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Allow only keeping a subset of slides for SlideSet #303

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Merged
alessiamarcolini merged 3 commits into from
Nov 15, 2021
Merged

Allow only keeping a subset of slides for SlideSet #303

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f091707
allow only keeping a subset of slides for SlideSet -- this would be u…
kheffah Jul 25, 2021
f8886fc
Typing improvements and parameter style changes according to CR
kheffah Jul 26, 2021
3c0da7d
remove underscore from list comprehension in Slide class
kheffah Jul 31, 2021
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19 changes: 15 additions & 4 deletions histolab/slide.py
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Original file line number Diff line number Diff line change
Expand Up @@ -510,11 +510,16 @@ class SlideSet:
"""Slideset object. It is considered a collection of Slides."""

def __init__(
self, slides_path: str, processed_path: str, valid_extensions: list
self,
slides_path: str,
processed_path: str,
valid_extensions: List[str],
keep_slides: List[str] = None,
) -> None:
self._slides_path = slides_path
self._processed_path = processed_path
self._valid_extensions = valid_extensions
self._keep_slides = keep_slides

def __iter__(self) -> Iterator[Slide]:
"""Slides of the slideset
Expand All @@ -523,11 +528,17 @@ def __iter__(self) -> Iterator[Slide]:
-------
generator of `Slide` objects.
"""
slide_names = [
name
for name in os.listdir(self._slides_path)
if (os.path.splitext(name)[1] in self._valid_extensions)
]
if self._keep_slides is not None:
slide_names = [name for name in slide_names if name in self._keep_slides]
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
Slide(os.path.join(self._slides_path, name), self._processed_path)
for name in slide_names
]
)

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21 changes: 17 additions & 4 deletions tests/unit/test_slide.py
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Original file line number Diff line number Diff line change
Expand Up @@ -453,15 +453,22 @@ def it_constructs_from_args(self, request):
_slides_path = "/foo/bar/"
_processed_path = "/foo/bar/wsislides/processed"
_valid_extensions = [".svs", ".tiff"]
_keep_slides = ["mywsi.svs"]

slideset = SlideSet(_slides_path, _processed_path, _valid_extensions)
slideset = SlideSet(
_slides_path, _processed_path, _valid_extensions, _keep_slides
)

_init_.assert_called_once_with(
ANY, _slides_path, _processed_path, _valid_extensions
ANY,
_slides_path,
_processed_path,
_valid_extensions,
_keep_slides,
)
assert isinstance(slideset, SlideSet)

def it_can_constructs_slides(self, request, tmpdir, Slide_):
def it_can_construct_slides(self, request, tmpdir, Slide_):
tmp_path_ = tmpdir.mkdir("myslide")
slides_ = method_mock(request, SlideSet, "__iter__")
slides_.return_value = [Slide_ for _ in range(10)]
Expand All @@ -475,9 +482,15 @@ def it_can_constructs_slides(self, request, tmpdir, Slide_):
def it_knows_its_slides(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")
image.save(os.path.join(tmp_path_, "mywsi1.svs"), "TIFF")
image.save(os.path.join(tmp_path_, "mywsi2.svs"), "TIFF")
slideset = SlideSet(tmp_path_, "proc", [".svs"])

assert len(slideset) == 2

# it can keep a subset of slides
slideset = SlideSet(tmp_path_, "proc", [".svs"], keep_slides=["mywsi1.svs"])

assert len(slideset) == 1

slideset = SlideSet(None, "proc", [".svs"])
Expand Down