/** Opens the file. */
private void openFile() {
if (!(data instanceof FileAnnotationData)) return;
FileAnnotationData fa = (FileAnnotationData) data;
Registry reg = MetadataViewerAgent.getRegistry();
UserNotifier un = reg.getUserNotifier();
OriginalFile f = (OriginalFile) fa.getContent();
Environment env = (Environment) reg.lookup(LookupNames.ENV);
DownloadAndLaunchActivityParam activity;
final long dataId = fa.getId();
final File dir =
new File(env.getOmeroFilesHome() + File.separatorChar + "file annotation " + dataId);
if (!dir.exists()) {
dir.mkdir();
}
if (f != null && f.isLoaded()) {
activity = new DownloadAndLaunchActivityParam(f, dir, null);
} else {
activity =
new DownloadAndLaunchActivityParam(
dataId, DownloadAndLaunchActivityParam.FILE_ANNOTATION, dir, null);
}
un.notifyActivity(model.getSecurityContext(), activity);
return;
}
/**
* Shuts downs the caching service.
*
* @param container Reference to the container.
*/
public static void shutdown(Container container) {
// NB: this can't be called outside of container b/c agents have no refs
// to the singleton container. So we can be sure this method is going to
// create services just once.
if (container == null) return;
Registry reg = container.getRegistry();
((CacheServiceImpl) reg.getCacheService()).shutDown();
}
/**
* Returns the compression quality related to the passed level.
*
* @param compressionLevel The level to handle.
* @return See above.
*/
static final float getCompressionQuality(int compressionLevel) {
Float value;
switch (compressionLevel) {
default:
case RenderingControl.UNCOMPRESSED:
case RenderingControl.MEDIUM:
value = (Float) registry.lookup(LookupNames.COMPRESSIOM_MEDIUM_QUALITY);
return value.floatValue();
case RenderingControl.LOW:
value = (Float) registry.lookup(LookupNames.COMPRESSIOM_LOW_QUALITY);
return value.floatValue();
}
}
/**
* Returns <code>true</code> if the proxy is used elsewhere.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
* @param pixelsID The id of the pixels set.
* @return See above.
*/
public static boolean isRenderingControlShared(Registry context, Long pixelsID) {
if (!(context.equals(registry)))
throw new IllegalArgumentException("Not allow to access method.");
if (!singleton.rndSvcProxiesCount.containsKey(pixelsID)) return false;
Integer count = singleton.rndSvcProxiesCount.get(pixelsID);
return (count > 1);
}
/**
* Resets the rendering engine.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
* @param pixelsID The ID of the pixels set.
* @param reList The {@link RenderingEngine}s.
* @param def The rendering def linked to the rendering engine. This is passed to speed up the
* initialization sequence.
* @return See above.
* @throws RenderingServiceException If an error occurred while setting the value.
* @throws DSOutOfServiceException If the connection is broken.
*/
public static RenderingControlProxy resetRenderingControl(
Registry context, long pixelsID, List<RenderingEnginePrx> reList, RenderingDef def)
throws RenderingServiceException, DSOutOfServiceException {
if (!(registry.equals(context)))
throw new IllegalArgumentException("Not allow to access method.");
if (reList == null || reList.size() == 0)
throw new IllegalArgumentException("No RE specified.");
RenderingControlProxy proxy = (RenderingControlProxy) singleton.rndSvcProxies.get(pixelsID);
if (proxy != null) {
RndProxyDef converted = convert(def);
proxy.resetRenderingEngine(reList.get(0), converted);
reList.remove(0);
List<RenderingControl> slaves = proxy.getSlaves();
if (slaves.size() == reList.size()) {
Iterator<RenderingControl> i = slaves.iterator();
int index = 0;
while (i.hasNext()) {
proxy = (RenderingControlProxy) i.next();
proxy.resetRenderingEngine(reList.get(index), converted);
}
index++;
}
}
return proxy;
}
/**
* Renders the specified {@link PlaneDef 2D-plane}.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
* @param pixelsID The id of the pixels set.
* @param pDef The plane to render.
