# encoding: utf-8
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# 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
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import numpy as np
from ..exceptions import FilterCompositionError
from ..util import lazyproperty
from . import image_filters as imf
from . import morphological_filters as mof
[docs]class FiltersComposition:
"""Provide appropriate filters compositions based on the ``cls_`` parameter.
Arguments
---------
cls_ : type, {Tile, Slide}
The class to get the appropriate filters composition for
Example:
>>> from histolab.filters.compositions import FiltersComposition
>>> from histolab.slide import Slide
>>> from histolab.tile import Tile
>>> filters_slide = FiltersComposition(Slide).tissue_mask_filters
>>> filters_tile = FiltersComposition(Tile).tissue_mask_filters
"""
def __new__(cls: type, cls_):
if not cls_:
raise FilterCompositionError("cls_ parameter cannot be None")
FiltersSubCls = {
"Tile": _TileFiltersComposition,
"Slide": _SlideFiltersComposition,
}.get(cls_.__name__)
if FiltersSubCls:
instance = super(FiltersComposition, FiltersSubCls).__new__(FiltersSubCls)
return instance
raise FilterCompositionError(
f"Filters composition for the class {cls_.__name__} is not available"
)
@lazyproperty
def tissue_mask_filters(self) -> imf.Compose:
"""Return filters composition based on the ``cls_`` parameter.
Returns
-------
imf.Compose
If the ``cls_`` parameter is the class ``Slide`` the returned filters chain
is composed of:
- `image_filters.RgbToGrayscale()
<image_filters.html#histolab.filters.image_filters.RgbToGrayscale>`_
- `image_filters.OtsuThreshold()
<image_filters.html#histolab.filters.image_filters.OtsuThreshold>`_
- `morphological_filters.BinaryDilation()
<morphological_filters.html#histolab.filters.morphological_filters.BinaryDilation>`_
- `morphological_filters.RemoveSmallHoles()
<morphological_filters.html#histolab.filters.morphological_filters.RemoveSmallHoles>`_
- `morphological_filters.RemoveSmallObjects()
<morphological_filters.html#histolab.filters.morphological_filters.RemoveSmallObjects>`_
If the ``cls_`` parameter is the class ``Tile`` the returned filters chain
is composed of:
- `image_filters.RgbToGrayscale()
<image_filters.html#histolab.filters.image_filters.RgbToGrayscale>`_
- `image_filters.OtsuThreshold()
<image_filters.html#histolab.filters.image_filters.OtsuThreshold>`_
- `morphological_filters.BinaryDilation()
<morphological_filters.html#histolab.filters.morphological_filters.BinaryDilation>`_
- `morphological_filters.BinaryFillHoles(structure=np.ones((5, 5)))
<morphological_filters.html#histolab.filters.morphological_filters.BinaryFillHoles>`_
"""
raise NotImplementedError("Must be implemented by each subclass")
class _SlideFiltersComposition(FiltersComposition):
@lazyproperty
def tissue_mask_filters(self) -> imf.Compose:
"""Filters composition for slide's tissue estimation.
Returns
-------
imf.Compose
Filters composition
"""
return imf.Compose(
[
imf.RgbToGrayscale(),
imf.OtsuThreshold(),
mof.BinaryDilation(),
mof.RemoveSmallHoles(),
mof.RemoveSmallObjects(),
]
)
class _TileFiltersComposition(FiltersComposition):
@lazyproperty
def tissue_mask_filters(self) -> imf.Compose:
"""Filters composition for tile's tissue estimation.
Returns
-------
imf.Compose
Filters composition
"""
return imf.Compose(
[
imf.RgbToGrayscale(),
imf.OtsuThreshold(),
mof.BinaryDilation(),
mof.BinaryFillHoles(structure=np.ones((5, 5))),
]
)