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Fix(BMZ export): torchvision version; model validation #257

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merged 2 commits into from
Oct 29, 2024
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Fix(BMZ export): torchvision version; model validation #257

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ff05fc1
fix: torchvision version in environment.yaml file
melisande-c Oct 21, 2024
fd3c0bc
fix: do not configure ModelDescr (error: decimal param was decimals; …
melisande-c Oct 21, 2024
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6 changes: 4 additions & 2 deletions src/careamics/model_io/bioimage/bioimage_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ def get_unzip_path(zip_path: Union[Path, str]) -> Path:
return zip_path.parent / (str(zip_path.name) + ".unzip")


def create_env_text(pytorch_version: str) -> str:
def create_env_text(pytorch_version: str, torchvision_version: str) -> str:
"""Create environment yaml content for the bioimage model.

This installs an environment with the specified pytorch version and the latest
Expand All @@ -32,6 +32,8 @@ def create_env_text(pytorch_version: str) -> str:
----------
pytorch_version : str
Pytorch version.
torchvision_version : str
Torchvision version.

Returns
-------
Expand All @@ -43,7 +45,7 @@ def create_env_text(pytorch_version: str) -> str:
f"dependencies:\n"
f" - python=3.10\n"
f" - pytorch={pytorch_version}\n"
f" - torchvision={pytorch_version}\n"
f" - torchvision={torchvision_version}\n"
f" - pip\n"
f" - pip:\n"
f" - git+https://github.com/CAREamics/careamics.git\n"
Expand Down
9 changes: 0 additions & 9 deletions src/careamics/model_io/bioimage/model_description.py
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Expand Up @@ -284,15 +284,6 @@ def create_model_description(
weights=weights_descr,
attachments=[FileDescr(source=config_path)],
cite=config.get_algorithm_citations(),
config={ # conversion from float32 to float64 creates small differences...
"bioimageio": {
"test_kwargs": {
"pytorch_state_dict": {
"decimals": 0, # ...so we relax the constraints on the decimals
}
}
}
},
)

return model
Expand Down
9 changes: 5 additions & 4 deletions src/careamics/model_io/bmz_io.py
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Expand Up @@ -8,7 +8,9 @@
import pkg_resources
from bioimageio.core import load_description, test_model
from bioimageio.spec import ValidationSummary, save_bioimageio_package
from torch import __version__, load, save
from torch import __version__ as PYTORCH_VERSION
from torch import load, save
from torchvision import __version__ as TORCHVISION_VERSION

from careamics.config import Configuration, load_configuration, save_configuration
from careamics.config.support import SupportedArchitecture
Expand Down Expand Up @@ -141,7 +143,6 @@ def export_to_bmz(
path_to_archive.parent.mkdir(parents=True, exist_ok=True)

# versions
pytorch_version = __version__
careamics_version = pkg_resources.get_distribution("careamics").version

# save files in temporary folder
Expand All @@ -151,7 +152,7 @@ def export_to_bmz(
# create environment file
# TODO move in bioimage module
env_path = temp_path / "environment.yml"
env_path.write_text(create_env_text(pytorch_version))
env_path.write_text(create_env_text(PYTORCH_VERSION, TORCHVISION_VERSION))

# export input and ouputs
inputs = temp_path / "inputs.npy"
Expand All @@ -174,7 +175,7 @@ def export_to_bmz(
inputs=inputs,
outputs=outputs,
weights_path=weight_path,
torch_version=pytorch_version,
torch_version=PYTORCH_VERSION,
careamics_version=careamics_version,
config_path=config_path,
env_path=env_path,
Expand Down
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