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Merged
merged 1,156 commits into from
Dec 23, 2023
Merged

Implement Data Preparation MLCube #74

merged 1,156 commits into from
Dec 23, 2023

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@aristizabal95
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@aristizabal95 aristizabal95 commented Sep 12, 2023 •
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This PR contains all the required logic for preparing a FeTS-related dataset with a medperf-compatible MLCube. It implements logic for manual steps in between automated ones, as well as resuming execution after a failure or input data modification

TODOs

  • Implement complete sanity check steps
  • Implement statistics

sarthakpati and others added 30 commits July 14, 2023 11:17
@sarthakpati
trying specific modules
2308da8
@sarthakpati
only want to install .py files in src/applications
8ec039f
@aristizabal95
Move mlcubes outside of src folder
5b9462f
@aristizabal95
Move mlcubes outside of src folder
7d38112
@aristizabal95
Implement efficient Dockerfile for data-prep
20cec29
@aristizabal95
Implement efficient Dockerfile for data-prep
41c6df4
@sarthakpati
trying without setuptools upgrade
41879e2
@sarthakpati
added py_modules in setup
f477ead
@sarthakpati
updated numpy version
2ec5ac1
@aristizabal95
Implement root-level dockerfile for data prep
c6ca685
@aristizabal95
Implement root-level dockerfile for data prep
c37b788
@aristizabal95
Update submodules
12b73f9
@aristizabal95
Update submodules
074ea92
@aristizabal95
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
df3eb72 
…reformat-prepare-script
@aristizabal95
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
0d18a61 
…reformat-prepare-script
@aristizabal95
Set submodules to correct hash
af2d4ef
@aristizabal95
Set submodules to correct hash
397b1ee
@sarthakpati
updated entrypoint
bade2be
@sarthakpati
fixed python path
2f0202d
@sarthakpati
fixed path
8072851
@sarthakpati
fixed path
60186e5
@aristizabal95
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
5c6aca4 
…reformat-prepare-script
@aristizabal95
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
7097678 
…reformat-prepare-script
@aristizabal95
Merge dockerfiles together
19c4317
@aristizabal95
Merge dockerfiles together
adf84b3
@sarthakpati
updated openvino version (per ST)
c177a9c
@sarthakpati
change to posixpath
074c990
@sarthakpati
started putting downloader in
4ea9122
@sarthakpati
updated ignore
a6b0204
@sarthakpati
made this a bit more generic
57ead10
aristizabal95 and others added 15 commits December 11, 2023 10:19
@aristizabal95
Merge branch 'separate-stages' of https://github.com/aristizabal95/Fe…
3e9ffb0 
…TS-AI-Front-End into nnunet
@aristizabal95
Import from extract for nnUNet
7a6366b
@aristizabal95
Remove report dependency. Handle empty stats
d79d5e3
@aristizabal95
Merge branch 'separate-stages' of https://github.com/aristizabal95/Fe…
d85b430 
…TS-AI-Front-End into nnunet
@aristizabal95
Sync generate_report with parent
08a9032
@aristizabal95
Remove stages file
f47a8a5
@aristizabal95
Merge branch 'separate-stages' of https://github.com/aristizabal95/Fe…
bca838b 
…TS-AI-Front-End into nnunet
@hasan7n
fix some permission issues inside the container
884a035
@aristizabal95
Handle alternative folder structures
644aaf6
@aristizabal95
Merge branch 'fix-container-perms' of https://github.com/hasan7n/Fron…
401319a 
…t-End into separate-stages
@aristizabal95
Support semi-prepared input data
87fa69a
@aristizabal95
Handle edge cases for semi-prepared data
72e9126
@aristizabal95
Merge branch 'separate-stages' of https://github.com/aristizabal95/Fe…
5f53fd9 
…TS-AI-Front-End into nnunet
@aristizabal95
Pass models through tarball. Fix skip issues
c97597d
@aristizabal95
Merge pull request #3 from aristizabal95/nnunet
c6f54af 
Use nnUNet for tumor segmentation
@aristizabal95 aristizabal95 marked this pull request as ready for review December 18, 2023 17:08
sarthakpati
sarthakpati approved these changes Dec 23, 2023
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LGTM

@sarthakpati sarthakpati merged commit 82b3bde into FeTS-AI:fets_2.0 Dec 23, 2023
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@hasan7n hasan7n hasan7n left review comments

@sarthakpati sarthakpati sarthakpati approved these changes

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4 participants

@aristizabal95 @sarthakpati @hasan7n @brandon-edwards