type the deepzoom generator

Signed-off-by: Sam Maxwell <[email protected]>

Author: sammaxwellxyz

openslide/deepzoom.py

@@ -25,6 +25,7 @@
 
 from io import BytesIO
 import math
+from typing import List, Tuple
 from xml.etree.ElementTree import Element, ElementTree, SubElement
 
 from PIL import Image
@@ -44,7 +45,13 @@ class DeepZoomGenerator:
         openslide.PROPERTY_NAME_BOUNDS_HEIGHT,
     )
 
-    def __init__(self, osr, tile_size=254, overlap=1, limit_bounds=False):
+    def __init__(
+        self,
+        osr: openslide.AbstractSlide,
+        tile_size: int = 254,
+        overlap: int = 1,
+        limit_bounds: bool = False,
+    ):
         """Create a DeepZoomGenerator wrapping an OpenSlide object.
 
         osr:          a slide object.
@@ -79,13 +86,13 @@ def __init__(self, osr, tile_size=254, overlap=1, limit_bounds=False):
                 for prop, l0_lim in zip(self.BOUNDS_SIZE_PROPS, osr.dimensions)
             )
             # Dimensions of active area
-            self._l_dimensions = tuple(
-                tuple(
-                    int(math.ceil(l_lim * scale))
-                    for l_lim, scale in zip(l_size, size_scale)
+            self._l_dimensions = [
+                (
+                    int(math.ceil(l_size[0] * size_scale[0])),
+                    int(math.ceil(l_size[1] * size_scale[1])),
                 )
                 for l_size in osr.level_dimensions
-            )
+            ]
         else:
             self._l_dimensions = osr.level_dimensions
             self._l0_offset = (0, 0)
@@ -94,25 +101,28 @@ def __init__(self, osr, tile_size=254, overlap=1, limit_bounds=False):
         z_size = self._l0_dimensions
         z_dimensions = [z_size]
         while z_size[0] > 1 or z_size[1] > 1:
-            z_size = tuple(max(1, int(math.ceil(z / 2))) for z in z_size)
+            z_size = (
+                max(1, int(math.ceil(z_size[0] / 2))),
+                max(1, int(math.ceil(z_size[1] / 2))),
+            )
             z_dimensions.append(z_size)
-        self._z_dimensions = tuple(reversed(z_dimensions))
+        self._z_dimensions = list(reversed(z_dimensions))
 
         # Tile
-        def tiles(z_lim):
+        def tiles(z_lim: int) -> int:
             return int(math.ceil(z_lim / self._z_t_downsample))
 
-        self._t_dimensions = tuple(
+        self._t_dimensions = [
             (tiles(z_w), tiles(z_h)) for z_w, z_h in self._z_dimensions
-        )
+        ]
 
         # Deep Zoom level count
         self._dz_levels = len(self._z_dimensions)
 
         # Total downsamples for each Deep Zoom level
-        l0_z_downsamples = tuple(
+        l0_z_downsamples: List[int] = [
             2 ** (self._dz_levels - dz_level - 1) for dz_level in range(self._dz_levels)
-        )
+        ]
 
         # Preferred slide levels for each Deep Zoom level
         self._slide_from_dz_level = tuple(
@@ -121,19 +131,19 @@ def tiles(z_lim):
 
         # Piecewise downsamples
         self._l0_l_downsamples = self._osr.level_downsamples
-        self._l_z_downsamples = tuple(
+        self._l_z_downsamples = [
             l0_z_downsamples[dz_level]
             / self._l0_l_downsamples[self._slide_from_dz_level[dz_level]]
             for dz_level in range(self._dz_levels)
-        )
+        ]
 
         # Slide background color
-        self._bg_color = '#' + self._osr.properties.get(
-            openslide.PROPERTY_NAME_BACKGROUND_COLOR, 'ffffff'
+        self._bg_color = "#" + self._osr.properties.get(
+            openslide.PROPERTY_NAME_BACKGROUND_COLOR, "ffffff"
         )
 
-    def __repr__(self):
-        return '{}({!r}, tile_size={!r}, overlap={!r}, limit_bounds={!r})'.format(
+    def __repr__(self) -> str:
+        return "{}({!r}, tile_size={!r}, overlap={!r}, limit_bounds={!r})".format(
             self.__class__.__name__,
             self._osr,
             self._z_t_downsample,
@@ -142,26 +152,26 @@ def __repr__(self):
         )
 
     @property
-    def level_count(self):
+    def level_count(self) -> int:
         """The number of Deep Zoom levels in the image."""
         return self._dz_levels
 
     @property
-    def level_tiles(self):
+    def level_tiles(self) -> List[Tuple[int, int]]:
         """A list of (tiles_x, tiles_y) tuples for each Deep Zoom level."""
         return self._t_dimensions
 
