // int numColumns = shape[1];
        // 
        // totalColumns += numColumns;
        }
        if (dataProcessingOutputInfo == null) {
            throw new RuntimeException("dataProcessingOutInfo null, thread = " + Thread.currentThread().getName());
        }
        final double[] vtp = dataProcessingOutputInfo.getVariableTimePoints();
        if (vtp == null) {
            throw new RuntimeException("getVariableTimePoints( ) null, thread = " + Thread.currentThread().getName());
        }
        final int numTimes = vtp.length;
        double[][] plotDatas = new double[totalColumns][numTimes];
        // assumes all times same
        plotDatas[0] = dataProcessingOutputInfo.getVariableTimePoints();
        String[] plotNames = new String[totalColumns - 1];
        int columnCount = 0;
        for (int v = 0; v < numSelectedVars; v++) {
            String varName = ((String) selectedObjects[v]);
            // remove the unit from name if exist
            if (// "_(" doesn't suppose to be the first char
            varName.indexOf("_(") > 0) {
                varName = varName.substring(0, varName.indexOf("_("));
            }
            // }
            for (int i = 0; i < /*numColumns*/
            1; i++) {
                String plotName = varName;
                if (i > 0) {
                    plotName += ": region " + (i - 1);
                }
                plotNames[columnCount] = plotName;
                if (columnCount >= plotDatas.length) {
                    throw new RuntimeException("invalid columnCount " + columnCount + " >= " + plotDatas.length);
                }
                for (int j = 0; j < numTimes; j++) {
                    // data.get(j, i);
                    double[] vars = dataProcessingOutputInfo.getVariableStatValues().get(varName);
                    if (j >= vars.length) {
                        throw new RuntimeException("invalid index " + j + " on " + varName + ", greater than " + vars.length);
                    }
                    plotDatas[columnCount + 1][j] = vars[j];
                }
                columnCount++;
            }
        }
        Plot2D plot2D = new SingleXPlot2D(null, null, ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
        plotPane.setPlot2D(plot2D);
    } catch (Exception e1) {
        VCDataIdentifier id = dataProcessingOutputInfo.getVCDataIdentifier();
        DialogUtils.ErrorContext ec = new DialogUtils.ErrorContext(VerboseDataIdentifier.parse(id));
        DialogUtils.showErrorDialog(this, e1.getMessage(), e1, ec);
        e1.printStackTrace();
    }
}

Example 29 with VCDataIdentifier

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

the class VFrapXmlHelper method LoadVFrapSpecialImages.

// // load and compute prebleach average and first postbleach images
// public void LoadVFrapSpecialImages(AnnotatedImageDataset annotatedImages, int startingIndexRecovery)
// {
// // unnormalized prebleach average
// prebleachAvg = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// for(int j = 0; j < prebleachAvg.length; j++)
// {
// double pixelTotal = 0;
// for(int i = 0 ; i < startingIndexRecovery; i++)
// {
// pixelTotal = pixelTotal + (annotatedImages.getImageDataset().getImage(0, 0, i).getPixels()[j] & 0x0000FFFF);
// }
// prebleachAvg[j] = pixelTotal/startingIndexRecovery;
// }
// 
// // unnormalized first post bleach
// firstPostBleach = new double[annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getNumXYZ()];
// short[] pixels = annotatedImages.getImageDataset().getImage(0, 0, startingIndexRecovery).getPixels();
// for(int i = 0; i< pixels.length; i++)
// {
// firstPostBleach[i] = pixels[i] & 0x0000FFFF;
// }
// }
// 
// Locate the special images within the vFrap files and load them in memory
// 
public static boolean LoadVFrapSpecialImages(Hashtable<String, Object> hashTable, Element vFrapRoot) throws IOException, DataAccessException, MathException, ImageException {
    // ------ parse the vfrap file and the log/zip files referred within -----
    // many channels of 1 timepoint each
    int NumTimePoints = 1;
    // the channels: prebleach, postbleach, roi1, roi2 ... roiN
    int NumChannels = tokenNames.length;
    String[] channelNames = new String[NumChannels];
    VariableType[] channelTypes = new VariableType[NumChannels];
    DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
    double[][][] pixData = new double[NumTimePoints][NumChannels][];
    // get the path of the file tagged with "ROIExternalDataInfoTag" and open it
    Element roiExternalDataInfoElement = vFrapRoot.getChild(MicroscopyXMLTags.ROIExternalDataInfoTag);
    if (roiExternalDataInfoElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    // <ROIExternalDataInfo Filename="c:\vFrap\VirtualMicroscopy\SimulationData\SimID_1282941232246_0_.log">
    // <ExternalDataIdentifier Name="timeData" KeyValue="1282941232246" OwnerName="SimulationData" OwnerKey="0" />
    // </ImageDatasetExternalDataInfo>
    // c:\VirtualMicroscopy\SimulationData\SimID_1284149203811_0_.log
    String filename = (roiExternalDataInfoElement).getAttributeValue("Filename");
    Element childElement = (roiExternalDataInfoElement).getChild("ExternalDataIdentifier");
    if (childElement == null) {
        // can't load FieldData for some reason, fall back to importing the biomodel only
        return false;
    }
    StringTokenizer tokens = new StringTokenizer(filename, "/\\.");
    final ArrayList<String> tokenArray = new ArrayList<String>();
    while (tokens.hasMoreElements()) {
        tokenArray.add(tokens.nextToken());
    }
    final String dataID = tokenArray.get(tokenArray.size() - 2);
    final String userName = tokenArray.get(tokenArray.size() - 3);
    VCDataIdentifier vcDataIdentifier = new VCDataIdentifier() {

