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Fix channel selector when duplicate channels present (resolve #11) #13

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merged 9 commits into from
Apr 25, 2024
Merged

Fix channel selector when duplicate channels present (resolve #11) #13

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760d5d9
Fix channel selector when duplicate channels present (resolve #11)
alanocallaghan Apr 22, 2024
5db23fa
Query server RGB-ness, not imageData fluoro-ness
alanocallaghan Apr 22, 2024
65d551d
Update InstanSegController.java
alanocallaghan Apr 23, 2024
e8d2d59
Fix channel selctor for fluoro at least
alanocallaghan Apr 24, 2024
293c550
Private fields
alanocallaghan Apr 24, 2024
2b2ce18
Move code + classes around
alanocallaghan Apr 24, 2024
9b3e2c2
Whitespace
alanocallaghan Apr 24, 2024
580d8d0
Use index not channel name
alanocallaghan Apr 25, 2024
db54e09
Address comments from #11
alanocallaghan Apr 25, 2024
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27 changes: 15 additions & 12 deletions src/main/java/qupath/ext/instanseg/ui/InstanSegController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,6 @@
import java.nio.file.WatchService;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.ResourceBundle;
Expand Down Expand Up @@ -153,7 +152,7 @@ private void addSetFromVisible(CheckComboBox<ColorTransforms.ColorTransform> com
var channelNames = activeChannels.stream().map(ChannelDisplayInfo::getName).toList();
var comboItems = comboChannels.getItems();
for (int i = 0; i < comboItems.size(); i++) {
if (channelNames.contains(comboItems.get(i).getName() + " (C" + (i+1) + ")")) {
if (channelNames.contains(comboItems.get(i).getName())) {
comboChannels.getCheckModel().check(i);
}
}
Expand All @@ -178,7 +177,7 @@ private void updateChannelPicker(ImageData<BufferedImage> imageData) {

private static Collection<ColorTransforms.ColorTransform> getAvailableChannels(ImageData<?> imageData) {
List<ColorTransforms.ColorTransform> list = new ArrayList<>();
for (var name : getAvailableUniqueChannelNames(imageData.getServer()))
for (var name : getAvailableChannelNames(imageData.getServer()))
list.add(ColorTransforms.createChannelExtractor(name));
var stains = imageData.getColorDeconvolutionStains();
if (stains != null) {
Expand All @@ -190,19 +189,23 @@ private static Collection<ColorTransforms.ColorTransform> getAvailableChannels(I
}

/**
* Create a collection representing available unique channel names, logging a warning if a channel name is duplicated
* @param server server containing channels
* @return set of channel names
* Create a collection representing available (possibly duplicate)
* channel names, logging a warning if a channel name is duplicated.
* @param server server that contains channels
* @return Collection of channel names
*/
private static Collection<String> getAvailableUniqueChannelNames(ImageServer<?> server) {
var set = new LinkedHashSet<String>();
private static Collection<String> getAvailableChannelNames(ImageServer<?> server) {
var set = new ArrayList<String>();
int i = 1;
for (var c : server.getMetadata().getChannels()) {
var name = c.getName();
if (!set.contains(name))
set.add(name);
else
logger.warn("Found duplicate channel name! Will skip channel " + i + " (name '" + name + "')");
if (server.isRGB()) {
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name += "(C" + i + ")";
}
set.add(name);
if (set.contains(name)) {
logger.warn("Found duplicate channel name! Channel " + i + " (name '" + name + "')");
}
i++;
}
return set;
Expand Down
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