/** 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);
}
/**
* Returns a collection of images composing the grid.
*
* @return See above.
*/
List<SplitImage> getSplitImages() {
if (splitImages == null) splitImages = new ArrayList<SplitImage>();
else splitImages.clear();
String n;
splitImages = new ArrayList<SplitImage>();
List<ChannelData> list = parent.getSortedChannelData();
Iterator<ChannelData> i = list.iterator();
ChannelData channel;
int j = 0;
int size = gridImages.size();
while (i.hasNext()) {
channel = i.next();
n = PREFIX + channel.getChannelLabeling();
if (j >= size) splitImages.add(new SplitImage(null, n));
else splitImages.add(new SplitImage(gridImages.get(j), n));
j++;
}
splitImages.add(new SplitImage(combinedImage, COMBINED));
return splitImages;
}
/**
* Returns the list of grid images for openGL.
*
* @return See above.
*/
List<GridImage> getGridImages() {
List<GridImage> list = new ArrayList<GridImage>();
List<ChannelData> l = parent.getSortedChannelData();
Iterator<ChannelData> i = l.iterator();
int index;
GridImage image;
// boolean[] rgb;
ChannelData data;
String label;
boolean b = isRenderedImageRGB();
if (!isModelRGB()) b = false;
while (i.hasNext()) {
data = i.next();
index = data.getIndex();
label = data.getChannelLabeling();
// rgb = new boolean[3];
if (parent.isChannelActive(index)) {
/*
if (b) {
rgb[0] = !parent.isChannelRed(index);
rgb[1] = !parent.isChannelGreen(index);
rgb[2] = !parent.isChannelBlue(index);
image = new GridImage(index, true, label, rgb);
} else {
image = new GridImage(index, true, label);
image.setTextureData(gridImagesAsTextures.get(index));
}
*/
image = new GridImage(index, true, label);
image.setTextureData(gridImagesAsTextures.get(index));
} else {
image = new GridImage(index, false, label);
}
list.add(image);
}
return list;
}
/**
* 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;
}