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ENH: Move get_wsireader to WSIReader.open #169

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Merged
merged 66 commits into from
Oct 27, 2021
Merged

ENH: Move get_wsireader to WSIReader.open #169

merged 66 commits into from
Oct 27, 2021

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@John-P
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@John-P John-P commented Oct 22, 2021 •
edited by shaneahmed
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  • Move get_wsireader to a WSIReader.open static method and add a deprecation notice to get_wsireader.

John-P and others added 30 commits May 19, 2021 15:14
@John-P
DEV: Add Tiffile Dependencies
addce62
@John-P
NEW: Add Reader For TIFF File Using tiffile + zarr
14a2a8c
@John-P
ENH: Add Check For Supported TIFF WSI Formats
f9ec2ab
@John-P
BUG: Remove Brackets from Property Access
cccc151
@John-P
WIP: Basic OME-TIFF Support with YX Indexing
eddd98a 
Add preliminary support for OME-TIFF using an ArrayView class to make indexing order consistent in YX order.
@John-P
MAINT: Typo Fixes
f9da0bd
@John-P
BUG: Swap Axes Order When Reading SYX OME-TIFFs
1c30415
@John-P
DOC: Add Docstring
7653d7d
@John-P
BUG: Fix Inability To Deepcopy tiffile Tags Attribute
b94a821
@John-P
TST: Add Sample OME-TIFF Download & Test
0e49a39
@John-P
Merge branch 'develop' into feature-tiffreader
426566b
@John-P
MAINT: Move Axes Information To WSIMeta
8928c7f
@John-P
TST: Add Parameterised TIFFWSIReader Tests
cf3df3c
@John-P
TST: Resolve Unused Import
7eaf125
@John-P
TST: Remove Unecessary Test
f613ca8
@deepsource-autofix
Autofix issues in 1 file
7441874 
Resolved issues in tiatoolbox/wsicore/wsireader.py via DeepSource Autofix
@John-P
STY: Make Args Consistent for read_rect/bounds
aa8a878
@John-P
Merge branch 'feature-tiffreader' of https://github.com/TIA-Lab/tiato…
4b82174 
…olbox into feature-tiffreader
@John-P
STY: Remove Unnecessary Dict Comprehension
76b452e
@John-P
ENH: Swap To Using defusedxml For Parsing OME-XML
ac1c794
@John-P
TST: Add skipcq For Test
1745049
@John-P
ENH: Add TIFFWSIReader Support For coord_space
a8bd386
@John-P
DOC: Add Docstring Line Breaks
6893554
@tialab
Merge branch 'develop' into feature-tiffreader
162f00a
@John-P
TST: Avoid Testing Very Small JP2 Levels
cbf3031
@John-P
DOC: Add Line Breaks To Docstrings
4926f38
@John-P
Merge branch 'feature-tiffreader' of https://github.com/TIA-Lab/tiato…
c502b3c 
…olbox into feature-tiffreader
@John-P
TST: Avoid Testing Very Small Levels (e.g. in JP2)
2a5f50c
@John-P
TST: Add Test For Invalid TIFFFile Axes
eceafef
@John-P
TST: Add Tests To Increase TIFFWSIReader Coverage
af6bc4a
shaneahmed and others added 12 commits October 21, 2021 11:30
@shaneahmed
BUG: Fix get_wsireader JP2 reader
e2b0f1c 
- Fix get_wsireader JP2 reader
@John-P
BUG: Handle Case For TIFF with No Series
eb4bc63
@John-P
TST: Add Test For get_wsireadre with OME-TIFF
cbd77d5
@John-P
Merge branch 'feature-tiffreader' of https://github.com/TIA-Lab/tiato…
b7b1eed 
…olbox into feature-tiffreader
@John-P
MAINT: Minor Refactor (Extract Variable)
dbb13d9
@John-P
BUG: Fix Wrong Line Causing Invalid Syntax
9b4eac1
@John-P
ENH: Add Check For None Series In TIFF
e4eaf99
@John-P
MAINT: Add skipqc For Non-Iterable PYL-e133
df2b90c
@John-P
BUG: Handle Special Case of 1x1 Resize
abda2cc 
OpenCV v4.5.4 no longer handles 1x1 images as input to resize correctly.
This adds a special case for those images.
@John-P
ENH: Simplify Check For 1x1
bf27c33
@John-P
STY: Sort Imports
d283823
@John-P
EHN: Move get_wsireader To WSIReader.open
ac40e38 
The original function is preserved with a deprecation warning.
@shaneahmed shaneahmed added the enhancement New feature or request label Oct 22, 2021
shaneahmed
shaneahmed reviewed Oct 25, 2021
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shaneahmed
shaneahmed reviewed Oct 25, 2021
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shaneahmed
shaneahmed reviewed Oct 25, 2021
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How about tests?

@shaneahmed
REV: Revert bug fix for cv2 v4.5.4
90addc0 
- Revert bug fix for cv2 v4.5.4
@shaneahmed
BUG: Fix a bug which was ignoring npy files.
3c605f3 
- Fix a bug which was ignoring npy files.
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codecov bot commented Oct 27, 2021 •
edited
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Codecov Report

Merging #169 (3c605f3) into develop (748ed2a) will increase coverage by 0.00%.
The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff            @@
##           develop     #169   +/-   ##
========================================
  Coverage    99.79%   99.79%           
========================================
  Files           40       40           
  Lines         2955     2959    +4     
  Branches       492      492           
========================================
+ Hits          2949     2953    +4     
  Misses           1        1           
  Partials         5        5
Impacted Files Coverage Δ
tiatoolbox/wsicore/wsireader.py 99.31% <100.00%> (+<0.01%) ⬆️
tiatoolbox/models/architecture/unet.py 100.00% <0.00%> (ø)
tiatoolbox/models/architecture/utils.py 100.00% <0.00%> (ø)
tiatoolbox/models/controller/semantic_segmentor.py 100.00% <0.00%> (ø)

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shaneahmed
shaneahmed approved these changes Oct 27, 2021
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Thanks @John-P

@shaneahmed shaneahmed merged commit a8c33e6 into develop Oct 27, 2021
@shaneahmed shaneahmed deleted the feature-wsireader-open branch October 27, 2021 11:36
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@shaneahmed shaneahmed shaneahmed approved these changes

@simongraham simongraham Awaiting requested review from simongraham

@Srijay-lab Srijay-lab Awaiting requested review from Srijay-lab

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