/** 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;
}
/**
* 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.");
}
