histolab · alessiamarcolini · Dec 31, 2020 · Dec 30, 2020 · Dec 30, 2020 · Dec 31, 2020
diff --git a/src/histolab/tile.py b/src/histolab/tile.py
@@ -153,25 +153,23 @@ def tissue_ratio(self) -> float:
 
     # ------- implementation helpers -------
 
-    def _has_only_some_tissue(self, near_zero_var_threshold: float = 0.1) -> np.bool_:
+    def _has_only_some_tissue(self, min_var: float = 150.0) -> np.bool_:
         """Check if the tile is composed by only some tissue.
 
         Parameters
         ----------
-        near_zero_var_threshold : float, optional
-            Minimum image variance after morphological operations (dilation, fill holes)
-            to consider the image to be composed by only some tissue, default is 0.1
+        min_var : float, optional
+            Minimum image variance to consider the image to be composed by only some
+            tissue, default is 150.
 
         Returns
         -------
         bool
             True if the image is composed by only some tissue. False if the tile is
             composed by all tissue or by no tissue at all.
         """
-        filters = FiltersComposition(Tile).tissue_mask_filters
-        tissue_mask = filters(self._image)
-
-        return np.var(tissue_mask) > near_zero_var_threshold
+        np_img = np.array(self._image.convert("L"))
+        return np.var(np_img) > min_var
 
     def _has_tissue_more_than_percent(self, tissue_percent: float = 80.0) -> bool:
         """Check if tissue represent more than ``tissue_percent`` % of the image.

diff --git a/...mu-1-small-region-tiles-location-grid.png → ...ages/cmu-1-small-region-tl-grid-false.png b/...mu-1-small-region-tiles-location-grid.png → ...ages/cmu-1-small-region-tl-grid-false.png
diff --git a/tests/expectations/tiles-location-images/cmu-1-small-region-tl-grid-true.png b/tests/expectations/tiles-location-images/cmu-1-small-region-tl-grid-true.png
diff --git a/...-1-small-region-tiles-location-random.png → ...es/cmu-1-small-region-tl-random-false.png b/...-1-small-region-tiles-location-random.png → ...es/cmu-1-small-region-tl-random-false.png
diff --git a/...-1-small-region-tiles-location-scored.png → ...ges/cmu-1-small-region-tl-random-true.png b/...-1-small-region-tiles-location-scored.png → ...ges/cmu-1-small-region-tl-random-true.png
diff --git a/tests/expectations/tiles-location-images/cmu-1-small-region-tl-scored-false.png b/tests/expectations/tiles-location-images/cmu-1-small-region-tl-scored-false.png
diff --git a/tests/expectations/tiles-location-images/cmu-1-small-region-tl-scored-true.png b/tests/expectations/tiles-location-images/cmu-1-small-region-tl-scored-true.png
diff --git a/...tations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tiles-location-scored.png b/...tations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tiles-location-scored.png
diff --git a/...r-7395-01a-01-ts1-tiles-location-grid.png → ...tcga-cr-7395-01a-01-ts1-tl-grid-false.png b/...r-7395-01a-01-ts1-tiles-location-grid.png → ...tcga-cr-7395-01a-01-ts1-tl-grid-false.png
diff --git a/tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-grid-true.png b/tests/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-grid-true.png
diff --git a/...7395-01a-01-ts1-tiles-location-random.png → ...ga-cr-7395-01a-01-ts1-tl-random-false.png b/...7395-01a-01-ts1-tiles-location-random.png → ...ga-cr-7395-01a-01-ts1-tl-random-false.png
diff --git a/...s/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-random-true.png b/...s/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-random-true.png
diff --git a/.../expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-scored-false.png b/.../expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-scored-false.png
diff --git a/...s/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-scored-true.png b/...s/expectations/tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-scored-true.png
diff --git a/tests/fixtures/tiles/liver-level2-10907-7808-11707-8608.png b/tests/fixtures/tiles/liver-level2-10907-7808-11707-8608.png
diff --git a/tests/fixtures/tiles/liver-level2-20914-13715-21714-14515.png b/tests/fixtures/tiles/liver-level2-20914-13715-21714-14515.png
diff --git a/tests/fixtures/tiles/liver-level2-38626-13514-39426-14315.png b/tests/fixtures/tiles/liver-level2-38626-13514-39426-14315.png
diff --git a/tests/fixtures/tiles/liver-level2-57138-8209-57938-9009.png b/tests/fixtures/tiles/liver-level2-57138-8209-57938-9009.png
diff --git a/tests/integration/test_tile.py b/tests/integration/test_tile.py
@@ -27,3 +27,17 @@ def it_knows_if_is_is_almost_white(self, tile_img, expected_result):
         is_almost_white = tile._is_almost_white
 