        public String getID() {
            return dataID;
        }

        public KeyValue getDataKey() {
            return null;
        }

        public User getOwner() {
            return new User(userName, new KeyValue("123345432334"));
        }
    };
    // ------- recover simulation data for this user name, load the images in memory ------------
    // ex  c:\\VirtualMicroscopy\\SimulationData
    String userDirName = filename.substring(0, filename.indexOf(dataID) - 1);
    File userDir = new File(userDirName);
    SimulationData.SimDataAmplistorInfo simDataAmplistorInfo = AmplistorUtils.getSimDataAmplistorInfoFromPropertyLoader();
    SimulationData simData = new SimulationData(vcDataIdentifier, userDir, null, simDataAmplistorInfo);
    // build a valid mesh in 2 steps, what we have in simData is incomplete
    CartesianMesh incompleteMesh = simData.getMesh();
    Extent extent = incompleteMesh.getExtent();
    ISize isize = new ISize(incompleteMesh.getSizeX(), incompleteMesh.getSizeY(), incompleteMesh.getSizeZ());
    Origin origin = new Origin(0, 0, 0);
    CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(origin, extent, isize, new RegionImage(new VCImageUncompressed(null, new byte[isize.getXYZ()], extent, isize.getX(), isize.getY(), isize.getZ()), 0, null, null, RegionImage.NO_SMOOTHING));
    DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
    double[] times = simData.getDataTimes();
    for (int i = 0; i < dataIdentifiers.length; i++) {
        // ex: prebleach_avg, postbleach_first, postbleach_last, bleached_mask, cell_mask, ring1_mask,... ring8_mask
        System.out.println(dataIdentifiers[i].getName());
        for (double time : times) {
            // this loops only once, we have just 1 timepoint for each "special" image
            SimDataBlock simDataBlock = simData.getSimDataBlock(null, dataIdentifiers[i].getName(), time);
            channelNames[i] = dataIdentifiers[i].getName();
            channelTypes[i] = VariableType.VOLUME;
            channelVFrapImageType[i] = SymbolEquivalence.typeFromToken(dataIdentifiers[i].getName());
            pixData[0][i] = simDataBlock.getData();
            // var = prebleach_avg, time = 0.0, data = { 1.0832530361887216 1.0832530361887216 1.0832530361887216 1.0 .... }
            System.out.print("var = " + dataIdentifiers[i].getName() + ", time = " + time + ", data = { ");
            // show a few
            for (int j = 0; j < 5; j++) {
                System.out.print(pixData[0][i][j] + " ");
            }
            // show a few
            ;
            // show a few
            System.out.println(" ... ");
        }
    }
    hashTable.put("mesh", mesh);
    hashTable.put("pixData", pixData);
    hashTable.put("channelNames", channelNames);
    hashTable.put("channelTypes", channelTypes);
    hashTable.put("channelVFrapImageType", channelVFrapImageType);
    return true;
}

Example 30 with VCDataIdentifier

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

the class SimResultsViewer method initialize.

/**
 * Insert the method's description here.
 * Creation date: (10/17/2005 11:37:52 PM)
 * @exception org.vcell.util.DataAccessException The exception description.
 */
private void initialize() throws DataAccessException {
    // create main viewer for jobIndex 0 and wire it up
    if (isODEData) {
        setMainViewer(createODEDataViewer());
    } else {
        setMainViewer(createPDEDataViewer());
    }
    java.beans.PropertyChangeListener pcl = new java.beans.PropertyChangeListener() {

        public void propertyChange(java.beans.PropertyChangeEvent evt) {
            if (evt.getSource() == SimResultsViewer.this && (evt.getPropertyName().equals("dataViewerManager"))) {
                try {
                    getMainViewer().setDataViewerManager(getDataViewerManager());
                } catch (java.beans.PropertyVetoException exc) {
                    exc.printStackTrace();
                }
            }
            if (evt.getSource() == SimResultsViewer.this && (evt.getPropertyName().equals("simulationModelInfo"))) {
                getMainViewer().setSimulationModelInfo(getSimulationModelInfo());
            }
        }
    };
    addPropertyChangeListener(pcl);
    // if necessarry, create parameter choices panel and wire it up
    if (getSimulation().getScanCount() > 1) {
        JPanel panel = new JPanel();
        panel.setLayout(new BorderLayout(5, 0));
        panel.setBorder(BorderFactory.createEtchedBorder());
        JLabel label = new JLabel("<html><b>Choose Parameter Values</b></html>");
        label.setHorizontalAlignment(SwingConstants.CENTER);
        label.setBorder(BorderFactory.createEmptyBorder(2, 2, 0, 2));
        panel.add(label, BorderLayout.NORTH);
        String[] scanParams = getSimulation().getMathOverrides().getScannedConstantNames();
        Arrays.sort(scanParams);
        JPanel tablePanel = new JPanel();
        tablePanel.setLayout(new BoxLayout(tablePanel, BoxLayout.X_AXIS));
        for (int i = 0; i < scanParams.length; i++) {
            Constant[] scanConstants = getSimulation().getMathOverrides().getConstantArraySpec(scanParams[i]).getConstants();
            String[][] values = new String[scanConstants.length][1];
            for (int j = 0; j < scanConstants.length; j++) {
                values[j][0] = scanConstants[j].getExpression().infix();
            }
            class ScanChoicesTableModel extends javax.swing.table.AbstractTableModel {

