From 7fb6ae0169f285da2629c64f569785531077d2d3 Mon Sep 17 00:00:00 2001
From: Pete <pete.bankhead@gmail.com>
Date: Mon, 13 Nov 2023 07:24:54 +0000
Subject: [PATCH] Bug fixes

Fix https://github.com/qupath/qupath-extension-wsinfer/issues/45
This uses zero-padding (other padding may be preferable).

Also fix threading bug when selected objects are updated from another thread (e.g. a script) and the dialog is showing.

Slightly reduce vertical height by reducing padding.
---
 .../java/qupath/ext/wsinfer/TileLoader.java   | 21 +++++++++++++++++--
 .../ext/wsinfer/ui/WSInferController.java     |  4 ++++
 .../ext/wsinfer/ui/wsinfer_control.fxml       |  2 +-
 .../qupath/ext/wsinfer/ui/wsinferstyles.css   |  2 +-
 4 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/src/main/java/qupath/ext/wsinfer/TileLoader.java b/src/main/java/qupath/ext/wsinfer/TileLoader.java
index b7ceee7..796c783 100644
--- a/src/main/java/qupath/ext/wsinfer/TileLoader.java
+++ b/src/main/java/qupath/ext/wsinfer/TileLoader.java
@@ -133,9 +133,26 @@ private TileBatch nextBatch() {
                 } else {
                     // Handle normal case of within-bounds coordinates
                     img = server.readRegion(downsample, x, y, width, height);
-                    if (resizeWidth > 0 && resizeHeight > 0)
-                        img = BufferedImageTools.resize(img, resizeWidth, resizeHeight, true);
                 }
+                if (resizeWidth > 0 && resizeHeight > 0) {
+                    // Using OpenCV is much faster tha BufferedImageTools/ImageJ,
+                    // but using BufferedImageTools (and ImageJ) seems to give more similar results to WSInfer Python.
+                    // For example, using the Python WSInfer 0.5.0 output for the image at
+                    // https://github.com/qupath/qupath-docs/issues/89 (30619 tiles):
+                    //  BufferedImageTools Tumor prob Mean Absolute Difference: 0.0026328298250342763
+                    //  OpenCV Tumor prob Mean Absolute Difference:             0.07625036735485102
+                    //
+                    // Note: If we activate this, then we should handle the if/else above separately to avoid
+                    // regenerating a Mat unnecessarily.
+//                        var mat = OpenCVTools.imageToMat(img);
+//                        var size = new Size(resizeWidth, resizeHeight);
+//                        opencv_imgproc.resize(mat, mat, size, 0, 0, opencv_imgproc.INTER_LINEAR);
+//                        img = OpenCVTools.matToBufferedImage(mat);
+//                        size.close();
+//                        mat.close();
+                    img = BufferedImageTools.resize(img, resizeWidth, resizeHeight, true);
+                }
+
                 Image input = BufferedImageFactory.getInstance().fromImage(img);
                 pathObjectBatch.add(pathObject);
                 inputs.add(input);
diff --git a/src/main/java/qupath/ext/wsinfer/ui/WSInferController.java b/src/main/java/qupath/ext/wsinfer/ui/WSInferController.java
index fc2c44a..ba2b38b 100644
--- a/src/main/java/qupath/ext/wsinfer/ui/WSInferController.java
+++ b/src/main/java/qupath/ext/wsinfer/ui/WSInferController.java
@@ -694,6 +694,10 @@ private void selectedPathObjectChanged(PathObject pathObjectSelected, PathObject
         }
 
         private void updateSelectedObjectCounts() {
+            if (!Platform.isFxApplicationThread()) {
+                Platform.runLater(this::updateSelectedObjectCounts);
+                return;
+            }
             var hierarchy = hierarchyProperty.getValue();
             if (hierarchy == null) {
                 numSelectedAnnotations.set(0);
diff --git a/src/main/resources/qupath/ext/wsinfer/ui/wsinfer_control.fxml b/src/main/resources/qupath/ext/wsinfer/ui/wsinfer_control.fxml
index e7b779d..572c64c 100644
--- a/src/main/resources/qupath/ext/wsinfer/ui/wsinfer_control.fxml
+++ b/src/main/resources/qupath/ext/wsinfer/ui/wsinfer_control.fxml
@@ -98,7 +98,7 @@
                             </Button>
                         </children>
                     </HBox>
-                    <Label id="labelWarning" fx:id="labelMessage" prefHeight="30.0" styleClass="error-message" text="%ui.error.no-selection" VBox.vgrow="ALWAYS" />
+                    <Label id="labelWarning" fx:id="labelMessage" styleClass="error-message" text="%ui.error.no-selection" VBox.vgrow="ALWAYS" />
                     <styleClass>
                         <String fx:value="standard-spacing" />
                         <String fx:value="standard-padding" />
diff --git a/src/main/resources/qupath/ext/wsinfer/ui/wsinferstyles.css b/src/main/resources/qupath/ext/wsinfer/ui/wsinferstyles.css
index a9075ad..4b58c22 100644
--- a/src/main/resources/qupath/ext/wsinfer/ui/wsinferstyles.css
+++ b/src/main/resources/qupath/ext/wsinfer/ui/wsinferstyles.css
@@ -37,7 +37,7 @@
 }
 
 .standard-padding {
-  -fx-padding: 4;
+  -fx-padding: 2;
 }
 
 /*download button*/