/** 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;
}
/**
* Handles the exception thrown if any while creating the images for the split view.
*
* @param e The exception to handle.
*/
private void handleGridImageCreationException(Exception e) {
UserNotifier un = ImViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo("Split View", "Unable to create the images for the view");
LogMessage msg = new LogMessage();
msg.print("Grid Images creation");
msg.print(e);
ImViewerAgent.getRegistry().getLogger().error(this, msg);
gridImages.clear();
gridImagesAsTextures.clear();
}
/**
* Creates or recycles the existing figure dialog.
*
* @param name The name to display.
* @param pixels The pixels object of reference.
* @param index One of the constants defined by this class.
* @return See above.
*/
FigureDialog createFigureDialog(String name, PixelsData pixels, int index) {
if (figureDialog != null) return figureDialog;
UserNotifier un = MetadataViewerAgent.getRegistry().getUserNotifier();
if (FigureDialog.needPixels(index) && pixels == null) {
un.notifyInfo("Figure", "The image is not valid," + " cannot create the figure.");
return null;
}
JFrame f = MetadataViewerAgent.getRegistry().getTaskBar().getFrame();
figureDialog = new FigureDialog(f, name, pixels, index, view.getRefObject().getClass());
figureDialog.addPropertyChangeListener(this);
return figureDialog;
}
/**
* Implemented as specified by the {@link Importer} interface.
*
* @see Importer#importData(ImportableObject)
*/
public void importData(ImportableObject data) {
if (model.getState() == DISCARDED) return;
if (data == null || data.getFiles() == null || data.getFiles().size() == 0) {
UserNotifier un = ImporterAgent.getRegistry().getUserNotifier();
un.notifyInfo("Import", "No Files to import.");
return;
}
view.showRefreshMessage(chooser.isRefreshLocation());
if (data.hasNewTags()) model.setTags(null);
ImporterUIElement element = view.addImporterElement(data);
if (model.getState() == IMPORTING) return;
importData(element);
}
/**
* Creates the {@link #displayedImage}. The method should be invoked after the {@link
* #setRenderedImage(BufferedImage)} method.
*/
void createDisplayedProjectedImage() {
if (projectedImage == null) return;
if (displayedProjectedImage != null) displayedProjectedImage.flush();
if (zoomFactor != ZoomAction.DEFAULT_ZOOM_FACTOR) {
BufferedImage img = null;
try {
img = Factory.magnifyImage(projectedImage, zoomFactor, 0);
} catch (Throwable e) {
UserNotifier un = ImViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo("Magnification", "An error occurred while magnifying the image.");
}
if (img != null) displayedProjectedImage = img;
} else displayedProjectedImage = projectedImage;
}
/**
* Opens a dialog box for users to enter a URL
*
* @see ActionListener#actionPerformed(ActionEvent)
*/
public void actionPerformed(ActionEvent e) {
JFrame f = EditorAgent.getRegistry().getTaskBar().getFrame();
InputDialog dialog = new InputDialog(f, "Enter ID of Editor File on Server", "");
int option = dialog.centerMsgBox();
if (option == InputDialog.SAVE) {
String newFileID = dialog.getText();
// could check valid ID (integer) etc?
if (EditorLinkParam.isLinkValidId(newFileID)) {
attributeEdited(TextParam.PARAM_VALUE, newFileID);
} else {
UserNotifier un = EditorAgent.getRegistry().getUserNotifier();
un.notifyInfo("Not valid ID", "Did not enter a valid Editor file ID");
}
}
}
/** Modifies the existing password. */
private void changePassword() {
UserNotifier un;
if (!oldPassword.isVisible()) {
StringBuffer buf = new StringBuffer();
buf.append(passwordNew.getPassword());
String newPass = buf.toString();
if (newPass == null || newPass.length() == 0) {
un = MetadataViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo(PASSWORD_CHANGE_TITLE, "Please enter the new password.");
passwordNew.requestFocus();
return;
}
un = MetadataViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo(PASSWORD_CHANGE_TITLE, "Password changed.");
passwordNew.setText("");
model.resetPassword(newPass);
return;
}
StringBuffer buf = new StringBuffer();
buf.append(passwordNew.getPassword());
String newPass = buf.toString();
String pass = buf.toString();
buf = new StringBuffer();
buf.append(passwordConfirm.getPassword());
String confirm = buf.toString();
buf = new StringBuffer();
buf.append(oldPassword.getPassword());
String old = buf.toString();
if (old == null || old.trim().length() == 0) {
un = MetadataViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo(PASSWORD_CHANGE_TITLE, "Please specify your old password.");
oldPassword.requestFocus();
return;
}
if (newPass == null || newPass.length() == 0) {
un = MetadataViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo(PASSWORD_CHANGE_TITLE, "Please enter your new password.");
passwordNew.requestFocus();
return;
}
if (pass == null || confirm == null || confirm.length() == 0 || !pass.equals(confirm)) {
un = MetadataViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo(
PASSWORD_CHANGE_TITLE, "The passwords entered do not match. " + "Please try again.");
passwordNew.setText("");
passwordConfirm.setText("");
passwordNew.requestFocus();
return;
}
model.changePassword(old, confirm);
}
/**
* 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;
}
/**
* Listens to property fired by the Editor dialog.