* @param largeImage Indicates to set the resolution to <code>0</code>.
* @param compression The compression level.
* @return The image representing the plane.
* @return See above.
* @throws RenderingServiceException If an error occurred while setting the value.
* @throws DSOutOfServiceException If the connection is broken.
*/
public static Object render(
Registry context,
SecurityContext ctx,
Long pixelsID,
PlaneDef pDef,
boolean largeImage,
int compression)
throws RenderingServiceException, DSOutOfServiceException {
if (!(context.equals(registry)))
throw new IllegalArgumentException("Not allow to access method.");
RenderingControlProxy proxy = (RenderingControlProxy) singleton.rndSvcProxies.get(pixelsID);
if (proxy == null)
throw new RuntimeException(
"No rendering service " + "initialized for the specified pixels set.");
int level = proxy.getSelectedResolutionLevel();
if (compression < RenderingControl.UNCOMPRESSED) compression = RenderingControl.UNCOMPRESSED;
if (compression > RenderingControl.LOW) compression = RenderingControl.LOW;
proxy.setCompression(compression);
if (largeImage) {
proxy.setSelectedResolutionLevel(0);
}
Object o = proxy.render(pDef);
if (largeImage) proxy.setSelectedResolutionLevel(level);
return o;
}
/**
* Creates a new data sink for the specified set of pixels.
*
* @param pixels The pixels set the data sink is for.
* @return See above.
*/
public static DataSink createDataSink(PixelsData pixels) {
if (pixels == null) throw new IllegalArgumentException("Pixels cannot be null.");
if (singleton.pixelsSource != null && singleton.pixelsSource.isSame(pixels.getId()))
return singleton.pixelsSource;
registry.getCacheService().clearAllCaches();
int size = getCacheSize();
if (size <= 0) size = 0;
singleton.pixelsSource = DataSink.makeNew(pixels, registry, size);
return singleton.pixelsSource;
}
/**
* Shuts downs the data sink attached to the specified pixels set.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
* @param pixelsID The ID of the pixels set.
*/
public static void shutDownDataSink(Registry context, long pixelsID) {
if (!(context.equals(registry)))
throw new IllegalArgumentException("Not allow to access method.");
if (singleton.pixelsSource != null && singleton.pixelsSource.isSame(pixelsID)) {
int size = getCacheSize();
boolean cacheInMemory = true;
if (size <= 0) cacheInMemory = false;
singleton.pixelsSource.clearCache();
singleton.pixelsSource.setCacheInMemory(cacheInMemory);
}
}
/**
* Returns the {@link RenderingControl} linked to the passed set of pixels, returns <code>null
* </code> if no proxy associated.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
* @param pixelsID The id of the pixels set.
* @param init Pass <code>true</code> if the rendering control is going to be initialized, <code>
* false</code> otherwise.
* @return See above.
*/
public static RenderingControl getRenderingControl(
Registry context, Long pixelsID, boolean init) {
if (!(context.equals(registry)))
throw new IllegalArgumentException("Not allow to access method.");
if (init && singleton.rndSvcProxiesCount.containsKey(pixelsID)) {
Integer count = singleton.rndSvcProxiesCount.get(pixelsID);
count++;
singleton.rndSvcProxiesCount.put(pixelsID, count);
}
return singleton.rndSvcProxies.get(pixelsID);
}
/**
* Creates a new {@link RenderingControl}. We pass a reference to the the registry to ensure that
* agents don't call the method.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
* @param reList The {@link RenderingEngine}s.
* @param pixels The pixels set.
* @param metadata The channel metadata.
* @param compression Pass <code>0</code> if no compression otherwise pass the compression used.
* @param defs The rendering defs linked to the rendering engine. This is passed to speed up the
* initialization sequence.
* @return See above.
* @throws IllegalArgumentException If an Agent try to access the method.
