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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 rms = DALConfig.getImageProvider().LoadRawMetasByRawDataFileAndName(getRdf().getRawDataFileId(), STR_CHANNELS_META);
if (rms != null && rms.size() > 0) { // update
RawMeta rm = rms.get(0);
rm.setModifyDate(new Date());
rm.setUserId(OrbitImageAnalysis.loginUser);
rm.setValue(vals);
if (DALConfig.getImageProvider().UpdateRawMeta(rm) && vals != null && vals.length() > 0) {
rdf.setFlagBit(RawDataFile.Flag_HAS_LINKED_CHANNELS);
DALConfig.getImageProvider().UpdateRawDataFile(rdf);
}
logger.debug("Channels updated in database. RawMeta: " + rm);
} else { // insert
RawMetaFactoryFile rmff = new RawMetaFactoryFile(getRdf().getRawDataFileId(), new Date(), OrbitImageAnalysis.loginUser);
RawMeta rm = rmff.createMetaStr(STR_CHANNELS_META, vals);
if (DALConfig.getImageProvider().InsertRawMeta(rm) > 0) {
// successful, so set flag in rdf
rdf.setFlagBit(RawDataFile.Flag_HAS_LINKED_CHANNELS);
DALConfig.getImageProvider().UpdateRawDataFile(rdf);
}
logger.debug("Channels saved to database. RawMeta: " + rm);
}
JOptionPane.showMessageDialog(this, "Channels successfully saved.", "Channels Saved", JOptionPane.INFORMATION_MESSAGE);
return true;
} catch (Exception e) {
logger.error("cannot insert or update raw meta into database", e);
return false;
}
} else {
logger.debug("Channels not saved because Orbit login is not ok or canceled.");
return false;
}
}
public boolean removeChannels() {
OrbitImageAnalysis.getInstance().forceLogin();
if (OrbitImageAnalysis.loginOk) {
try {
//String vals = channelsToString();
List rms = DALConfig.getImageProvider().LoadRawMetasByRawDataFileAndName(getRdf().getRawDataFileId(), STR_CHANNELS_META);
if (rms != null && rms.size() > 0) {
for (RawMeta rm : rms) {
if (DALConfig.getImageProvider().DeleteRawMeta(rm.getRawMetaId())) {
logger.debug("RawMeta deleted: " + rm.getRawMetaId());
// successful, so unset has linked channels flag
rdf.unsetFlagBit(RawDataFile.Flag_HAS_LINKED_CHANNELS);
DALConfig.getImageProvider().UpdateRawDataFile(rdf);
}
}
}
// unset channels
recognitionFrame.bimg.setRedChannel(null);
recognitionFrame.bimg.setGreenChannel(null);
recognitionFrame.bimg.setBlueChannel(null);
recognitionFrame.bimg.setRedChannelRdfId(0);
recognitionFrame.bimg.setGreenChannelRdfId(0);
recognitionFrame.bimg.setBlueChannelRdfId(0);
repaint();
JOptionPane.showMessageDialog(this, "Channels successfully removed.", "Channels Removed", JOptionPane.INFORMATION_MESSAGE);
return true;
} catch (Exception e) {
logger.error("cannot remove raw meta from database", e);
return false;
}
} else {
logger.debug("Channels not removed because Orbit login is not ok or canceled.");
return false;
}
}
public void loadChannels() {
if (rdf == null) return;
try {
List channelMeta = DALConfig.getImageProvider().LoadRawMetasByRawDataFileAndName(getRdf().getRawDataFileId(), STR_CHANNELS_META);
if ((!ScaleoutMode.SCALEOUTMODE.get()) && channelMeta != null && channelMeta.size() > 0) {
if (JOptionPane.showConfirmDialog(this,
"Linked channels (red/green/blue) found. Do you want to load and link the channels?",
"Load Linked Channels?", JOptionPane.YES_NO_OPTION)
== JOptionPane.YES_OPTION) {
String[] vals = channelMeta.get(0).getValue().split(",");
if (vals != null && vals.length >= 3) {
for (String val : vals) {
String[] split = val.split(":");
String channel = split[0];
int rdfId = Integer.parseInt(split[1]);
if (rdfId > 0) {
loadChannel(rdfId, channel);
repaint();
}
}
}
} // really load?
