/**
* 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++;
}
/**
* Reacts to slider moves.
*
* @see ChangeListener#stateChanged(javax.swing.event.ChangeEvent)
*/
public void stateChanged(ChangeEvent e) {
if (zSlider == null || tSlider == null || coord == null || state != State.READY) return;
Coord3D thisCoord = new Coord3D(zSlider.getValue() - 1, tSlider.getValue() - 1);
if (coord.equals(thisCoord)) return;
if (!pixelStats.containsKey(thisCoord)) return;
Object[] nameColour = (Object[]) channelSelection.getSelectedItem();
String string = (String) nameColour[1];
if (!nameMap.containsKey(string)) {
state = State.READY;
return;
}
selectedChannelName = string;
int channel = nameMap.get(string);
if (channel == -1) return;
if (!pixelStats.get(thisCoord).containsKey(channel)) return;
state = State.ANALYSING;
populateData(thisCoord, channel);
repaint();
if (shape != null) view.selectFigure(shape.getFigure());
state = State.READY;
}
/**
* Outputs the summary information from the shape map.
*
* @param writer The Excel writer.
* @param shapeMap see above.
* @throws IOException
*/
private void outputSummary(ExcelWriter writer, TreeMap<Coord3D, ROIShape> shapeMap) {
int rowIndex = 0;
printSummaryHeader(writer, rowIndex);
rowIndex++;
Coord3D start = shapeMap.firstKey();
Coord3D end = shapeMap.lastKey();
Coord3D coord;
List<Integer> channels = new ArrayList<Integer>(channelName.keySet());
for (Integer c : channels) {
for (int z = start.getZSection(); z <= end.getZSection(); z++)
for (int t = start.getTimePoint(); t <= end.getTimePoint(); t++) {
coord = new Coord3D(z, t);
populateData(coord, c);
outputSummaryRow(writer, rowIndex, c, z, t);
rowIndex++;
}
}
}
/**
* 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;
}
