com.actelion.research.orbit.imageAnalysis.tasks.SambaMRResultsView 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 dateFormat = new ThreadLocal() {
@Override
protected SimpleDateFormat initialValue() {
return new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
}
};
private String shareName = "spark";
public SambaMRResultsView() throws Exception {
taskList.setCellRenderer(new DefaultListCellRenderer() {
@Override
public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
return super.getListCellRendererComponent(list, task2String((TaskResultGeneric) value), index, isSelected, cellHasFocus);
}
});
taskList.addListSelectionListener(new ListSelectionListener() {
public void valueChanged(ListSelectionEvent arg0) {
updateValues(true);
}
});
refreshBtn.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
updateValues(false);
}
});
fillTaskList();
// layout
setLayout(new BorderLayout());
setBounds(10, 10, 1100, 800);
JPanel upperPanel = new JPanel(new BorderLayout());
upperPanel.add(refreshBtn, BorderLayout.WEST);
upperPanel.add(statusField, BorderLayout.CENTER);
roiAreaCb.setToolTipText("Compute and report the ROI area per image. This might take some time!");
JPanel taskPanel = new JPanel(new BorderLayout());
taskPanel.add(new JScrollPane(taskList), BorderLayout.CENTER);
taskPanel.add(roiAreaCb, BorderLayout.SOUTH);
JSplitPane splitter = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, new JScrollPane(taskPanel), new JScrollPane(resultView));
add(upperPanel, BorderLayout.NORTH);
add(splitter, BorderLayout.CENTER);
setVisible(true);
}
protected void updateValues(final boolean selectionChange) {
if (updating.get()) return;
updating.set(true);
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
try {
setCursor(new Cursor(Cursor.WAIT_CURSOR));
TaskResultGeneric task = (TaskResultGeneric) taskList.getSelectedValue();
if (task == null && (!selectionChange)) { // nothing selected, take last task
task = selectedTask;
}
if (task != null) {
selectedTask = task;
String res = "Results not ready";
try {
fillTaskList();
statusField.setText("Status of task " + task2String(task) + ": " + task.getStatus());
if (task.getStatus() == 0) { // 0 means finished
Map map = task.getResults();
ITaskResultProducer worker = TaskResultProducerFactoryMapReduce.createTaskResultProducer(task.getClassName());
TaskResult taskResult = worker.produceTaskResult(map, roiAreaCb.isSelected());
res = OrbitUtils.text2SmartHtml(taskResult.getResultStr());
} // task finished
} catch (Exception e) {
logger.error("Error retrieving results", e);
}
resultView.setText(res);
resultView.setCaretPosition(0);
resultView.repaint();
}
} finally {
setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
updating.set(false);
}
}
;
});
}
protected void fillTaskList() throws InstantiationException, IllegalAccessException, ClassNotFoundException, SQLException, IOException {
IRemoteContextStore store = DALConfig.getScaleOut().getRemoteContextStore();
List filenames = store.listFilenames(shareName);
DefaultListModel model = new DefaultListModel();
for (String s : filenames) {
System.out.println(s);
byte[] bytes = store.readFromRemote(shareName + "/" + s);
ObjectInputStream ois = null;
try {
ois = new ObjectInputStream(new GZIPInputStream(new ByteArrayInputStream(bytes)));
TaskResultGeneric taskResult = (TaskResultGeneric) ois.readObject();
taskResult.setStringId(s);
model.addElement(taskResult);
} catch (Exception e) {
logger.error("cannot read taskresult", e);
} finally {
if (ois != null) ois.close();
}
}
taskList.setModel(model);
}
public String getShareName() {
return shareName;
}
public void setShareName(String shareName) {
this.shareName = shareName;
}
protected String task2String(TaskResultGeneric task) {
String name = "";
if (task.getClassName() != null) name = task.getClassName();
if (name.contains(".")) name = name.substring(name.lastIndexOf(".") + 1);
//if (task.getNumericId()>0) name += " ("+dateFormat.get().format(new Date(task.getNumericId()))+")";
name += " [" + task.getStringId() + "]";
return name;
}
public static void main(String[] args) throws Exception {
SambaMRResultsView view = new SambaMRResultsView();
view.setVisible(true);
}
}