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Add tile padding as an option #70

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merged 2 commits into from
Sep 9, 2024
Merged

Add tile padding as an option #70

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0637cc6
Add tile padding as an option
petebankhead Sep 9, 2024
6bd3f0c
Tooltips, cloud icon, output channel fix
petebankhead Sep 9, 2024
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12 changes: 10 additions & 2 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 @@ -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;
Expand Down Expand Up @@ -173,6 +175,7 @@ private InstanSegController(QuPathGUI qupath) throws IOException {

// Options
configureTileSizes();
configureTilePadding();
configureDeviceChoices();
configureThreadSpinner();
configureInputChannelCombo();
Expand Down Expand Up @@ -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();
}
}
Expand Down Expand Up @@ -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));
}
Expand Down
8 changes: 8 additions & 0 deletions src/main/java/qupath/ext/instanseg/ui/InstanSegPreferences.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
Expand Down Expand Up @@ -82,6 +86,10 @@ static IntegerProperty tileSizeProperty() {
return tileSizeProperty;
}

static IntegerProperty tilePaddingProperty() {
return tilePaddingProperty;
}

static BooleanProperty makeMeasurementsProperty() {
return makeMeasurementsProperty;
}
Expand Down
14 changes: 10 additions & 4 deletions src/main/java/qupath/ext/instanseg/ui/InstanSegTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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();
Expand All @@ -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)
Expand All @@ -88,6 +92,7 @@ protected Void call() {
.%s
.outputChannels(%s)
.tileDims(%d)
.interTilePadding(%d)
.nThreads(%d)
.makeMeasurements(%s)
.randomColors(%s)
Expand All @@ -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();
Expand Down
3 changes: 2 additions & 1 deletion src/main/java/qupath/ext/instanseg/ui/ModelListCell.java
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Original file line number Diff line number Diff line change
@@ -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;
Expand Down Expand Up @@ -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);
}

}
51 changes: 44 additions & 7 deletions src/main/resources/qupath/ext/instanseg/ui/instanseg_control.fxml
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand Down
2 changes: 2 additions & 0 deletions src/main/resources/qupath/ext/instanseg/ui/strings.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down