Fix handling of pyramid index when creating instance (#161)

* Fix handling of pyramid index when creating instance

CHANGELOG.md

@@ -7,7 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [0.20.2] - 2024-02-22
+## [0.20.3] - 2024-03-20
+
+### Fixed
+
+- Missing handling of pyramid index when creating `WsiInstance` using `create_instance()`.
+
+## [0.20.2] - 2024-03-18
 
 ### Fixed
 
@@ -353,7 +359,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Initial release of wsidicom
 
-[Unreleased]: https://github.com/imi-bigpicture/wsidicom/compare/0.20.2..HEAD
+[Unreleased]: https://github.com/imi-bigpicture/wsidicom/compare/0.20.3..HEAD
+[0.20.3]: https://github.com/imi-bigpicture/wsidicom/compare/v0.20.2..v0.20.3
 [0.20.2]: https://github.com/imi-bigpicture/wsidicom/compare/v0.20.1..v0.20.2
 [0.20.1]: https://github.com/imi-bigpicture/wsidicom/compare/v0.20.0..v0.20.1
 [0.20.0]: https://github.com/imi-bigpicture/wsidicom/compare/v0.19.1..v0.20.0

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "wsidicom"
-version = "0.20.2"
+version = "0.20.3"
 description = "Tools for handling DICOM based whole scan images"
 authors = ["Erik O Gabrielsson <[email protected]>"]
 license = "Apache-2.0"

tests/conftest.py

@@ -14,19 +14,23 @@
 
 import json
 import os
+import random
+import sys
 from enum import Enum
 from io import BufferedReader
 from pathlib import Path
 from typing import Any, Dict, Iterable, List, Optional, Tuple
 
 import pytest
 from dicomweb_client import DICOMfileClient
-from pydicom.uid import JPEGBaseline8Bit
+from pydicom.uid import UID, JPEGBaseline8Bit
 from upath import UPath
 
 from tests.data_gen import create_layer_file
+from tests.file.io.test_wsidicom_writer import WsiDicomTestImageData
 from wsidicom import WsiDicom
 from wsidicom.config import settings
+from wsidicom.geometry import Size
 from wsidicom.web.wsidicom_web_client import WsiDicomWebClient
 
 SLIDE_FOLDER = Path(os.environ.get("WSIDICOM_TESTDIR", "tests/testdata/slides"))
@@ -195,3 +199,68 @@ def open_wsi(
         wsi.close()
     for stream in streams:
         stream.close()
+
+
+@pytest.fixture()
+def tiled_size():
+    yield Size(2, 2)
+
+
+@pytest.fixture()
+def frame_count(tiled_size: Size):
+    yield tiled_size.area
+
+
+@pytest.fixture()
+def rng():
+    SEED = 0
+    yield random.Random(SEED)
+
+
+@pytest.fixture()
+def bits():
+    yield 8
+
+
+@pytest.fixture
+def samples_per_pixel():
+    yield 3
+
+
+@pytest.fixture
+def tile_size():
+    yield Size(10, 10)
+
+
+@pytest.fixture()
+def transfer_syntax():
+    yield JPEGBaseline8Bit
+
+
+@pytest.fixture()
+def frames(
+    rng: random.Random,
+    transfer_syntax: UID,
+    frame_count: int,
+    bits: int,
+    samples_per_pixel: int,
+    tile_size: Size,
+):
+    if not transfer_syntax.is_encapsulated:
+        min_frame_length = bits * tile_size.area * samples_per_pixel // 8
+        max_frame_length = min_frame_length
+    else:
+        min_frame_length = 2
+        max_frame_length = 100
+    lengths = [
+        rng.randint(min_frame_length, max_frame_length) for i in range(frame_count)
+    ]
+    yield [
+        rng.getrandbits(length * 8).to_bytes(length, sys.byteorder)
+        for length in lengths
+    ]
+
+
+@pytest.fixture()
+def image_data(frames: List[bytes], tiled_size: Size):
+    yield WsiDicomTestImageData(frames, tiled_size)

tests/file/io/test_wsidicom_writer.py

@@ -14,8 +14,6 @@
 
 import math
 import os
-import random
-import sys
 from pathlib import Path
 from typing import List, Optional, OrderedDict, Sequence
 
@@ -155,66 +153,6 @@ def _get_encoded_tile(self, tile: Point, z: float, path: str) -> bytes:
         return self._data[tile.x + tile.y * self.tiled_size.width]
 