*/
public static RenderingControl createRenderingControl(
Registry context,
SecurityContext ctx,
List<RenderingEnginePrx> reList,
Pixels pixels,
List<ChannelData> metadata,
int compression,
List<RndProxyDef> defs) {
if (!(context.equals(registry)))
throw new IllegalArgumentException("Not allow to access method.");
return singleton.makeNew(ctx, reList, pixels, metadata, compression, defs);
}
/**
* Renders the specified {@link PlaneDef 2D-plane}.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
* @param pixelsID The id of the pixels set.
* @param pDef The plane to render.
* @param tableID The id of the table hosting the mask.
* @param overlays The overlays to render or <code>null</code>.
* @return See above.
* @throws RenderingServiceException If an error occurred while setting the value.
* @throws DSOutOfServiceException If the connection is broken.
*/
public static Object renderOverlays(
Registry context, long pixelsID, PlaneDef pd, long tableID, Map<Long, Integer> overlays)
throws RenderingServiceException, DSOutOfServiceException {
if (!(context.equals(registry)))
throw new IllegalArgumentException("Not allow to access method.");
RenderingControlProxy proxy = (RenderingControlProxy) singleton.rndSvcProxies.get(pixelsID);
if (proxy == null)
throw new RuntimeException(
"No rendering service " + "initialized for the specified pixels set.");
proxy.setOverlays(tableID, overlays);
return proxy.render(pd);
}
/**
* Creates a new {@link CacheService}.
*
* @param container Reference to the container.
* @return See above.
*/
public static CacheService makeNew(Container container) {
// NB: this can't be called outside of container b/c agents have no refs
// to the singleton container. So we can be sure this method is going to
// create services just once.
if (container == null) return null;
// If caching is off, then we return the no-op adapter.
Registry reg = container.getRegistry();
Boolean isCachingOn = (Boolean) reg.lookup(LookupNames.CACHE_ON);
if (!isCachingOn.booleanValue()) return makeNoOpCache();
// Ok we have to cache, so try and read the config file.
InputStream config = loadConfig(container.getConfigFileRelative(CACHE_CONFIG_FILE));
if (config == null) return makeNoOpCache();
// We have a config file, set up ehcache.
CacheService cache = new CacheServiceImpl(config, container.getRegistry().getLogger());
try {
config.close();
} catch (Exception e) {
}
return cache;
}
/**
* Checks if the rendering controls are still active. Shuts the inactive ones.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
*/
public static void checkRenderingControls(Registry context) {
// TODO Auto-generated method stub
if (!(context.equals(registry)))
throw new IllegalArgumentException("Not allow to access method.");
RenderingControlProxy proxy;
Entry<Long, RenderingControl> e;
Iterator<Entry<Long, RenderingControl>> i = singleton.rndSvcProxies.entrySet().iterator();
Long value = (Long) context.lookup(LookupNames.RE_TIMEOUT);
long timeout = 60000; // 1min
if (value != null && value.longValue() > timeout) timeout = value.longValue();
Logger logger = context.getLogger();
while (i.hasNext()) {
e = i.next();
proxy = (RenderingControlProxy) e.getValue();
if (!proxy.isProxyActive(timeout)) {
if (!proxy.shutDown(true))
logger.info(singleton, "Rendering Engine shut down: PixelsID " + e.getKey());
}
}
}
/**
* Creates a new instance. This can't be called outside of container b/c agents have no refs to
* the singleton container. So we can be sure this method is going to create services just once.
*
* @param c Reference to the container.
* @return The sole instance.
* @throws NullPointerException If the reference to the {@link Container} is <code>null</code>.
*/
public static PixelsServicesFactory getInstance(Container c) {
if (c == null) throw new NullPointerException(); // An agent called this method?
if (singleton == null) {
registry = c.getRegistry();
singleton = new PixelsServicesFactory();
// Retrieve the maximum heap size.
MemoryUsage usage = ManagementFactory.getMemoryMXBean().getHeapMemoryUsage();
String message = "Heap memory usage: max " + usage.getMax();
registry.getLogger().info(singleton, message);
// percentage of memory used for caching.
maxSize = (int) (RATIO * usage.getMax()) / FACTOR;
}
return singleton;
}
/**
* Renders the projected images.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
* @param pixelsID The id of the pixels set.
