Fix EOT writing. Fallback to EOT if BOT fails (#132)

CHANGELOG.md

@@ -7,8 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+
+- Fallback to EOT when overflowing BOT.
+
 ### Fixed
 
+- Missing empty BOT when writing EOT.
 - Fixed accessing settings for PillowEncoder.
 
 ## [0.14.0] - 2023-11-29

tests/test_wsidicom_file_target.py

@@ -19,6 +19,7 @@
 from pydicom.uid import generate_uid
 from tests.conftest import WsiTestDefinitions
 from wsidicom import WsiDicom
+from wsidicom.file.wsidicom_file_base import OffsetTableType
 from wsidicom.file.wsidicom_file_target import WsiDicomFileTarget
 from wsidicom.series.levels import Levels
 
@@ -34,7 +35,9 @@ def test_save_levels(
         expected_levels_count = len(wsi.levels)
 
         # Act
-        with WsiDicomFileTarget(tmp_path, generate_uid, 1, 16, "bot") as target:
+        with WsiDicomFileTarget(
+            tmp_path, generate_uid, 1, 16, OffsetTableType.BASIC, False
+        ) as target:
             target.save_levels(wsi.levels)
 
         # Assert
@@ -57,7 +60,9 @@ def test_save_levels_add_missing(
         levels_missing_smallest_levels = Levels(levels_larger_than_tile_size)
 
         # Act
-        with WsiDicomFileTarget(tmp_path, generate_uid, 1, 16, "bot", True) as target:
+        with WsiDicomFileTarget(
+            tmp_path, generate_uid, 1, 16, OffsetTableType.BASIC, True
+        ) as target:
             target.save_levels(levels_missing_smallest_levels)
 
         # Assert

tests/test_wsidicom_file_writer.py

@@ -503,7 +503,7 @@ def test_write_pixel_end(
 
         # Act
         with WsiDicomFileWriter.open(filepath, JPEGBaseline8Bit) as write_file:
-            write_file._write_pixel_data_end()
+            write_file._write_pixel_data_end_tag()
 
         # Assert
         with WsiDicomTestFile(
@@ -659,7 +659,8 @@ def test_create_child(
             generate_uid,
             1,
             100,
-            "bot",
+            OffsetTableType.BASIC,
+            False,
         ) as target:
             target._save_and_open_level(source_level, wsi.pixel_spacing, 2)
 

wsidicom/errors.py

@@ -96,3 +96,7 @@ class WsiDicomNoResolutionError(Exception):
 
 class WsiDicomNotSupportedError(Exception):
     """Raised if opened instance is not supported."""
+
+
+class WsiDicomBotOverflow(Exception):
+    """Raised if image data is to large to fit into basic table offset."""

wsidicom/file/wsidicom_file.py

@@ -493,7 +493,10 @@ def _parse_pixel_data(self) -> Tuple[List[Tuple[int, int]], OffsetTableType]:
         )
         if table_type == OffsetTableType.BASIC:
             table = self._read_bot()
-        elif table_type == OffsetTableType.EMPTY:
+        elif (
+            table_type == OffsetTableType.EMPTY
+            or table_type == OffsetTableType.EXTENDED
+        ):
             self._read_bot_length()
 
         if table_type == OffsetTableType.NONE:

wsidicom/file/wsidicom_file_base.py

@@ -29,9 +29,9 @@ class OffsetTableType(Enum):
     EXTENDED = "EOT"
 
     @classmethod
-    def from_string(cls, offset_table: Optional[str]) -> "OffsetTableType":
+    def from_string(cls, offset_table: str) -> "OffsetTableType":
         """Return OffsetTableType parsed from string."""
-        if offset_table is None:
+        if offset_table == "none":
             return OffsetTableType.NONE
         if offset_table.strip().lower() == "empty":
             return OffsetTableType.EMPTY
@@ -60,7 +60,8 @@ def __init__(
         owned: bool = False
             If the stream should be closed by this instance.
         """
-        self._file = DicomFileLike(stream)
+        self._stream = stream
+        self._file = DicomFileLike(self._stream)
         self._filepath = filepath
         self._owned = owned
         self.__enter__()

wsidicom/file/wsidicom_file_target.py

@@ -40,8 +40,8 @@ def __init__(
         uid_generator: Callable[..., UID],
         workers: int,
         chunk_size: int,
-        offset_table: Optional[str],
-        add_missing_levels: bool = False,
+        offset_table: OffsetTableType,
+        add_missing_levels: bool,
     ):
         """
         Create a WsiDicomFileTarget.
@@ -57,14 +57,13 @@ def __init__(
         chunk_size: int
             Chunk size (number of tiles) to process at a time. Actual chunk
             size also depends on minimun_chunk_size from image_data.
-        offset_table: Optional[str]
-            Offset table to use, 'bot' basic offset table, 'eot' extended
-            offset table, None - no offset table.
-        add_missing_levels: bool = False
+        offset_table: OffsetTableType
+            Offset table to use.
+        add_missing_levels: bool
             If to add missing dyadic levels up to the single tile level.
         """
         self._output_path = output_path
-        self._offset_table = OffsetTableType.from_string(offset_table)
+        self._offset_table = offset_table
         self._filepaths: List[Path] = []
         self._opened_files: List[WsiDicomFile] = []
         super().__init__(uid_generator, workers, chunk_size, add_missing_levels)
@@ -135,7 +134,7 @@ def _save_group(self, group: Group, scale: int = 1) -> List[Path]:
         filepaths: List[Path] = []
         for instances in self._group_instances_to_file(group):
             uid = self._uid_generator()
-            filepath = Path(self._output_path).joinpath(uid + ".dcm")
+            filepath = self._output_path.joinpath(uid + ".dcm")
             transfer_syntax = instances[0].image_data.transfer_syntax
             image_data_list = self._list_image_data(instances)
             focal_planes, optical_paths, tiled_size = self._get_frame_information(