com.actelion.research.orbit.imageAnalysis.components.AdjustPanel 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 ;con:;r:;g;b;gamma:;deconvChan:;deconvName:
*
* @param vals
*/
public void setAdjustmentValues(String vals) {
OrbitUtils.ImageAdjustments ia = OrbitUtils.parseImageAdjustments(vals);
brightnessSlider.setValue(ia.getBrightness());
contrastSlider.setValue(ia.getContrast());
redSlider.setValue(ia.getRed());
greenSlider.setValue(ia.getGreen());
blueSlider.setValue(ia.getBlue());
gammaSlider.setValue(ia.getGamma());
redCb.setSelected(true);
greenCb.setSelected(true);
blueCb.setSelected(true);
deconvCb.setSelectedItem(ia.getDeconvName());
deconvChannel0.setSelected(true);
if (ia.getDeconvChannel() == 1) deconvChannel1.setSelected(true);
if (ia.getDeconvChannel() == 2) deconvChannel2.setSelected(true);
if (ia.getDeconvChannel() == 3) deconvChannel3.setSelected(true);
}
/**
* returns bri:;con:;r:;g;b
* for storing the string as a meta value
*
* @return
*/
private String adjustmentsToString() {
String deconvName = Colour_Deconvolution.DECONV_NONE;
if (deconvCb.getSelectedItem() != null) deconvName = (String) deconvCb.getSelectedItem();
int deconvChannel = 0;
if (deconvChannel1.isSelected()) deconvChannel = 1;
if (deconvChannel2.isSelected()) deconvChannel = 2;
if (deconvChannel3.isSelected()) deconvChannel = 3;
String channelContributions = "";
IOrbitImageMultiChannel oim = getMultiChannelImage();
if (oim!=null) {
if (oim.getChannelContributions()!=null && oim.getChannelContributions().length>0) {
for (int c=0; c0) {
s += ";channelContributions:"+channelContributions;
}
System.out.println("s: "+s);
return s;
}
private boolean saveAdjustments() {
OrbitImageAnalysis.getInstance().forceLogin();
if (OrbitImageAnalysis.loginOk) {
ImageFrame iFrame = OrbitImageAnalysis.getInstance().getIFrame();
if (iFrame != null && iFrame.getRdf() != null) {
try {
String vals = adjustmentsToString();
List rms = DALConfig.getImageProvider().LoadRawMetasByRawDataFileAndName(iFrame.getRdf().getRawDataFileId(), RawUtilsCommon.STR_META_IMAGEADJUSTMENTS);
if (rms != null && rms.size() > 0) { // update
RawMeta rm = rms.get(0);
rm.setModifyDate(new Date());
rm.setUserId(OrbitImageAnalysis.loginUser);
rm.setValue(vals);
DALConfig.getImageProvider().UpdateRawMeta(rm);
logger.debug("Image adjustments updated in database. RawMeta: " + rm);
} else { // insert
RawMetaFactoryFile rmff = new RawMetaFactoryFile(iFrame.getRdf().getRawDataFileId(), new Date(), OrbitImageAnalysis.loginUser);
RawMeta rm = rmff.createMetaStr(RawUtilsCommon.STR_META_IMAGEADJUSTMENTS, vals);
DALConfig.getImageProvider().InsertRawMeta(rm);
logger.debug("Image adjustments saved to database. RawMeta: " + rm);
}
JOptionPane.showMessageDialog(this, "Image adjustments successfully saved.", "Image Adjustments Saved", JOptionPane.INFORMATION_MESSAGE);
return true;
} catch (Exception e) {
logger.error("cannot insert or update raw meta into database", e);
return false;
}
} else {
logger.error("Cannot save image adjustment data because image is not stored in the Orbit database or no image is selected.");
return false;
}
} else {
logger.debug("Image adjustments not saved because Orbit login is not ok or canceled.");
return false;
}
}
private IOrbitImageMultiChannel getMultiChannelImage() {
ImageFrame iFrame = OrbitImageAnalysis.getInstance().getIFrame();
if (iFrame!=null) {
OrbitTiledImage2 img = iFrame.recognitionFrame.bimg.getImage();
if (img instanceof OrbitTiledImageIOrbitImage) {