* @param startZ The first optical section.
* @param endZ The last optical section.
* @param stepping Stepping value to use while calculating the projection.
* @param type One of the projection type defined by this class.
* @param channels The collection of channels to project.
* @return See above.
* @throws RenderingServiceException If an error occurred while setting the value.
* @throws DSOutOfServiceException If the connection is broken.
*/
public static BufferedImage renderProjected(
Registry context,
Long pixelsID,
int startZ,
int endZ,
int type,
int stepping,
List<Integer> channels)
throws RenderingServiceException, DSOutOfServiceException {
if (!(context.equals(registry)))
throw new IllegalArgumentException("Not allow to access method.");
RenderingControlProxy proxy = (RenderingControlProxy) singleton.rndSvcProxies.get(pixelsID);
if (proxy == null)
throw new RuntimeException(
"No rendering service " + "initialized for the specified pixels set.");
return proxy.renderProjected(startZ, endZ, stepping, type, channels);
}
/**
* Shuts downs the rendering service attached to the specified pixels set. Returns <code>true
* </code> if the rendering control is shared, <code>false</code> otherwise.
*
* @param context Reference to the registry. To ensure that agents cannot call the method. It must
* be a reference to the container's registry.
* @param pixelsID The ID of the pixels set.
* @return See above.
*/
public static boolean shutDownRenderingControl(Registry context, long pixelsID) {
if (!(context.equals(registry)))
throw new IllegalArgumentException("Not allow to access method.");
RenderingControlProxy proxy = (RenderingControlProxy) singleton.rndSvcProxies.get(pixelsID);
Integer count = singleton.rndSvcProxiesCount.get(pixelsID);
if (proxy != null) {
if (count == 1) {
proxy.shutDown();
singleton.rndSvcProxies.remove(pixelsID);
singleton.rndSvcProxiesCount.remove(pixelsID);
getCacheSize();
} else {
count--;
singleton.rndSvcProxiesCount.put(pixelsID, count);
}
return (singleton.rndSvcProxiesCount.containsKey(pixelsID));
}
return false;
}
/**
* Builds the UI component hosting the UI component used to modify the password.
*
* @return See above.
*/
private JPanel buildPasswordPanel() {
JPanel content = new JPanel();
content.setBackground(UIUtilities.BACKGROUND_COLOR);
Registry reg = MetadataViewerAgent.getRegistry();
String ldap = (String) reg.lookup(LookupNames.USER_AUTHENTICATION);
if (ldap != null && ldap.length() > 0) {
content.setBorder(BorderFactory.createTitledBorder("LDAP Authentication"));
content.setLayout(new FlowLayout(FlowLayout.LEFT));
content.add(new JLabel(ldap));
return content;
}
content.setBorder(BorderFactory.createTitledBorder("Change Password"));
content.setLayout(new GridBagLayout());
GridBagConstraints c = new GridBagConstraints();
c.fill = GridBagConstraints.HORIZONTAL;
c.anchor = GridBagConstraints.WEST;
c.insets = new Insets(0, 2, 2, 0);
c.gridx = 0;
c.gridy = 0;
c.gridwidth = GridBagConstraints.RELATIVE; // next-to-last
c.fill = GridBagConstraints.NONE; // reset to default
c.weightx = 0.0;
if (MetadataViewerAgent.isAdministrator()) {
content.add(UIUtilities.setTextFont(PASSWORD_NEW), c);
c.gridx++;
c.gridwidth = GridBagConstraints.REMAINDER; // end row
c.fill = GridBagConstraints.HORIZONTAL;
c.weightx = 1.0;
content.add(passwordNew, c);
} else {
content.add(UIUtilities.setTextFont(PASSWORD_OLD), c);
c.gridx++;
c.gridwidth = GridBagConstraints.REMAINDER; // end row
c.fill = GridBagConstraints.HORIZONTAL;
c.weightx = 1.0;
content.add(oldPassword, c);
