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Use containers with hugging face model storage
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Uses updated containers that pulled the models from HuggingFace
instead of datacommons.
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johnbradley committed Jul 25, 2023
1 parent 807bb05 commit c054a42
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions workflow/Snakefile
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ rule generate_metadata:
mask = 'Mask/{image}_mask.png'
log: 'logs/generate_metadata_{image}.log'
container:
'docker://ghcr.io/hdr-bgnn/drexel_metadata:0.5'
'docker://ghcr.io/hdr-bgnn/drexel_metadata:0.6'
shell: 'gen_metadata.py {input} --device cpu --outfname {output.metadata} --maskfname {output.mask} > {log} 2>&1'

# Transform metadata into a format compatible with the following rules
Expand Down Expand Up @@ -52,7 +52,7 @@ rule segment_image:
output: 'Segmented/{image}_segmented.png'
log: 'logs/segment_image_{image}.log'
container:
'docker://ghcr.io/hdr-bgnn/bgnn-trait-segmentation:0.0.6'
'docker://ghcr.io/hdr-bgnn/bgnn-trait-segmentation:0.0.7'
shell:
'segmentation_main_rescale_origin.py {input} {output} > {log} 2>&1'

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