                String[] columnNames;

                Object[][] rowData;

                ScanChoicesTableModel(Object[][] argData, String[] argNames) {
                    columnNames = argNames;
                    rowData = argData;
                }

                public String getColumnName(int column) {
                    return columnNames[column].toString();
                }

                public int getRowCount() {
                    return rowData.length;
                }

                public int getColumnCount() {
                    return columnNames.length;
                }

                public Object getValueAt(int row, int col) {
                    return rowData[row][col];
                }

                public boolean isCellEditable(int row, int column) {
                    return false;
                }

                public void setValueAt(Object value, int row, int col) {
                    rowData[row][col] = value;
                    fireTableCellUpdated(row, col);
                }
            }
            ;
            ScanChoicesTableModel tm = new ScanChoicesTableModel(values, new String[] { scanParams[i] });
            final JTable table = new JTable(tm);
            choicesHash.put(scanParams[i], table);
            table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
            table.getSelectionModel().setSelectionInterval(0, 0);
            final ListSelectionListener[] nextListSelectionListener = new ListSelectionListener[1];
            nextListSelectionListener[0] = new javax.swing.event.ListSelectionListener() {

                public void valueChanged(javax.swing.event.ListSelectionEvent e) {
                    if (!e.getValueIsAdjusting()) {
                        DefaultListSelectionModel list = (DefaultListSelectionModel) e.getSource();
                        int selected = list.getAnchorSelectionIndex();
                        final int previous = (selected == e.getFirstIndex() ? e.getLastIndex() : e.getFirstIndex());
                        ListReset listReset = new ListReset() {

                            @Override
                            public void reset(VCDataIdentifier myVcDataIdentifier) {
                                if (myVcDataIdentifier instanceof VCSimulationDataIdentifier) {
                                    int paramScanIndex = ((VCSimulationDataIdentifier) myVcDataIdentifier).getJobIndex();
                                    table.getSelectionModel().removeListSelectionListener(nextListSelectionListener[0]);
                                    try {
                                        table.setRowSelectionInterval(paramScanIndex, paramScanIndex);
                                    } finally {
                                        table.getSelectionModel().addListSelectionListener(nextListSelectionListener[0]);
                                    }
                                } else {
                                    table.setRowSelectionInterval(previous, previous);
                                }
                            }
                        };
                        updateScanParamChoices("SimResultsViewer set paramScan index=" + getSelectedParamScanJobIndex(), listReset);
                    }
                }
            };
            table.getSelectionModel().addListSelectionListener(nextListSelectionListener[0]);
            JScrollPane scr = new JScrollPane(table);
            JPanel p = new JPanel();
            scr.setPreferredSize(new java.awt.Dimension(100, Math.min(150, table.getPreferredSize().height + table.getTableHeader().getPreferredSize().height + 5)));
            p.setLayout(new java.awt.BorderLayout());
            p.add(scr, java.awt.BorderLayout.CENTER);
            p.setBorder(BorderFactory.createEmptyBorder(4, 4, 4, 4));
            tablePanel.add(p);
        }
        panel.add(tablePanel, BorderLayout.CENTER);
        if (isODEData) {
            JPanel buttonPanel = new JPanel(new FlowLayout());
            JButton button = new JButton("Time Plot with Multiple Parameter Value Sets");
            buttonPanel.add(button);
            panel.add(buttonPanel, BorderLayout.SOUTH);
            button.addActionListener(new ActionListener() {

                public void actionPerformed(ActionEvent e) {
                    mainViewer.showTimePlotMultipleScans(dataManager);
                }
            });
        } else {
            pdeDataViewer.setSimNameSimDataID(new ExportSpecs.SimNameSimDataID(getSimulation().getName(), getSimulation().getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), SimResultsViewer.getParamScanInfo(getSimulation(), getSelectedParamScanJobIndex())));
        }
        setParamChoicesPanel(panel);
    }
    // put things together
    setLayout(new java.awt.BorderLayout());
    add(getMainViewer(), java.awt.BorderLayout.CENTER);
    if (getSimulation().getScanCount() > 1) {
        add(getParamChoicesPanel(), java.awt.BorderLayout.SOUTH);
    }
}