Make SlideSet iterable

src/histolab/slide.py

@@ -25,7 +25,7 @@
 import os
 import pathlib
 from functools import lru_cache
-from typing import List, Tuple, Union
+from typing import Iterator, List, Tuple, Union
 
 import ntpath
 import numpy as np
@@ -460,6 +460,30 @@ def __init__(
         self._processed_path = processed_path
         self._valid_extensions = valid_extensions
 
+    def __iter__(self) -> Iterator[Slide]:
+        """Slides of the slideset
+
+        Returns
+        -------
+        generator of `Slide` objects.
+        """
+        return iter(
+            [
+                Slide(os.path.join(self._slides_path, _path), self._processed_path)
+                for _path in os.listdir(self._slides_path)
+                if os.path.splitext(_path)[1] in self._valid_extensions
+            ]
+        )
+
+    def __len__(self) -> int:
+        """Total number of the slides of this Slideset
+
+        Returns
+        -------
+        int representing the number of the Slides.
+        """
+        return len(list(self.__iter__()))
+
     # ---public interface methods and properties---
 
     def save_scaled_slides(self, scale_factor: int = 32, n: int = 0) -> None:
@@ -475,7 +499,7 @@ def save_scaled_slides(self, scale_factor: int = 32, n: int = 0) -> None:
         """
         os.makedirs(self._processed_path, exist_ok=True)
         n = self.total_slides if (n > self.total_slides or n == 0) else n
-        for slide in self.slides[:n]:
+        for slide in list(self.__iter__())[:n]:
             slide.save_scaled_image(scale_factor)
 
     def save_thumbnails(self, n: int = 0) -> None:
@@ -489,23 +513,9 @@ def save_thumbnails(self, n: int = 0) -> None:
         """
         os.makedirs(self._processed_path, exist_ok=True)
         n = self.total_slides if (n > self.total_slides or n == 0) else n
-        for slide in self.slides[:n]:
+        for slide in list(self.__iter__())[:n]:
             slide.save_thumbnail()
 
-    @lazyproperty
-    def slides(self) -> List[Slide]:
-        """Retrieve all the slides of the slideset
-
-        Returns
-        ----------
-        slides: list, list of `Slide` objects
-        """
-        return [
-            Slide(os.path.join(self._slides_path, _path), self._processed_path)
-            for _path in os.listdir(self._slides_path)
-            if os.path.splitext(_path)[1] in self._valid_extensions
-        ]
-
     @lazyproperty
     def slides_stats(self) -> dict:
         """Retrieve statistic/graphs of slides files contained in the dataset.
@@ -536,7 +546,7 @@ def total_slides(self) -> int:
         n: int
             Number of slides.
         """
-        return len(self.slides)
+        return self.__len__()
 
     # ---private interface methods and properties---
 
@@ -591,9 +601,9 @@ def _slides_dimensions(self) -> List[dict]:
                 "height": slide.dimensions[1],
                 "size": slide.dimensions[0] * slide.dimensions[1],
             }
-            for slide in self.slides
+            for slide in list(self.__iter__())
         ]
 
     @lazyproperty
     def _slides_dimensions_list(self):
-        return [slide.dimensions for slide in self.slides]
+        return [slide.dimensions for slide in list(self.__iter__())]

tests/unit/test_slide.py

@@ -4,7 +4,6 @@
 import math
 import os
 from collections import namedtuple
-from unittest.mock import call
 
 import numpy as np
 import openslide
@@ -603,16 +602,15 @@ def it_constructs_from_args(self, request):
         )
         assert isinstance(slideset, SlideSet)
 
-    def it_can_constructs_slides(self, request, tmpdir):
+    def it_can_constructs_slides(self, request, tmpdir, Slide_):
         tmp_path_ = tmpdir.mkdir("myslide")
-        slides_ = tuple(instance_mock(request, Slide) for _ in range(10))
-        _slides_ = property_mock(request, SlideSet, "slides")
-        _slides_.return_value = slides_
+        slides_ = method_mock(request, SlideSet, "__iter__")
+        slides_.return_value = [Slide_ for _ in range(10)]
         slideset = SlideSet(tmp_path_, os.path.join(tmp_path_, "b"), [".svs"])
 
-        slides = slideset.slides
+        slides = slideset.__iter__()
 