     @property
-    def level_dimensions(self):
+    def level_dimensions(self) -> List[Tuple[int, int]]:
         """A list of (pixels_x, pixels_y) tuples for each Deep Zoom level."""
         return self._z_dimensions
 
     @property
-    def tile_count(self):
+    def tile_count(self) -> int:
         """The total number of Deep Zoom tiles in the image."""
         return sum(t_cols * t_rows for t_cols, t_rows in self._t_dimensions)
 
-    def get_tile(self, level, address):
+    def get_tile(self, level: int, address: Tuple[int, int]) -> Image.Image:
         """Return an RGB PIL.Image for a tile.
 
         level:     the Deep Zoom level.
@@ -171,25 +181,27 @@ def get_tile(self, level, address):
         # Read tile
         args, z_size = self._get_tile_info(level, address)
         tile = self._osr.read_region(*args)
-        profile = tile.info.get('icc_profile')
+        profile = tile.info.get("icc_profile")
 
         # Apply on solid background
-        bg = Image.new('RGB', tile.size, self._bg_color)
+        bg = Image.new("RGB", tile.size, self._bg_color)
         tile = Image.composite(tile, bg, tile)
 
         # Scale to the correct size
         if tile.size != z_size:
             # Image.Resampling added in Pillow 9.1.0
             # Image.LANCZOS removed in Pillow 10
-            tile.thumbnail(z_size, getattr(Image, 'Resampling', Image).LANCZOS)
+            tile.thumbnail(z_size, getattr(Image, "Resampling", Image).LANCZOS)
 
         # Reference ICC profile
         if profile is not None:
-            tile.info['icc_profile'] = profile
+            tile.info["icc_profile"] = profile
 
         return tile
 
-    def _get_tile_info(self, dz_level, t_location):
+    def _get_tile_info(
+        self, dz_level: int, t_location: Tuple[int, int]
+    ) -> Tuple[Tuple[Tuple[int, int], int, Tuple[int, int]], Tuple[int, int]]:
         # Check parameters
         if dz_level < 0 or dz_level >= self._dz_levels:
             raise ValueError("Invalid level")
@@ -208,42 +220,62 @@ def _get_tile_info(self, dz_level, t_location):
         )
 
         # Get final size of the tile
-        z_size = tuple(
-            min(self._z_t_downsample, z_lim - self._z_t_downsample * t) + z_tl + z_br
-            for t, z_lim, z_tl, z_br in zip(
-                t_location, self._z_dimensions[dz_level], z_overlap_tl, z_overlap_br
+        z_size = (
+            min(
+                self._z_t_downsample,
+                self._z_dimensions[dz_level][0] - self._z_t_downsample * t_location[0],
+            )
+            + z_overlap_tl[0]
+            + z_overlap_br[0],
+            min(
+                self._z_t_downsample,
+                self._z_dimensions[dz_level][1] - self._z_t_downsample * t_location[1],
             )
+            + z_overlap_tl[1]
+            + z_overlap_br[1],
         )
 
         # Obtain the region coordinates
-        z_location = [self._z_from_t(t) for t in t_location]
-        l_location = [
-            self._l_from_z(dz_level, z - z_tl)
-            for z, z_tl in zip(z_location, z_overlap_tl)
-        ]
+        z_location = (self._z_from_t(t_location[0]), self._z_from_t(t_location[1]))
+        l_location = (
+            self._l_from_z(dz_level, z_location[0] - z_overlap_tl[0]),
+            self._l_from_z(dz_level, z_location[1] - z_overlap_tl[1]),
+        )
         # Round location down and size up, and add offset of active area
-        l0_location = tuple(
-            int(self._l0_from_l(slide_level, l) + l0_off)
-            for l, l0_off in zip(l_location, self._l0_offset)
+        l0_location = (
+            int(self._l0_from_l(slide_level, l_location[0]) + self._l0_offset[0]),
+            int(self._l0_from_l(slide_level, l_location[1]) + self._l0_offset[1]),
         )
-        l_size = tuple(
-            int(min(math.ceil(self._l_from_z(dz_level, dz)), l_lim - math.ceil(l)))
-            for l, dz, l_lim in zip(l_location, z_size, self._l_dimensions[slide_level])
+        l_size = (
+            int(
+                min(
+                    math.ceil(self._l_from_z(dz_level, z_size[0])),
+                    self._l_dimensions[slide_level][0] - math.ceil(l_location[0]),
+                )
+            ),
+            int(
+                min(
+                    math.ceil(self._l_from_z(dz_level, z_size[1])),
+                    self._l_dimensions[slide_level][1] - math.ceil(l_location[1]),
+                )
+            ),
         )
 
         # Return read_region() parameters plus tile size for final scaling
         return ((l0_location, slide_level, l_size), z_size)
 
-    def _l0_from_l(self, slide_level, l):
+    def _l0_from_l(self, slide_level: int, l: float) -> float:
         return self._l0_l_downsamples[slide_level] * l
 
-    def _l_from_z(self, dz_level, z):
+    def _l_from_z(self, dz_level: int, z: int) -> float:
         return self._l_z_downsamples[dz_level] * z
 
-    def _z_from_t(self, t):
+    def _z_from_t(self, t: int) -> int:
         return self._z_t_downsample * t
 
-    def get_tile_coordinates(self, level, address):
+    def get_tile_coordinates(
+        self, level: int, address: Tuple[int, int]
+    ) -> Tuple[Tuple[int, int], int, Tuple[int, int]]:
         """Return the OpenSlide.read_region() arguments for the specified tile.
 
