Merge pull request #70 from petebankhead/tile-padding

Add tile padding as an option
qupath · Sep 9, 2024 · 0fc6355 · 0fc6355
2 parents 21af929 + 6bd3f0c
commit 0fc6355
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Showing 6 changed files with 76 additions and 14 deletions.
diff --git a/src/main/java/qupath/ext/instanseg/ui/InstanSegController.java b/src/main/java/qupath/ext/instanseg/ui/InstanSegController.java
@@ -88,6 +88,8 @@ public class InstanSegController extends BorderPane {
     @FXML
     private ChoiceBox<Integer> tileSizeChoiceBox;
     @FXML
+    private ChoiceBox<Integer> tilePaddingChoiceBox;
+    @FXML
     private Spinner<Integer> threadSpinner;
     @FXML
     private ToggleButton selectAllAnnotationsButton;
@@ -173,6 +175,7 @@ private InstanSegController(QuPathGUI qupath) throws IOException {
 
         // Options
         configureTileSizes();
+        configureTilePadding();
         configureDeviceChoices();
         configureThreadSpinner();
         configureInputChannelCombo();
@@ -455,7 +458,7 @@ private void refreshModelChoice() {
         var nOutputs = model.getOutputChannels().orElse(1);
         comboOutputChannels.getCheckModel().clearChecks();
         comboOutputChannels.getItems().setAll(OutputChannelItem.getOutputsForChannelCount(nOutputs));
-        if (!outputChannelCache.restoreChecks()) {
+        if (!outputChannelCache.restoreChecks() || comboOutputChannels.getCheckModel().isEmpty()) {
             comboOutputChannels.getCheckModel().checkAll();
         }
     }
@@ -590,13 +593,18 @@ private static List<InstanSegModel> getRemoteModels() {
         return List.copyOf(models);
     }
 
+    private void configureTilePadding() {
+        tilePaddingChoiceBox.getItems().addAll(16, 32, 48, 64, 80, 96);
+        tilePaddingChoiceBox.setValue(InstanSegPreferences.tilePaddingProperty().getValue());
+        tilePaddingChoiceBox.valueProperty().addListener((v, o, n) -> InstanSegPreferences.tilePaddingProperty().set(n));
+    }
+
 
     private void configureTileSizes() {
         // The use of 32-bit signed ints for coordinates of the intermediate sparse matrix *might* be
         // an issue for very large tile sizes - but I haven't seen any evidence of this.
         // We definitely can't have very small tiles, because they must be greater than 2 x the padding.
         tileSizeChoiceBox.getItems().addAll(256, 512, 1024, 2048);
-        tileSizeChoiceBox.getSelectionModel().select(Integer.valueOf(512));
         tileSizeChoiceBox.setValue(InstanSegPreferences.tileSizeProperty().getValue());
         tileSizeChoiceBox.valueProperty().addListener((v, o, n) -> InstanSegPreferences.tileSizeProperty().set(n));
     }

diff --git a/src/main/java/qupath/ext/instanseg/ui/InstanSegPreferences.java b/src/main/java/qupath/ext/instanseg/ui/InstanSegPreferences.java
@@ -41,6 +41,10 @@ enum OnlinePermission {
             "intanseg.tile.size",
             512);
 
+    private static final IntegerProperty tilePaddingProperty = PathPrefs.createPersistentPreference(
+            "intanseg.tile.padding",
+            32);
+
     private static final BooleanProperty makeMeasurementsProperty = PathPrefs.createPersistentPreference(
             "intanseg.measurements",
             true);
@@ -82,6 +86,10 @@ static IntegerProperty tileSizeProperty() {
         return tileSizeProperty;
     }
 
+    static IntegerProperty tilePaddingProperty() {
+        return tilePaddingProperty;
+    }
+
     static BooleanProperty makeMeasurementsProperty() {
         return makeMeasurementsProperty;
     }

diff --git a/src/main/java/qupath/ext/instanseg/ui/InstanSegTask.java b/src/main/java/qupath/ext/instanseg/ui/InstanSegTask.java
@@ -48,9 +48,10 @@ class InstanSegTask extends Task<Void> {
 