-        _slides_.assert_called_once_with()
+        slides_.assert_called_once_with(slideset)
         assert len(slides) == 10
 
     def it_knows_its_slides(self, tmpdir):
@@ -621,46 +619,37 @@ def it_knows_its_slides(self, tmpdir):
         image.save(os.path.join(tmp_path_, "mywsi.svs"), "TIFF")
         slideset = SlideSet(tmp_path_, "proc", [".svs"])
 
-        slides = slideset.slides
-
-        assert len(slides) == 1
+        assert len(slideset) == 1
 
         slideset = SlideSet(None, "proc", [".svs"])
 
-        slides = slideset.slides
-
-        assert len(slides) == 0
+        assert len(slideset) == 0
 
         with pytest.raises(FileNotFoundError) as err:
             slideset = SlideSet("fake/path", "proc", [".svs"])
-            slides = slideset.slides
+            list(slideset)
 
         assert isinstance(err.value, FileNotFoundError)
         assert err.value.errno == errno.ENOENT
 
-    def it_constructs_its_sequence_of_slides_to_help(self, request, Slide_, tmpdir):
-        slides_path = tmpdir.mkdir("mypath")
-        for i in range(4):
-            open(os.path.join(slides_path, f"myfile{i}.svs"), "a")
-        slides_ = tuple(instance_mock(request, Slide) for _ in range(4))
-        Slide_.side_effect = iter(slides_)
-        slide_set = SlideSet(
-            slides_path=slides_path,
-            processed_path=os.path.join(slides_path, "processed"),
-            valid_extensions=[".svs"],
-        )
-        slides = tuple(slide_set.slides)
+    def it_constructs_its_sequence_of_slides_to_help(self, tmpdir):
+        tmp_path_ = tmpdir.mkdir("myslide")
+        image = PILIMG.RGBA_COLOR_500X500_155_249_240
+        image.save(os.path.join(tmp_path_, "mywsi.svs"), "TIFF")
+        image2 = PILIMG.RGBA_COLOR_50X50_155_0_0
+        image2.save(os.path.join(tmp_path_, "mywsi2.svs"), "TIFF")
+        slideset = SlideSet(tmp_path_, "proc", [".svs"])
+        expected_slides = [
+            Slide(os.path.join(tmp_path_, _path), "proc")
+            for _path in os.listdir(tmp_path_)
+        ]
 
-        assert sorted(Slide_.call_args_list) == sorted(
-            [
-                call(
-                    os.path.join(slides_path, f"myfile{i}.svs"),
-                    os.path.join(slides_path, "processed"),
-                )
-                for i in range(4)
-            ]
-        )
-        assert slides == slides_
+        slides = slideset.__iter__()
+
+        for i, slide in enumerate(slides):
+            np.testing.assert_array_almost_equal(
+                slide.resampled_array(), expected_slides[i].resampled_array()
+            )
 
     def it_knows_the_slides_dimensions(self, tmpdir):
         tmp_path_ = tmpdir.mkdir("myslide")
@@ -691,11 +680,11 @@ def it_knows_its_slides_dimensions_list(self, tmpdir):
         assert sorted(_slides_dimensions_list) == sorted([(500, 500), (50, 50)])
 
     def it_knows_its_total_slides(self, request, Slide_):
-        slides = property_mock(request, SlideSet, "slides")
+        slides = method_mock(request, SlideSet, "__iter__")
         slides.return_value = [Slide_ for _ in range(4)]
         slideset = SlideSet("the/path", "proc", [".svs"])
 
-        total_slides = slideset.total_slides
+        total_slides = len(slideset)
 
         assert total_slides == 4
 
@@ -819,7 +808,7 @@ def it_can_save_scaled_slides(self, request, tmpdir):
         slide2 = instance_mock(request, Slide)
 
         slideset = SlideSet(tmp_path_, os.path.join(tmp_path_, "processed"), [])
-        slides = property_mock(request, SlideSet, "slides")
+        slides = method_mock(request, SlideSet, "__iter__")
         slides.return_value = [slide1, slide2]
         slideset.save_scaled_slides(32, 2)
 
@@ -832,7 +821,7 @@ def it_can_save_thumbnails(self, request, tmpdir):
         slide2 = instance_mock(request, Slide)
 
         slideset = SlideSet(tmp_path_, os.path.join(tmp_path_, "processed"), [])
-        slides = property_mock(request, SlideSet, "slides")
+        slides = method_mock(request, SlideSet, "__iter__")
         slides.return_value = [slide1, slide2]
         slideset.save_thumbnails(2)