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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 classList = new ArrayList();
//classList.add("");
String selected = "";
OrbitModel model = OrbitImageAnalysis.getInstance().getModel();
if (model != null) {
OrbitModel classModel = model;
if (model.getSegmentationModel() != null) classModel = model.getSegmentationModel();
int i = 0;
for (ClassShape cs : classModel.getClassShapes()) {
String cleanCS = cs.getName().replaceAll(";", ",");
classList.add(cleanCS);
if (featureDescription.getFeatureClasses() != null) {
for (int fc : featureDescription.getFeatureClasses()) {
if (i == fc) {
selected += cleanCS + "; ";
}
}
}
i++;
}
}
cbFeatureClasses = new JComboCheckBox(classList);
cbFeatureClasses.setText(selected);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Classes for retrieving features/histograms:");
panel.add(lab);
panel.add(cbFeatureClasses);
setCompBounds(panel, frameWidth - 50, 0);
panelClassification.add(panel);
// fluo channels
if (featureDescription.getActiveFluoChannels()!=null) {
setCbActiveFluoChannels(featureDescription.getActiveFluoChannels());
}
else {
IOrbitImageMultiChannel multiChanImage = getOpenMultiChannelImage();
if (multiChanImage!=null && multiChanImage.getChannelNames()!=null && multiChanImage.getChannelNames().length>0) {
setCbActiveFluoChannels(multiChanImage.getChannelNames());
}
}
if (cbFluoChannels==null)
cbFluoChannels = new JComboCheckBox();
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Active fluorescence channels:");
panel.add(lab);
panel.add(cbFluoChannels);
setCompBounds(panel, frameWidth - 50, 0);
panelClassification.add(panel);
tabs.add("Classification", panelClassification);
// segmentation
JPanel panelSegmentation = new JPanel();
panelSegmentation.setLayout(new FlowLayout(FlowLayout.LEFT, 20, 15));
final OrbitModel modelFin = model;
cbForSecondarySegmentationModel = new JCheckBox("Set Features for Secondary Segmentation", featureDescription.isForSecondarySegmentationModel());
cbForSecondarySegmentationModel.setToolTipText("set the segmentation features for the secondary segmentation model");
cbForSecondarySegmentationModel.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
// attention: we use always the segmentation model for feature description!!! (this might go wrong...)
if (modelFin.getSegmentationModel() != null) {
FeatureDescription fd = modelFin.getSegmentationModel().getFeatureDescription();
if (cbForSecondarySegmentationModel.isSelected() && modelFin.getSecondarySegmentationModel() != null) {
fd = modelFin.getSecondarySegmentationModel().getFeatureDescription();
}
updateValues(fd);
}
}
});
setCompBounds(cbForSecondarySegmentationModel, frameWidth, 0);
panelSegmentation.add(cbForSecondarySegmentationModel);
cbCytoplasmaSegmentation = new JCheckBox("Cytoplasma Segmentation", featureDescription.isCytoplasmaSegmentation());
cbCytoplasmaSegmentation.setToolTipText("performs a cytoplasma segmentation based on a nuclei staining");
setCompBounds(cbCytoplasmaSegmentation, frameWidth, 0);
panelSegmentation.add(cbCytoplasmaSegmentation);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Minimum segmentation size:");
panel.add(lab);
tfMinSegmentationSize = new JTextField();
tfMinSegmentationSize.setText(Integer.toString(featureDescription.getMinSegmentationSize()));
tfMinSegmentationSize.setInputVerifier(new IntInputVerifier(3, 1, 2000));
tfMinSegmentationSize.setToolTipText("the minimum area (in pixel) a segmented object must have");
tfMinSegmentationSize.setColumns(4);
panel.add(tfMinSegmentationSize);
setCompBounds(panel, frameWidth - 50, 0);
panelSegmentation.add(panel);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Maximum segmentation length:");
panel.add(lab);
