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Refactor to depend on deepcell_auth. #130

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Refactor to depend on deepcell_auth. #130

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6 changes: 4 additions & 2 deletions cellSAM/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,10 +20,12 @@ def download_training_data(version=None):
- 1.2 (latest)
- 1.0
"""
from . import _auth
from deepcell_auth import _auth

manifest = _auth.load_manifest()

version = "1.2" if version is None else version
record = _auth._data_versions[version]
record = manifest["datasets"]["cellsam"][version]

_auth.fetch_data(
record["asset_key"], cache_subdir="datasets", file_hash=record["asset_hash"]
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195 changes: 0 additions & 195 deletions cellSAM/_auth.py
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10 changes: 6 additions & 4 deletions cellSAM/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
fill_holes_and_remove_small_masks,
subtract_boundaries,
)
from . import _auth
from deepcell_auth import _auth


__all__ = ["segment_cellular_image"]
Expand Down Expand Up @@ -76,13 +76,15 @@ def get_model(model="cellsam_general", version=None) -> nn.Module:
the latest released version will be used.

"""
model_version_dict = _auth.load_manifest()["models"]["cellsam"]

version = "1.2" if version is None else version
if version not in _auth._model_versions:
if version not in model_version_dict:
raise ValueError(
f"Model version {version} not recognized, must be one of:\n"
f"{list(_auth._model_versions)}"
f"{list(model_version_dict)}"
)
record = _auth._model_versions[version]
record = model_version_dict[version]
archive_name = record["asset_key"].split("/")[-1]

cellsam_assets_dir = Path.home() / f".deepcell/models"
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3 changes: 1 addition & 2 deletions pyproject.toml
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Expand Up @@ -17,8 +17,7 @@ dependencies = [
'torchvision',
'kornia',
# Model access
'requests',
'tqdm',
'deepcell_auth@git+https://github.com/vanvalenlab/deepcell-auth.git',
# Whole-slide imaging
'dask[distributed]',
'dask-image',
Expand Down