From 0bb8c1cbfdc201d8c629ff7228bbbe03d0f3f44f Mon Sep 17 00:00:00 2001
From: Pete <pete.bankhead@gmail.com>
Date: Wed, 4 Sep 2024 19:22:41 +0100
Subject: [PATCH] Fix pixel size/downsample inconsistency

Introduced in https://github.com/qupath/qupath-extension-instanseg/pull/59 I forgot to rename the variable in the builder.
---
 .../ext/instanseg/core/DetectionMeasurer.java    | 16 ++++++++++------
 .../qupath/ext/instanseg/core/InstanSeg.java     |  2 +-
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/src/main/java/qupath/ext/instanseg/core/DetectionMeasurer.java b/src/main/java/qupath/ext/instanseg/core/DetectionMeasurer.java
index 55979f9..cfa0184 100644
--- a/src/main/java/qupath/ext/instanseg/core/DetectionMeasurer.java
+++ b/src/main/java/qupath/ext/instanseg/core/DetectionMeasurer.java
@@ -93,15 +93,19 @@ public static class Builder {
                 .filter(m -> m != ObjectMeasurements.Measurements.VARIANCE) // Skip variance - we have standard deviation
                 .toList();
         private Collection<ObjectMeasurements.ShapeFeatures> shapeFeatures = Arrays.asList(ObjectMeasurements.ShapeFeatures.values());
-        private double pixelSize;
+        private double downsample;
 
         /**
-         * Set the pixel size that measurements should be made at.
-         * @param pixelSize The pixel size that detections/annotations/etc were made at.
+         * Set the downsample that the measurer should use.
+         * The measurer is assumed to be short-lived and used for a single image, and so doesn't need to maintain a
+         * value related to pixel size. Therefore, it takes an explicit downsample to avoid any risk that the
+         * pixel-size-to-downsample calculation here wouldn't match that done during detection.
+         *
+         * @param downsample The downsample that detections/annotations/etc should be made at.
          * @return A modified builder.
          */
-        public Builder pixelSize(double pixelSize) {
-            this.pixelSize = pixelSize;
+        public Builder downsample(double downsample) {
+            this.downsample = downsample;
             return this;
         }
 
@@ -140,7 +144,7 @@ public Builder shapeFeatures(Collection<ObjectMeasurements.ShapeFeatures> shapeF
          * @return An immutable detection measurer.
          */
         public DetectionMeasurer build() {
-            return new DetectionMeasurer(compartments, measurements, shapeFeatures, pixelSize);
+            return new DetectionMeasurer(compartments, measurements, shapeFeatures, downsample);
         }
     }
 }
diff --git a/src/main/java/qupath/ext/instanseg/core/InstanSeg.java b/src/main/java/qupath/ext/instanseg/core/InstanSeg.java
index 74d2945..360e089 100644
--- a/src/main/java/qupath/ext/instanseg/core/InstanSeg.java
+++ b/src/main/java/qupath/ext/instanseg/core/InstanSeg.java
@@ -126,7 +126,7 @@ public static Builder builder() {
     public void makeMeasurements(ImageData<BufferedImage> imageData, Collection<? extends PathObject> detections) {
         double downsample = model.getPreferredDownsample(imageData.getServer().getPixelCalibration());
         DetectionMeasurer.builder()
-                .pixelSize(downsample)
+                .downsample(downsample)
                 .build()
                 .makeMeasurements(imageData, detections);
     }