/** Creates the combobox holding the channel list. */
private void createComboBox() {
Object[][] channelCols = new Object[channelName.size()][2];
List<ChannelData> metadata = model.getMetadata();
Iterator<ChannelData> i = metadata.iterator();
ChannelData channelData;
int channel;
int index = 0;
while (i.hasNext()) {
channelData = i.next();
channel = channelData.getIndex();
if (channelName.containsKey(channel)) {
channelCols[index] = new Object[] {channelColour.get(channel), channelName.get(channel)};
index++;
}
}
// if (channelCols.length == 0)
// return;
channelSelection.setModel(new DefaultComboBoxModel(channelCols));
channelSelection.setRenderer(new ColorListRenderer());
if (selectedChannelName != null)
if (nameMap.containsKey(selectedChannelName))
selectedChannel = nameMap.get(selectedChannelName);
else selectedChannel = 0;
else selectedChannel = 0;
if (selectedChannel >= channelSelection.getItemCount() || selectedChannel < 0) return;
channelSelection.setSelectedIndex(selectedChannel);
channelSelection.setEnabled(true);
}
/** Toggles the value of the boolean under the current selection. */
private void toggleValue() {
int col = fieldTable.getSelectedColumn();
int row = fieldTable.getSelectedRow();
Object v = (Boolean) fieldTable.getModel().getValueAt(row, col);
Boolean value = Boolean.valueOf(false);
if (v != null) value = (Boolean) v;
boolean newValue = !(value.booleanValue());
fieldTable.getModel().setValueAt(Boolean.valueOf(newValue), row, col);
model.getDrawingView().repaint();
}
/**
* 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++;
}
/** Rebuilds Tree */
void rebuildTable() {
TreeMap<Long, ROI> roiList = model.getROI();
Iterator<ROI> iterator = roiList.values().iterator();
ROI roi;
TreeMap<Coord3D, ROIShape> shapeList;
Iterator<ROIShape> shapeIterator;
objectsTable.clear();
while (iterator.hasNext()) {
roi = iterator.next();
shapeList = roi.getShapes();
shapeIterator = shapeList.values().iterator();
while (shapeIterator.hasNext()) objectsTable.addROIShape(shapeIterator.next());
}
objectsTable.collapseAll();
}
/** Initializes the component composing the display. */
private void initComponents() {
infoLabel = new JLabel(MAGNIFICATION + " is " + model.getDrawingView().getScaleFactor());
// create the table
fieldTable = new FigureTable(new FigureTableModel(attributeFields, COLUMN_NAMES));
fieldTable.getTableHeader().setReorderingAllowed(false);
fieldTable.setRowHeight(26);
fieldTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
fieldTable.setCellSelectionEnabled(true);
fieldTable.setColumnSelectionAllowed(true);
fieldTable.addMouseListener(
new MouseAdapter() {
public void mouseClicked(MouseEvent e) {
int col = fieldTable.getSelectedColumn();
int row = fieldTable.getSelectedRow();
Object value = fieldTable.getValueAt(row, col);
if (e.getClickCount() == 1) {
if (value instanceof Boolean) {
toggleValue();
}
} else if (e.getClickCount() > 1) {
e.consume();
if (value instanceof Color) {
// Only if the figure is not read only.
FigureTableModel ftm = (FigureTableModel) fieldTable.getModel();
ROIFigure figure = ftm.getFigure();
if (figure != null && !figure.isReadOnly())
if (figure.canEdit()) controller.showColorPicker((Color) value);
} else if (value instanceof Boolean) {
toggleValue();
}
}
}
});
fieldTable.addPropertyChangeListener(
new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent evt) {
String name = evt.getPropertyName();
if (FigureTable.VALUE_CHANGED_PROPERTY.equals(name)) {
handleValueChanged((String) evt.getNewValue());
}
}
});
}
private void handleValueChanged(String text) {
int row = fieldTable.getEditingRow();
if (row < 0 || row >= attributeFields.size()) {
return;
}
AttributeKey attr = getAttributeKey(row);
FigureTableModel ftm = (FigureTableModel) fieldTable.getModel();
ROIFigure figure = ftm.getFigure();
if (attr.equals(MeasurementAttributes.TEXT)) {
if (TextHolderFigure.class.isAssignableFrom(figure.getClass())) {
((TextHolderFigure) figure).setText(text);
}
} else if (attr.equals(MeasurementAttributes.FONT_SIZE)) {
double d = parseDouble(text);
figure.setAttribute(MeasurementAttributes.FONT_SIZE, d);
figure.changed();
} else if (attr.equals(MeasurementAttributes.STROKE_WIDTH)) {
double d = parseDouble(text);
figure.setAttribute(MeasurementAttributes.STROKE_WIDTH, d);
} else if (attr.equals(MeasurementAttributes.WIDTH)) {
try {
double d = parseDouble(text);
setFigureDimension(figure, MeasurementAttributes.WIDTH, d);
if (isScaleProportionally()) {
setFigureDimension(figure, MeasurementAttributes.HEIGHT, d);
}
} catch (Exception e) {
}
} else if (attr.equals(MeasurementAttributes.HEIGHT)) {
try {
double d = parseDouble(text);
setFigureDimension(figure, MeasurementAttributes.HEIGHT, d);
if (isScaleProportionally()) {
setFigureDimension(figure, MeasurementAttributes.WIDTH, d);
}
} catch (Exception e) {
}
}
model.getDrawingView().repaint();
}
/**
* Returns the selected figures.
