Tile size level matching (#181)

* Config for allowing non-uniform tile size across levels

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - Cache for compressed and decompressed tiles.
+- Setting `strict_tile_size_check`, defaulting to `True`, to enable parsing of levels with  different tile size.
 
 ### Changed
 

wsidicom/config.py

@@ -24,13 +24,14 @@ class Settings:
 
     def __init__(self) -> None:
         self._strict_uid_check = False
+        self._strict_tile_size_check = True
         self._strict_attribute_check = False
+        self._strict_specimen_identifier_check = True
         self._focal_plane_distance_threshold = 0.000001
         self._pyramids_origin_threshold = 0.02
         self._prefered_decoder: Optional[str] = None
         self._open_web_theads: Optional[int] = None
         self._pillow_resampling_filter = Pillow.Resampling.BILINEAR
-        self._strict_specimen_identifier_check = True
         self._ignore_specimen_preparation_step_on_validation_error = True
         self._truncate_long_dicom_strings = False
         self._decoded_frame_cache_size = 1000
@@ -54,6 +55,27 @@ def strict_attribute_check(self) -> bool:
     def strict_attribute_check(self, value: bool) -> None:
         self._strict_attribute_check = value
 
+    @property
+    def strict_specimen_identifier_check(self) -> bool:
+        """If `True` the issuer of two specimen identifiers needs to match or both be
+        None for the identifiers to match. If `False` the identifiers will match also if
+        either issuer is None. Either way the identifier needs to match."""
+        return self._strict_specimen_identifier_check
+
+    @strict_specimen_identifier_check.setter
+    def strict_specimen_identifier_check(self, value: bool) -> None:
+        self._strict_specimen_identifier_check = value
+
+    @property
+    def strict_tile_size_check(self) -> bool:
+        """If tile size need to match for levels. If `False` the tile size accross
+        levels are allowed to be non-uniform."""
+        return self._strict_tile_size_check
+
+    @strict_tile_size_check.setter
+    def strict_tile_size_check(self, value: bool) -> None:
+        self._strict_tile_size_check = value
+
     @property
     def focal_plane_distance_threshold(self) -> float:
         """Threshold in mm for which distances between focal planes are
@@ -104,17 +126,6 @@ def pillow_resampling_filter(self) -> Pillow.Resampling:
     def pillow_resampling_filter(self, value: Pillow.Resampling) -> None:
         self._pillow_resampling_filter = value
 
-    @property
-    def strict_specimen_identifier_check(self) -> bool:
-        """If `True` the issuer of two specimen identifiers needs to match or both be
-        None for the identifiers to match. If `False` the identifiers will match also if
-        either issuer is None. Either way the identifier needs to match."""
-        return self._strict_specimen_identifier_check
-
-    @strict_specimen_identifier_check.setter
-    def strict_specimen_identifier_check(self, value: bool) -> None:
-        self._strict_specimen_identifier_check = value
-
     @property
     def ignore_specimen_preparation_step_on_validation_error(self) -> bool:
         """If ignore specimen preparation steps that fails to validate. If false all

wsidicom/file/wsidicom_file_source.py

@@ -31,6 +31,7 @@
 from pydicom.uid import UID, MediaStorageDirectoryStorage
 from upath import UPath
 
+from wsidicom.config import settings
 from wsidicom.errors import (
     WsiDicomNotFoundError,
     WsiDicomNotSupportedError,
@@ -99,7 +100,9 @@ def base_dataset(self) -> WsiDataset:
     def level_instances(self) -> Iterable[WsiInstance]:
         """The level instances parsed from the source."""
         return self._create_instances(
-            self._levels, self._slide_uids, self._base_tile_size
+            self._levels,
+            self._slide_uids,
+            self._base_tile_size if settings.strict_tile_size_check else None,
         )
 
     @property

wsidicom/group/level.py

@@ -17,12 +17,12 @@
 
 from PIL.Image import Image
 
+from wsidicom import settings
 from wsidicom.errors import WsiDicomNoResolutionError, WsiDicomOutOfBoundsError
 from wsidicom.geometry import Point, Region, Size, SizeMm
 from wsidicom.group.group import Group
 from wsidicom.instance import WsiInstance
 from wsidicom.stringprinting import dict_pretty_str
-from wsidicom import settings
 
 
 class Level(Group):
@@ -110,7 +110,10 @@ def matches(self, other_level: "Level") -> bool:
         return (
             self.uids.matches(other_level.uids)
             and other_level.image_type == self.image_type
-            and other_level.tile_size == self.tile_size
+            and (
+                not settings.strict_tile_size_check
+                or other_level.tile_size == self.tile_size
+            )
         )
 
     def get_highest_level(self) -> int:

wsidicom/web/wsidicom_web_source.py

@@ -161,10 +161,12 @@ def create_instance(
                     key=lambda instance: instance.dataset.image_size.width,
                 )
             )
+
         except StopIteration:
             WsiDicomNotFoundError(
                 "No level instances found", f"{study_uid}, {series_uids}"
             )
+        self._base_tile_size = self._base_dataset.tile_size
 
     @property
     def base_dataset(self) -> WsiDataset:
@@ -174,6 +176,12 @@ def base_dataset(self) -> WsiDataset:
     @property
     def level_instances(self) -> List[WsiInstance]:
         """The level instances parsed from the source."""
+        if settings.strict_tile_size_check:
+            return [
+                level
+                for level in self._level_instances
+                if level.dataset.tile_size == self._base_tile_size
+            ]
         return self._level_instances
 
     @property