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dvc.yaml
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dvc.yaml
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stages:
convert_sly_to_int:
cmd:
- rm -rf data/interim || true
- python src/data/convert_sly_to_int.py
deps:
- src/data/convert_sly_to_int.py
- src/data/utils_sly.py
- configs/convert_sly_to_int.yaml
- data/sly
outs:
- data/interim/img
- data/interim/metadata.xlsx
segment_lungs:
cmd:
- rm -rf data/interim_lungs || true
- python src/segment_lungs.py
deps:
- src/segment_lungs.py
- src/models/lung_segmenter.py
- configs/segment_lungs.yaml
- data/interim/img
- models/lung_segmentation/DeepLabV3
- models/lung_segmentation/FPN
- models/lung_segmentation/MAnet
outs:
- data/interim_lungs
fuse_maps:
cmd:
- rm -rf data/interim_fused || true
- python src/fuse_maps.py
deps:
- src/fuse_maps.py
- src/models/map_fuser.py
- src/models/mask_processor.py
- src/data/utils_sly.py
- configs/fuse_maps.yaml
- data/interim_lungs
outs:
- data/interim_fused/map
- data/interim_fused/mask
- data/interim_fused/metadata.xlsx
convert_int_to_final:
cmd:
- rm -rf data/final || true
- python src/data/convert_int_to_final.py
deps:
- src/data/convert_int_to_final.py
- src/data/utils_final.py
- configs/convert_int_to_final.yaml
- data/interim/img
- data/interim/metadata.xlsx
- data/interim_fused/metadata.xlsx
outs:
- data/final/img
- data/final/metadata.xlsx
convert_final_to_coco:
cmd:
- rm -rf data/coco || true
- python src/data/convert_final_to_coco.py
deps:
- src/data/convert_final_to_coco.py
- src/data/utils_coco.py
- src/data/utils_sly.py
- configs/convert_final_to_coco.yaml
- data/final/img
- data/final/metadata.xlsx
outs:
- data/coco/train
- data/coco/test
- data/coco/metadata.xlsx