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multi_scan

plantimager.cli.multi_scan Link

Multiple imaging with varying parameters to assess/test acquisition or reconstruction pipelines.

load_config_from_directory Link

load_config_from_directory(path)

Load TOML & JSON configuration files from path.

Parameters:

Name Type Description Default
path str

Path to where the configuration file(s) should be.

 required

Returns:

Type Description
dict

The configuration dictionary, if loaded from the files.
Notes

We exclude the backup files SCAN_TOML & PIPE_TOML from the list of loadable files.

Source code in plantimager/cli/multi_scan.py 
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def load_config_from_directory(path):
    """Load TOML & JSON configuration files from path.

    Parameters
    ----------
    path : str
        Path to where the configuration file(s) should be.

    Returns
    -------
    dict
        The configuration dictionary, if loaded from the files.

    Notes
    -----
    We exclude the backup files ``SCAN_TOML`` & ``PIPE_TOML`` from the list of loadable files.

    """
    # List TOML config files:
    toml_list = glob.glob(os.path.join(path, "*.toml"))
    toml_list = [cfg for cfg in toml_list if cfg.split("/")[-1] not in (SCAN_TOML, PIPE_TOML)]
    # List JSON config files:
    json_list = glob.glob(os.path.join(path, "*.json"))

    if len(toml_list) == 0 and len(json_list) == 0:
        logger.critical(f"Could not find any TOML or JSON configuration file in '{path}'!")
        sys.exit("Configuration file missing!")

    config = {}
    # Read TOML configs
    for f in toml_list:
        try:
            c = toml.load(open(f))
            config = {**config, **c}
        except:
            logger.warning(f"Could not process TOML config file: {f}")
        else:
            logger.info(f"Loaded configuration file: {f}")
    # Read JSON configs:
    for f in json_list:
        try:
            c = json.load(open(f))
            config = {**config, **c}
        except:
            logger.warning(f"Could not process JSON config file: {f}")
        else:
            logger.info(f"Loaded configuration file: {f}")

    return config

load_config_from_file Link

load_config_from_file(path)

Load TOML or JSON configuration file from path.

Parameters:

Name Type Description Default
path str

Path to the configuration file to load.

 required

Returns:

Type Description
dict

The configuration dictionary.
Source code in plantimager/cli/multi_scan.py 
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def load_config_from_file(path):
    """Load TOML or JSON configuration file from path.

    Parameters
    ----------
    path : str
        Path to the configuration file to load.

    Returns
    -------
    dict
        The configuration dictionary.

    """
    config = None
    if path.endswith("toml"):
        try:
            config = toml.load(open(path))
        except:
            logger.critical(f"Could not load TOML configuration file '{path}'!")
    elif path.endswith("json"):
        try:
            config = json.load(open(path))
        except:
            logger.critical(f"Could not load JSON configuration file '{path}'!")
    else:
        logger.critical(f"Unsupported configuration file format, should be TOML or JSON!")

    if config is None:
        sys.exit(f"Error while loading configuration file!")

    return config