Release version 4.0.0 #587

mathieuboudreau · 2022-01-12T14:59:04Z

Checklist

I've given this PR a concise, self-descriptive, and meaningful title
I've linked relevant issues in the PR body
I've applied the relevant labels to this PR
I've added relevant tests for my contribution
I've updated the documentation and/or added correct docstrings
I've assigned a reviewer
I've consulted ADS's internal developer documentation to ensure my contribution is in line with any relevant design decisions

Description

Release version 4.0.0 of AxonDeepSeg that integrated IVADOMED into the project and provides Mac M1 compatibility.

Linked issues

…fter IVADOMED transition (#539) * Delete files/functions we suspect will be no longer necessary after IVADOMED transition, see https://docs.google.com/document/d/1Ipd6_nK6I6CKlDI_KpkLXH_jY2C547W_ootalfKnFlU/edit?usp=sharing' * Restore visualize segmentation * Remove imports from files that have been deleted * Remove imports from files that have been deleted Co-authored-by: Mathieu Boudreau <mathieuboudreau@Mathieus-MacBook-Pro.local>

…entation. Remove FSLeyes (temporarily) (#546) * Remove dependencies: TF, Keras, and Albumentation * Remove TF import and tf reset graph calls in tests * Update environment file for compatibility with Mac M1 ARM current setup with MiniForge (upgrade to python > 3.7 and update scikit versions * Update run_tests.yaml * Loosen fsleyes req * Downgrade to Python 3.8 for IVADOMED-compatibility * Downgrade python in the testing environment too

* Add IVADOMED in the requirements * Add IVADOMED in environment files * Add test IVADOMED SEM model * Update download_model.py * Update download_model.py * Update model * Early implementation of segmentation wrapper * Update missing import * Fix syntax * Convert Path() object to str() * Fix typo in string * Fix full path * Remove hardoced output filename * Save merge mask * Add missing import * Cleanup * Cleanup * Cleanup * Cleanup * Cleanup * Cleanup * Debug * Debug * Add tests for segment module * Try implementing segment_image * Debug * Initial implementation of segment_image for IVADOMED wrapper * Initial implementation of segment_folders for ivadomed * Make necessary changes to test_segment_folders_runs_with_relative_path * Resolve failing tests * Resolve test * Implement CLI for ivadomed * Update IVADOMED pixel_size option syntax * Update ads plugin for IVADOMED compatibility * Change ivadomed installation to pip * Updated notebooks for IVADOMED; deleted training notebooks * Update SEM model * Fix broken link * Refactor * Fix typo * Change missed line * Debug * Fix * Add TEM model * Final fixes * Add TEM * Fix typo * Fix IVADOMED related folder name * Add TEM option * Update release versions * Fix TEM model * Update release * Fix model names * Add pytest ini file * Resolve warnings * Resolve warnings * Test upgrading versions * Try Windows fix * Add find links * Update test files link * Update test files version * Update release * Update release version * Add OM model * Minor fixes * Minor fixes * Update release version * Update release version * Update release version * Implement IVADOMED into the ADS plugin * Fix bug where if no gratio and myelin stats were not initialized * Update test files release versions * Change convention from giving default NaNs to gratio and myelin stats to 0, for more robust save/load behaviours * Update one test * Change OM to BF nomenclature * Minor cleanup. Add documentation * Update environment.yml * Update AxonDeepSeg/integrity_test.py Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com> * Update AxonDeepSeg/morphometrics/compute_morphometrics.py Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com> * Review changes * Convert from 0 to np.nans * Remove duplicate line * Remove unnecessary line * Minor fixes in notebooks * Change filename convention * Switch from is to == to remove warnings * Add default pixel unit * Workaround to testing saved and loaded morphometrics with NaNs * #547 updated the plugin file Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com> Co-authored-by: Stoyan I. Asenov <43790661+Stoyan-I-A@users.noreply.github.com>

mathieuboudreau · 2022-01-12T15:29:27Z

@mariehbourget this branch is ready for review.

coveralls · 2022-01-12T15:40:42Z

Coverage remained the same at 87.769% when pulling 20aae92 on v4 into 45e7da0 on master.

mathieuboudreau · 2022-01-12T15:42:21Z

Hmm the coverage dropped, but that may be because of all the tests we removed when we removed the training files. Let me look into it, I could increase the limit temporarily if that's the case.

mariehbourget · 2022-01-12T15:44:46Z

Thank you @mathieuboudreau, I should be able to review by the end of the week.