IOrbitImage oi = ((OrbitTiledImageIOrbitImage) img).getOrbitImage();
if (oi instanceof IOrbitImageMultiChannel) {
final IOrbitImageMultiChannel oim = (IOrbitImageMultiChannel) oi;
return oim;
}
}
}
return null;
}
private List getMultiChannelImages() {
List images = new ArrayList<>();
List iFrames = OrbitImageAnalysis.getInstance().getIFrames();
if (iFrames!=null) {
for (ImageFrame iFrame : iFrames) {
OrbitTiledImage2 img = iFrame.recognitionFrame.bimg.getImage();
if (img instanceof OrbitTiledImageIOrbitImage) {
IOrbitImage oi = ((OrbitTiledImageIOrbitImage) img).getOrbitImage();
if (oi instanceof IOrbitImageMultiChannel) {
final IOrbitImageMultiChannel oim = (IOrbitImageMultiChannel) oi;
images.add(oim);
}
}
}
}
return images;
}
public boolean loadAdjustments(final ImageFrame iFrame) {
boolean adjustmentsSet = false;
// other adjustments
if (iFrame != null && iFrame.getRdf() != null) {
try {
List rms = DALConfig.getImageProvider().LoadRawMetasByRawDataFileAndName(iFrame.getRdf().getRawDataFileId(), RawUtilsCommon.STR_META_IMAGEADJUSTMENTS);
if (rms != null && rms.size() > 0) {
RawMeta rm = rms.get(0);
setAdjustmentValues(rm.getValue());
logger.debug("Image adjustments loaded. RawMeta: " + rm);
iFrame.recognitionFrame.bimg.setBrightness(brightnessSlider.getValue());
iFrame.recognitionFrame.bimg.setContrast(contrastSlider.getValue());
iFrame.recognitionFrame.bimg.setRedAdjust(redSlider.getValue());
iFrame.recognitionFrame.bimg.setGreenAdjust(greenSlider.getValue());
iFrame.recognitionFrame.bimg.setBlueAdjust(blueSlider.getValue());
iFrame.recognitionFrame.bimg.setGamma(gammaSlider.getValue());
if (deconvCb.getSelectedItem() != null)
iFrame.recognitionFrame.bimg.setDeconvName((String) deconvCb.getSelectedItem());
if (deconvChannel0.isSelected()) iFrame.recognitionFrame.bimg.setDeconvChannel(0);
if (deconvChannel1.isSelected()) iFrame.recognitionFrame.bimg.setDeconvChannel(1);
if (deconvChannel2.isSelected()) iFrame.recognitionFrame.bimg.setDeconvChannel(2);
if (deconvChannel3.isSelected()) iFrame.recognitionFrame.bimg.setDeconvChannel(3);
// channel contributions
OrbitUtils.ImageAdjustments ia = OrbitUtils.parseImageAdjustments(rm.getValue());
if (ia!=null) {
IOrbitImageMultiChannel oim = getMultiChannelImage();
if (!iFrame.isChannelContributionsLoaded() && oim!=null) {
iFrame.setChannelContributionsLoaded(true);
oim.setChannelContributions(ia.getChannelContributions());
}
}
} else adjustmentsSet = false;
adjustmentsSet = true;
} catch (Exception e) {
logger.error("Cannot load image adjustment meta data from database", e);
}
}
// add multichannel components
if (iFrame!=null) {
OrbitTiledImage2 img = iFrame.recognitionFrame.bimg.getImage();
if (img instanceof OrbitTiledImageIOrbitImage) {
IOrbitImage oi = ((OrbitTiledImageIOrbitImage) img).getOrbitImage();
if (oi instanceof IOrbitImageMultiChannel) {
final IOrbitImageMultiChannel oim = (IOrbitImageMultiChannel) oi;
if (oim.getChannelNames()!=null && oim.getChannelNames().length>0) {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
multiChannelPanel.removeAll();
JLabel fluoLabel = new JLabel("Fluorescence Channels:");
Box b1 = Box.createHorizontalBox();
b1.setBorder(BorderFactory.createEmptyBorder(13,0,7,0));
b1.add(fluoLabel);
b1.add(Box.createHorizontalGlue());
multiChannelPanel.add(b1);
JPanel cp = new JPanel(new GridBagLayout());
Insets insetsL = new Insets(5, 5, 0, 5);
Insets insetsCP = new Insets(6, 5, 0, 5);
Insets insets = new Insets(0, 5, 0, 5);
int y = 0;
final float multiplier = 0.01f;
for (int c=0; c