Merge 865c766 into e673dd4

src/histolab/exceptions.py

@@ -1,3 +1,22 @@
+# encoding: utf-8
+
+# ------------------------------------------------------------------------
+# Copyright 2020 All Histolab Contributors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+
+
 class HistolabException(Exception):
     """Histolab custom exception main class"""
 

src/histolab/scorer.py

@@ -1,3 +1,21 @@
+# encoding: utf-8
+
+# ------------------------------------------------------------------------
+# Copyright 2020 All Histolab Contributors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+
 import operator
 from abc import abstractmethod
 
@@ -15,16 +33,22 @@
 
 
 @runtime_checkable
-class Scorer(Protocol):
-    """General scorer object"""
+class _Scorer(Protocol):
+    """General scorer object
+
+    .. automethod:: __call__
+    """
 
     @abstractmethod
     def __call__(self, tile: Tile) -> float:
         raise NotImplementedError
 
 
-class RandomScorer(Scorer):
-    """Implement a Scorer that returns a random float score between 0 and 1."""
+class RandomScorer(_Scorer):
+    """Implement a Scorer that returns a random float score between 0 and 1.
+
+    .. automethod:: __call__
+    """
 
     def __call__(self, tile: Tile) -> float:
         """Return the random score associated with the tile.
@@ -42,7 +66,7 @@ def __call__(self, tile: Tile) -> float:
         return np.random.random()
 
 
-class NucleiScorer(Scorer):
+class NucleiScorer(_Scorer):
     r"""Implement a Scorer that estimates the presence of nuclei in an H&E-stained tile.
 
     A higher presence of nuclei is associated with a higher scorer, following this
@@ -51,6 +75,8 @@ class NucleiScorer(Scorer):
     .. math::
 
         score = nuclei\_ratio \cdot tanh(tissue\_ratio)
+
+    .. automethod:: __call__
     """
 
     def __call__(self, tile: Tile) -> float:

src/histolab/tile.py

@@ -1,3 +1,21 @@
+# encoding: utf-8
+
+# ------------------------------------------------------------------------
+# Copyright 2020 All Histolab Contributors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+
 import os
 from pathlib import Path
 from typing import Callable, Union

src/histolab/tiler.py

@@ -1,12 +1,30 @@
+# encoding: utf-8
+
+# ------------------------------------------------------------------------
+# Copyright 2020 All Histolab Contributors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ------------------------------------------------------------------------
+
 import csv
 import os
 from abc import abstractmethod
-from typing import List, Tuple
+from typing import List, Tuple, Union
 
 import numpy as np
 
 from .exceptions import LevelError
-from .scorer import Scorer
+from .scorer import RandomScorer, NucleiScorer
 from .slide import Slide
 from .tile import Tile
 from .types import CoordinatePair
@@ -337,7 +355,7 @@ def __init__(
         check_tissue: bool = True,
         prefix: str = "",
         suffix: str = ".png",
-        max_iter: int = 1e4,
+        max_iter: float = 1e4,
     ):
 
         super().__init__()
@@ -519,7 +537,7 @@ class ScoreTiler(GridTiler):
 
     def __init__(
         self,
-        scorer: Scorer,
+        scorer: Union[NucleiScorer, RandomScorer],
         tile_size: Tuple[int, int],
         n_tiles: int = 0,
         level: int = 0,

src/histolab/types.py

@@ -20,3 +20,5 @@
 
 CoordinatePair = namedtuple("CoordinatePair", ("x_ul", "y_ul", "x_br", "y_br"))
 Region = namedtuple("Region", ("index", "area", "bbox", "center"))
+
+CP = CoordinatePair

src/histolab/util.py

@@ -15,6 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 # ------------------------------------------------------------------------
+
 import functools
 import warnings
 from collections import deque

tests/integration/test_tile.py

@@ -1,7 +1,7 @@
 import pytest
 
 from histolab.tile import Tile
-from histolab.types import CoordinatePair
+from histolab.types import CP
 
 from ..fixtures import TILES
 
@@ -21,7 +21,7 @@ class Describe_Tile:
         ),
     )
     def it_knows_if_is_is_almost_white(self, tile_img, expected_result):
-        coords = CoordinatePair(0, 512, 0, 512)
+        coords = CP(0, 512, 0, 512)
         tile = Tile(tile_img, coords)
 
         is_almost_white = tile._is_almost_white