shnitsel.io.newtonx.format_reader#

Attributes#

DataType

_newtonx_default_pattern_regex

_newtonx_default_pattern_glob

Classes#

NewtonXFormatInformation

Information to keep track of relevant information for

NewtonXFormatReader

Class for providing the NewtonX format reading functionality in the standardized FormatReader interface

Module Contents#

class NewtonXFormatInformation#

Bases: shnitsel.io.format_reader_base.FormatInformation

Information to keep track of relevant information for

nx_log_path: pathlib.Path | None = None#
positions_file_path: pathlib.Path | None = None#
DataType#
_newtonx_default_pattern_regex#
_newtonx_default_pattern_glob = 'TRAJ*'#
class NewtonXFormatReader#

Bases: shnitsel.io.format_reader_base.FormatReader

Class for providing the NewtonX format reading functionality in the standardized FormatReader interface

find_candidates_in_directory(path)#

Function to return a all potential matches for the current file format within a provided directory at path. :param path: The path to a directory to check for potential candidate files or subdirectories :type path: PathOptionsType

Returns:

  • list[pathlib.Path] – A list of paths that should be checked in detail for whether they represent the format of this FormatReader.

  • None – If no potential candidates were found

Parameters:

path (shnitsel.io.shared.helpers.PathOptionsType)

Return type:

list[pathlib.Path] | None

check_path_for_format_info(path, hints_or_settings=None)#

Check if the path is a NewtonX-style output directory.

Designed for a single input trajectory.

Parameters:

  • path (PathOptionsType) – The path to check for NewtonX data

  • hints_or_settings (dict | None, optional) – Configuration options provided to the reader by the user, by default None

Returns:

The object holding all relevant format information for the path contents if it matches the NewtonX format

Return type:

FormatInformation

Raises:
read_from_path(path, *, format_info, loading_parameters=None, expect_dtype=None)#

Read a NewtonX-style trajcetory from path at path. Implements FormatReader.read_from_path()

Parameters:

  • path (pathlib.Path) – Path to a NewtonX-format directory.

  • format_info (FormatInformation) – Format information on the provided path that has been previously parsed.

  • loading_parameters (LoadingParameters | None, optional) – Loading parameters to e.g. override default state names, units or configure the error reporting behavior, by default None

  • expect_dtype (type[DataType] | TypeForm[DataType] | None, optional) – An optional parameter to specify the return type. For this class, it should be xr.Dataset, Trajectory or Frames, by default None

Returns:

The loaded Shnitsel-conforming trajectory.

Return type:

xr.Dataset | Trajectory | Frames | None

Raises:

  • ValueError – Not enough loading information was provided via path and format_info, e.g. if both are None.

  • FileNotFoundError – Path was not found or was not of appropriate NewtonX format

get_units_with_defaults(unit_overrides=None)#

Apply units to the default unit dictionary of the format NewtonX

Parameters:

unit_overrides (Dict[str, str] | None, optional) – Units denoted by the user to override format default settings., by default None

Returns:

The resulting, overridden default units

Return type:

dict[str, str]