tfMaxSegmentationLength = new IntegerTextField(featureDescription.getMaxSegmentationLength(), 500, 5, 20000);
tfMaxSegmentationLength.setText(Integer.toString(featureDescription.getMaxSegmentationLength()));
tfMaxSegmentationLength.setToolTipText("the maximum border path-length (in pixel) a segmented cell can have");
tfMaxSegmentationLength.setHorizontalAlignment(JTextField.LEFT);
tfMaxSegmentationLength.setColumns(4);
panel.add(tfMaxSegmentationLength);
setCompBounds(panel, frameWidth - 50, 0);
panelSegmentation.add(panel);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Maximum open distance:");
panel.add(lab);
tfMaxOpenDistance = new IntegerTextField(featureDescription.getMaxOpenDistance(), 3, 0, 100);
tfMaxOpenDistance.setText(Integer.toString(featureDescription.getMaxOpenDistance()));
tfMaxOpenDistance.setToolTipText("maximum distance (in pixel) between start and end of the path of an object");
tfMaxOpenDistance.setHorizontalAlignment(JTextField.LEFT);
tfMaxOpenDistance.setColumns(4);
panel.add(tfMaxOpenDistance);
setCompBounds(panel, frameWidth - 50, 0);
panelSegmentation.add(panel);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Segmentation scale factor:");
panel.add(lab);
tfSegmentationScale = new DoubleTextField(1, 1, 0.1, 10);
tfSegmentationScale.setHorizontalAlignment(JTextField.LEFT);
tfSegmentationScale.setText(featureDescription.getSegmentationScale() + "");
tfSegmentationScale.setColumns(4);
panel.add(tfSegmentationScale);
setCompBounds(panel, frameWidth - 50, 0);
panelSegmentation.add(panel);
cbDisableWatershed = new JCheckBox("Disable object splitting", featureDescription.isDisableWatershed());
cbDisableWatershed.setToolTipText("disable splitting of overlapping objects (do not apply watershed algorithm)");
setCompBounds(cbDisableWatershed, frameWidth, 0);
panelSegmentation.add(cbDisableWatershed);
cbDoCombineCrossTiles = new JCheckBox("Combine cross tile objects (slow)", featureDescription.isCombineObjectsCrossTiles());
cbDoCombineCrossTiles.setToolTipText("combine objects across tiles");
setCompBounds(cbDoCombineCrossTiles, frameWidth, 0);
panelSegmentation.add(cbDoCombineCrossTiles);
cbFilterTileEdgeShapes = new JCheckBox("Discard tile border objects", featureDescription.isFilterTileEdgeShapes());
cbFilterTileEdgeShapes.setToolTipText("discards objects at tile borders, e.g. objects which are divided by tiles");
setCompBounds(cbFilterTileEdgeShapes, frameWidth, 0);
panelSegmentation.add(cbFilterTileEdgeShapes);
panel = new JPanel(new GridLayout(1, 2));
cbMFS = new JCheckBox("Mumford-Shah segmentation (cell clusters):",featureDescription.isMumfordShahSegmentation());
cbMFS.setToolTipText("enable mumford-shah segmentation (good for cell clusters)");
cbMFS.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
if (cbMFS.isSelected() && !cbDisableWatershed.isSelected()) {
cbDisableWatershed.setSelected(true);
JOptionPane.showMessageDialog(FeaturesAdminFrame.this,"Mumford-Shah segmentation has its own object splitting algorithm, thus the additional object splitting has been disabled.\nHowever, you can enable it again in addition and try if the additional splitting (watershed algorithm) gives better results.","Additional object splitting has been disabled",JOptionPane.INFORMATION_MESSAGE);
}
}
});
panel.add(cbMFS);
JPanel mfsParamPanel = new JPanel();
mfsParamPanel.setBorder(BorderFactory.createEmptyBorder());
JPanel mfsSizePanel = new JPanel();
mfsSizePanel.setBorder(BorderFactory.createEmptyBorder());
JLabel mfsSizeLabel = new JLabel("Obj size [px]");
mfsSizeLabel.setToolTipText("Expected size of objects in pixels. Smaller values will split objects more frequently.");
tfMFSCellSize = new IntegerTextField(18, 18, 1, 1000);
tfMFSCellSize.setHorizontalAlignment(JTextField.LEFT);
tfMFSCellSize.setInt(featureDescription.getMumfordShahCellSize());
tfMFSCellSize.setColumns(3);