}
} catch (Exception e) {
logger.error("error loading channel meta data", e);
}
}
private void loadChannel(int rdfId, String channel) {
try {
RawDataFile rdf = DALConfig.getImageProvider().LoadRawDataFile(rdfId);
String ch = "red";
if (channel.equalsIgnoreCase("g")) ch = "green";
if (channel.equalsIgnoreCase("b")) ch = "blue";
if (channel.equalsIgnoreCase("o")) ch = "overlay";
OrbitImageAnalysis.getInstance().loadFile(rdf, rdf.getFileName() + " [" + ch + "]", false);
RecognitionFrame rf = new RecognitionFrame(rdf, false);
if (channel.equalsIgnoreCase("r")) {
setTIPChannel(recognitionFrame.bimg, rdfId, rf.bimg, TiledImagePainter.CHANNEL_RED);
} else if (channel.equalsIgnoreCase("g")) {
setTIPChannel(recognitionFrame.bimg, rdfId, rf.bimg, TiledImagePainter.CHANNEL_GREEN);
} else if (channel.equalsIgnoreCase("b")) {
setTIPChannel(recognitionFrame.bimg, rdfId, rf.bimg, TiledImagePainter.CHANNEL_BLUE);
} else if (channel.equalsIgnoreCase("o")) {
setTIPChannel(recognitionFrame.bimg, rdfId, rf.bimg, TiledImagePainter.CHANNEL_OVERLAY);
}
} catch (Exception e) {
logger.error("error loading channel", e);
}
}
private void setTIPChannel(TiledImagePainter tip, int rdfId, TiledImagePainter channel, int chanNr) {
tip.setChannelRdfId(rdfId, chanNr);
tip.setChannel(channel.getImage(), chanNr);
// TODO remove work around
if (OrbitImageAnalysis.getInstance().loadAllLayersMultiChannel.isSelected()) {
if (tip.hasMipMaps()) {
for (int i = 0; i < tip.getMipMaps().length; i++) {
tip.getMipMaps()[i].setChannelRdfId(rdfId, chanNr);
tip.getMipMaps()[i].setChannel(channel.getMipMaps()[i].getImage(), chanNr);
}
}
}
}
private String channelsToString() {
return "r:" + recognitionFrame.bimg.getRedChannelRdfId()
+ ",g:" + recognitionFrame.bimg.getGreenChannelRdfId()
+ ",b:" + recognitionFrame.bimg.getBlueChannelRdfId()
+ ",o:" + recognitionFrame.bimg.getOverlayChannelRdfId();
}
public void componentHidden(ComponentEvent e) {
}
public void componentMoved(ComponentEvent e) {
}
public void componentResized(ComponentEvent e) {
if (recognitionFrame != null) {
recognitionFrame.setViewPortSize(getSize());
recognitionFrame.prepareBuffer();
recognitionFrame.repaint();
}
if (renderGrid != null) {
renderGrid.setViewportSize(getSize());
if (recognitionFrame != null)
renderGrid.setViewportPosition(recognitionFrame.getViewPortOffset());
renderGrid.repaint();
}
}
public void componentShown(ComponentEvent e) {
}
@Override
public Point getMousePosition() throws HeadlessException {
if (!exclusive) return super.getMousePosition();
else
return MouseInfo.getPointerInfo().getLocation(); // e.g. in fullscreen mode
}
@Override
public Dimension getSize() {
if (!exclusive) return super.getSize();
else {
// exclusive
return Toolkit.getDefaultToolkit().getScreenSize();
}
}
public RecognitionFrame getRecognitionFrame() {
return recognitionFrame;
}
public void setRecognitionFrame(RecognitionFrame recognitionFrame) {
this.recognitionFrame = recognitionFrame;
}
public RenderGrid getRenderGrid() {
return renderGrid;
}
public void setRenderGrid(RenderGrid renderGrid) {
this.renderGrid = renderGrid;
}
public JSlider getOpacitySlider() {
return opacitySlider;
}
public void setOpacitySlider(JSlider opacitySlider) {
this.opacitySlider = opacitySlider;
}
public RawDataFile getRdf() {
return rdf;
}
public void setRdf(RawDataFile rdf) {
this.rdf = rdf;
}
public boolean isExclusive() {
return exclusive;
}
public void setExclusive(boolean exclusive) {
this.exclusive = exclusive;
}
public int getMipLayer() {
return mipLayer;
}
public void setMipLayer(int mipLayer) {
this.mipLayer = mipLayer;
}
public boolean isChannelContributionsLoaded() {
return channelContributionsLoaded;
}
public void setChannelContributionsLoaded(boolean channelContributionsLoaded) {
this.channelContributionsLoaded = channelContributionsLoaded;
}
}