     @Override
     protected Void call() {
+        int nThreads = InstanSegPreferences.numThreadsProperty().get();
         var taskRunner = new TaskRunnerFX(
                 QuPathGUI.getInstance(),
-                InstanSegPreferences.numThreadsProperty().getValue());
+                nThreads);
 
         var selectedObjects = imageData.getHierarchy().getSelectionModel().getSelectedObjects();
         Optional<Path> path = model.getPath();
@@ -69,13 +70,16 @@ protected Void call() {
         if (nChecked > 0 && nChecked < nOutputs) {
             outputChannels = this.outputChannels.stream().mapToInt(Integer::intValue).toArray();
         }
+        int tileSize = InstanSegPreferences.tileSizeProperty().get();
+        int tilePadding = InstanSegPreferences.tilePaddingProperty().get();
 
         var instanSeg = InstanSeg.builder()
                 .model(model)
                 .device(device)
                 .inputChannels(channels.stream().map(InputChannelItem::getTransform).toList())
                 .outputChannels(outputChannels)
-                .tileDims(InstanSegPreferences.tileSizeProperty().get())
+                .tileDims(tileSize)
+                .interTilePadding(tilePadding)
                 .taskRunner(taskRunner)
                 .makeMeasurements(makeMeasurements)
                 .randomColors(randomColors)
@@ -88,6 +92,7 @@ protected Void call() {
                                 .%s
                                 .outputChannels(%s)
                                 .tileDims(%d)
+                                .interTilePadding(%d)
                                 .nThreads(%d)
                                 .makeMeasurements(%s)
                                 .randomColors(%s)
@@ -100,8 +105,9 @@ protected Void call() {
                 outputChannels.length == 0 ? "" : Arrays.stream(outputChannels)
                         .mapToObj(Integer::toString)
                         .collect(Collectors.joining(", ")),
-                InstanSegPreferences.tileSizeProperty().get(),
-                InstanSegPreferences.numThreadsProperty().getValue(),
+                tileSize,
+                tilePadding,
+                nThreads,
                 makeMeasurements,
                 randomColors
         ).strip();

diff --git a/src/main/java/qupath/ext/instanseg/ui/ModelListCell.java b/src/main/java/qupath/ext/instanseg/ui/ModelListCell.java
@@ -1,5 +1,6 @@
 package qupath.ext.instanseg.ui;
 
+import javafx.scene.control.ContentDisplay;
 import javafx.scene.control.ListCell;
 import javafx.scene.control.Tooltip;
 import org.controlsfx.glyphfont.FontAwesome;
@@ -46,7 +47,7 @@ public void updateItem(InstanSegModel model, boolean empty) {
 
     private Glyph createOnlineIcon() {
         GlyphFont fontAwesome = GlyphFontRegistry.font("FontAwesome");
-        return fontAwesome.create(FontAwesome.Glyph.DOWNLOAD);
+        return fontAwesome.create(FontAwesome.Glyph.CLOUD);
     }
 