mfsSizePanel.add(mfsSizeLabel);
mfsSizePanel.add(tfMFSCellSize);
mfsParamPanel.add(mfsSizePanel);
JPanel mfsAlphaPanel = new JPanel();
mfsAlphaPanel.setBorder(BorderFactory.createEmptyBorder());
JLabel mfsAlphaLabel = new JLabel("Intens split [1-50]");
mfsAlphaLabel.setToolTipText("Object splitting based on intensity. Smaller values will split objects more frequently.\nRecommended range: [1,50], allowed range: [1,255].\n"+
"This value corresponds to the alpha value of the mumford-shah functional which is responsible for the smoothing of the image.\nHigher values will smooth the image more and thus split objects less.");
tfMFSAlpha = new IntegerTextField(5, 5, 1, 255);
tfMFSAlpha.setHorizontalAlignment(JTextField.LEFT);
tfMFSAlpha.setInt(featureDescription.getMumfordShahAlpha());
tfMFSAlpha.setColumns(3);
mfsAlphaPanel.add(mfsAlphaLabel);
mfsAlphaPanel.add(tfMFSAlpha);
mfsParamPanel.add(mfsAlphaPanel);
panel.add(mfsParamPanel);
setCompBounds(panel, frameWidth - 50, 0);
panel.setPreferredSize(new Dimension((int)panel.getPreferredSize().getWidth(),(int)mfsAlphaPanel.getPreferredSize().getHeight()));
panelSegmentation.add(panel);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Dilate:");
panel.add(lab);
tfNumDilate = new IntegerTextField(featureDescription.getNumDilate(), 10, 0, 10);
tfNumDilate.setText(Integer.toString(featureDescription.getNumDilate()));
tfNumDilate.setToolTipText("dilate foreground before object segmentation");
tfNumDilate.setHorizontalAlignment(JTextField.LEFT);
tfNumDilate.setColumns(4);
panel.add(tfNumDilate);
setCompBounds(panel, frameWidth - 50, 0);
panelSegmentation.add(panel);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Erode:");
panel.add(lab);
tfNumErode = new IntegerTextField(featureDescription.getNumErode(), 10, 0, 10);
tfNumErode.setText(Integer.toString(featureDescription.getNumErode()));
tfNumErode.setToolTipText("erode foreground before object segmentation");
tfNumErode.setHorizontalAlignment(JTextField.LEFT);
tfNumErode.setColumns(4);
panel.add(tfNumErode);
setCompBounds(panel, frameWidth - 50, 0);
panelSegmentation.add(panel);
cbDilateBeforeErode = new JCheckBox("Dilate before erode", featureDescription.isDilateBeforeErode());
cbDilateBeforeErode.setToolTipText("otherwise erode before dilate");
setCompBounds(cbDilateBeforeErode, frameWidth, 0);
panelSegmentation.add(cbDilateBeforeErode);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Despeckle: [0-50]");
panel.add(lab);
tfRemoveOutliers = new IntegerTextField(featureDescription.getRemoveOutliers(), 0, 0, 50);
tfRemoveOutliers.setText(Integer.toString(featureDescription.getRemoveOutliers()));
tfRemoveOutliers.setToolTipText("despeckle foerground before object segmentation (remove outliers)");
tfRemoveOutliers.setHorizontalAlignment(JTextField.LEFT);
tfRemoveOutliers.setColumns(4);
panel.add(tfRemoveOutliers);
setCompBounds(panel, frameWidth - 50, 0);
panelSegmentation.add(panel);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Smooth objects (GraphCut): [0-100]");
panel.add(lab);
tfGraphCut = new DoubleTextField(featureDescription.getGraphCut(), 10, 0, 100);
tfGraphCut.setText(Double.toString(featureDescription.getGraphCut()));
tfGraphCut.setToolTipText("smooth objects and fill holes");
tfGraphCut.setHorizontalAlignment(JTextField.LEFT);
tfGraphCut.setColumns(4);
panel.add(tfGraphCut);
setCompBounds(panel, frameWidth - 50, 0);
panelSegmentation.add(panel);
cbNerveDetectionMode = new JCheckBox("Nerve Detection Mode", featureDescription.isDeactivateWatershed()); // large object detection
cbNerveDetectionMode.setToolTipText("activate for nerve detection (large object detection)");
setCompBounds(cbNerveDetectionMode, frameWidth, 0);
panelSegmentation.add(cbNerveDetectionMode);
tabs.add("Segmentation", panelSegmentation);
