- Use PHOTOMETRIC-enum from tifffile for photometric interpretation. (#…

…47)

- Use PHOTOMETRIC-enum from tifffile for photometric interpretation.
- Update imagecodecs to 2022.9.26.

CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased] - ...
 
+
+## [0.4.2] - 2022-11-24
+### Fixed
+- Use PHOTOMETRIC-enum from tifffile for photometric interpretation.
+- Update imagecodecs to 2022.9.26.
+
 ## [0.4.1] - 2022-11-24
 ### Fixed
 - Added missing tag in Philips tiff tiler.
@@ -59,7 +65,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Initial release of opentile.
 
-[Unreleased]: https://github.com/imi-bigpicture/opentile/compare/v0.4.1..HEAD
+[Unreleased]: https://github.com/imi-bigpicture/opentile/compare/v0.4.2..HEAD
+[0.4.2]: https://github.com/imi-bigpicture/opentile/compare/v0.4.1..v0.4.2
 [0.4.1]: https://github.com/imi-bigpicture/opentile/compare/v0.4.0..v0.4.1
 [0.4.0]: https://github.com/imi-bigpicture/opentile/compare/v0.3.0..v0.4.0
 [0.3.0]: https://github.com/imi-bigpicture/opentile/compare/v0.2.0..v0.3.0

opentile/__init__.py

@@ -14,4 +14,4 @@
 
 from opentile.interface import OpenTile
 
-__version__ = '0.4.1'
+__version__ = '0.4.2'

opentile/common.py

@@ -19,8 +19,8 @@
 from typing import List, Optional, Sequence, Tuple
 
 import numpy as np
-from tifffile.tifffile import (COMPRESSION, FileHandle, TiffFile, TiffPage,
-                               TiffPageSeries, TiffTags)
+from tifffile.tifffile import (COMPRESSION, PHOTOMETRIC, FileHandle, TiffFile,
+                               TiffPage, TiffPageSeries, TiffTags)
 
 from opentile.geometry import Point, Region, Size, SizeMm
 from opentile.jpeg import Jpeg
@@ -136,9 +136,9 @@ def compression(self) -> COMPRESSION:
         return COMPRESSION(self._page.compression)
 
     @property
-    def photometric_interpretation(self) -> str:
+    def photometric_interpretation(self) -> PHOTOMETRIC:
         """Return photometric interpretation, e.g. 'YCBCR" or "RGB"."""
-        return str(self._page.photometric).split('.', maxsplit=1)[1]
+        return PHOTOMETRIC(self._page.photometric)
 
     @property
     def subsampling(self) -> Optional[Tuple[int, int]]:

opentile/histech_tiff_tiler.py

@@ -15,7 +15,8 @@
 from pathlib import Path
 from typing import Dict, Optional, Tuple, Union
 
-from tifffile.tifffile import FileHandle, TiffFile, TiffPage, TiffPageSeries
+from tifffile.tifffile import (PHOTOMETRIC, FileHandle, TiffFile, TiffPage,
+                               TiffPageSeries)
 
 from opentile.common import NativeTiledPage, Tiler
 from opentile.geometry import Size, SizeMm
@@ -63,14 +64,11 @@ def mpp(self) -> SizeMm:
         return self._mpp
 
     @property
-    def photometric_interpretation(self) -> str:
-        photometric_interpretation = str(
-            self._page.photometric
-        ).split('.', maxsplit=1)[1]
-        if photometric_interpretation == 'PALETTE':
-            return 'MINISBLACK'
-        else:
-            return photometric_interpretation
+    def photometric_interpretation(self) -> PHOTOMETRIC:
+        photometric_interpretation = PHOTOMETRIC(self._page.photometric)
+        if photometric_interpretation == PHOTOMETRIC.PALETTE:
+            return PHOTOMETRIC.MINISBLACK
+        return photometric_interpretation
 