c.gridy++;
c.gridx = 0;
c.gridwidth = GridBagConstraints.RELATIVE; // next-to-last
c.fill = GridBagConstraints.NONE; // reset to default
c.weightx = 0.0;
content.add(UIUtilities.setTextFont(PASSWORD_NEW), c);
c.gridx++;
c.gridwidth = GridBagConstraints.REMAINDER; // end row
c.fill = GridBagConstraints.HORIZONTAL;
c.weightx = 1.0;
content.add(passwordNew, c);
c.gridy++;
c.gridx = 0;
c.gridwidth = GridBagConstraints.RELATIVE; // next-to-last
c.fill = GridBagConstraints.NONE; // reset to default
c.weightx = 0.0;
content.add(UIUtilities.setTextFont(PASSWORD_CONFIRMATION), c);
c.gridx++;
c.gridwidth = GridBagConstraints.REMAINDER; // end row
c.fill = GridBagConstraints.HORIZONTAL;
c.weightx = 1.0;
content.add(passwordConfirm, c);
c.gridy++;
c.gridx = 0;
}
JPanel p = new JPanel();
p.setBackground(UIUtilities.BACKGROUND_COLOR);
p.setLayout(new BoxLayout(p, BoxLayout.Y_AXIS));
p.add(content);
JPanel buttonPanel = UIUtilities.buildComponentPanel(passwordButton);
buttonPanel.setBackground(UIUtilities.BACKGROUND_COLOR);
p.add(buttonPanel);
return p;
}
/**
* Logs off from the current server.
*
* @see java.awt.event.ActionListener#actionPerformed(ActionEvent)
*/
public void actionPerformed(ActionEvent e) {
Registry reg = TreeViewerAgent.getRegistry();
reg.getEventBus().post(new LogOff());
}
/**
* Implemented as specified by the {@link Importer} interface.
*
* @see Importer#logOff()
*/
public void logOff() {
if (model.getState() == IMPORTING) return;
Registry reg = ImporterAgent.getRegistry();
reg.getEventBus().post(new LogOff());
}
/**
* Returns an implementation of {@link ExecMonitor} that works as an adapter to notify the
* specified <code>observer</code> of execution events. Specifically, the returned adapter will
* notify the <code>observer</code> of the tree's execution progress and of the eventual outcome
* of the computation.
*
* @param observer The adaptee.
* @return The adapter.
* @see BatchCallMonitor
*/
protected ExecMonitor getMonitor(AgentEventListener observer) {
MonitorFactory mf = (MonitorFactory) context.lookup(LookupNames.MONITOR_FACTORY);
return mf.makeNew(this, observer);
}
/**
* Returns a concrete {@link CmdProcessor} to {@link #exec(AgentEventListener) execute} the call
* tree.
*
* @return See above.
*/
protected CmdProcessor getProcessor() {
return (CmdProcessor) context.lookup(LookupNames.CMD_PROCESSOR);
}
/**
* Sets the file to edit. If the file cannot be read by {@link TreeModelFactory#getTree()} then
* the state of this model is re-set to {@link Editor#NEW}.
*
* @param file The file to edit.
* @return See above.
*/
boolean setFileToEdit(File file) {
if (file == null) {
fileToEdit = null;
state = Editor.NEW;
fileName = EditorFactory.BLANK_MODEL;
return false;
}
TreeModel treeModel = null;
// try opening file as recognised OMERO.editor file (pro.xml or cpe.xml)
try {
treeModel = TreeModelFactory.getTree(file);
fileToEdit = file;
} catch (ParsingException e) {
// may get a parsing exception simply because the file was not
// recognised as Editor File..
Registry reg = EditorAgent.getRegistry();
UserNotifier un = reg.getUserNotifier();
// ... try opening as ANY xml file
try {
treeModel = TreeModelFactory.getTreeXml(file);
// if this worked, we have an XML file converted to cpe.xml
// .. tell user..
un.notifyInfo(
"File not recognised",
"File was converted from an unrecognised format into\n"
+ "OMERO.editor's cpe.xml format.\nOverwriting the "
+ "original file will erase the original XML format.");
// must avoid overwriting the original file...
