biopsykit.utils.file_handling module

Helper functions for file handling.

biopsykit.utils.file_handling.mkdirs(dir_list)

Batch-create a list of directories.

Conveniently create a list of directories, e.g. directories for storing processing results, figures, and statistic reports, using mkdir(). If parent directories do not exist yet, they are created (pathlib option parent=True), if directories already exist no Error is thrown (pathlib option exist_ok=True).

Parameters

dir_list (list of path or str) – list of directory names to create

Return type

None

Examples

>>> from biopsykit.utils.file_handling import mkdirs
>>> path_list = [Path("processing_results"), Path("exports/figures"), Path("exports/statistics")]
>>> mkdirs(path_list)

biopsykit.utils.file_handling.get_subject_dirs(base_path, pattern)

Filter for subject directories using a name pattern.

Parameters

• base_path (path or str) – base path to filter for directories

• pattern (str) – name pattern as regex

Returns

a list of path or an empty list if no subfolders matched the pattern

Return type

list of path

Raises

FileNotFoundError – if no subfolders in base_path match pattern.

Examples

>>> from biopsykit.utils.file_handling import get_subject_dirs
>>> base_path = Path(".")
>>> get_subject_dirs(base_path, "Vp*")

biopsykit.utils.file_handling.export_figure(fig, filename, base_dir, formats=None, use_subfolder=True, **kwargs)

Export matplotlib figure to file(s).

This function allows to export a matplotlib figure in multiple file formats, each format being optionally saved in its own output subfolder.

Parameters

• fig (Figure) – matplotlib figure object

• filename (Path or str) – name of the output file

• base_dir (path or str) – base directory to export figures to

• formats (list of str, optional) – list of file formats to export or None to export as pdf. Default: None

• use_subfolder (bool, optional) – whether to create an own output subfolder per file format or not. Default: True

• **kwargs – additional keyword arguments to pass to savefig()

Examples

>>> fig = plt.Figure()
>>>
>>> base_dir = "./img"
>>> filename = "plot"
>>> formats = ["pdf", "png"]
>>> # Export into subfolders (default)
>>> export_figure(fig, filename=filename, base_dir=base_dir, formats=formats)
>>> # | img/
>>> # | - pdf/
>>> # | - - plot.pdf
>>> # | - png/
>>> # | - - plot.png

>>> # Export into one folder
>>> export_figure(fig, filename=filename, base_dir=base_dir, formats=formats, use_subfolder=False)
>>> # | img/
>>> # | - plot.pdf
>>> # | - plot.png

biopsykit.utils.file_handling.is_excel_file(file_name, raise_exception=True)

Check whether the file name is an Excel file.

Parameters

• file_name (Path or str) – file name to check

• raise_exception (bool, optional) – whether to raise an exception or return a bool value

Returns

• True if file_name is an Excel file, i.e. has the suffix .xlsx

• False otherwise (if raise_exception is False)

Raises

ValidationError – if raise_exception is True and file_name is not an Excel file

Return type

Optional[bool]

biopsykit.utils.exceptions module biopsykit.utils.functions module