// roi
JPanel panelROI = new JPanel();
panelROI.setLayout(new FlowLayout(FlowLayout.LEFT, 20, 15));
List annotationGroups = new ArrayList(12);
annotationGroups.add(new AnnotationGroupLabel(-1, "Ignore"));
annotationGroups.add(new AnnotationGroupLabel(0, "All Groups"));
for (int g = 1; g < (OrbitUtils.ANNOTATION_GROUPS + 1); g++)
annotationGroups.add(new AnnotationGroupLabel(g, "Group " + g));
cbAnnotationROI = new JComboBox(annotationGroups.toArray(new AnnotationGroupLabel[0]));
cbAnnotationROI.setSelectedIndex(0);
int groupIdx = OrbitImageAnalysis.getInstance().getModel().getAnnotationGroup() + 1; // +1 because 'ignore' is -1
if (cbAnnotationROI.getItemCount() > groupIdx)
cbAnnotationROI.setSelectedIndex(groupIdx);
cbAnnotationROI.setToolTipText("Use annotations (excl/incl/ROI) to build the ROI?");
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Use annotations as ROI:");
panel.add(lab);
panel.add(cbAnnotationROI);
setCompBounds(panel, frameWidth - 50, 0);
panelROI.add(panel);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("Fixed circular ROI (pixel):");
panel.add(lab);
tfFixedROI = new JTextField();
tfFixedROI.setText(Integer.toString(OrbitImageAnalysis.getInstance().getModel().getFixedCircularROI()));
tfFixedROI.setInputVerifier(new IntInputVerifier(0));
panel.add(tfFixedROI);
setCompBounds(panel, frameWidth - 50, 0);
panelROI.add(panel);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("ROI offset X:");
panel.add(lab);
tfROIX = new JTextField();
tfROIX.setText(Integer.toString(OrbitImageAnalysis.getInstance().getModel().getFixedROIOffsetX()));
tfROIX.setInputVerifier(new IntInputVerifier(0));
panel.add(tfROIX);
setCompBounds(panel, frameWidth - 50, 0);
panelROI.add(panel);
panel = new JPanel(new GridLayout(1, 2));
lab = new JLabel("ROI offset Y:");
panel.add(lab);
tfROIY = new JTextField();
tfROIY.setText(Integer.toString(OrbitImageAnalysis.getInstance().getModel().getFixedROIOffsetY()));
tfROIY.setInputVerifier(new IntInputVerifier(0));
panel.add(tfROIY);
setCompBounds(panel, frameWidth - 50, 0);
panelROI.add(panel);
tabs.add("ROI", panelROI);
// image adjustments
JPanel panelImageAdjustments = new JPanel();
panelImageAdjustments.setLayout(new FlowLayout(FlowLayout.LEFT, 20, 15));
cbUseImageAdjustments = new JCheckBox("Use image adjustments *", featureDescription.isUseImageAdjustments());
cbUseImageAdjustments.setToolTipText("load image adjustments from database before classification (brightness, contrast, gamma) - use with care!");
setCompBounds(cbUseImageAdjustments, frameWidth, 0);
panelImageAdjustments.add(cbUseImageAdjustments);
JLabel imageAdjustmentWarning = new JLabel("* If activated, image adjustments like gamma, brightness and contrast from the image
adjustment panel are taken into account." +
"
Please use it with care, because it will influence the quantification results,
thus you might get an unwanted bias." +
"
If you really want to use it, please double-check that the image adjustments are saved.");
panelImageAdjustments.add(imageAdjustmentWarning);
tabs.add("Image Adjustments", panelImageAdjustments);
// layout
setLayout(new BorderLayout());
add(tabs, BorderLayout.CENTER);
btnOK = new JButton("OK");
add(btnOK, BorderLayout.SOUTH);
tabs.setSelectedIndex(FeaturesAdminFrame.selectedTab);
tabs.addChangeListener(new ChangeListener() {
@Override
public void stateChanged(ChangeEvent e) {
logger.trace("selected tab: "+ tabs.getSelectedIndex());
FeaturesAdminFrame.selectedTab = tabs.getSelectedIndex();
}
});
addActionListeners();
Toolkit toolkit = getToolkit();
Dimension size = toolkit.getScreenSize();
setLocation((size.width - getWidth()) / 2, (size.height - getHeight()) / 2);
}
/**
* returns the IOrbitImageMultiChannel if an image is open and selected and a IOrbitImageMultiChannel image, null otherwise.
