Merge pull request #83 from erikogabrielsson/icc-profile

Add color_profile property and profile to Pil images if available

tiffslide/tests/test_compatibility.py

@@ -84,7 +84,14 @@ def ts_slide(file_name):
 
 @pytest.fixture()
 def os_slide(file_name):
-    from openslide import OpenSlide
+    import os
+    if hasattr(os, 'add_dll_directory'):
+        openslide_path = os.getenv("OPENSLIDE_PATH")
+        if openslide_path is not None:
+            with os.add_dll_directory(openslide_path):
+                from openslide import OpenSlide
+    else:
+        from openslide import OpenSlide
 
     yield OpenSlide(file_name)
 
@@ -233,3 +240,28 @@ def test_read_region_equality_level_common_max(ts_slide, os_slide, file_name):
 
     max_difference = np.max(np.abs(ts_arr.astype(int) - os_arr.astype(int)))
     assert max_difference <= (0 if exact else 1)
+
+def test_color_profile_property(ts_slide, os_slide):
+    if os_slide.color_profile is None:
+        assert ts_slide.color_profile is None
+    else:
+        assert ts_slide.color_profile.tobytes() == os_slide.color_profile.tobytes()
+
+def test_icc_profile_in_thumbnail(ts_slide, os_slide):
+    ts_slide_thumbnail = ts_slide.get_thumbnail((200, 200))
+    os_slide_thumbnail = os_slide.get_thumbnail((200, 200))
+
+    if os_slide_thumbnail.info.get("icc_profile") is None:
+        assert ts_slide_thumbnail.info.get("icc_profile") is None
+    else:
+        assert os_slide_thumbnail.info["icc_profile"] == ts_slide_thumbnail.info["icc_profile"]
+
+
+def test_icc_profile_in_region(ts_slide, os_slide):
+    ts_slide_region = ts_slide.read_region((0, 0), 0, (200, 200))
+    os_slide_region = os_slide.read_region((0, 0), 0, (200, 200))
+
+    if os_slide_region.info.get("icc_profile") is None:
+        assert ts_slide_region.info.get("icc_profile") is None
+    else:
+        assert os_slide_region.info["icc_profile"] == ts_slide_region.info["icc_profile"]

tiffslide/tiffslide.py

@@ -1,4 +1,5 @@
 from __future__ import annotations
+import io
 
 import math
 import os.path
@@ -13,7 +14,6 @@
 from typing import Iterator
 from typing import Literal
 from typing import Mapping
-from typing import Optional
 from typing import TypeVar
 from typing import overload
 from warnings import warn
@@ -25,7 +25,7 @@
 from fsspec.core import url_to_fs
 from fsspec.implementations.local import LocalFileSystem
 from fsspec.implementations.reference import ReferenceFileSystem
-from PIL import Image
+from PIL import Image, ImageCms
 from tifffile import TiffFile
 from tifffile import TiffFileError as TiffFileError
 from tifffile import TiffPage
@@ -240,6 +240,13 @@ def associated_images(self) -> _LazyAssociatedImagesDict:
         series = self.ts_tifffile.series[idx + 1 :]
         return _LazyAssociatedImagesDict(series)
 
+    @cached_property
+    def color_profile(self) -> ImageCms.ImageCmsProfile | None:
+        """return the color profile of the image if present"""
+        if self._profile is None:
+            return None
+        return ImageCms.getOpenProfile(io.BytesIO(self._profile))
+
     def get_best_level_for_downsample(self, downsample: float) -> int:
         """return the best level for a given downsampling factor"""
         if downsample <= 1.0:
@@ -411,9 +418,12 @@ def read_region(
         if as_array:
             return arr
         elif axes == "YX":
-            return Image.fromarray(arr[..., 0])
+            image = Image.fromarray(arr[..., 0])
         else:
-            return Image.fromarray(arr)
+            image = Image.fromarray(arr)
+        if self._profile is not None:
+            image.info['icc_profile'] = self._profile
+        return image
 
     def _read_region_loc_transform(
         self, location: tuple[int, int], level: int
@@ -484,8 +494,16 @@ def get_thumbnail(
         except ValueError:
             # see: https://github.com/python-pillow/Pillow/blob/95cff6e959/src/libImaging/Resample.c#L559-L588
             thumb.thumbnail(size, _NEAREST)
+        if self._profile is not None:
+            thumb.info['icc_profile'] = self._profile
         return thumb
 
+    @cached_property
+    def _profile(self) -> bytes | None:
+        """return the color profile of the image if present"""
+        parser = _IccParser(self._tifffile)
+        return parser.parse()
+
 
 class NotTiffSlide(TiffSlide):
     # noinspection PyMissingConstructor
@@ -771,6 +789,7 @@ def parse_aperio(self) -> dict[str, Any]:
 
         # collect level info
         md.update(self.collect_level_info(series0))
+
         return md
 
     def parse_leica(self) -> dict[str, Any]:
@@ -1031,6 +1050,21 @@ def _parse_metadata_leica(image_description: str) -> dict[str, Any]:
 
     return md
 
+class _IccParser:
+    """parse ICC profile from tiff tags"""
+
+    def __init__(self, tf: TiffFile) -> None:
+        self._tf = tf
+
+    def parse(self) -> bytes | None:
+        """return the ICC profile if present"""
+        page = self._tf.pages[0]
+        if isinstance(page, TiffPage) and "InterColorProfile" in page.tags:
+            icc_profile = page.tags["InterColorProfile"].value
+            if isinstance(icc_profile, bytes):
+                return icc_profile
+        return None
+
 
 # --- helper functions --------------------------------------------------------