         Most users should call get_tile() rather than calling
@@ -254,28 +286,30 @@ def get_tile_coordinates(self, level, address):
                    tuple."""
         return self._get_tile_info(level, address)[0]
 
-    def get_tile_dimensions(self, level, address):
+    def get_tile_dimensions(
+        self, level: int, address: Tuple[int, int]
+    ) -> Tuple[int, int]:
         """Return a (pixels_x, pixels_y) tuple for the specified tile.
 
         level:     the Deep Zoom level.
         address:   the address of the tile within the level as a (col, row)
                    tuple."""
         return self._get_tile_info(level, address)[1]
 
-    def get_dzi(self, format):
+    def get_dzi(self, format: str) -> str:
         """Return a string containing the XML metadata for the .dzi file.
 
         format:    the format of the individual tiles ('png' or 'jpeg')"""
         image = Element(
-            'Image',
+            "Image",
             TileSize=str(self._z_t_downsample),
             Overlap=str(self._z_overlap),
             Format=format,
-            xmlns='http://schemas.microsoft.com/deepzoom/2008',
+            xmlns="http://schemas.microsoft.com/deepzoom/2008",
         )
         w, h = self._l0_dimensions
-        SubElement(image, 'Size', Width=str(w), Height=str(h))
+        SubElement(image, "Size", Width=str(w), Height=str(h))
         tree = ElementTree(element=image)
         buf = BytesIO()
-        tree.write(buf, encoding='UTF-8')
-        return buf.getvalue().decode('UTF-8')
+        tree.write(buf, encoding="UTF-8")
+        return buf.getvalue().decode("UTF-8")

tests/test_deepzoom.py

@@ -36,7 +36,7 @@ def tearDown(self):
     def test_repr(self):
         self.assertEqual(
             repr(self.dz),
-            ('DeepZoomGenerator(%r, tile_size=254, overlap=1, ' + 'limit_bounds=False)')
+            ("DeepZoomGenerator(%r, tile_size=254, overlap=1, " + "limit_bounds=False)")
             % self.osr,
         )
 
@@ -45,7 +45,7 @@ def test_metadata(self):
         self.assertEqual(self.dz.tile_count, 11)
         self.assertEqual(
             self.dz.level_tiles,
-            (
+            [
                 (1, 1),
                 (1, 1),
                 (1, 1),
@@ -56,11 +56,11 @@ def test_metadata(self):
                 (1, 1),
                 (1, 1),
                 (2, 1),
-            ),
+            ],
         )
         self.assertEqual(
             self.dz.level_dimensions,
-            (
+            [
                 (1, 1),
                 (2, 1),
                 (3, 2),
@@ -71,7 +71,7 @@ def test_metadata(self):
                 (75, 63),
                 (150, 125),
                 (300, 250),
-            ),
+            ],
         )
 
     def test_get_tile(self):
@@ -80,7 +80,7 @@ def test_get_tile(self):
     def test_tile_color_profile(self):
         if self.CLASS is OpenSlide and not lowlevel.read_icc_profile.available:
             self.skipTest("requires OpenSlide 4.0.0")
-        self.assertEqual(len(self.dz.get_tile(9, (1, 0)).info['icc_profile']), 588)
+        self.assertEqual(len(self.dz.get_tile(9, (1, 0)).info["icc_profile"]), 588)
 
     def test_get_tile_bad_level(self):
         self.assertRaises(ValueError, lambda: self.dz.get_tile(-1, (0, 0)))
@@ -100,15 +100,15 @@ def test_get_tile_dimensions(self):
 
     def test_get_dzi(self):
         self.assertTrue(
-            'http://schemas.microsoft.com/deepzoom/2008' in self.dz.get_dzi('jpeg')
+            "http://schemas.microsoft.com/deepzoom/2008" in self.dz.get_dzi("jpeg")
         )
 
 
 class TestSlideDeepZoom(_BoxesDeepZoomTest, unittest.TestCase):
     CLASS = OpenSlide
-    FILENAME = 'boxes.tiff'
+    FILENAME = "boxes.tiff"
 
 
 class TestImageDeepZoom(_BoxesDeepZoomTest, unittest.TestCase):
     CLASS = ImageSlide
-    FILENAME = 'boxes.png'
+    FILENAME = "boxes.png"