     def _get_mpp_from_page(self) -> SizeMm:
         items_split = self._page.description.split('|')

opentile/jpeg.py

@@ -203,7 +203,7 @@ def encode(self, data: np.ndarray) -> bytes:
         bytes:
             Encoded frame of data.
         """
-        return self._turbo_jpeg.encode(data)
+        return self._turbo_jpeg.encode(data, pixel_format=TJPF_RGB)
 
     def crop_multiple(
         self,

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "opentile"
-version = "0.4.1"
+version = "0.4.2"
 description = "Read tiles from wsi-TIFF files"
 authors = ["Erik O Gabrielsson <[email protected]>"]
 license = "Apache-2.0"
@@ -20,7 +20,7 @@ tifffile = "^2022.5.4"
 numpy = "^1.22.0"
 PyTurboJPEG = "^1.6.1"
 Pillow = "^9.1.1"
-imagecodecs = "^2021.8.26"
+imagecodecs = "^2022.9.26"
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.2"

tests/test_histech_tiff_tiler.py

@@ -16,6 +16,8 @@
 from hashlib import md5
 
 import pytest
+from tifffile.tifffile import PHOTOMETRIC
+
 from opentile.histech_tiff_tiler import HistechTiffTiler
 
 from .filepaths import histech_file_path
@@ -56,7 +58,7 @@ def test_get_tile(self):
 
     def test_photometric_interpretation(self):
         self.assertEqual(
-            'YCBCR',
+            PHOTOMETRIC.YCBCR,
             self.tiler.get_level(0).photometric_interpretation
         )
 

tests/test_ndpi_tiler.py

@@ -12,12 +12,14 @@
 #    See the License for the specific language governing permissions and
 #    limitations under the License.
 
-from datetime import datetime
 import unittest
+from datetime import datetime
 from hashlib import md5
 from typing import cast
 
 import pytest
+from tifffile.tifffile import PHOTOMETRIC
+
 from opentile.geometry import Point, Size
 from opentile.ndpi_tiler import (NdpiCache, NdpiFrameJob, NdpiStripedPage,
                                  NdpiTile, NdpiTiler)
@@ -314,7 +316,7 @@ def test_adjust_tile_size(self):
 
     def test_photometric_interpretation(self):
         self.assertEqual(
-            'YCBCR',
+            PHOTOMETRIC.YCBCR,
             self.tiler.get_level(0).photometric_interpretation
         )
 

tests/test_philips_tiff_tiler.py

@@ -12,11 +12,13 @@
 #    See the License for the specific language governing permissions and
 #    limitations under the License.
 
-from datetime import datetime
 import unittest
+from datetime import datetime
 from hashlib import md5
 
 import pytest
+from tifffile.tifffile import PHOTOMETRIC
+
 from opentile.philips_tiff_tiler import PhilipsTiffTiler
 
 from .filepaths import philips_file_path
@@ -56,7 +58,7 @@ def test_get_tile(self):
 
     def test_photometric_interpretation(self):
         self.assertEqual(
-            'YCBCR',
+            PHOTOMETRIC.YCBCR,
             self.tiler.get_level(0).photometric_interpretation
         )
 

tests/test_svs_tiler.py

@@ -12,12 +12,14 @@
 #    See the License for the specific language governing permissions and
 #    limitations under the License.
 
-from datetime import datetime
 import unittest
+from datetime import datetime
 from hashlib import md5
 from typing import cast
 
 import pytest
+from tifffile.tifffile import PHOTOMETRIC
+
 from opentile.geometry import Point
 from opentile.svs_tiler import SvsTiledPage, SvsTiler
 
@@ -91,7 +93,7 @@ def test_detect_corrupt_edges(self):
 
     def test_photometric_interpretation(self):
         self.assertEqual(
-            'RGB',
+            PHOTOMETRIC.RGB,
             self.tiler.get_level(0).photometric_interpretation
         )