         assert is_almost_white == expected_result
+
+    @pytest.mark.parametrize(
+        "tile_image, expected_value",
+        (
+            (TILES.LIVER_LEVEl2_10907_7808_11707_8608, False),  # all tissue
+            (TILES.LIVER_LEVEl2_20914_13715_21714_14515, True),  # some tissue
+            (TILES.LIVER_LEVEl2_57138_8209_57938_9009, True),  # some tissue
+            (TILES.LIVER_LEVEl2_38626_13514_39426_14315, False),  # no tissue
+        ),
+    )
+    def it_knows_if_it_has_only_some_tissue(self, tile_image, expected_value):
+        tile = Tile(tile_image, CP(5, 5, 5, 5))
+
+        assert tile._has_only_some_tissue() == expected_value
diff --git a/tests/integration/test_tiler.py b/tests/integration/test_tiler.py
@@ -15,25 +15,37 @@
 
 class DescribeRandomTiler:
     @pytest.mark.parametrize(
-        "fixture_slide, expectation",
+        "fixture_slide, check_tissue, expectation",
         [
             (
                 SVS.CMU_1_SMALL_REGION,
-                "tiles-location-images/cmu-1-small-region-tiles-location-random",
+                False,
+                "tiles-location-images/cmu-1-small-region-tl-random-false",
             ),
             (
                 SVS.TCGA_CR_7395_01A_01_TS1,
-                "tiles-location-images/tcga-cr-7395-01a-01-ts1-tiles-location-random",
+                False,
+                "tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-random-false",
+            ),
+            (
+                SVS.CMU_1_SMALL_REGION,
+                True,
+                "tiles-location-images/cmu-1-small-region-tl-random-true",
+            ),
+            (
+                SVS.TCGA_CR_7395_01A_01_TS1,
+                True,
+                "tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-random-true",
             ),
         ],
     )
     def it_locates_tiles_on_the_slide(
-        self, request, fixture_slide, expectation, tmpdir
+        self, request, fixture_slide, check_tissue, expectation, tmpdir
     ):
         slide = Slide(fixture_slide, os.path.join(tmpdir, "processed"))
         slide.save_scaled_image(10)
         random_tiles_extractor = RandomTiler(
-            tile_size=(512, 512), n_tiles=2, level=0, seed=42, check_tissue=False
+            tile_size=(512, 512), n_tiles=2, level=0, seed=42, check_tissue=check_tissue
         )
         expected_img = load_expectation(
             expectation,
@@ -43,68 +55,88 @@ def it_locates_tiles_on_the_slide(
         # --- Expanding test report with actual and expected images ---
         expand_tests_report(request, actual=tiles_location_img, expected=expected_img)
 
-        np.testing.assert_array_almost_equal(
-            np.asarray(tiles_location_img), expected_img
-        )
+        np.testing.assert_array_almost_equal(tiles_location_img, expected_img)
 
 
 class DescribeGridTiler:
     @pytest.mark.parametrize(
-        "fixture_slide, expectation",
+        "fixture_slide, check_tissue, expectation",
         [
             (
                 SVS.CMU_1_SMALL_REGION,
-                "tiles-location-images/cmu-1-small-region-tiles-location-grid",
+                False,
+                "tiles-location-images/cmu-1-small-region-tl-grid-false",
             ),
             (
                 SVS.TCGA_CR_7395_01A_01_TS1,
-                "tiles-location-images/tcga-cr-7395-01a-01-ts1-tiles-location-grid",
+                False,
+                "tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-grid-false",
+            ),
+            (
+                SVS.CMU_1_SMALL_REGION,
+                True,
+                "tiles-location-images/cmu-1-small-region-tl-grid-true",
+            ),
+            (
+                SVS.TCGA_CR_7395_01A_01_TS1,
+                True,
+                "tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-grid-true",
             ),
         ],
     )
     def it_locates_tiles_on_the_slide(
-        self, request, fixture_slide, expectation, tmpdir
+        self, request, fixture_slide, check_tissue, expectation, tmpdir
     ):
         slide = Slide(fixture_slide, os.path.join(tmpdir, "processed"))
         grid_tiles_extractor = GridTiler(
             tile_size=(512, 512),
             level=0,
-            check_tissue=False,
+            check_tissue=check_tissue,
         )
         expected_img = load_expectation(expectation, type_="png")
         tiles_location_img = grid_tiles_extractor.locate_tiles(slide, scale_factor=10)
         # --- Expanding test report with actual and expected images ---
         expand_tests_report(request, expected=expected_img, actual=tiles_location_img)
 
