MSEval module

class MSEval.Background(isotope, laser_on, laser_off, width=0.8, offset=0.15)

Bases: object

Class for calculating and visualising background.

Parameters:

  • isotope (MSData.Isotope) – Isotope from which background is calculated

  • laser_on (list) – List of sets, where each set has 2 values (start of the laser and end of the laser.) indicating when the laser was fireing.

  • laser_off (list) – List of sets, where each set has 2 values (end of the laser and start of the laser.) indicating when the laser wasn’t fireing.

  • offset (float (Optional)) – Parameter for outlier removal. 1-offset = upper treshold for percentile filtering. Accepts values between 0 and 1. Default is 0.15.

  • width (float (Optional)) – Parameter for outlier removal. Width od returned values, where 1-offset-width = lower treshold for percentile filtering. Accepts values between 0 and 1. Default is 0.8.

class MSEval.DataReader(filename, filetype=None, instrument=None)

Bases: object

Reads data into pandas Dataframe from a file.

Parameters:

  • filename (str) – Path to file to read.

  • filetype (str) – Type of the file to read. If not specified, csv is used. Possible options are csv, xlsx and asc.

  • instrument (str) – Type of the instrument used for measurement. If not specified, raw data is expected. Possible options are Agilent, and Element.

read(filename, filetype, instrument)

Reads data into pandas Dataframe from a file.

Parameters:

  • filename (str) – Path to file to read.

  • filetype (str) – Type of the file to read. If not specified, csv is used. Possible options are csv, xlsx and asc.

  • instrument (str) – Type of the instrument used for measurement. If not specified, raw data is expected. Possible options are Agilent, MC Nu-Sapphire, and Element.

Returns:

data – data as a dataframe, which can be passed to MSData.

Return type:

dataframe

class MSEval.Iolite(path)

Bases: object

Class holding Iolite data.

Parameters:

path (str) – Path to Iolite .csv file.

names_from_iolite()

Return peak names from iolite.

on_and_off_times()
read_iolite(path)

Read Iolite file.

Parameters:

path (str) – Path to Iolite .csv file.

class MSEval.Param(path, logger=None)

Bases: object

Class holding meta data and parameters of analysis.

Parameters:

path (str) – Path to param .xlsx file.

read_is_coef()

Read sheet with internal standard coefficients from Param file.

Returns:

internal_std – DataFrame with internal standard coefficients.

Return type:

DataFrame

read_names()

Read sheet with peak names from Param file.

Returns:

names – List of peak names.

Return type:

list

read_ts_coef()

Read sheet with total sum correction coefficients from Param file.

Returns:

internal_std – DataFrame with total sum correction coefficients .

Return type:

dict

class MSEval.Selector(ms_data, s=60, sdmul=10, iolite=None, logger=None)

Bases: object

Class for peak and background identification.

Parameters:

  • ms_data (MSData) – Mass spectrometry data class, for which the selector will be used.

  • s (float (Optional)) – Start of first peak in seconds for synchronisation with Iolite data if using method Iolite or for calculation of backround standard deviation if using method treshold. Default is 60s.

  • sdmul (int (Optional)) – Multiplier for backround standard deviation in method treshold. Default is 10.

  • iolite (MSEval.Iolite (Optional)) – Iolite class, only necessary if method is Iolite. Default is None.

  • logger (logger class (optional)) – If logger is pssed all methods of Selector will log in the activity.

create_on_off(starts, ends)

From starts and ends of ablation create laser_on and laser_off with skipped values.

create_selector_iolite()

Select starts and ends of ablation using iolite file.

create_selector_treshold()

Select starts and ends of ablation based on selected element or sum of all using treshold calculated from background.

set_skip(bcg_s=None, bcg_e=None, sig_s=None, sig_e=None)

Set time skipped on start and end of background and ablation in seconds.