Add Feature read a region from whole slide image #10
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shaneahmed
commented
Jul 2, 2020
shaneahmed
commented
- Add feature to read a region from whole slide image in WSIReader class.
- Add the option to display or save specific region from whole slide images using command line
added 16 commits
July 2, 2020 19:55
Add feature read_region to WSIReader class in wsireader.py
Configure setup.py
Rearrange examples in doc to be within 88 characters
Add test read_region and slide_info directly through WSIReader object.
Fix travis bug due to image path.
Add command line for read regions
Fix travis bug for read region
Fix travis bug for read region
Fix Travis bug
Fix Travis bug
Fix Travis bug
Fix Travis bug file list empty
Add command line test for read region
Fix docstring for test_wsireader_read_region
Fix Travis error for command line read region
Update docstring
Update docstring to fix issues with Sphinx build
Codecov Report
@@ Coverage Diff @@
## develop #10 +/- ##
============================================
+ Coverage 56.55% 77.12% +20.56%
============================================
Files 9 9
Lines 122 153 +31
Branches 9 14 +5
============================================
+ Hits 69 118 +49
+ Misses 50 25 -25
- Partials 3 10 +7
Continue to review full report at Codecov.
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Merge pull request #5 from docs-readthedocs-config Create Read the Docs configuration file (.readthedocs.yml) specifying to use conda setup to create environment using requiremetns.conda.yml. - Add Conda Forge OpenSlide To Requirements - Add OpenSlide to conda requirements file. - Add Pixman < 0.38.0 (0.38.0 breaks OpenSlide). - Removed version numbers from others so that latest is used. - Pin Setup Tools Verions <= 45.1 - Pin OpenCV Version >4.0 In Conda Requirements File - Add requirements.txt and requirements.win64.conda.yml - Modify setup.py to add dependencies - Make version numbers for various packages in requirements and conda yaml consistent. Pin version numbers if necessary. Co-authored-by: shaneahmed <sa>
Add feature read_region to WSIReader class in wsireader.py
Rearrange examples in doc to be within 88 characters
Add test read_region and slide_info directly through WSIReader object.
Fix travis bug due to image path.
Add command line for read regions
Fix travis bug for read region
Fix travis bug for read region
Fix Travis bug
added 9 commits
July 3, 2020 14:22
Fix Travis bug
Fix Travis bug
Fix Travis bug file list empty
Add command line test for read region
Fix docstring for test_wsireader_read_region
Fix Travis error for command line read region
Update docstring
Update docstring to fix issues with Sphinx build
John-P
approved these changes
Jul 3, 2020
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John-P
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All looks good to me. Just that one minor point about the naming of the function to write to disk. I suggested keeping a neutral rather than specifying that is uses cv2 in case we change it to use a different / multiple libraries later e.g. we might find that the Nvidia libraries are faster and can swap it out etc. and the name would still make sense.
added 3 commits
July 3, 2020 15:25
Replace cv2_imwrite with imwrite for flexibility
Update usage.rst to include imwrite in doc
Update README.rst to update `pip install -r requirements.txt` instead of `pip install requirements_dev.txt`
simongraham
reviewed
Jul 7, 2020
simongraham
reviewed
Jul 7, 2020
simongraham
reviewed
Jul 7, 2020
simongraham
approved these changes
Jul 7, 2020
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simongraham
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simongraham
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Overall- looks good -> few very minor things to consider before merging.
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