From a988db273f950b707a8149dfcfa52eacbe07df52 Mon Sep 17 00:00:00 2001
From: miriam-groeneveld <miriam.groeneveld.diag@gmail.com>
Date: Wed, 4 Oct 2023 17:12:40 +0200
Subject: [PATCH] fix writing pyramid levels fix mypy errors

---
 panimg/contrib/wsi_dcm_to_tiff/dcm_to_tiff.py | 23 ++++++++++---------
 panimg/models.py                              |  9 +++++---
 2 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/panimg/contrib/wsi_dcm_to_tiff/dcm_to_tiff.py b/panimg/contrib/wsi_dcm_to_tiff/dcm_to_tiff.py
index f1427d3..a2ce711 100644
--- a/panimg/contrib/wsi_dcm_to_tiff/dcm_to_tiff.py
+++ b/panimg/contrib/wsi_dcm_to_tiff/dcm_to_tiff.py
@@ -228,6 +228,7 @@ def dcm_to_tiff(input_dir, output_path):
 
     with TiffWriter(output_path, bigtiff=True) as tif:
         tile_size = image.levels[0].default_instance.tile_size.width
+        test_tile = np.array(image.read_tile(0, (0, 0)))
 
         def tiler(getter, level, cols, rows):
             for row in range(rows):
@@ -235,29 +236,27 @@ def tiler(getter, level, cols, rows):
                     im = np.array(getter(level, (col, row)))
                     yield im
 
-        for level in range(0, len(image.levels.levels)):
-            cols = int(math.ceil(image.levels[level].size.width / tile_size))
-            rows = int(math.ceil(image.levels[level].size.height / tile_size))
+        for level in image.levels:
+            cols = int(math.ceil(level.size.width / tile_size))
+            rows = int(math.ceil(level.size.height / tile_size))
 
-            test_tile = np.array(image.read_tile(0, (0, 0)))
             dtype = test_tile.dtype
             shape = (
-                image.levels[level].size.height,
-                image.levels[level].size.width,
+                level.size.height,
+                level.size.width,
                 3,
             )
 
-            level_tiler = tiler(image.read_tile, level, cols, rows)
+            level_tiler = tiler(image.read_tile, level.level, cols, rows)
 
             extratags = [(274, 3, 1, 1, False)]  # Orientation TOPLEFT
 
             resolution = (
-                int(10 / image.levels[level].pixel_spacing.width),
-                int(10 / image.levels[level].pixel_spacing.height),
-                "CENTIMETER",
+                int(10 / level.pixel_spacing.width),
+                int(10 / level.pixel_spacing.height),
             )
 
-            subfiletype = 1 if level != 0 else 0
+            subfiletype = 1 if level.level != 0 else 0
 
             tif.write(
                 level_tiler,
@@ -268,6 +267,8 @@ def tiler(getter, level, cols, rows):
                 compression="jpeg",
                 subsampling=(1, 1),
                 resolution=resolution,
+                resolutionunit="CENTIMETER",
                 description="Converted from DICOM",
                 subfiletype=subfiletype,
+                extratags=extratags,
             )
diff --git a/panimg/models.py b/panimg/models.py
index 1da3842..e48f6bb 100644
--- a/panimg/models.py
+++ b/panimg/models.py
@@ -10,8 +10,9 @@
 
 import numpy as np
 import SimpleITK
-from pydantic import BaseModel, ConfigDict, field_validator
+from pydantic import BaseModel, ConfigDict
 from pydantic.dataclasses import dataclass
+from pydantic.functional_validators import field_validator
 from SimpleITK import GetArrayViewFromImage, Image, WriteImage
 
 from panimg.exceptions import ValidationError
@@ -185,7 +186,9 @@ class SimpleITKImage(BaseModel):
     spacing_valid: bool
     eye_choice: EyeChoice = EyeChoice.NOT_APPLICABLE
 
-    model_config = ConfigDict(arbitrary_types_allowed=True, frozen=True)
+    model_config: ConfigDict = ConfigDict(
+        arbitrary_types_allowed=True, frozen=True
+    )
 
     @property
     def width(self) -> int:
@@ -408,7 +411,7 @@ class TIFFImage(BaseModel):
     eye_choice: EyeChoice = EyeChoice.NOT_APPLICABLE
     segments: Optional[FrozenSet[int]] = None
 
-    model_config = ConfigDict(frozen=True)
+    model_config: ConfigDict = ConfigDict(frozen=True)
 
     def save(self, output_directory: Path) -> Tuple[PanImg, Set[PanImgFile]]:
         pk = uuid4()