Bioimage

Create environment yaml content for the bioimage model.

This installs an environment with the specified pytorch version and the latest changes to careamics.

Parameters:

• pytorch_version (str) –

  Pytorch version.

• torchvision_version (str) –

  Torchvision version.

Returns:

• str –

  Environment text.

Create model description.

Parameters:

• config (Configuration) –

  CAREamics configuration.

• name (str) –

  Name of the model.

• general_description (str) –

  General description of the model.

• data_description (str) –

  Description of the data the model was trained on.

• authors (list[Author]) –

  Authors of the model.

• inputs (Union[Path, str]) –

  Path to input .npy file.

• outputs (Union[Path, str]) –

  Path to output .npy file.

• weights_path (Union[Path, str]) –

  Path to model weights.

• torch_version (str) –

  Pytorch version.

• careamics_version (str) –

  CAREamics version.

• config_path (Union[Path, str]) –

  Path to model configuration.

• env_path (Union[Path, str]) –

  Path to environment file.

• covers (list of pathlib.Path or str) –

  Paths to cover images.

• channel_names (Optional[list[str]], default: None ) –

  Channel names, by default None.

• model_version (str, default: "0.1.0" ) –

  Model version.

Returns:

• ModelDescr –

  Model description.

Return the relative path to the weights and configuration files.

Parameters:

• model_desc (ModelDescr) –

  Model description.

Returns:

• tuple of (path, path) –

  Weights and configuration paths.

Generate unzipped folder path from the bioimage.io model path.

Parameters:

• zip_path (Path) –

  Path to the bioimage.io model.

Returns:

• Path –

  Path to the unzipped folder.