// 'Save' won't work.
if (fileID > 0) { // try to read a file downloaded
file.delete();
}
fileToEdit = null;
setFileAnnotationData(null);
} catch (ParsingException ex) {
LogMessage message = new LogMessage();
message.print(ex);
reg.getLogger().error(this, message);
// ...and notify the user. Use the exception message.
String errMsg = ex.getMessage();
un.notifyInfo("File Failed to Open", errMsg);
}
}
if (treeModel == null) {
fileToEdit = null;
state = Editor.NEW;
fileName = EditorFactory.BLANK_MODEL;
return false;
}
fileName = file.getName();
browser.setTreeModel(treeModel);
state = Editor.READY;
return true;
}
/** Save the results to an Excel File. */
private void saveResults() {
channelsSelectionForm = new ChannelSelectionForm(channelName);
FileChooser chooser = view.createSaveToExcelChooser();
chooser.addComponentToControls(channelsSelectionForm);
int results = chooser.showDialog();
if (results != JFileChooser.APPROVE_OPTION) return;
File file = chooser.getFormattedSelectedFile();
// TODO: Modify that code when we have various writer.
if (!file.getAbsolutePath().endsWith(ExcelFilter.EXCEL)) {
String fileName = file.getAbsolutePath() + "." + ExcelFilter.EXCEL;
file = new File(fileName);
}
List<Integer> channels = channelsSelectionForm.getUserSelection();
if (channels == null || channels.size() == 0) {
UserNotifier un = MeasurementAgent.getRegistry().getUserNotifier();
un.notifyInfo("Save Results", " Please select at least a channel.");
view.setStatus("No Channel selected to output.");
return;
}
try {
ExcelWriter writer = new ExcelWriter(file.getAbsolutePath());
writer.openFile();
writer.createSheet("Channel Summary");
Iterator<Coord3D> coordMapIterator = shapeMap.keySet().iterator();
Coord3D currentCoord;
int n = channels.size();
Integer channel;
if (channelSummarySelected(channels)) outputSummary(writer, shapeMap);
BufferedImage originalImage = model.getRenderedImage();
if (originalImage != null) {
BufferedImage image = Factory.copyBufferedImage(originalImage);
// Add the ROI for the current plane to the image.
// TODO: Need to check that.
model.setAttributes(MeasurementAttributes.SHOWID, true);
model.getDrawingView().print(image.getGraphics());
model.setAttributes(MeasurementAttributes.SHOWID, false);
try {
writer.addImageToWorkbook("ThumbnailImage", image);
} catch (Exception e) {
// TODO
}
int col = writer.getMaxColumn(0);
writer.writeImage(0, col + 1, 256, 256, "ThumbnailImage");
}
if (channelSummarySelected(channels) && channels.size() != 1)
while (coordMapIterator.hasNext()) {
currentCoord = coordMapIterator.next();
for (int i = 0; i < n; i++) {
channel = channels.get(i);
if (channel == ChannelSelectionForm.SUMMARYVALUE) continue;
if (!nameMap.containsKey(channelName.get(channel))) continue;
int rowIndex = 0;
writer.createSheet("Channel Number " + channelName.get(channel));
writeHeader(writer, rowIndex, currentCoord);
channel = nameMap.get(channelName.get(channel));
writeData(writer, rowIndex, currentCoord, channel.intValue());
}
}
writer.close();
} catch (Exception e) {
Logger logger = MeasurementAgent.getRegistry().getLogger();
logger.error(this, "Cannot save ROI results: " + e.toString());
UserNotifier un = MeasurementAgent.getRegistry().getUserNotifier();
String message = "An error occurred while trying to" + " save the data.\nPlease try again.";
if (e instanceof NumberFormatException) {
message =
"We only support the British/American style of "
+ "representing numbers,\nusing a decimal point rather "
+ "than a comma.";
}
un.notifyInfo("Save Results", message);
return;
}
Registry reg = MeasurementAgent.getRegistry();
UserNotifier un = reg.getUserNotifier();
un.notifyInfo("Save ROI results", "The ROI results have been " + "successfully saved.");
}