*/
private IOrbitImageMultiChannel getOpenMultiChannelImage() {
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 void updateValues(FeatureDescription featureDescription) {
this.featureDescription = featureDescription;
tfWindowSize.setText(Integer.toString(featureDescription.getWindowSize()));
tfNumBlur.setText(Integer.toString(featureDescription.getNumBlur()));
cbRed.setSelected(!featureDescription.isSkipRed());
cbGreen.setSelected(!featureDescription.isSkipGreen());
cbBlue.setSelected(!featureDescription.isSkipBlue());
cbDeconvName.setSelectedIndex(0);
if (featureDescription.getDeconvName() != null && featureDescription.getDeconvName().length() > 0 && (!featureDescription.getDeconvName().equals(Colour_Deconvolution.DECONV_NONE)))
setDeconvName(featureDescription.getDeconvName());
setDeconvChannel(featureDescription.getDeconvChannel());
List classList = new ArrayList();
//classList.add("");
String selected = "";
OrbitModel model = OrbitImageAnalysis.getInstance().getModel();
if (model != null) {
OrbitModel classModel = model;
if (model.getSegmentationModel() != null) classModel = model.getSegmentationModel();
if (featureDescription.isForSecondarySegmentationModel() && model.getSecondarySegmentationModel() != null)
classModel = model.getSecondarySegmentationModel();
int i = 0;
for (ClassShape cs : classModel.getClassShapes()) {
String cleanCS = cs.getName().replaceAll(";", ",");
classList.add(cleanCS);
if (featureDescription.getFeatureClasses() != null) {
for (int fc : featureDescription.getFeatureClasses()) {
if (i == fc) {
selected += cleanCS + "; ";
}
}
}
i++;
}
}
cbFeatureClasses.setChoices(classList);
cbFeatureClasses.setText(selected);
cbUseImageAdjustments.setSelected(featureDescription.isUseImageAdjustments());
// segmentation
//cbForSecondarySegmentationModel.setSelected(featureDescription.isForSecondarySegmentationModel());
tfMinSegmentationSize.setText(Integer.toString(featureDescription.getMinSegmentationSize()));
tfMaxSegmentationLength.setText(Integer.toString(featureDescription.getMaxSegmentationLength()));
tfMaxOpenDistance.setText(Integer.toString(featureDescription.getMaxOpenDistance()));
tfSegmentationScale.setText(featureDescription.getSegmentationScale() + "");
cbDisableWatershed.setSelected(featureDescription.isDisableWatershed());
cbDoCombineCrossTiles.setSelected(featureDescription.isCombineObjectsCrossTiles());
cbFilterTileEdgeShapes.setSelected(featureDescription.isFilterTileEdgeShapes());
tfNumDilate.setText(Integer.toString(featureDescription.getNumDilate()));
tfNumErode.setText(Integer.toString(featureDescription.getNumErode()));
cbDilateBeforeErode.setSelected(featureDescription.isDilateBeforeErode());
tfRemoveOutliers.setText(Integer.toString(featureDescription.getRemoveOutliers()));
tfGraphCut.setText(Double.toString(featureDescription.getGraphCut()));
cbNerveDetectionMode.setSelected(featureDescription.isDeactivateWatershed()); // large object detection
cbMFS.setSelected(featureDescription.isMumfordShahSegmentation());
tfMFSAlpha.setInt(featureDescription.getMumfordShahAlpha());
tfMFSCellSize.setInt(featureDescription.getMumfordShahCellSize());
// roi
cbAnnotationROI.setSelectedIndex(0);
int groupIdx = OrbitImageAnalysis.getInstance().getModel().getAnnotationGroup() + 1; // +1 because 'ignore' is -1
if (cbAnnotationROI.getItemCount() > groupIdx)
cbAnnotationROI.setSelectedIndex(groupIdx);
tfFixedROI.setText(Integer.toString(OrbitImageAnalysis.getInstance().getModel().getFixedCircularROI()));
tfROIX.setText(Integer.toString(OrbitImageAnalysis.getInstance().getModel().getFixedROIOffsetX()));
