Add option to make measurements (#45)

qupath · Aug 21, 2024 · 9ab48e8 · 9ab48e8
1 parent ac62573
commit 9ab48e8
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Showing 3 changed files with 32 additions and 15 deletions.
diff --git a/src/main/java/qupath/ext/instanseg/ui/InstanSegController.java b/src/main/java/qupath/ext/instanseg/ui/InstanSegController.java
@@ -89,6 +89,8 @@ public class InstanSegController extends BorderPane {
     private ToggleButton selectAllTMACoresButton;
     @FXML
     private CheckBox nucleiOnlyCheckBox;
+    @FXML
+    private CheckBox makeMeasurementsCheckBox;
 
     private final ExecutorService pool = Executors.newSingleThreadExecutor(ThreadTools.createThreadFactory("instanseg", true));
     private final QuPathGUI qupath;
@@ -440,7 +442,7 @@ protected Void call() {
                     InstanSegPreferences.numThreadsProperty().getValue());
 
             var imageData = qupath.getImageData();
-            var selectedObjects = qupath.getImageData().getHierarchy().getSelectionModel().getSelectedObjects();
+            var selectedObjects = imageData.getHierarchy().getSelectionModel().getSelectedObjects();
             var instanSeg = InstanSeg.builder()
                     .model(model)
                     .imageData(imageData)
@@ -452,10 +454,6 @@ protected Void call() {
                     .taskRunner(taskRunner)
                     .build();
             instanSeg.detectObjects(selectedObjects);
-            for (PathObject po: selectedObjects) {
-                instanSeg.makeMeasurements(instanSeg.getImageData(), po.getChildObjects());
-            }
-            qupath.getImageData().getHierarchy().fireHierarchyChangedEvent(this);
 
 
             String cmd = String.format("""
@@ -474,19 +472,27 @@ protected Void call() {
                                 .nThreads(%d)
                                 .build();
                             instanSeg.detectObjects(instanSegObjects);
+                            """,
+                            model.getPath(),
+                            deviceChoices.getSelectionModel().getSelectedItem(),
+                            nucleiOnlyCheckBox.isSelected() ? 1 : 2,
+                            ChannelSelectItem.toConstructorString(channels),
+                            InstanSegPreferences.tileSizeProperty().get(),
+                            model.getPixelSizeX() / (double) server.getPixelCalibration().getAveragedPixelSize(),
+                            InstanSegPreferences.numThreadsProperty().getValue()
+                    );
+                    if (makeMeasurementsCheckBox.isSelected()) {
+                        cmd += """
                             for (PathObject po: instanSegObjects) {
                                 instanSeg.makeMeasurements(instanSeg.getImageData(), po.getChildObjects());
                             }
-                            """,
-                    model.getPath(),
-                    deviceChoices.getSelectionModel().getSelectedItem(),
-                    nucleiOnlyCheckBox.isSelected() ? 1 : 2,
-                    ChannelSelectItem.toConstructorString(channels),
-                    InstanSegPreferences.tileSizeProperty().get(),
-                    model.getPixelSizeX() / (double) server.getPixelCalibration().getAveragedPixelSize(),
-                    InstanSegPreferences.numThreadsProperty().getValue()
-            );
-            qupath.getImageData().getHistoryWorkflow()
+                            """;
+                        for (PathObject po: selectedObjects) {
+                            instanSeg.makeMeasurements(instanSeg.getImageData(), po.getChildObjects());
+                        }
+                    }
+            imageData.getHierarchy().fireHierarchyChangedEvent(this);
+            imageData.getHistoryWorkflow()
                     .addStep(
                             new DefaultScriptableWorkflowStep(resources.getString("workflow.title"), cmd)
                     );

diff --git a/src/main/resources/qupath/ext/instanseg/ui/instanseg_control.fxml b/src/main/resources/qupath/ext/instanseg/ui/instanseg_control.fxml
@@ -141,6 +141,15 @@
                                 </CheckComboBox>
                             </children>
                         </HBox>
+                        <HBox alignment="CENTER" styleClass="standard-spacing">
+                            <children>
+                                <CheckBox styleClass="regular" fx:id="makeMeasurementsCheckBox" text="%ui.options.makeMeasurements">
+                                    <tooltip>
+                                        <Tooltip text="%ui.options.makeMeasurements.tooltip" />
+                                    </tooltip>
+                                </CheckBox>
+                            </children>
+                        </HBox>
                         <Separator prefWidth="200.0" />
 
         <!--            Model Directory Selection-->

diff --git a/src/main/resources/qupath/ext/instanseg/ui/strings.properties b/src/main/resources/qupath/ext/instanseg/ui/strings.properties
@@ -55,6 +55,8 @@ 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.makeMeasurements = Make measurements
+ui.options.makeMeasurements.tooltip = Make shape and intensity measurements after detecting objects
 ui.options.noChannelSelected = No channels selected!
 ui.options.oneChannelSelected = 1 channel selected
 ui.options.nChannelSelected = %d channels selected