 }
diff --git a/src/main/resources/qupath/ext/instanseg/ui/instanseg_control.fxml b/src/main/resources/qupath/ext/instanseg/ui/instanseg_control.fxml
@@ -136,7 +136,10 @@
                                 <Insets left="10" right="10" top="10" />
                             </padding>
                             <children>
-                                <Label styleClass="regular" text="%ui.options.device" />
+                                <Label styleClass="regular" text="%ui.options.device">
+                           <tooltip>
+                              <Tooltip text="%ui.options.device.tooltip" />
+                           </tooltip></Label>
                                 <Pane minWidth="5" HBox.hgrow="ALWAYS" />
                                 <ChoiceBox fx:id="deviceChoices" prefWidth="75.0">
                                     <tooltip><Tooltip text="%ui.options.device.tooltip" /></tooltip>
@@ -149,7 +152,10 @@
                                 <Insets left="10" right="10" />
                             </padding>
                             <children>
-                                <Label styleClass="regular" text="%ui.options.threads" />
+                                <Label styleClass="regular" text="%ui.options.threads">
+                           <tooltip>
+                              <Tooltip text="%ui.options.threads.tooltip" />
+                           </tooltip></Label>
                                 <Pane minWidth="5" HBox.hgrow="ALWAYS" />
                                 <Spinner fx:id="threadSpinner" prefWidth="75.0">
                                     <tooltip>
@@ -167,7 +173,10 @@
                                 <Insets left="10" right="10" />
                             </padding>
                             <children>
-                                <Label styleClass="regular" text="%ui.options.tilesize" />
+                                <Label styleClass="regular" text="%ui.options.tilesize">
+                           <tooltip>
+                              <Tooltip text="%ui.options.tilesize.tooltip" />
+                           </tooltip></Label>
                                 <Pane minWidth="5" HBox.hgrow="ALWAYS" />
                                 <ChoiceBox fx:id="tileSizeChoiceBox" prefWidth="75.0">
                                     <tooltip>
@@ -176,13 +185,33 @@
                                 </ChoiceBox>
                             </children>
                         </HBox>
+                  <HBox alignment="CENTER_RIGHT" styleClass="standard-spacing">
+                     <padding>
+                        <Insets left="10" right="10" />
+                     </padding>
+                     <children>
+                        <Label styleClass="regular" text="%ui.options.tileboundary">
+                           <tooltip>
+                              <Tooltip text="%ui.options.tileboundary.tooltip" />
+                           </tooltip></Label>
+                        <Pane minWidth="5" HBox.hgrow="ALWAYS" />
+                        <ChoiceBox fx:id="tilePaddingChoiceBox" prefWidth="75.0">
+                           <tooltip>
+                              <Tooltip text="%ui.options.tileboundary.tooltip" />
+                           </tooltip>
+                        </ChoiceBox>
+                     </children>
+                  </HBox>
         <!--            Channel Selection-->
                         <HBox alignment="CENTER_RIGHT" styleClass="standard-spacing">
                             <padding>
                                 <Insets left="10" right="10" />
                             </padding>
                             <children>
-                                <Label styleClass="regular" text="%ui.options.input-channels" />
+                                <Label styleClass="regular" text="%ui.options.input-channels">
+                           <tooltip>
+                              <Tooltip text="%ui.options.input-channels.tooltip" />
+                           </tooltip></Label>
                                 <Pane minWidth="5" HBox.hgrow="ALWAYS" />
                                 <CheckComboBox fx:id="comboInputChannels">
                                     <tooltip>
@@ -196,7 +225,10 @@
                                 <Insets left="10" right="10" />
                             </padding>
                             <children>
-                                <Label styleClass="regular" text="%ui.options.output-channels" />
+                                <Label styleClass="regular" text="%ui.options.output-channels">
+                           <tooltip>
+                              <Tooltip text="%ui.options.output-channels.tooltip" />
+                           </tooltip></Label>
                                 <Pane minWidth="5" HBox.hgrow="ALWAYS" />
                         <CheckComboBox id="checkComboOutputs" fx:id="comboOutputChannels">
                            <tooltip>
@@ -209,7 +241,10 @@
                                 <Insets left="10.0" right="10.0" />
                             </padding>
                             <children>
-                                <Label text="%ui.options.makeMeasurements" />
+                                <Label text="%ui.options.makeMeasurements">
+                           <tooltip>
+                              <Tooltip text="%ui.options.makeMeasurements.tooltip" />
+                           </tooltip></Label>
                                 <Pane minWidth="5" HBox.hgrow="ALWAYS" />
                                 <CheckBox fx:id="makeMeasurementsCheckBox" styleClass="regular">
                                     <tooltip>
@@ -224,7 +259,9 @@
                      </padding>
                      <children>
                         <Label text="%ui.options.randomColors">
-                        </Label>
+                           <tooltip>
+                              <Tooltip text="%ui.options.randomColors.tooltip" />
+                           </tooltip></Label>
                         <Pane minWidth="5" HBox.hgrow="ALWAYS" />
                         <CheckBox fx:id="randomColorsCheckBox" styleClass="regular">
                            <tooltip>

diff --git a/src/main/resources/qupath/ext/instanseg/ui/strings.properties b/src/main/resources/qupath/ext/instanseg/ui/strings.properties
@@ -56,6 +56,8 @@ ui.options.threads = Threads
 ui.options.threads.tooltip = Define the preferred number of threads
 ui.options.tilesize = Tile size
 ui.options.tilesize.tooltip = Define the approximate tile size
+ui.options.tileboundary = Tile padding
+ui.options.tileboundary.tooltip = Define how much padding to add on tile boundaries.\nSmaller values can make processing faster, but may cause objects to be split or broken at tile boundaries.
 ui.options.input-channels = Input channels
 ui.options.input-channels.tooltip = Define the set of channels to be used in inference
 ui.options.makeMeasurements = Make measurements