-        np.testing.assert_array_almost_equal(
-            np.asarray(tiles_location_img), expected_img
-        )
+        np.testing.assert_array_almost_equal(tiles_location_img, expected_img)
 
 
 class DescribeScoreTiler:
     @pytest.mark.parametrize(
-        "fixture_slide, expectation",
+        "fixture_slide, check_tissue, expectation",
         [
             (
                 SVS.CMU_1_SMALL_REGION,
-                "tiles-location-images/cmu-1-small-region-tiles-location-scored",
+                False,
+                "tiles-location-images/cmu-1-small-region-tl-scored-false",
+            ),
+            (
+                SVS.TCGA_CR_7395_01A_01_TS1,
+                False,
+                "tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-scored-false",
+            ),
+            (
+                SVS.CMU_1_SMALL_REGION,
+                True,
+                "tiles-location-images/cmu-1-small-region-tl-scored-true",
             ),
             (
                 SVS.TCGA_CR_7395_01A_01_TS1,
-                "tiles-location-images/tcga-cr-7395-01a-01-ts1-tiles-location-scored",
+                True,
+                "tiles-location-images/tcga-cr-7395-01a-01-ts1-tl-scored-true",
             ),
         ],
     )
     def it_locates_tiles_on_the_slide(
-        self, request, fixture_slide, expectation, tmpdir
+        self, request, fixture_slide, check_tissue, expectation, tmpdir
     ):
         slide = Slide(fixture_slide, os.path.join(tmpdir, "processed"))
         scored_tiles_extractor = ScoreTiler(
             scorer=NucleiScorer(),
             tile_size=(512, 512),
             n_tiles=2,
             level=0,
-            check_tissue=True,
+            check_tissue=check_tissue,
         )
         expected_img = load_expectation(
             expectation,
@@ -114,6 +146,4 @@ def it_locates_tiles_on_the_slide(
         # --- Expanding test report with actual and expected images ---
         expand_tests_report(request, expected=expected_img, actual=tiles_location_img)
 
-        np.testing.assert_array_almost_equal(
-            np.asarray(tiles_location_img), expected_img
-        )
+        np.testing.assert_array_almost_equal(tiles_location_img, expected_img)
diff --git a/tests/unit/test_tile.py b/tests/unit/test_tile.py
@@ -6,7 +6,7 @@
 from histolab.filters.compositions import _TileFiltersComposition
 from histolab.filters.image_filters import Compose
 from histolab.tile import Tile
-from histolab.types import CoordinatePair
+from histolab.types import CP
 
 from ..base import COMPLEX_MASK
 from ..unitutil import (
@@ -24,7 +24,7 @@ def it_constructs_from_args(self, request):
         _init = initializer_mock(request, Tile)
         _image = PILIMG.RGBA_COLOR_50X50_155_0_0
         _level = 0
-        _coords = CoordinatePair(0, 0, 50, 50)
+        _coords = CP(0, 0, 50, 50)
 
         tile = Tile(_image, _coords, _level)
 
@@ -35,14 +35,14 @@ def but_it_has_wrong_image_type(self):
         """This test simulates a wrong user behaviour, using a None object instead of a
         PIL Image for image param"""
         with pytest.raises(AttributeError) as err:
-            tile = Tile(None, CoordinatePair(0, 0, 50, 50), 0)
+            tile = Tile(None, CP(0, 0, 50, 50), 0)
             tile.has_enough_tissue()
 
         assert isinstance(err.value, AttributeError)
         assert str(err.value) == "'NoneType' object has no attribute 'convert'"
 
     def it_knows_its_coords(self):
-        _coords = CoordinatePair(0, 0, 50, 50)
+        _coords = CP(0, 0, 50, 50)
         tile = Tile(None, _coords, 0)
 
         coords = tile.coords
@@ -144,30 +144,20 @@ def it_knows_if_has_tissue_more_than_percent(
 
     def it_calls_tile_tissue_mask_filters(
         self,
-        request,
         RgbToGrayscale_,
         OtsuThreshold_,
         BinaryDilation_,
         BinaryFillHoles_,
     ):
-        _tissue_mask_filters = property_mock(
-            request, _TileFiltersComposition, "tissue_mask_filters"
-        )
-        BinaryFillHoles_.return_value = np.zeros((50, 50))
-        _tissue_mask_filters.return_value = Compose(
-            [RgbToGrayscale_, OtsuThreshold_, BinaryDilation_, BinaryFillHoles_]
-        )
         image = PILIMG.RGBA_COLOR_50X50_155_0_0
         tile = Tile(image, None, 0)
 
         tile._has_only_some_tissue()
 
-        _tissue_mask_filters.assert_called_once()
         assert type(tile._has_only_some_tissue()) == np.bool_
 
     def it_knows_its_tissue_mask(
         self,
-        request,
         RgbToGrayscale_,
         OtsuThreshold_,
         BinaryDilation_,