From f9108138fd8b7efdf28ff5fddb697d57675b58fb Mon Sep 17 00:00:00 2001
From: Max Gamill <mcgamill1@sheffield.ac.uk>
Date: Tue, 10 Dec 2024 12:40:52 +0000
Subject: [PATCH 1/4] adds ability to import older topostats unet models

---
 topostats/grains.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/topostats/grains.py b/topostats/grains.py
index 2e2ac4cd61..64fcdfd8f1 100644
--- a/topostats/grains.py
+++ b/topostats/grains.py
@@ -17,6 +17,7 @@
 from topostats.logs.logs import LOGGER_NAME
 from topostats.thresholds import threshold
 from topostats.unet_masking import (
+    iou_loss,
     make_bounding_box_square,
     mean_iou,
     pad_bounding_box,
@@ -611,7 +612,9 @@ def improve_grain_segmentation_unet(
         # You may also get an error referencing a "group_1" parameter, this is discussed in this issue:
         # https://github.com/keras-team/keras/issues/19441 which also has an experimental fix that we can try but
         # I haven't tested it yet.
-        unet_model = keras.models.load_model(unet_config["model_path"], custom_objects={"mean_iou": mean_iou})
+        unet_model = keras.models.load_model(
+            unet_config["model_path"], custom_objects={"mean_iou": mean_iou, "iou_loss": iou_loss}, compile=False
+        )
         LOGGER.debug(f"Output shape of UNet model: {unet_model.output_shape}")
 
         # Initialise an empty mask to iteratively add to for each grain, with the correct number of class channels based on

From 24d93dca83923b5e9883e5a6b01d01097bdb28d5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 10 Dec 2024 13:11:54 +0000
Subject: [PATCH 2/4] [pre-commit.ci] Fixing issues with pre-commit

---
 topostats/grains.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/topostats/grains.py b/topostats/grains.py
index 362b3ede11..1e3cd5c53b 100644
--- a/topostats/grains.py
+++ b/topostats/grains.py
@@ -660,7 +660,7 @@ def improve_grain_segmentation_unet(
 
         try:
             unet_model = keras.models.load_model(
-              unet_config["model_path"], custom_objects={"mean_iou": mean_iou, "iou_loss": iou_loss}, compile=False
+                unet_config["model_path"], custom_objects={"mean_iou": mean_iou, "iou_loss": iou_loss}, compile=False
             )
         except Exception as e:
             LOGGER.debug(f"Python executable: {sys.executable}")

From 6988cb60168d928463ce4822d9a5847442ce535f Mon Sep 17 00:00:00 2001
From: Max Gamill <mcgamill1@sheffield.ac.uk>
Date: Tue, 10 Dec 2024 15:20:11 +0000
Subject: [PATCH 3/4] re(?)-add mean_iou func as import

---
 topostats/grains.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/topostats/grains.py b/topostats/grains.py
index 1e3cd5c53b..8ed3a42cac 100644
--- a/topostats/grains.py
+++ b/topostats/grains.py
@@ -21,6 +21,7 @@
 from topostats.unet_masking import (
     iou_loss,
     make_bounding_box_square,
+    mean_iou,
     pad_bounding_box,
     predict_unet,
 )

From ba118973e70bb7de6d6789f53c8a064cce77e4ea Mon Sep 17 00:00:00 2001
From: Neil Shephard <n.shephard@sheffield.ac.uk>
Date: Wed, 11 Dec 2024 11:01:26 +0000
Subject: [PATCH 4/4] Update topostats/unet_masking.py

---
 topostats/unet_masking.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/topostats/unet_masking.py b/topostats/unet_masking.py
index 79bc55e427..7700fbc36f 100644
--- a/topostats/unet_masking.py
+++ b/topostats/unet_masking.py
@@ -18,7 +18,6 @@
 # pylint: disable=too-many-locals
 
 
-# DICE Loss
 def dice_loss(y_true: npt.NDArray[np.float32], y_pred: npt.NDArray[np.float32], smooth: float = 1e-5) -> tf.Tensor:
     """
     DICE loss function.