tfROIY.setText(Integer.toString(OrbitImageAnalysis.getInstance().getModel().getFixedROIOffsetY()));
setCbActiveFluoChannels(featureDescription.getActiveFluoChannels());
}
private void setCbActiveFluoChannels(final String[] activeFluoChannels) {
List fluoChannels = new ArrayList<>();
String selectedChannels = "";
if (activeFluoChannels!=null &&activeFluoChannels.length>0) {
for (int i=0;i0) {
for (String channel: multiChanImage.getChannelNames()) {
channel = OrbitUtils.cleanChannelName(channel);
if (!fluoChannels.contains(channel)) {
fluoChannels.add(channel);
}
}
}
if (fluoChannels.size()>0) {
Collections.sort(fluoChannels);
}
else {
selectedChannels = OrbitUtils.CHANNEL_NAME_ALL;
fluoChannels.add(OrbitUtils.CHANNEL_NAME_ALL);
}
if (cbFluoChannels==null) {
cbFluoChannels = new JComboCheckBox(fluoChannels);
} else {
cbFluoChannels.setChoices(fluoChannels);
}
cbFluoChannels.setText(selectedChannels);
}
private void setCompBounds(Component comp, int width, int y) {
comp.setMaximumSize(new Dimension(width, btnHeight));
comp.setPreferredSize(new Dimension(width, btnHeight));
comp.setMinimumSize(new Dimension(width, btnHeight));
//comp.setBounds((frameWidth/3) + 200, y, comp.getWidth(), comp.getHeight());
}
private void addActionListeners() {
ActionListener okAction = new ActionListener() {
public void actionPerformed(ActionEvent arg0) {
exitProcedure();
}
};
btnOK.addActionListener(okAction);
}
private void setDeconvChannel(int channel) {
switch (channel) {
case 0: {
deconvChannel0.setSelected(true);
break;
}
case 1: {
deconvChannel1.setSelected(true);
break;
}
case 2: {
deconvChannel2.setSelected(true);
break;
}
case 3: {
deconvChannel3.setSelected(true);
break;
}
default: {
deconvChannel0.setSelected(true);
break;
}
}
}
private int getDeconvChannel() {
if (deconvChannel0.isSelected()) return 0;
if (deconvChannel1.isSelected()) return 1;
if (deconvChannel2.isSelected()) return 2;
if (deconvChannel3.isSelected()) return 3;
return 0;
}
private String getDeconvName() {
String name = Colour_Deconvolution.DECONV_NONE;
if (cbDeconvName.getSelectedItem() != null)
name = (String) cbDeconvName.getSelectedItem();
return name;
}
private void setDeconvName(String name) {
cbDeconvName.setSelectedItem(name);
}
public void exitProcedure() {
if (cbForSecondarySegmentationModel.isSelected() && cbCytoplasmaSegmentation.isSelected()) {
JOptionPane.showMessageDialog(FeaturesAdminFrame.this, "Cytoplasma segmentation cannot be activated for secondary segmentation model.\nPlease select either cytoplasma segmentation or 'for secondary segmentation model', but not both.", "Secondary Segmentation model and cytoplasma segmentation cannot be used together.", JOptionPane.ERROR_MESSAGE);
return;
}
// if (cbDoCombineCrossTiles.isSelected() && cbCytoplasmaSegmentation.isSelected()) {
// JOptionPane.showMessageDialog(FeaturesAdminFrame.this, "'Combine large connecting objects' and Cytoplasma Segmentation cannot be used together.\n(It would result in exactly one large object because all cytoplasma borders are connecting.)", "Cytoplasma Segmentation and Combine Objects active.", JOptionPane.ERROR_MESSAGE);
// return;
// }
OrbitImageAnalysis.getInstance().getModel().setFixedCircularROI(OrbitUtils.parseInt(tfFixedROI.getText(), 0));
OrbitImageAnalysis.getInstance().getModel().setFixedROIOffsetX(OrbitUtils.parseInt(tfROIX.getText(), 0));
OrbitImageAnalysis.getInstance().getModel().setFixedROIOffsetY(OrbitUtils.parseInt(tfROIY.getText(), 0));
OrbitImageAnalysis.getInstance().getModel().setAnnotationGroup(-1);
