tesliper.extraction.spectra_parser

Parser for spectra files.

Classes

SpectraParser()

Parser for files containing spectral data.
class tesliper.extraction.spectra_parser.SpectraParser[source]

Parser for files containing spectral data. It can parse .txt (in “x y” format) and .csv files, returning an numpy.ndarray with loaded spectrum. Parsing process may be customized by specifying what delimiter of values should be expected and in which column x- and y-values are, if there are more than 2 columns of data. If file contains any header, it is ignored.

parse(filename: Union[str, pathlib.Path], delimiter: Optional[str] = None, xcolumn: int = 0, ycolumn: int = 1) → numpy.ndarray[source]

Loads spectral data from file to numpy.array. Currently supports only .txt, .xy, and .csv files.

Parameters

  • filename (str) – path to file containing spectral data

  • delimiter (str, optional) – character used to delimit columns in file, defaults to whitespace

  • xcolumn (int, optional) – column, that should be used as points on x axis, defaults to 0 (first column)

  • ycolumn (int, optional) – column, that should be used as values on y axis, defaults to 1 (second column)

Returns

two-dimensional numpy array ([[x-values], [y-values]]) of data type float

Return type

numpy.array

initial(filename: str)[source]

An initial parser state.

A default implementation checks if any of defined triggers matches a line and sets an associated state as parser’s workhorse, if it does. This is an abstract method and should be overridden in subclass. Its default implementation can be used, however, by calling super().initial(line) in subclass’s method.

Notes

initial() method is always registered as parser’s state.

Parameters

line (str) – currently parsed line

Returns

empty dictionary

Return type

dict

parse_txt(file: pathlib.Path)[source]

Loads spectral data from .txt or .xy file to numpy.array.

Parameters

  • file (str) – path to file containing spectral data

  • delimiter (str, optional) – character used to delimit columns in file, defaults to whitespace

  • xcolumn (int, optional) – column, that should be used as points on x axis, defaults to 0 (first column)

  • ycolumn (int, optional) – column, that should be used as values on y axis, defaults to 1 (second column)

Returns

  • numpy.array – two-dimensional numpy array ([[x-values], [y-values]]) of data type ‘float’

  • Rises

  • —–

  • ValueError – if file passed was read to end, but no spectral data was found; this includes columns’ numbers out of range and usage of inappropriate delimiter

parse_csv(file: pathlib.Path)[source]

Loads spectral data from csv file to numpy.array.

Parameters

  • file (str) – path to file containing spectral data

  • delimiter (str, optional) – character used to delimit columns in file, defaults to ‘,’

  • xcolumn (int, optional) – column, that should be used as points on x axis, defaults to 0 (first column)

  • ycolumn (int, optional) – column, that should be used as values on y axis, defaults to 1 (second column)

Returns

two-dimensional numpy array ([[x-values], [y-values]]) of data type ‘float’

Return type

numpy.array

parse_spc(file)[source]

Loads spectral data from spc file to numpy.array.

Notes

This method is not implemented yet, it will raise an error when called.

Parameters

file (str) – path to file containing spectral data

Returns

two-dimensional numpy array ([[x-values], [y-values]]) of data type ‘float’

Return type

numpy.array

Raises

NotImplementedError – Whenever called, as this functionality is not implemented yet.

add_state(state: Callable, name: str = '', trigger: str = '')

Register callable as parser’s state.

This method registers a callable under name key in states dictionary. If trigger parameter is given, it is registered under the same key in triggers dictionary.

Parameters

  • state (Callable) – callable, that is to be registered as parser’s state

  • name (str, optional) – name under which the callable should be registered; defaults to callable.__name__

  • trigger (str, optional) – string with regular expression, that will be compiled with re module

Returns

callable object registered as state

Return type

Callable

remove_state(name: str)

Removes the state from parser’s registered states.

Parameters

name (str) – name of state, that should be unregistered

Raises

InvalidStateError – if no callable was registered under the name ‘name’

static state(state=None, trigger=None)

Convenience decorator for registering a method as parser’s state. It can be with or without ‘trigger’ parameter, like this:

>>> @ParserBase.state
... def method(self, arg): pass

or

>>> @ParserBase.state(trigger='triggering regex')
... def method(self, arg): pass

This function marks a method state as parser’s state by defining is_state attribute on said method and setting its values to True. If trigger is given, it is stored in method’s attribute trigger. During instantiation of ParserBase’s subclass, methods marked as states are registered under method.__name__ key in its states (and possibly triggers) attribute. It is meaningless if used outside of ParserBase’s subclass definition.

Parameters

  • state (Callable) – callable, that is to be registered as parser’s state

  • trigger (str, optional) – string with regular expression, that will be compiled with re module

Returns

callable object registered as state if ‘state’ was given or decorator if only ‘trigger’ was given

Return type

Callable

Raises

  • TypeError – if no arguments given

  • InvalidStateError – if state argument is not callable

property workhorse: Callable

Callable marked as a current state used by parser object.

Setter can take a callable or a string as a parameter. If name as string is passed to setter, it will be translated to a method registered as state. If no method was registered under this name, InvalidStateError will be raised. No other checks are performed when argument is callable.