*
* @see PropertyChangeListener#propertyChange(PropertyChangeEvent)
*/
public void propertyChange(PropertyChangeEvent evt) {
String name = evt.getPropertyName();
if (EditorDialog.CREATE_NO_PARENT_PROPERTY.equals(name)) {
// reset text and tooltip
String text = "";
String description = "";
AnnotationData annotation = null;
if (data instanceof TagAnnotationData
|| data instanceof TermAnnotationData
|| data instanceof XMLAnnotationData) {
annotation = (AnnotationData) data;
text = annotation.getContentAsString();
text = EditorUtil.truncate(text, TEXT_LENGTH, false);
}
if (data instanceof DoubleAnnotationData) {
annotation = (AnnotationData) data;
text = "" + ((DoubleAnnotationData) data).getDataValue();
}
if (data instanceof LongAnnotationData) {
annotation = (AnnotationData) data;
text = "" + ((LongAnnotationData) data).getDataValue();
}
if (data instanceof BooleanAnnotationData) {
annotation = (AnnotationData) data;
text = "" + ((BooleanAnnotationData) data).getValue();
}
description = model.getAnnotationDescription(annotation);
if (annotation == null) return;
label.setText(text);
label.setToolTipText(formatToolTip(annotation, null));
originalName = text;
originalDescription = description;
firePropertyChange(AnnotationUI.EDIT_TAG_PROPERTY, null, this);
} else if (FileChooser.APPROVE_SELECTION_PROPERTY.equals(name)) {
if (data == null) return;
FileAnnotationData fa = (FileAnnotationData) data;
OriginalFile f = (OriginalFile) fa.getContent();
File folder;
Object o = evt.getNewValue();
if (o instanceof String) {
String path = (String) o;
if (!path.endsWith(File.separator)) {
path += File.separator;
}
path += fa.getFileName();
folder = new File(path);
} else {
File[] files = (File[]) o;
folder = files[0];
}
if (folder == null) folder = UIUtilities.getDefaultFolder();
UserNotifier un = MetadataViewerAgent.getRegistry().getUserNotifier();
IconManager icons = IconManager.getInstance();
DownloadActivityParam activity =
new DownloadActivityParam(f, folder, icons.getIcon(IconManager.DOWNLOAD_22));
// Check Name space
activity.setLegend(fa.getDescription());
un.notifyActivity(model.getSecurityContext(), activity);
}
}
/** Message displayed when one of the required fields is left blank. */
private void showRequiredField() {
UserNotifier un = MetadataViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo("Edit Profile", "The required fields cannot be left " + "blank.");
return;
}
/**
* Saves the displayed images.
*
* @param init Pass <code>true</code> to initialize the images to save, <code>false</code>
* otherwise.
*/
void saveImage(boolean init) {
UserNotifier un = ImViewerAgent.getRegistry().getUserNotifier();
if (init) createImages(uiDelegate.getSavingType());
// Builds the image to display.
boolean unitBar = model.isUnitBar();
String v = getUnitBarValue();
int s = (int) getUnitBarSize();
boolean constrain;
try {
String name = uiDelegate.getSelectedFilePath();
// make sure the parent directory paths all exist
FileUtils.forceMkdir(new File(name).getParentFile());
if (imageComponents == null) {
constrain =
unitBar && v != null && s < mainImage.getWidth() && imageType == ImgSaverUI.IMAGE;
writeSingleImage(mainImage, constrain, name);
} else {
if (mainImage == null) return;
Iterator i;
int h, w;
BufferedImage newImage;
Graphics2D g2;
if (uiDelegate.isSaveImagesInSeparatedFiles()) {
constrain =
unitBar && v != null && s < mainImage.getWidth() && imageType == ImgSaverUI.IMAGE;
writeSingleImage(mainImage, constrain, name);
i = imageComponents.iterator();
int j = 0;
while (i.hasNext()) {
constrain = unitBar && v != null && imageType != ImgSaverUI.LENS_IMAGE_AND_COMPONENTS;
writeSingleImage((BufferedImage) i.next(), constrain, name + "_" + j);
j++;
}
} else {
int width = mainImage.getWidth();
h = mainImage.getHeight();
int n = imageComponents.size();
w = width * (n + 1) + ImgSaverPreviewer.SPACE * (n - 1);
newImage = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB);
g2 = (Graphics2D) newImage.getGraphics();
g2.setColor(Color.WHITE);
ImagePaintingFactory.setGraphicRenderingSettings(g2);
// Paint the original image.
i = imageComponents.iterator();
int x = 0;
while (i.hasNext()) {
g2.drawImage((BufferedImage) i.next(), null, x, 0);
if (unitBar && v != null && imageType != ImgSaverUI.LENS_IMAGE_AND_COMPONENTS)
ImagePaintingFactory.paintScaleBar(g2, x + width - s - 10, h - 10, s, v);
x += width;
g2.fillRect(x, 0, ImgSaverPreviewer.SPACE, h);
x += ImgSaverPreviewer.SPACE;
}
g2.drawImage(mainImage, null, x, 0);
if (unitBar
&& v != null
&& !(imageType == ImgSaverUI.LENS_IMAGE_AND_COMPONENTS
|| imageType == ImgSaverUI.LENS_IMAGE))
ImagePaintingFactory.paintScaleBar(g2, x + width - s - 10, h - 10, s, v);
writeImage(newImage, name);
}
}
} catch (Exception e) {
if (e instanceof IOException || e.getCause() instanceof IOException)
un.notifyInfo(
"Save Image failure",
"Could not access file "
+ uiDelegate.getSelectedFilePath()
+ "\nMake sure you have the necessary permissions to perform this action.");
else un.notifyError("Save Image failure", "An error occurred while saving the image.", e);
return;
}
notifySave(getExtendedName(uiDelegate.getSelectedFilePath(), format));
if (uiDelegate.isSetDefaultFolder())
UIUtilities.setDefaultFolder(uiDelegate.getCurrentDirectory());
}
/** 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.");
}
