Thumbnails

CHANGELOG.md

@@ -7,6 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.15.0] - 2025-01-30
+
+### Added
+
+- Reading out thumbnails from supported formats.
+
 ## [0.14.0] - 2025-01-29
 
 ### Added
@@ -237,7 +243,8 @@ 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/v0.14.0..HEAD
+[Unreleased]: https://github.com/imi-bigpicture/opentile/compare/v0.15.0..HEAD
+[0.15.0]: https://github.com/imi-bigpicture/opentile/compare/v0.14.0..v0.15.0
 [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

opentile/__init__.py

@@ -17,4 +17,4 @@
 from opentile.opentile import OpenTile
 from opentile.metadata import Metadata
 
-__version__ = "0.14.0"
+__version__ = "0.15.0"

opentile/formats/histech/histech_tiff_tiler.py

@@ -73,6 +73,9 @@ def get_label(self, page: int = 0) -> TiffImage:
     def get_overview(self, page: int = 0) -> TiffImage:
         raise NotImplementedError()
 
+    def get_thumbnail(self, page: int = 0) -> TiffImage:
+        raise NotImplementedError()
+
     @staticmethod
     def _is_level_series(series: TiffPageSeries) -> bool:
         return series.index == 0
@@ -86,3 +89,8 @@ def _is_overview_series(series: TiffPageSeries) -> bool:
     def _is_label_series(series: TiffPageSeries) -> bool:
         """Return true if series is a label series."""
         return False
+
+    @staticmethod
+    def _is_thumbnail_series(series: TiffPageSeries) -> bool:
+        """Return true if series is a thumbnail series."""
+        return False

opentile/formats/ndpi/ndpi_tiler.py

@@ -103,6 +103,11 @@ def _is_label_series(series: TiffPageSeries) -> bool:
         """Return true if series is a label series."""
         return False
 
+    @staticmethod
+    def _is_thumbnail_series(series: TiffPageSeries) -> bool:
+        """Return true if series is a thumbnail series."""
+        return False
+
     @staticmethod
     def _adjust_tile_size(
         requested_tile_width: int, smallest_stripe_width: Optional[int] = None
@@ -224,3 +229,6 @@ def get_overview(self, page: int = 0) -> TiffImage:
         return NdpiCroppedImage(
             tiff_page, self._file, self._jpeg, (self._label_crop_position, 1.0)
         )
+
+    def get_thumbnail(self, page: int = 0) -> TiffImage:
+        raise NotImplementedError()

opentile/formats/ome/ome_tiff_tiler.py

@@ -73,8 +73,10 @@ def supported(cls, tiff_file: TiffFile) -> bool:
         return tiff_file.is_ome
 
     def _is_level_series(self, series: TiffPageSeries) -> bool:
-        return not self._is_label_series(series) and not self._is_overview_series(
-            series
+        return (
+            not self._is_label_series(series)
+            and not self._is_overview_series(series)
+            and not self._is_thumbnail_series(series)
         )
 
     def _is_label_series(self, series: TiffPageSeries) -> bool:
@@ -83,6 +85,9 @@ def _is_label_series(self, series: TiffPageSeries) -> bool:
     def _is_overview_series(self, series: TiffPageSeries) -> bool:
         return series.name.strip() == "macro"
 
+    def _is_thumbnail_series(self, series: TiffPageSeries) -> bool:
+        return series.name.strip() == "thumbnail"
+
     def _get_mpp(self, series_index: int) -> SizeMm:
         mpp = self._get_optional_mpp(series_index)
         if mpp is None:
@@ -134,6 +139,12 @@ def get_overview(self, page: int = 0) -> TiffImage:
             raise ValueError("No overview detected in file")
         return self._get_associated_image(self._overview_series_index, page)
 
+    @lru_cache(None)
+    def get_thumbnail(self, page: int = 0) -> TiffImage:
+        if self._thumbnail_series_index is None:
+            raise ValueError("No thumbnail detected in file")
+        return self._get_associated_image(self._thumbnail_series_index, page)
+
     def _get_associated_image(self, series: int, page: int = 0) -> TiffImage:
         tiff_page = self._get_tiff_page(series, 0, page)
         return OmeTiffImage(

opentile/formats/philips/philips_tiff_tiler.py

@@ -72,6 +72,9 @@ def get_label(self, page: int = 0) -> TiffImage:
     def get_overview(self, page: int = 0) -> TiffImage:
         return self._get_image(self._overview_series_index, 0, page)
 