 
-@pytest.fixture()
-def tiled_size():
-    yield Size(2, 2)
-
-
-@pytest.fixture()
-def frame_count(tiled_size: Size):
-    yield tiled_size.area
-
-
-@pytest.fixture()
-def rng():
-    SEED = 0
-    yield random.Random(SEED)
-
-
-@pytest.fixture()
-def bits():
-    yield 8
-
-
-@pytest.fixture
-def samples_per_pixel():
-    yield 3
-
-
-@pytest.fixture
-def tile_size():
-    yield Size(10, 10)
-
-
-@pytest.fixture()
-def frames(
-    rng: random.Random,
-    transfer_syntax: UID,
-    frame_count: int,
-    bits: int,
-    samples_per_pixel: int,
-    tile_size: Size,
-):
-    if not transfer_syntax.is_encapsulated:
-        min_frame_length = bits * tile_size.area * samples_per_pixel // 8
-        max_frame_length = min_frame_length
-    else:
-        min_frame_length = 2
-        max_frame_length = 100
-    lengths = [
-        rng.randint(min_frame_length, max_frame_length) for i in range(frame_count)
-    ]
-    yield [
-        rng.getrandbits(length * 8).to_bytes(length, sys.byteorder)
-        for length in lengths
-    ]
-
-
-@pytest.fixture()
-def image_data(frames: List[bytes], tiled_size: Size):
-    yield WsiDicomTestImageData(frames, tiled_size)
-
-
 @pytest.fixture()
 def dataset(image_data: ImageData, frame_count: int):
     assert image_data.pixel_spacing is not None

tests/test_wsi_dataset.py

@@ -6,8 +6,8 @@
 from pydicom.uid import UID, generate_uid
 
 from wsidicom.geometry import SizeMm
-from wsidicom.instance import TileType
-from wsidicom.instance.dataset import WsiDataset
+from wsidicom.instance import ImageData, TileType
+from wsidicom.instance.dataset import ImageType, WsiDataset
 from wsidicom.tags import LossyImageCompressionRatioTag
 
 
@@ -265,3 +265,30 @@ def test_spacing_between_slices(
 
         # Assert
         assert read_spacing_between_slices == spacing_between_slices
+
+    @pytest.mark.parametrize(
+        ["image_type", "pyramid_index", "expected_image_type"],
+        [
+            (ImageType.VOLUME, 0, ["ORIGINAL", "PRIMARY", "VOLUME", "NONE"]),
+            (ImageType.VOLUME, 1, ["ORIGINAL", "PRIMARY", "VOLUME", "RESAMPLED"]),
+            (ImageType.LABEL, None, ["ORIGINAL", "PRIMARY", "LABEL", "NONE"]),
+            (ImageType.OVERVIEW, None, ["ORIGINAL", "PRIMARY", "OVERVIEW", "NONE"]),
+        ],
+    )
+    def test_create_instance_dataset(
+        self,
+        image_data: ImageData,
+        image_type: ImageType,
+        pyramid_index: Optional[int],
+        expected_image_type: Sequence[str],
+    ):
+        # Arrange
+        dataset = Dataset()
+
+        # Act
+        instance_dataset = WsiDataset.create_instance_dataset(
+            dataset, image_type, image_data, pyramid_index
+        )
+
+        # Assert
+        assert instance_dataset.ImageType == expected_image_type

wsidicom/__init__.py

@@ -30,7 +30,7 @@
 from wsidicom.web import WsiDicomWebClient
 from wsidicom.wsidicom import WsiDicom
 
-__version__ = "0.20.2"
+__version__ = "0.20.3"
 
 __all__ = [
     "settings",

wsidicom/instance/dataset.py

@@ -740,16 +740,21 @@ def create_instance_dataset(
             Type of instance ('VOLUME', 'LABEL', 'OVERVIEW)
         image_data:
             Image data to create dataset for.
+        pyramid_index: Optional[int] = None
+            Pyramid index. of image data, if volume image.
 
         Returns
         -------
         WsiDataset
             Dataset for instance.
         """
-        if image_type == ImageType.VOLUME and pyramid_index == 0:
-            resampled = "NONE"
-        else:
-            resampled = "RESAMPLED"
+        resampled = "NONE"
+        if image_type == ImageType.VOLUME:
+            if pyramid_index is None:
+                raise ValueError("Pyramid index must be set for volume image.")
+            if pyramid_index > 0:
+                resampled = "RESAMPLED"
+
         dataset.ImageType = ["ORIGINAL", "PRIMARY", image_type.value, resampled]
         dataset.SOPInstanceUID = generate_uid(prefix=None)
         shared_functional_group_sequence = Dataset()

wsidicom/instance/instance.py

@@ -209,7 +209,11 @@ def create_label(
 
     @classmethod
     def create_instance(
-        cls, image_data: ImageData, base_dataset: Dataset, image_type: ImageType
+        cls,
+        image_data: ImageData,
+        base_dataset: Dataset,
+        image_type: ImageType,
+        pyramid_index: Optional[int] = None,
     ) -> "WsiInstance":
         """Create WsiInstance from ImageData.
 
@@ -221,14 +225,16 @@ def create_instance(
             Base dataset to include.
         image_type: ImageType
             Type of instance to create.
+        pyramid_index: Optional[int] = None
+            Pyramid index. of image data, if volume image.
 
         Returns
         -------
         WsiInstance
             Created WsiInstance.
         """
         instance_dataset = WsiDataset.create_instance_dataset(
-            base_dataset, image_type, image_data
+            base_dataset, image_type, image_data, pyramid_index
         )
 
         return cls(instance_dataset, image_data)