/**
* Create summary table with horizontal columns.
*
* @param writer The Excel writer.
* @param rowIndex The selected row.
*/
private void printSummaryHeader(ExcelWriter writer, int rowIndex) {
writer.writeElement(rowIndex, 0, "channel");
writer.writeElement(rowIndex, 1, "zsection");
writer.writeElement(rowIndex, 2, "time");
for (int y = 0; y < channelSummaryTable.getRowCount(); y++)
writer.writeElement(rowIndex, 3 + y, channelSummaryTable.getValueAt(y, 0));
}
/**
* Adds the any remaining fields (min, max, mean, stdDev) to the file being saved.
*
* @param writer The Excel writer.
* @param rowIndex The selected row.
* @param channel The channel to output.
* @param z z-section to output.
* @param t timepoint to output.
*/
private void outputSummaryRow(ExcelWriter writer, int rowIndex, Integer channel, int z, int t) {
writer.writeElement(rowIndex, 0, channelName.get(channel));
writer.writeElement(rowIndex, 1, z + "");
writer.writeElement(rowIndex, 2, t + "");
int col;
String v;
for (int y = 0; y < channelSummaryTable.getRowCount(); y++) {
col = getColumn(channelName.get(channel));
if (col == -1) continue;
v = (String) channelSummaryTable.getValueAt(y, col);
if (v.contains(".") && v.contains(",")) {
v = v.replace(".", "");
v = v.replace(",", ".");
}
writer.writeElement(rowIndex, 3 + y, new Double(v));
}
}
/**
* Writes the header information for the file, image, projects, dataset.
*
* @param writer The Excel writer.
* @param rowIndex The selected row.
* @param currentCoord The coord of the shape being written.
* @throws IOException Thrown if the data cannot be written.
*/
private void writeHeader(ExcelWriter writer, int rowIndex, Coord3D currentCoord) {
writer.writeElement(rowIndex, 0, "Image ");
writer.writeElement(rowIndex, 1, model.getImageName());
rowIndex++;
writer.writeElement(rowIndex, 0, "Z ");
writer.writeElement(rowIndex, 1, (currentCoord.getZSection() + 1));
rowIndex++;
writer.writeElement(rowIndex, 0, "T ");
writer.writeElement(rowIndex, 1, (currentCoord.getTimePoint() + 1));
rowIndex++;
}
/**
* Writes the channel intensities and stats to the files.
*
* @param writer The Excel writer.
* @param rowIndex The selected row.
* @param coord The specified coordinate.
* @param channel The channel to output.
*/
private void writeData(ExcelWriter writer, int rowIndex, Coord3D coord, int channel) {
populateData(coord, channel);
writer.writeTableToSheet(rowIndex, 0, tableModel);
}
/** 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.");
}