Path manager¶

class dendrotweaks.path_manager.PathManager(path_to_model: str)[source]¶

Bases: object

A manager class for handling file and directory paths related to models data.

Parameters:: path_to_model (str) – The path to the model directory.

path_to_model¶

The path to the model directory.

Type:: str

paths¶

A dictionary of paths for different file types.

Type:: Dict[str, str]

property path_to_data¶: The path to the data directory, which is always the parent directory of path_to_model.

copy_default_mod_files()[source]¶: Copy default mod files to the data directory.

copy_template_files()[source]¶: Copy template files to the data directory.

remove_folder(relative_path: str) → None[source]¶

Remove a folder and all its contents.

Parameters:: relative_path (str) – The absolute path to the folder to be removed.

get_abs_path(relative_path: str, create_dirs: bool = False) → str[source]¶

Get the absolute path to a file or directory based on a relative path.

Parameters:

relative_path (str) – Path relative to one of the registered roots.
create_dirs (bool, default False) – If True, create the parent directories if they don’t exist.

Returns:

Absolute path in OS-native format.

Return type:

str

Examples

>>> pm = PathManager('/path/to/model')
>>> pm.get_abs_path('stimuli/depolarizing/protocol.json')
'/path/to/model/stimuli/depolarizing/protocol.json'

list_folders(relative_path: str) → List[str][source]¶

List all folders in a given directory.

Parameters:: relative_path (str) – Path relative to one of the registered roots.
Returns:: A list of folder names.
Return type:: List[str]

Examples

>>> pm = PathManager('/path/to/model')
>>> pm.list_folders('stimuli')
['depolarizing_current', 'hyperpolarizing_current']

list_files(relative_path: str, extension: str | None = None) → List[str][source]¶

List all files in a given directory with an optional extension filter. If the extension is None, su

Parameters:

relative_path (str) – Path relative to one of the registered roots.
extension (str) – The file extension to filter by (e.g., ‘mod’, ‘swc’).

Returns:

A list of file names.

Return type:

List[str]

list_morphologies(extension: str = '.swc') → List[str][source]¶

List all SWC files.

Returns:: A list of SWC file names.
Return type:: List[str]

list_stimuli() → List[str][source]¶

List all JSON files.

Returns:: A list of JSON file names.
Return type:: List[str]

list_biophys()[source]¶

List all biophysics files.

Returns:: A list of biophysics file names.
Return type:: List[str]

print_directory_tree(subfolder=None) → None[source]¶

Print a directory tree for a given file type.

Parameters:: file_type (str) – The type of file (e.g., ‘mod’, ‘swc’).

get_channel_paths(mechanism_name: str, python_template_name: str = None) → Dict[str, str][source]¶

Get all necessary paths for creating a channel.

Parameters:

mechanism_name (str) – The name of the mechanism.
python_template_name (str, optional) – The name of the Python template file.

Returns:

A dictionary of paths.

Return type:

Dict[str, str]

get_standard_channel_paths(mechanism_name: str, python_template_name: str = None, mod_template_name: str = None) → Dict[str, str][source]¶

Get all necessary paths for creating a standard channel.

Parameters:

mechanism_name (str) – The name of the mechanism.
python_template_name (str, optional) – The name of the Python template file.
mod_template_name (str, optional) – The name of the MOD template file.

Returns:

A dictionary of paths.

Return type:

Dict[str, str]