Merge branch 'main' of github.com:qupath/qupath-extension-instanseg

qupath · Aug 6, 2024 · 959639d · 959639d
2 parents 52f1b5b + 3b30495
commit 959639d
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Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/src/main/java/qupath/ext/instanseg/core/InstanSeg.java b/src/main/java/qupath/ext/instanseg/core/InstanSeg.java
@@ -1,8 +1,6 @@
 package qupath.ext.instanseg.core;
 
 import ai.djl.Device;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import qupath.lib.images.ImageData;
 import qupath.lib.images.servers.ColorTransforms;
 import qupath.lib.objects.PathAnnotationObject;
@@ -23,7 +21,6 @@
 import java.util.stream.IntStream;
 
 public class InstanSeg {
-    private static final Logger logger = LoggerFactory.getLogger(InstanSeg.class);
 
     private final int tileDims;
     private final double downsample;

diff --git a/src/main/java/qupath/ext/instanseg/core/MatTranslator.java b/src/main/java/qupath/ext/instanseg/core/MatTranslator.java
@@ -13,7 +13,7 @@ class MatTranslator implements Translator<Mat, Mat> {
 
     private final String inputLayoutNd;
     private final String outputLayoutNd;
-    private boolean nucleiOnly = false;
+    private final boolean firstChannelOnly;
 
     /**
      * Create a translator from InstanSeg input to output.
@@ -24,7 +24,7 @@ class MatTranslator implements Translator<Mat, Mat> {
     MatTranslator(String inputLayoutNd, String outputLayoutNd, boolean firstChannelOnly) {
         this.inputLayoutNd = inputLayoutNd;
         this.outputLayoutNd = outputLayoutNd;
-        this.nucleiOnly = firstChannelOnly;
+        this.firstChannelOnly = firstChannelOnly;
     }
 
     /**
@@ -37,7 +37,7 @@ public NDList processInput(TranslatorContext ctx, Mat input) {
         var manager = ctx.getNDManager();
         var ndarray = DjlTools.matToNDArray(manager, input, inputLayoutNd);
         var out = new NDList(ndarray);
-        if (nucleiOnly) {
+        if (firstChannelOnly) {
             var inds = new int[]{1, 0};
             var array = manager.create(inds, new Shape(2));
             var arrayCPU = array.toDevice(Device.cpu(), false);

diff --git a/src/main/java/qupath/ext/instanseg/core/PytorchManager.java b/src/main/java/qupath/ext/instanseg/core/PytorchManager.java
@@ -64,7 +64,7 @@ public static Collection<String> getAvailableDevices() {
     }
 
     /**
-     * Query if the PyTorch engine is already available, without a need to downlaod.
+     * Query if the PyTorch engine is already available, without a need to download.
      * @return
      */
     public static boolean hasPyTorchEngine() {

diff --git a/src/main/java/qupath/ext/instanseg/ui/InstanSegController.java b/src/main/java/qupath/ext/instanseg/ui/InstanSegController.java
@@ -183,10 +183,10 @@ private static String getCheckComboBoxText(CheckComboBox<ChannelSelectItem> comb
                 .toList()
                 .size();
         if (n == 0)
-            return "No channels selected!";
+            return resources.getString("ui.options.noChannelSelected");
         if (n == 1)
-            return "1 channel selected";
-        return n + " channels selected";
+            return resources.getString("ui.options.oneChannelSelected");
+        return String.format(resources.getString("ui.options.nChannelSelected"), n);
     }
 
     /**

diff --git a/src/main/resources/qupath/ext/instanseg/ui/strings.properties b/src/main/resources/qupath/ext/instanseg/ui/strings.properties
@@ -55,6 +55,9 @@ ui.options.tilesize = Tile Size:
 ui.options.tilesize.tooltip = Define the approximate tile size
 ui.options.channel = Channels:
 ui.options.channel.tooltip = Define the set of channels to be used in inference
+ui.options.noChannelSelected = No channels selected!
+ui.options.oneChannelSelected = 1 channel selected
+ui.options.nChannelSelected = %d channels selected
 ui.options.directory = Downloaded model directory:
 ui.options.directory.tooltip = Choose the directory where models should be stored