if (cbAnnotationROI.getSelectedItem() != null) {
OrbitImageAnalysis.getInstance().getModel().setAnnotationGroup(((AnnotationGroupLabel) cbAnnotationROI.getSelectedItem()).getNum());
}
int ws = Integer.parseInt(tfWindowSize.getText());
int minSegSize = Integer.parseInt(tfMinSegmentationSize.getText());
int numBlur = Integer.parseInt(tfNumBlur.getText());
featureDescription.setWindowSize(ws);
featureDescription.setMinSegmentationSize(minSegSize);
featureDescription.setMaxSegmentationLength(tfMaxSegmentationLength.getInt());
featureDescription.setMaxOpenDistance(tfMaxOpenDistance.getInt());
featureDescription.setDeactivateWatershed(cbNerveDetectionMode.isSelected());
featureDescription.setNumBlur(numBlur);
featureDescription.setSkipRed(!cbRed.isSelected());
featureDescription.setSkipGreen(!cbGreen.isSelected());
featureDescription.setSkipBlue(!cbBlue.isSelected());
featureDescription.setSegmentationScale(tfSegmentationScale.getDouble());
List featureClasses = new ArrayList();
OrbitModel model = OrbitImageAnalysis.getInstance().getModel();
if (model != null) {
OrbitModel classModel = model;
if (model.getSegmentationModel() != null) classModel = model.getSegmentationModel();
int i = 0;
String[] selectedClasses = cbFeatureClasses.getCheckedItems();
if (selectedClasses != null) {
for (ClassShape cs : classModel.getClassShapes()) {
String cleanCS = cs.getName().replaceAll(";", ",");
for (String sc : selectedClasses) {
if (sc.equals(cleanCS)) {
featureClasses.add(i);
break;
}
}
i++;
}
}
}
featureDescription.setFeatureClasses(null);
if (featureClasses.size() > 0) {
int[] fca = new int[featureClasses.size()];
for (int i = 0; i < featureClasses.size(); i++) {
fca[i] = featureClasses.get(i);
}
featureDescription.setFeatureClasses(fca);
}
featureDescription.setDeconvName(getDeconvName());
featureDescription.setDeconvChannel(getDeconvChannel());
// v2 features
featureDescription.setDisableWatershed(cbDisableWatershed.isSelected());
featureDescription.setCombineObjectsCrossTiles(cbDoCombineCrossTiles.isSelected());
featureDescription.setFilterTileEdgeShapes(cbFilterTileEdgeShapes.isSelected());
featureDescription.setDilateBeforeErode(cbDilateBeforeErode.isSelected());
featureDescription.setNumDilate(tfNumDilate.getInt());
featureDescription.setNumErode(tfNumErode.getInt());
featureDescription.setRemoveOutliers(tfRemoveOutliers.getInt());
featureDescription.setGraphCut(tfGraphCut.getDouble());
featureDescription.setUseImageAdjustments(cbUseImageAdjustments.isSelected());
featureDescription.setForSecondarySegmentationModel(cbForSecondarySegmentationModel.isSelected());
featureDescription.setCytoplasmaSegmentation(cbCytoplasmaSegmentation.isSelected());
featureDescription.setMumfordShahSegmentation(cbMFS.isSelected());
featureDescription.setMumfordShahAlpha(tfMFSAlpha.getInt());
featureDescription.setMumfordShahCellSize(tfMFSCellSize.getInt());
// fluo channels
String[] activeFluoChannels = cbFluoChannels.getCheckedItems();
if (activeFluoChannels!=null && activeFluoChannels.length>0) {
featureDescription.setActiveFluoChannels(activeFluoChannels);
}
firePropertyChange(FEATURES_DONE, null, featureDescription);
this.dispose();
}
public class AnnotationGroupLabel implements Serializable {
private static final long serialVersionUID = 1L;
private int num;
private String name;
public AnnotationGroupLabel(int num, String name) {
this.num = num;
this.name = name;
}
public int getNum() {
return num;
}
public void setNum(int num) {
this.num = num;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
@Override
public String toString() {
return name;
}
}
}