Compressed size (#84)

* Add property for compressed size of image

* Change from cytomine to openslide test data

* Revert to installed turbojpeg

.github/workflows/pytests.yaml

@@ -60,9 +60,6 @@ jobs:
       - name: Set up Ubuntu
         if: matrix.os == 'ubuntu-latest'
         run: sudo apt-get install -y libturbojpeg
-      - name: Set up libjpegturbo OSX
-        if: matrix.os == 'macos-latest'
-        run: brew unlink jpeg-turbo && brew install jpeg-turbo --HEAD
       - name: Set up libjpegturbo Windows
         shell: pwsh
         if: matrix.os == 'windows-latest'

CHANGELOG.md

@@ -5,7 +5,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased] -
+## [Unreleased]
+
+## [0.14.0] - 2025-01-29
+
+### Added
+
+- Property `compressed_size` returning the size of all frames, with jpeg headers if separated.
 
 ## [0.13.4] - 2024-11-06
 
@@ -231,7 +237,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Initial release of opentile.
 
-[Unreleased]: https://github.com/imi-bigpicture/opentile/compare/v0.13.4..HEAD
+[Unreleased]: https://github.com/imi-bigpicture/opentile/compare/v0.14.0..HEAD
+[0.14.0]: https://github.com/imi-bigpicture/opentile/compare/v0.13.3..v0.14.0
 [0.13.4]: https://github.com/imi-bigpicture/opentile/compare/v0.13.2..v0.13.3
 [0.13.3]: https://github.com/imi-bigpicture/opentile/compare/v0.13.2..v0.13.3
 [0.13.2]: https://github.com/imi-bigpicture/opentile/compare/v0.13.1..v0.13.2

opentile/__init__.py

@@ -17,4 +17,4 @@
 from opentile.opentile import OpenTile
 from opentile.metadata import Metadata
 
-__version__ = "0.13.4"
+__version__ = "0.14.0"

opentile/tiff_image.py

@@ -14,6 +14,7 @@
 
 """Base image classes."""
 
+from functools import cached_property
 import math
 from abc import ABCMeta, abstractmethod
 from pathlib import Path
@@ -165,6 +166,18 @@ def pyramid_index(self) -> int:
         images not in pyramidal series."""
         return self._pyramid_index
 
+    @cached_property
+    def compressed_size(self) -> int:
+        """Return the size of the compressed image data."""
+        frames = sum(self._page.databytecounts)
+        if self._page.jpegheader is not None:
+            jpeg_header_length = len(self._page.jpegheader)
+        elif self._page.jpegtables is not None:
+            jpeg_header_length = len(self._page.jpegtables)
+        else:
+            jpeg_header_length = 0
+        return frames + len(self._page.dataoffsets) * jpeg_header_length
+
     @abstractmethod
     def get_tile(self, tile_position: Tuple[int, int]) -> bytes:
         """Should return image bytes for tile at tile position.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "opentile"
-version = "0.13.4"
+version = "0.14.0"
 description = "Read tiles from wsi-TIFF files"
 authors = ["Erik O Gabrielsson <erik.o.gabrielsson@sectra.com>"]
 license = "Apache-2.0"

tests/download_test_images.py

@@ -20,11 +20,11 @@
 
 FILES: Dict[str, Dict[str, Any]] = {
     "svs/CMU-1/CMU-1.svs": {
-        "url": "https://data.cytomine.coop/open/openslide/aperio-svs/CMU-1.svs",  # NOQA
+        "url": "https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/CMU-1.svs",  # NOQA
         "md5": {"CMU-1.svs": "751b0b86a3c5ff4dfc8567cf24daaa85"},
     },
     "ndpi/CMU-1/CMU-1.ndpi": {
-        "url": "https://data.cytomine.coop/open/openslide/hamamatsu-ndpi/CMU-1.ndpi",  # NOQA
+        "url": "https://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu/CMU-1.ndpi",  # NOQA
         "md5": {"CMU-1.ndpi": "fb89dea54f85fb112e418a3cf4c7888a"},
     },
 }

tests/test_histech_tiff_tiler.py

@@ -109,3 +109,12 @@ def test_sumples_per_pixel(self, level: TiffImage):
 
         # Assert
         assert samples_per_pixel == 3
+
+    def test_compressed_size(self, level: TiffImage):
+        # Arrange
+
+        # Act
+        compressed_size = level.compressed_size
+
+        # Assert
+        assert compressed_size == 425684721

tests/test_ndpi_tiler.py

@@ -484,3 +484,12 @@ def test_overview(self, tiler: NdpiTiler):
 
         # Assert
         assert md5(overview).hexdigest() == "c663698334b10cd57484a2d503b3bafa"
+
+    def test_compressed_size(self, level: TiffImage):
+        # Arrange
+
+        # Act
+        compressed_size = level.compressed_size
+
+        # Assert
+        assert compressed_size == 262256667

tests/test_ome_tiff_tiler.py

@@ -72,3 +72,12 @@ def test_sumples_per_pixel(self, level: TiffImage):
 
         # Assert
         assert samples_per_pixel == 3
+
+    def test_compressed_size(self, level: TiffImage):
+        # Arrange
+
+        # Act
+        compressed_size = level.compressed_size
+
+        # Assert
+        assert compressed_size == 104115549

tests/test_philips_tiff_tiler.py

@@ -146,3 +146,12 @@ def test_metadata_aquisition_datetime(self, tiler: PhilipsTiffTiler):
 
         # Assert
         assert aquisition_datetime == datetime(2013, 7, 1, 18, 59, 4)
+
+    def test_compressed_size(self, level: TiffImage):
+        # Arrange
+
+        # Act
+        compressed_size = level.compressed_size
+
+        # Assert
+        assert compressed_size == 486105413

tests/test_svs_tiler.py

@@ -21,6 +21,7 @@
 
 from opentile.formats import SvsTiler
 from opentile.formats.svs.svs_image import SvsTiledImage
+from opentile.tiff_image import TiffImage
 from opentile.geometry import Point
 
 from .filepaths import svs_file_path
@@ -181,3 +182,12 @@ def test_metadata_aquisition_datetime(self, tiler: SvsTiler):
 
         # Assert
         assert aquisition_datetime == datetime(2009, 12, 29, 9, 59, 15)
+
+    def test_compressed_size(self, level: TiffImage):
+        # Arrange
+
+        # Act
+        compressed_size = level.compressed_size
+
+        # Assert
+        assert compressed_size == 163831603