Quick notes:

We will need to update the documentation for v4 in this PR.
We should probably do a "last" v3 release before the merge as well.

mathieuboudreau · 2022-01-12T15:45:37Z

Looks like the cause was that we removed the tests for visualize.py, but we didn't remove the source file itself when we were doing cleanup in 3c903dc. I just deleted it

mathieuboudreau · 2022-01-12T16:11:03Z

Hmm, not sure why the deleted file is still being counted in the number of lines during Coveralls

mariehbourget · 2022-01-12T19:27:09Z

Hmm, not sure why the deleted file is still being counted in the number of lines during Coveralls

Looks good now with +5% 🚀

mariehbourget · 2022-01-12T19:27:22Z

The training microscopy tutorial in ivadomed is now merged if we want to link to it in the documentation.

mathieuboudreau · 2022-01-14T01:38:32Z

When we're ready to merge this branch, I'll update the checks settings from Python 3.7 to 3.8 to make them pass (we moved to 3.8 in this PR).

mathieuboudreau · 2022-01-14T01:42:19Z

We should probably do a "last" v3 release before the merge as well.

Being done in #588

mathieuboudreau · 2022-01-14T01:49:47Z

We will need to update the documentation for v4 in this PR.

Done in 61c59a3

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

mathieuboudreau · 2022-02-02T23:40:37Z

@mariehbourget I just accepted all suggestions, and fixed the bug in reading resolutions in commit d0abfaa

mariehbourget

Thank you @mathieuboudreau!

I think everything is working as expected.
I left some minor comment/suggestions but approve the PR since they are small details.

Question: I saw that #592 and #584 are approved, do we want to integrate them before merging?

AxonDeepSeg/apply_model.py

CHANGELOG.md

Co-authored-by: Armand <83031821+hermancollin@users.noreply.github.com>

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

mathieuboudreau · 2022-02-03T15:16:36Z

Question: I saw that #592 and #584 are approved, do we want to integrate them before merging?

Done, just merged them into this branch.

…Leyes plugin (#592)

mathieuboudreau · 2022-02-03T15:31:07Z

@mariehbourget I've merged the two PRs, accepted your suggestions, and updated the Changelog per your suggestion.

If this is ready to merge, please give it one final approval!

mariehbourget

Thanks @mathieuboudreau!
2 small things, I promise to approve after that! :)

CHANGELOG.md

AxonDeepSeg/segment.py

mathieuboudreau · 2022-02-03T17:34:09Z

Thanks @mathieuboudreau!
2 small things, I promise to approve after that! :)

Perfect! Done and done =)

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

mathieuboudreau · 2022-02-03T17:47:50Z

Sorry, I clicked commit changed but it didn't work the first time! It should be there now.

-- Mathieu Boudreau, PhD Research Fellow | Montreal Heart Institute Software Developer | qMRLab and AxonDeepSeg Lead Editor | MRM Highlights<http://linkedin.com/company/mrm-highlights/><https://www.linkedin.com/company/mrm-highlights/>

________________________________ From: mariehbourget ***@***.***> Sent: Thursday, February 3, 2022 13:44 To: neuropoly/axondeepseg ***@***.***> Cc: Mathieu Boudreau ***@***.***>; Mention ***@***.***> Subject: Re: [neuropoly/axondeepseg] Release version 4.0.0 (PR #587) @mariehbourget commented on this pull request.

