com.actelion.research.orbit.imageAnalysis.modules.ManualBoxCountModule Maven / Gradle / Ivy
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Orbit, a versatile image analysis software for biological image-based quantification
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2018 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see areaCache = new ConcurrentHashMap();
protected Random rand = new Random();
public ManualBoxCountModule(boolean withGui) {
if (withGui) {
if (OrbitImageAnalysis.getInstance().getLoadedModelFilename().equals("none")) {
JOptionPane.showMessageDialog(this, "No model loaded. Please create or load an appropriate model (see help).", "Please load or create a model", JOptionPane.INFORMATION_MESSAGE);
}
cellRenderer = new SpotCellRenderer();
init2();
addPropertyChangeListener(NumSpotsClassifiedListener.NUMSPOTSCLASSIFIED, new NumSpotsClassifiedListener(100));
}
}
@Override
protected int getClassNumOffset() {
return 0;
}
public void init2() {
list.setCellRenderer(cellRenderer);
list.addKeyListener(new SpotModuleKeyListener());
btnGenerateSpots.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
generateSpots(true);
}
});
btnShowStatistics.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
showStatistics();
}
});
btnSaveSpots.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
saveSpots(true);
}
});
btnLoadSpots.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
loadSpots();
}
});
list.addListSelectionListener(new ListSelectionListener() {
public void valueChanged(ListSelectionEvent e) {
final ImageFrame iFrame = OrbitImageAnalysis.getInstance().getIFrame();
if (list.getSelectedValue() != null && iFrame != null) {
ImageAnnotation ann = (ImageAnnotation) list.getSelectedValue();
PolygonExt shape = (PolygonExt) ann.getShape().getShapeList().get(0);
Rectangle bb = shape.getScaledInstance(100, new Point(0, 0)).getBounds();
double sc = iFrame.recognitionFrame.getScale() / 100d;
final Point targetP = new Point((int) (bb.getCenterX() * sc) - iFrame.recognitionFrame.getWidth() / 2, (int) (bb.getCenterY() * sc) - iFrame.recognitionFrame.getHeight() / 2);
// set annotation as selected for highlightning in recognitionframe and unset all others
for (ImageAnnotation annotation : iFrame.getRecognitionFrame().getAnnotations()) {
if (annotation instanceof SpotAnnotation) {
annotation.setSelected(false);
}
}
if (ann instanceof SpotAnnotation) {
ann.setSelected(true);
}
iFrame.setViewPortPositionAndAdjust(targetP);
}
}
}
);
// layout
JMenuBar menuBar = new JMenuBar();
JMenu menu = new JMenu("Spots");
JMenuItem item = new JMenuItem("Remove Selected");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
removeSpots();
repaintFrameAndList();
}
});
menu.add(item);
item = new JMenuItem("Remove in ROI");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
removeSpotsInROI();
repaintFrameAndList();
}
});
menu.add(item);
menu.addSeparator();
item = new JMenuItem("Reset all Boxes");
item.setToolTipText("set class to 'undefined'");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
resetAllSpots();
}
});
menu.add(item);
menuBar.add(menu);
menu = new JMenu("Sort");
item = new JMenuItem("Shuffle");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
shuffle();
}
});
menu.add(item);
item = new JMenuItem("Sort by Class");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
sortByClass(false);
}
});
menu.add(item);
menuBar.add(menu);
menu = new JMenu("Help");
item = new JMenuItem("Show Help");
item.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
showHelp();
}
});
menu.add(item);
menuBar.add(menu);
JPanel mainPanel = new JPanel();
mainPanel.setLayout(new GridBagLayout());
JScrollPane scrollPane = new JScrollPane(list, JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
mainPanel.add(scrollPane, new GridBagConstraints(0, 0, GridBagConstraints.REMAINDER, 1, 0, 1, GridBagConstraints.NORTHWEST, GridBagConstraints.BOTH, new Insets(1, 1, 0, 1), 0, 0));
mainPanel.add(btnGenerateSpots, new GridBagConstraints(0, 1, 1, 1, 1, 0, GridBagConstraints.SOUTHWEST, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
mainPanel.add(btnShowStatistics, new GridBagConstraints(1, 1, 1, 1, 1, 0, GridBagConstraints.SOUTHEAST, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
mainPanel.add(btnLoadSpots, new GridBagConstraints(0, 2, 1, 1, 1, 0, GridBagConstraints.SOUTHWEST, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
mainPanel.add(btnSaveSpots, new GridBagConstraints(1, 2, 1, 1, 1, 0, GridBagConstraints.SOUTHEAST, GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
setLayout(new BorderLayout());
add(menuBar, BorderLayout.NORTH);
add(mainPanel, BorderLayout.CENTER);
}
protected void sortByClass(final boolean useProposedClass) {
DefaultListModel listModel = (DefaultListModel) list.getModel();
List annotationList = new ArrayList(listModel.size());
for (int i = 0; i < listModel.getSize(); i++) {
SpotAnnotation annotation = (SpotAnnotation) listModel.get(i);
annotationList.add(annotation);
}
Collections.sort(annotationList, new Comparator() {
public int compare(SpotAnnotation o1, SpotAnnotation o2) {
if (useProposedClass)
return o1.getProposedClassNum() - o2.getProposedClassNum();
else return o1.getClassNum() - o2.getClassNum(); // real class
}
});
clear();
DefaultListModel newModel = new DefaultListModel();
for (SpotAnnotation annotation : annotationList) {
newModel.addElement(annotation);
}
list.setModel(newModel);
}
private void showHelp() {
final OrbitImageAnalysis oia = OrbitImageAnalysis.getInstance();
String color = OrbitUtils.DARKUI ? " color=white" : "";
String h = "" +
"Manual Box Count Module
" +
"Prerequisites
" +
"" +
"- Create (F4) or load an appropriate model. The model should contain count classes, e.g. class names from '0' till '9'.
" +
"- Load an image from Orbit
" +
"- Activate the manual box count module (Tools->Manuel Box Count Module)
" +
"
" +
"Create Count Boxes
" +
"" +
"- Create annotations on the image where you want to count (if not already done).
" +
"- Click the 'Generate' button. Enter the box size and the percentage and click 'ok'. The percentage will be the percentage areawhich will be covert by the boxes in each annotation. Ensure that the box size is small enough that Orbit is able is place enough boxes.
" +
"
" +
"Load Existing Boxes
" +
"" +
"- Click on the 'Load' button to see if already detected boxes have been persisted and load them.
" +
"
" +
"Count Objects in Boxes
" +
"" +
"- Click on the first box entry in the list.
" +
"- Use the keyboard and press a number (e.g. 0-9) to assign a count number to the selected box.
The selection will automatically jump to the next box. By holding down the ctrl key you can prevent this and the selection will stay on the selected item. " +
"- With backspace you can mark spots as unseen (undefined).
" +
"- Once you think you counted enough boxes, click on 'Statistics' to retrieve a statistic.
" +
"- Click on 'Save' to persist your boxes and counts. You can always continue the quantification by pressing the 'Load' button after you opened the same image.
" +
"
" +
"