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Refactor#38

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taxe10 merged 86 commits intomlexchange:mainfrom
taxe10:refactor
Dec 4, 2025
Merged

Refactor#38
taxe10 merged 86 commits intomlexchange:mainfrom
taxe10:refactor

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@taxe10 taxe10 commented Nov 14, 2025 •
edited by xiaoyachong
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Companion PRs:
tomo: mlexchange/mlex_tomo_framework#16
prefect worker: mlexchange/mlex_prefect_worker#26
mlex_utils: mlexchange/mlex_utils#5
highres_seg: mlexchange/mlex_highres_segmentation#201

TibbersHao added 30 commits June 28, 2024 14:56
@TibbersHao
added functions to load yaml and validate params
40d0398
@TibbersHao
added functions to initialize tiled dataset
6d5f688
@TibbersHao
added function for normalization, tensor conversion and qlty cropping
e29ac4f
@TibbersHao
added DLSIA prefix for all model names
565a0cb
@TibbersHao
updated qlty version to 0.2.0
16c6be2
@TibbersHao
added function and tests for dataloader construction
6831c46
@TibbersHao
temporary degrade to pydantic 1.10.15 to deal with old tiled catalog …
c456aef 
…package compatibility
@TibbersHao
changed network names with DLSIA Prefix
d4805d4
@TibbersHao
changed model name
fdb8711
@TibbersHao
added training function and tests
803e15d
@TibbersHao
added pytest folders
ffea05e
@TibbersHao
modified parameters and added tests for model training/saving
0b8e238
@TibbersHao
modified var name to specifically reflect to network name
ac0e602
@TibbersHao
added function and tests for model loading
20c501d
@TibbersHao
added full inference function
59ca883
@TibbersHao
pre-commit format fix
44ead0f
@TibbersHao
cleared unnecessary tests and added monkeypatch tests for device dete…
82e7886 
…ction
@TibbersHao
trimmed one-line functions and got rid of unnecessary pytests
d9fa680
@TibbersHao
added utility functions for segmentation, breaking down big functions…
aba3f4b 
…, added pytests
@TibbersHao
move dvc import inside loop to speed up process
a8738aa
@TibbersHao
enable pytest order as temp solution for dependency issues
3fe5ee1
@TibbersHao
rearrange fixtures
b77bbd7
@TibbersHao
modified to local tiled server for testing purpose
46040af
@TibbersHao
fixed name mismatch
31773fd
@TibbersHao
added dimension check for data_shape
87ad30b
@TibbersHao
fixed dimension mismatch when building network
bc794e6
@TibbersHao
format change
c2d8dc6
@TibbersHao
fixed model name mismatch
d1e1b23
@TibbersHao
adjusments for full inference
31461c2
@TibbersHao
pytest rearrangement and parameterization
08cbd4d
@taxe10 taxe10 mentioned this pull request Nov 14, 2025
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@taxe10 taxe10 requested review from Wiebke and xiaoyachong November 14, 2025 17:11
xiaoyachong
xiaoyachong reviewed Nov 20, 2025
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Thanks for your PR! It looks good. The only potential issue is that it currently has conflicts with the main branch. Could you merge main into your branch and resolve the conflicts on your side? Once that’s done, I can test it together with the other PRs.

Comment thread mlex_dlsia/main.py
Comment thread mlex_dlsia/network.py Outdated
Comment thread mlex_dlsia/train.py Outdated
Comment thread pyproject.toml
Comment thread _tests/example_bad_params.yaml
Comment thread _tests/test_3-train.py
@taxe10 taxe10 marked this pull request as ready for review November 21, 2025 16:44
@taxe10 taxe10 mentioned this pull request Nov 21, 2025
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taxe10 commented Nov 21, 2025 •
edited by xiaoyachong
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Companion PR: mlexchange/mlex_highres_segmentation#201

xiaoyachong
xiaoyachong reviewed Nov 21, 2025
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Thank you for your PR! I found a few issues with the refactor and left some comments.

Comment thread mlex_dlsia/train.py Outdated
Comment thread mlex_dlsia/parameters.py
Comment thread mlex_dlsia/network.py Outdated
Comment thread mlex_dlsia/main.py Outdated
Comment thread mlex_dlsia/train.py Outdated
@xiaoyachong xiaoyachong mentioned this pull request Nov 24, 2025
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This was referenced Nov 24, 2025
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xiaoyachong
xiaoyachong approved these changes Nov 25, 2025
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@taxe10 @Wiebke This PR has been tested on my end alongside the companion PRs, and everything works as expected.

@taxe10 taxe10 merged commit 76bf4d3 into mlexchange:main Dec 4, 2025
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@xiaoyachong xiaoyachong xiaoyachong approved these changes

@Wiebke Wiebke Awaiting requested review from Wiebke

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4 participants

@taxe10 @xiaoyachong @TibbersHao @Wiebke