________________________________ In AxonDeepSeg/segment.py<#587 (comment)>:

requiredName.add_argument('-i', '--imgpath', required=True, nargs='+', help='Path to the image to segment or path to the folder \n'+

'where the image(s) to segment is/are located.') - ap.add_argument("-m", "--model", required=False, help='Folder where the model is located. \n'+ - 'The default SEM model path is: \n'+str(default_SEM_path)+'\n'+ - 'The default TEM model path is: \n'+str(default_TEM_path)+'\n'+ - 'The default OM model path is: \n'+str(model_seg_pns_bf_path)+'\n') + ap.add_argument("-m", "--model", required=False, help='Folder where the model is located, if different from the default model.') ap.add_argument('-s', '--sizepixel', required=False, help='Pixel size of the image(s) to segment, in micrometers. \n'+ 'If no pixel size is specified, a pixel_size_in_micrometer.txt \n'+ 'file needs to be added to the image folder path. The pixel size \n'+ 'in that file will be used for the segmentation.', default=None) ap.add_argument('-v', '--verbose', required=False, type=int, choices=list(range(0,4)), help='Verbosity level. \n'+ Hey @mathieuboudreau<https://github.com/mathieuboudreau>, I don't see this change, is it normal? — Reply to this email directly, view it on GitHub<#587 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAK25ZJEMZGCNPTNOBQUTODUZK5GFANCNFSM5LZGIOJQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

mariehbourget

Thank you so much @mathieuboudreau for coordinating this project. 🚀
Version 4 is ready! 😀

mathieuboudreau · 2022-02-03T18:00:53Z

Thank you so much @mathieuboudreau for coordinating this project. 🚀
Version 4 is ready! 😀

Thank you for your very rigourous review @mariehbourget and all your suggestsions !!

mathieuboudreau and others added 4 commits July 15, 2021 11:48

Merge branch 'master' into v4

92f1013

mathieuboudreau requested a review from mariehbourget January 12, 2022 14:59

mathieuboudreau changed the title V4 Release Version 4 Jan 12, 2022

mathieuboudreau added 2 commits January 12, 2022 11:07

Bump ADS version to 4.0.0

a2fbfd1

Update changelog

75e9539

Update python version in setup classifier

59a4d91

Remove unused file

9c7de92

mariehbourget mentioned this pull request Jan 12, 2022

Create a CLI in ADS using ivadomed API for segmentation #309

Closed

Update documentation

61c59a3

mathieuboudreau changed the title ~~Release Version 4~~ Release Version 4.0.0 Jan 14, 2022

mathieuboudreau changed the title ~~Release Version 4.0.0~~ Release version 4.0.0 Jan 14, 2022

mathieuboudreau and others added 4 commits February 2, 2022 19:25

Update ads_plugin.py

d3e8baf

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

Update docs/source/documentation.rst

dedef5a

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

Update ads_plugin.py

700b60b

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

Fix read resolution bug

d0abfaa

mathieuboudreau requested a review from mariehbourget February 2, 2022 23:40

mariehbourget previously approved these changes Feb 3, 2022

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changed all instances of imageio_imread by ads_utils.imread (#584)

5c01d3e

Co-authored-by: Armand <83031821+hermancollin@users.noreply.github.com>

mathieuboudreau dismissed mariehbourget’s stale review via 5c01d3e February 3, 2022 15:14

Update AxonDeepSeg/apply_model.py

9eca5f4

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

Stoyan-I-A and others added 2 commits February 3, 2022 11:26

#587 Fix NaNs not appearing when generating morphometrics with the FS…

4dfec07

…Leyes plugin (#592)

Update CHANGELOG.md

dea20b0

mathieuboudreau requested a review from mariehbourget February 3, 2022 15:30

mariehbourget reviewed Feb 3, 2022

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Update CHANGELOG.md

ad42fe6

mathieuboudreau requested a review from mariehbourget February 3, 2022 17:33

Update AxonDeepSeg/segment.py

7627d77

Co-authored-by: mariehbourget <54086142+mariehbourget@users.noreply.github.com>

mariehbourget previously approved these changes Feb 3, 2022

View reviewed changes

Update environment.yml

52fa7d3

mathieuboudreau dismissed mariehbourget’s stale review via 52fa7d3 February 3, 2022 18:28

mathieuboudreau added 2 commits February 3, 2022 15:14

Update environment.yml

370c666

Reduce verbosity level to appropriate new value of 1

20aae92

mathieuboudreau requested a review from mariehbourget February 3, 2022 20:55

mariehbourget approved these changes Feb 3, 2022

View reviewed changes

mathieuboudreau merged commit 805868e into master Feb 3, 2022

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Release version 4.0.0 #587

Release version 4.0.0 #587

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Release version 4.0.0 #587

Release version 4.0.0 #587

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