+    def get_thumbnail(self, page: int = 0) -> TiffImage:
+        return self._get_image(self._thumbnail_series_index, 0, page)
+
     @lru_cache(None)
     def _get_image(self, series: int, level: int, page: int = 0) -> TiffImage:
         """Return PhilipsTiffTiledPage for series, level, page."""
@@ -101,6 +104,13 @@ def _is_label_series(series: TiffPageSeries) -> bool:
         assert isinstance(page, TiffPage)
         return page.description.find("Label") > -1
 
+    @staticmethod
+    def _is_thumbnail_series(series: TiffPageSeries) -> bool:
+        """Return true if series is a thumbnail series."""
+        page = series.pages[0]
+        assert isinstance(page, TiffPage)
+        return page.description.find("Thumbnail") > -1
+
     @staticmethod
     def _get_associated_mpp_from_page(page: TiffPage):
         """Return mpp (um/pixel) for associated image (label or

opentile/formats/svs/svs_tiler.py

@@ -82,6 +82,10 @@ def _is_label_series(series: TiffPageSeries) -> bool:
     def _is_overview_series(series: TiffPageSeries) -> bool:
         return series.name == "Macro"
 
+    @staticmethod
+    def _is_thumbnail_series(series: TiffPageSeries) -> bool:
+        return series.name == "Thumbnail"
+
     @lru_cache(None)
     def get_level(self, level: int, page: int = 0) -> TiffImage:
         series = self._level_series_index
@@ -117,3 +121,13 @@ def get_overview(self, page: int = 0) -> TiffImage:
             self._file,
             self._jpeg,
         )
+
+    @lru_cache(None)
+    def get_thumbnail(self, page: int = 0) -> TiffImage:
+        if self._thumbnail_series_index is None:
+            raise ValueError("No overview detected in file")
+        return SvsStripedImage(
+            self._get_tiff_page(self._thumbnail_series_index, 0, page),
+            self._file,
+            self._jpeg,
+        )

opentile/tiler.py

@@ -53,13 +53,16 @@ def __init__(
         self._level_series_index = 0
         self._overview_series_index: Optional[int] = None
         self._label_series_index: Optional[int] = None
+        self._thumbnail_series_index: Optional[int] = None
         for series_index, series in enumerate(self.series):
             if self._is_level_series(series):
                 self._level_series_index = series_index
             if self._is_label_series(series):
                 self._label_series_index = series_index
             elif self._is_overview_series(series):
                 self._overview_series_index = series_index
+            elif self._is_thumbnail_series(series):
+                self._thumbnail_series_index = series_index
         self._icc_profile: Optional[bytes] = None
         base_page = self.series[self._level_series_index].pages[0]
         assert isinstance(base_page, TiffPage)
@@ -124,6 +127,18 @@ def overviews(self) -> List[TiffImage]:
             )
         ]
 
+    @property
+    def thumbnails(self) -> List[TiffImage]:
+        """Return list of thumbnail TiffImage."""
+        if self._thumbnail_series_index is None:
+            return []
+        return [
+            self.get_thumbnail(page_index)
+            for page_index, page in enumerate(
+                self.series[self._thumbnail_series_index].pages
+            )
+        ]
+
     @property
     def icc_profile(self) -> Optional[bytes]:
         """Return icc profile if found in file."""
@@ -191,6 +206,22 @@ def get_overview(self, page: int = 0) -> TiffImage:
         """
         raise NotImplementedError()
 
+    @abstractmethod
+    def get_thumbnail(self, page: int = 0) -> TiffImage:
+        """Return thumbnail TiffImage.
+
+        Parameters
+        ----------
+        page: int = 0
+            Index of page to get.
+
+        Returns
+        ----------
+        TiffImage
+            Thumbnail TiffImage.
+        """
+        raise NotImplementedError()
+
     @staticmethod
     @abstractmethod
     def _is_level_series(series: TiffPageSeries) -> bool:
@@ -209,6 +240,12 @@ def _is_label_series(series: TiffPageSeries) -> bool:
         """Return true if series is a label series."""
         raise NotImplementedError()
 
+    @staticmethod
+    @abstractmethod
+    def _is_thumbnail_series(series: TiffPageSeries) -> bool:
+        """Return true if series is a thumbnail series."""
+        raise NotImplementedError()
+
     def close(self) -> None:
         """Close tiff file."""
         self._file.close()