*
* @return See above.
*/
Collection<Figure> getSelectedFigures() {
return model.getSelectedFigures();
}
/** Invokes when new figures are selected. */
void onSelectedFigures() {
objectsTable.onSelectedFigures(model.getSelectedFigures());
}
/** Resets the component. */
void reset() {
model.getROIComponent().reset();
}
/**
* Get the analysis results from the model and convert to the necessary array. data types using
* the ROIStats wrapper then create the appropriate table data and summary statistics.
*/
void displayAnalysisResults() {
if (state == State.ANALYSING) return;
this.ROIStats = model.getAnalysisResults();
if (ROIStats == null || ROIStats.size() == 0) return;
state = State.ANALYSING;
channelSelection.setVisible(true);
clearMaps();
shapeStatsList = new TreeMap<Coord3D, Map<StatsType, Map>>(new Coord3D());
pixelStats = new TreeMap<Coord3D, Map<Integer, Map<Point, Double>>>(new Coord3D());
shapeMap = new TreeMap<Coord3D, ROIShape>(new Coord3D());
minStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D());
maxStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D());
meanStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D());
sumStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D());
stdDevStats = new TreeMap<Coord3D, Map<Integer, Double>>(new Coord3D());
Entry entry;
Iterator j = ROIStats.entrySet().iterator();
channelName = new TreeMap<Integer, String>();
nameMap = new LinkedHashMap<String, Integer>();
int minZ = Integer.MAX_VALUE, maxZ = Integer.MIN_VALUE;
int minT = Integer.MAX_VALUE, maxT = Integer.MIN_VALUE;
clearAllValues();
Coord3D c3D;
Map<StatsType, Map> shapeStats;
ChannelData channelData;
int channel;
Iterator<ChannelData> i;
List<ChannelData> metadata = model.getMetadata();
while (j.hasNext()) {
entry = (Entry) j.next();
shape = (ROIShape) entry.getKey();
c3D = shape.getCoord3D();
minT = Math.min(minT, c3D.getTimePoint());
maxT = Math.max(maxT, c3D.getTimePoint());
minZ = Math.min(minZ, c3D.getZSection());
maxZ = Math.max(maxZ, c3D.getZSection());
shapeMap.put(c3D, shape);
if (shape.getFigure() instanceof MeasureTextFigure) {
state = State.READY;
return;
}
shapeStats = AnalysisStatsWrapper.convertStats((Map) entry.getValue());
shapeStatsList.put(c3D, shapeStats);
minStats.put(c3D, shapeStats.get(StatsType.MIN));
maxStats.put(c3D, shapeStats.get(StatsType.MAX));
meanStats.put(c3D, shapeStats.get(StatsType.MEAN));
sumStats.put(c3D, shapeStats.get(StatsType.SUM));
stdDevStats.put(c3D, shapeStats.get(StatsType.STDDEV));
pixelStats.put(c3D, shapeStats.get(StatsType.PIXEL_PLANEPOINT2D));
/* really inefficient but hey.... quick hack just now till refactor */
channelName.clear();
nameMap.clear();
channelColour.clear();
i = metadata.iterator();
List<String> names = new ArrayList<String>();
String name;
while (i.hasNext()) {
channelData = i.next();
channel = channelData.getIndex();
if (model.isChannelActive(channel)) {
name = channelData.getChannelLabeling();
if (names.contains(name)) name += " " + channel;
channelName.put(channel, name);
nameMap.put(channelName.get(channel), channel);
channelColour.put(channel, (Color) model.getActiveChannels().get(channel));
}
}
}
if (channelName.size() != channelColour.size() || nameMap.size() == 0) {
createComboBox();
List<String> names = channelSummaryModel.getRowNames();
List<String> channelNames = new ArrayList<String>();
Double data[][] = new Double[channelName.size()][names.size()];
channelSummaryModel = new ChannelSummaryModel(names, channelNames, data);
channelSummaryTable.setModel(channelSummaryModel);
saveButton.setEnabled(false);
showIntensityTable.setEnabled(false);
if (intensityDialog != null) intensityDialog.setVisible(false);
state = State.READY;
return;
}
saveButton.setEnabled(true);
showIntensityTable.setEnabled(true);
maxZ = maxZ + 1;
minZ = minZ + 1;
maxT = maxT + 1;
minT = minT + 1;
createComboBox();
Object[] nameColour = (Object[]) channelSelection.getSelectedItem();
String string = (String) nameColour[1];
selectedChannel = nameMap.get(string);
zSlider.setMaximum(maxZ);
zSlider.setMinimum(minZ);
tSlider.setMaximum(maxT);
tSlider.setMinimum(minT);
zSlider.setVisible((maxZ != minZ));
tSlider.setVisible((maxT != minT));
tSlider.setValue(model.getCurrentView().getTimePoint() + 1);
zSlider.setValue(model.getCurrentView().getZSection() + 1);
coord = new Coord3D(zSlider.getValue() - 1, tSlider.getValue() - 1);
shape = shapeMap.get(coord);
populateData(coord, selectedChannel);
saveButton.setEnabled(tableModel.getRowCount() > 0);
state = State.READY;
}
/** 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.");
}
/** Updates the display when the magnification factor changes. */
void onMagnificationChanged() {
infoLabel.setText(MAGNIFICATION + " is " + model.getDrawingView().getScaleFactor());
}
