Merge 965f7f3 into d5945e1

setup.py

@@ -31,7 +31,6 @@ def ascii_bytes_from(path, *paths):
     "Pillow",
     "scikit-image",
     "scipy",
-    "sparse",
     "openslide-wrapper",
     "typing_extensions",
 ]

src/histolab/exceptions.py

@@ -0,0 +1,14 @@
+class LevelError(Exception):
+    """Raised when a requested level is not available"""
+
+    def __init__(self, *args) -> None:
+        if args:
+            self.message = args[0]
+        else:
+            self.message = None
+
+    def __str__(self):
+        if self.message:
+            return self.message
+        else:
+            return ""

src/histolab/scorer.py

@@ -0,0 +1,22 @@
+from abc import abstractmethod
+
+import numpy as np
+
+from histolab.tile import Tile
+
+try:
+    from typing import Protocol, runtime_checkable
+except ImportError:
+    from typing_extensions import Protocol, runtime_checkable
+
+
+@runtime_checkable
+class Scorer(Protocol):
+    @abstractmethod
+    def __call__(self, tile: Tile) -> float:
+        raise NotImplementedError
+
+
+class RandomScorer(Scorer):
+    def __call__(self, tile: Tile) -> float:
+        return np.random.random()

src/histolab/slide.py

@@ -30,8 +30,8 @@
 import numpy as np
 import openslide
 import PIL
-import sparse
 
+from .exceptions import LevelError
 from .filters import image_filters as imf
 from .filters import morphological_filters as mof
 from .tile import Tile
@@ -42,7 +42,6 @@
     polygon_to_mask_array,
     region_coordinates,
     regions_from_binary_mask,
-    resize_mask,
     scale_coordinates,
 )
 
@@ -97,20 +96,32 @@ def level_dimensions(self, level: int = 0) -> Tuple[int, int]:
         try:
             return self._wsi.level_dimensions[level]
         except IndexError:
-            raise ValueError(
+            raise LevelError(
                 f"Level {level} not available. Number of available levels: "
                 f"{len(self._wsi.level_dimensions)}"
             )
 
+    @lazyproperty
+    def levels(self) -> List[int]:
+        """Return the slide's available levels
+
+        Returns
+        -------
+        List[int]
+            The levels available
+        """
+        return list(range(len(self._wsi.level_dimensions)))
+
     @lazyproperty
     @lru_cache(maxsize=100)
-    def biggest_tissue_box_mask(self) -> sparse._coo.core.COO:
-        """Return the binary mask of the box containing the max area of tissue.
+    def biggest_tissue_box_mask(self) -> np.ndarray:
+        """Return the thumbnail binary mask of the box containing the max tissue area.
 
         Returns
         -------
-        mask: sparse._coo.core.COO
-            Binary mask of the box containing the max area of tissue.
+        mask: np.ndarray
+            Binary mask of the box containing the max area of tissue. The dimensions are
+            those of the thumbnail.
 
         """
         thumb = self._wsi.get_thumbnail(self._thumbnail_size)
@@ -123,8 +134,7 @@ def biggest_tissue_box_mask(self) -> sparse._coo.core.COO:
         thumb_bbox_mask = polygon_to_mask_array(
             self._thumbnail_size, biggest_region_coordinates
         )
-        thumb_bbox_mask_sparse = sparse.COO(thumb_bbox_mask)
-        return resize_mask(thumb_bbox_mask_sparse, self.dimensions)
+        return thumb_bbox_mask
 
     def extract_tile(self, coords: CoordinatePair, level: int) -> Tile:
         """Extract a tile of the image at the selected level.