Add NucleiScorer #132

alessiamarcolini · 2020-09-01T22:07:32Z

Example

from PIL import Image

from histolab.scorer import NucleiScorer
from histolab.tile import Tile

im = Image.open("image.png")
tile = Tile(im, None, 0)
ns = NucleiScorer()
score = ns(tile)

src/histolab/filters/compositions.py

src/histolab/tile.py

tests/integration/test_scorer.py

tests/unit/filters/test_util.py

ernestoarbitrio

Some minor comments + in general I would include more integration tests for the nuclei scorer. I'd like to cover much corner cases as possible.

…compositions module

…he tissue ratio of a tile

… a np array

Co-authored-by: Ernesto Arbitrio <ernesto.arbitrio.gmail.com>

…mpositionError

… FiltersComposition

…shold' to 'below the threshold'

…ort with the scaled scores

src/histolab/tile.py

src/histolab/scorer.py

src/histolab/filters/image_filters.py

src/histolab/tiler.py

src/histolab/filters/image_filters_functional.py

src/histolab/filters/morphological_filters.py

src/histolab/tiler.py

src/histolab/scorer.py

nicolebussola

minor changes wrt docstrings

ernestoarbitrio

left some comments :D ...

nicolebussola

LGTM

alessiamarcolini added the 0.1.0 label Sep 1, 2020

alessiamarcolini requested review from ernestoarbitrio and nicolebussola September 1, 2020 22:07

alessiamarcolini force-pushed the nuclei-scorer branch from 052221e to f3373cc Compare September 1, 2020 22:08

ernestoarbitrio reviewed Sep 2, 2020

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alessiamarcolini force-pushed the nuclei-scorer branch 2 times, most recently from fcde4e8 to b82930a Compare September 5, 2020 20:06

alessiamarcolini added 18 commits September 7, 2020 20:57

Refactor filter composition used in tile to detect tissue in its own …

6323499

…compositions module

Add method for applying filters on a tile + add method to calculate t…

0d64586

…he tissue ratio of a tile

Add dosctring to RandomScorer

fe1ea3f

Add Yen's thresholding method to filters

83919fb

Add test for composition module

36a319a

Add test for apply filters method of tile with a filter which returns…

ec9dea8

… a np array

Add White Top Hat morphological filter

1a0df02

Add mask differnce function

57ea9f6

Refactor Filters Composition

6e248d0

Co-authored-by: Ernesto Arbitrio <ernesto.arbitrio.gmail.com>

Add unit tests for FiltersComposition + add custom exception FilterCo…

5090ecd

…mpositionError

Refactor tissue_ratio property of Tile

85c658b

Add NucleiScorer

7815c3a

Add dosctring for NucleiScorer

1caff6b

Move filters composition to find tissue in a Slide in the appropriate…

59603bf

… FiltersComposition

Add unit and integration tests for NucleiScorer

abd9f3e

Fix typo

0fd2d42

Update docstring

fce1479

Flake8 fix

0206168

alessiamarcolini added 10 commits September 7, 2020 20:58

Real fix on saving the tiles in the correct folder

1087062

Fix failing test

0a2342e

Add test cases for NucleiScorer integration test

794c4a7

Change formula to compute nuclei score

676b4ea

Change default thresholding result of Yen filter from 'above the thre…

ad86a48

…shold' to 'below the threshold'

Update scorer based on new Yen Threshold

d16f09e

Handle exception in case of no tiles are extracted

ddda46a

Fix after rebase

58d61ce

Fix float representation issue in tests

27986ce

Scale scores between 0 and 1 and save an additional column in the rep…

a3e07c9

…ort with the scaled scores

alessiamarcolini force-pushed the nuclei-scorer branch from 43a1846 to a3e07c9 Compare September 7, 2020 19:58

alessiamarcolini requested a review from ernestoarbitrio September 7, 2020 20:10

ernestoarbitrio reviewed Sep 8, 2020

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