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Getting code ready for the next major release #58

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Getting code ready for the next major release #58

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@sarthakpati sarthakpati commented May 11, 2023 •
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Fixes issue #N.A.

Proposed Changes

  • removed the FeTS 1.0 inference executables, since they were designed for pre-op GBM
  • added docker image construction
  • added helper python script CreateCSVForDICOMs.py and updated PrepareDataset.py to handle post-op cases
  • added a setup.py to aid in install-time environment creation
  • Removed unnecessary files

@sarthakpati sarthakpati marked this pull request as draft May 11, 2023 20:27
@sarthakpati sarthakpati changed the title Removing a lot of stuff for the next release Getting code ready for the next major release Jun 19, 2023
aristizabal95 and others added 28 commits July 24, 2023 18:04
@aristizabal95
Simplify build copy. Rename stages
675bb2e
@aristizabal95
Simplify build copy. Rename stages
4ea515a
@aristizabal95
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
4dcb96e 
…separate-stages
@aristizabal95
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
678eee4 
…separate-stages
@sarthakpati
added example for tumor segmentation models
75b1bed
@sarthakpati
added example for tumor segmentation models
54d5159
@sarthakpati
updated to use the example models
e6f72c7
@sarthakpati
updated to use the example models
8d7ecd9
@sarthakpati
added brats nomenclature
760c0da
@sarthakpati
added brats nomenclature
734dd04
@sarthakpati
updated nomenclature
3243bee
@sarthakpati
updated nomenclature
00470e6
@sarthakpati
fixed list issue
99a3a2e
@sarthakpati
fixed list issue
f672747
@sarthakpati
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
b8eadb1 
…fets_2.0
@sarthakpati
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
3c1bcb4 
…fets_2.0
@sarthakpati
updated hash
440376a
@sarthakpati
version update
9fe207b
@sarthakpati
Merge branch 'master' of https://github.com/FeTS-AI/Front-End into fe…
60aae62 
…ts_2.0
@sarthakpati
Merge branch 'master' of https://github.com/FeTS-AI/Front-End into fe…
57d7a38 
…ts_2.0
@aristizabal95
Move downloaded models to MLCube
b7b918b
@aristizabal95
Move downloaded models to MLCube
eb53a4b
@aristizabal95
Fix prev stage removal from brain_extraction
85cb2bf
@aristizabal95
Fix prev stage removal from brain_extraction
94b8588
@aristizabal95
Fix get row information retrieval
ee47c95
@aristizabal95
Fix get row information retrieval
c421040
@aristizabal95
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
b5cd751 
…separate-stages
@aristizabal95
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
33aabc7 
…separate-stages
sarthakpati
sarthakpati commented Dec 23, 2023
View reviewed changes
.github/workflows/docker-image.yml Outdated
@@ -117,7 +117,9 @@ jobs:
# Run the image from the base entrypoint as a test
- name: Test container with entrypoint
# Run a tag we generated from the metadata extraction above -- they're all the same image, but echo it regardless just so we know.
run: docker run --rm ghcr.io/fets-ai/front-end:latest -h
run: |
docker run --rm ghcr.io/fets-ai/front-end:latest -h
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@sarthakpati sarthakpati Dec 23, 2023 •
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Should there be some other (or additional) check(s) here, @aristizabal95 @hasan7n? Maybe something specific to mlcubes?

aristizabal95 and others added 23 commits January 4, 2024 15:03
@aristizabal95
Fix issue with hardcoded input paths
16293bd
@aristizabal95
Fix datatype conversion on csv read
e34bd1e
@aristizabal95
Fix gt not found error. Create mlcube constants
9f9a7b7
@aristizabal95
update is_done functions
1114439
@aristizabal95
Remove resolved TODO
e4e0d21
@aristizabal95
Fix csv stage using wrong status code
127d7bd
@hasan7n
gpu support
35b97ea
@sarthakpati
Merge pull request #77 from aristizabal95/separate-stages
fe05957 
Separate stages
@hasan7n
add cuda visible devices env var
64818a4
@aristizabal95
Generate dataset statistics instead of DICOM ones
e64bdd9
@sarthakpati
added a check for nifti files
91358e7
@aristizabal95
Merge branch 'fets_2.0' of https://github.com/FeTS-AI/Front-End into …
47218ae 
…separate-stages
@aristizabal95
Fix non-preprocessed NIfTIs not being detected
ebb7edb
@sarthakpati
Merge pull request #78 from aristizabal95/separate-stages
cb90aab 
MLCube: Support for GPUs and non-preprocessed NIfTI images
@sarthakpati
Update Dockerfile
0bc3aa1
@aristizabal95
Write documentation for RANO
51d4c25
@aristizabal95
Remove unused image
405b89d
@sarthakpati
Merge pull request #80 from aristizabal95/rano_docs
c58b76a 
Write documentation for RANO
@sarthakpati
Merge branch 'master' of https://github.com/FeTS-AI/Front-End into fe…
69b1dd6 
…ts_2.0
@sarthakpati
end of file updated
dd1dab9
@sarthakpati
Merge pull request #82 from FeTS-AI/fets_2.0_master_sync
3df09a5 
Fets 2.0 master sync
@sarthakpati
Update Dockerfile
d11351d
@sarthakpati
using an environment variable and falling back to temp dir
6f374ec
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4 participants
@sarthakpati @aristizabal95 @hasan7n @brandon-edwards