Merge 983e824 into 036429b

src/histolab/slide.py

@@ -175,6 +175,17 @@ def name(self) -> str:
         """
         return ntpath.basename(self._path).split(".")[0]
 
+    @lazyproperty
+    def processed_path(self) -> str:
+        """Retrieve the path to store processed files generated from the slide.
+
+        Returns
+        -------
+        str
+            Path to store processed files generated from the slide
+        """
+        return self._processed_path
+
     def resampled_array(self, scale_factor: int = 32) -> np.array:
         """Retrieve the resampled array from the original slide
 

src/histolab/tiler.py

@@ -1,3 +1,4 @@
+import os
 from abc import abstractmethod
 from typing import Tuple
 
@@ -178,7 +179,9 @@ def extract(self, slide: Slide):
 
         for tiles_counter, (tile, tile_wsi_coords) in enumerate(grid_tiles):
             tile_filename = self._tile_filename(tile_wsi_coords, tiles_counter)
-            tile.save(tile_filename)
+            root_folder = slide.processed_path
+            full_tile_path = os.path.join(root_folder, tile_filename)
+            tile.save(full_tile_path)
             print(f"\t Tile {tiles_counter} saved: {tile_filename}")
 
         print(f"{tiles_counter+1} Grid Tiles have been saved.")
@@ -410,7 +413,8 @@ def extract(self, slide: Slide):
         tiles_counter = 0
         for tiles_counter, (tile, tile_wsi_coords) in enumerate(random_tiles):
             tile_filename = self._tile_filename(tile_wsi_coords, tiles_counter)
-            tile.save(tile_filename)
+            full_tile_path = os.path.join(slide.processed_path, tile_filename)
+            tile.save(full_tile_path)
             print(f"\t Tile {tiles_counter} saved: {tile_filename}")
         print(f"{tiles_counter+1} Random Tiles have been saved.")
 

tests/unit/test_tiler.py

@@ -297,6 +297,38 @@ def it_knows_its_box_mask_lvl(
             box_mask_lvl.todense(), expected_box_mask_lvl.todense()
         )
 
+    def it_can_extract_random_tiles(self, request, tmpdir):
+        tmp_path_ = tmpdir.mkdir("myslide")
+        image = PILImageMock.DIMS_500X500_RGBA_COLOR_155_249_240
+        image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
+        slide_path = os.path.join(tmp_path_, "mywsi.png")
+        slide = Slide(slide_path, os.path.join(tmp_path_, "processed"))
+        _random_tiles_generator = method_mock(
+            request, RandomTiler, "_random_tiles_generator"
+        )
+        coords = CoordinatePair(0, 10, 0, 10)
+        tile = Tile(image, coords)
+        _random_tiles_generator.return_value = [(tile, coords), (tile, coords)]
+        _tile_filename = method_mock(request, RandomTiler, "_tile_filename")
+        _tile_filename.side_effect = [
+            os.path.join(tmp_path_, "processed", f"tile_{i}_level2_0-10-0-10.png")
+            for i in range(2)
+        ]
+        random_tiler = RandomTiler((10, 10), n_tiles=2, level=2)
+
+        random_tiler.extract(slide)
+
+        assert _tile_filename.call_args_list == [
+            call(random_tiler, coords, 0),
+            call(random_tiler, coords, 1),
+        ]
+        assert os.path.exists(
+            os.path.join(tmp_path_, "processed", "tile_0_level2_0-10-0-10.png")
+        )
+        assert os.path.exists(
+            os.path.join(tmp_path_, "processed", "tile_1_level2_0-10-0-10.png")
+        )
+
     # fixtures -------------------------------------------------------
 
     @pytest.fixture(
@@ -515,7 +547,9 @@ def it_can_generate_grid_tiles(
         generated_tiles = list(grid_tiler._grid_tiles_generator(slide))
 
