/**
* 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));
}
/** Invokes when ROI are removed. */
void onFigureRemoved() {
channelSelection.setEnabled(false);
showIntensityTable.setEnabled(false);
saveButton.setEnabled(false);
channelSelection.setVisible(false);
channelSummaryTable.setVisible(false);
}
/**
* Populate the summary table with the list of values for the ROI at coord.
*
* @param coord see above.
*/
private void populateChannelSummaryTable(Coord3D coord) {
List<String> statNames = new ArrayList<String>();
List<String> channelNames = new ArrayList<String>();
ROIFigure fig = shape.getFigure();
int count = 0;
statNames.add("Min");
statNames.add("Max");
statNames.add("Sum");
statNames.add("Mean");
statNames.add("Std Dev.");
statNames.add("NumPixels");
if (areaFigure(fig)) addAreaStats(statNames);
else if (lineFigure(fig)) addLineStats(statNames);
else if (pointFigure(fig)) addPointStats(statNames);
Iterator<Integer> channelIterator = channelName.keySet().iterator();
while (channelIterator.hasNext()) channelNames.add(channelName.get(channelIterator.next()));
Double data[][] = new Double[channelName.size()][statNames.size()];
channelIterator = channelName.keySet().iterator();
int channel;
count = 0;
while (channelIterator.hasNext()) {
channel = channelIterator.next();
populateSummaryColumn(fig, data, channel, count);
count++;
}
channelSummaryModel = new ChannelSummaryModel(statNames, channelNames, data);
channelSummaryTable.setModel(channelSummaryModel);
}
/**
* 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));
}
}
/**
* 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;
}
/**
* Populates the table and fields with the data.
*
* @param coord the coordinate of the shape being analysed.
* @param channel the channel to be analysed.
*/
private void populateData(Coord3D coord, int channel) {
channelSummaryTable.setVisible(true);
interpretResults(coord, channel);
populateChannelSummaryTable(coord);
}