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Conversion from RGB to HED preserves HED color space range #334

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Merged
alessiamarcolini merged 19 commits into from
Nov 3, 2021
Merged

Conversion from RGB to HED preserves HED color space range #334

alessiamarcolini merged 19 commits into from
Nov 3, 2021

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@alessiamarcolini alessiamarcolini commented Oct 20, 2021 •
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Description

This PR fixes rgb_to_hed filter and related (hematoxylin_channel, eosin_channel and dab_channel)

TODO:

  • fix NucleiScorer accordingly
  • fix CellularityScorer accordingly
  • fix ScoreTiler.locate_tiles accordingly
  • update figures in documentation

However, to enable possible roundtrip transformation, I had to change the np_to_pil function. Therefore there are some filters for which I need to recompute the expectations, listed below.

TODO 2:

  • adaptive_equalization
  • histogram_equalization
  • update figures in documentation

Types of Changes

  • Core
  • Bugfix
  • New feature
  • Enhancement/optimization
  • Documentation

Issues Fixed or Closed by This PR

Checklist

  • My code follows the code style of this project.
  • My change requires a change to the documentation.
  • I have updated the documentation accordingly.
  • I have read the CONTRIBUTING document.
  • I have added tests to cover my changes.
  • I have tested the changes and verified that they work and don't break anything (as well as I can manage).

ernestoarbitrio
ernestoarbitrio requested changes Oct 28, 2021
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as per comments

alessiamarcolini added a commit that referenced this pull request Oct 29, 2021
@alessiamarcolini
Remove wrong color space conversions image in docs
1eeb8ad 
also related to #334
alessiamarcolini added a commit that referenced this pull request Nov 1, 2021
@alessiamarcolini
Remove wrong color space conversions image in docs
8780624 
also related to #334
@alessiamarcolini alessiamarcolini added the bug Something isn't working label Nov 1, 2021
@alessiamarcolini alessiamarcolini added this to the 0.2.7 milestone Nov 1, 2021
alessiamarcolini added a commit that referenced this pull request Nov 2, 2021
@alessiamarcolini
Remove wrong color space conversions image in docs
9a3d971 
also related to #334
@alessiamarcolini
Make rgb_to_hed return HED array with correct range
6b94f05
@alessiamarcolini
Add hed_to_rgb conversion and enable round-trip transformations
dbae351
@alessiamarcolini
Manually clip values, waiting for skimage fix
3fede33
@alessiamarcolini
RGB<->HED actually not possible
21d3c1e
@alessiamarcolini
Fix hematoxylin channel extraction
3b60e9a
@alessiamarcolini
Fix eosin channel extraction
ce52c60
@alessiamarcolini
Fix DAB channel extraction
463079d
@alessiamarcolini
Fix NucleiScorer according to new HematoxylinChannel filter
c713042
@alessiamarcolini
Docstring improvements
0bb06c4
@alessiamarcolini
Fix CellularityScorer according to new HematoxylinChannel filter
caa4dd3
@alessiamarcolini
Fix locate_tiles according to new NucleiScorer
6377335
@alessiamarcolini
Update HED channels figure in docs
fc93675
@alessiamarcolini
Update expectations of adaptive_equalization filter
ddf84b8
@alessiamarcolini
Update expectations of histogram_equalization filter
c2b1b33
@alessiamarcolini
Update figure of HistogramEqualization
5448a8f
@alessiamarcolini
Update figure of AdaptiveEqualization
fb827cb
@alessiamarcolini
Fix path in HedToRgb example
2951134
@alessiamarcolini
Fix codefactor
52cc333
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codecov bot commented Nov 2, 2021 •
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Codecov Report

Merging #334 (e07b6c6) into master (c4f75d3) will not change coverage.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff            @@
##            master      #334   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           17        17           
  Lines         1305      1313    +8     
  Branches       128       128           
=========================================
+ Hits          1305      1313    +8
Impacted Files Coverage Δ
histolab/scorer.py 100.00% <ø> (ø)
histolab/filters/image_filters.py 100.00% <100.00%> (ø)
histolab/filters/image_filters_functional.py 100.00% <100.00%> (ø)
histolab/util.py 100.00% <100.00%> (ø)

Continue to review full report at Codecov.

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@alessiamarcolini alessiamarcolini mentioned this pull request Nov 2, 2021
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ernestoarbitrio
ernestoarbitrio approved these changes Nov 3, 2021
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👏🏽 👏🏽

@alessiamarcolini alessiamarcolini merged commit 37db202 into master Nov 3, 2021
@alessiamarcolini alessiamarcolini deleted the fix-hed-filter branch November 3, 2021 11:21
@alessiamarcolini alessiamarcolini linked an issue Nov 3, 2021 that may be closed by this pull request
Re-write H&E filter #254
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@alessiamarcolini alessiamarcolini mentioned this pull request Nov 9, 2021
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Conversion from RGB to HED must preserve HED color space range Re-write H&E filter

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