         _grid_coordinates_generator.assert_called_once_with(grid_tiler, slide)
-        _extract_tile.call_args_list == ([call(coords1, 0), call(coords2, 0)])
+        assert _extract_tile.call_args_list == (
+            [call(slide, coords1, 0), call(slide, coords2, 0)]
+        )
         assert len(generated_tiles) == expected_n_tiles
         if expected_n_tiles == 2:
             assert generated_tiles == [(tile1, coords1), (tile2, coords2)]
@@ -524,6 +558,31 @@ def it_can_generate_grid_tiles(
         if expected_n_tiles == 0:
             assert generated_tiles == []
 
+    def but_with_wrong_coordinates(self, request, tmpdir):
+        tmp_path_ = tmpdir.mkdir("myslide")
+        image = PILImageMock.DIMS_500X500_RGBA_COLOR_155_249_240
+        image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
+        slide_path = os.path.join(tmp_path_, "mywsi.png")
+        slide = Slide(slide_path, "processed")
+        _has_enough_tissue = method_mock(request, Tile, "has_enough_tissue")
+        _has_enough_tissue.return_value = False
+        _grid_coordinates_generator = method_mock(
+            request, GridTiler, "_grid_coordinates_generator"
+        )
+        coords1 = CoordinatePair(600, 610, 600, 610)
+        coords2 = CoordinatePair(0, 10, 0, 10)
+        _grid_coordinates_generator.return_value = [coords1, coords2]
+        grid_tiler = GridTiler((10, 10), level=0, check_tissue=False)
+
+        generated_tiles = list(grid_tiler._grid_tiles_generator(slide))
+
+        _grid_coordinates_generator.assert_called_once_with(grid_tiler, slide)
+        assert len(generated_tiles) == 1
+        # generated_tiles[0][0] is a Tile object but we don't know what object it is
+        # because Slide.extract_tile is not mocked (for the exception to happen inside)
+        assert isinstance(generated_tiles[0][0], Tile)
+        assert generated_tiles[0][1] == coords2
+
     def and_doesnt_raise_error_with_wrong_coordinates(self, request, tmpdir):
         tmp_path_ = tmpdir.mkdir("myslide")
         image = PILImageMock.DIMS_500X500_RGBA_COLOR_155_249_240
@@ -541,6 +600,36 @@ def and_doesnt_raise_error_with_wrong_coordinates(self, request, tmpdir):
         assert len(generated_tiles) == 0
         _grid_coordinates_generator.assert_called_once_with(grid_tiler, slide)
 
+    def it_can_extract_grid_tiles(self, request, tmpdir):
+        tmp_path_ = tmpdir.mkdir("myslide")
+        image = PILImageMock.DIMS_500X500_RGBA_COLOR_155_249_240
+        image.save(os.path.join(tmp_path_, "mywsi.png"), "PNG")
+        slide_path = os.path.join(tmp_path_, "mywsi.png")
+        slide = Slide(slide_path, os.path.join(tmp_path_, "processed"))
+        _grid_tiles_generator = method_mock(request, GridTiler, "_grid_tiles_generator")
+        coords = CoordinatePair(0, 10, 0, 10)
+        tile = Tile(image, coords)
+        _grid_tiles_generator.return_value = [(tile, coords), (tile, coords)]
+        _tile_filename = method_mock(request, GridTiler, "_tile_filename")
+        _tile_filename.side_effect = [
+            os.path.join(tmp_path_, "processed", f"tile_{i}_level2_0-10-0-10.png")
+            for i in range(2)
+        ]
+        grid_tiler = GridTiler((10, 10), level=2)
+
+        grid_tiler.extract(slide)
+
+        assert _tile_filename.call_args_list == [
+            call(grid_tiler, coords, 0),
+            call(grid_tiler, coords, 1),
+        ]
+        assert os.path.exists(
+            os.path.join(tmp_path_, "processed", "tile_0_level2_0-10-0-10.png")
+        )
+        assert os.path.exists(
+            os.path.join(tmp_path_, "processed", "tile_1_level2_0-10-0-10.png")
+        )
+
     # fixtures -------------------------------------------------------
 
     @pytest.fixture(