OrgAlkCalc

This is a package which you can use to compute organic alkalinity from titration: see OrgAlkCalc.py: Estimation of organic alkalinity quantities and acid-base properties with proof of concept in Dublin Bay

Usage

This toolbox contains two basic classes which may be used to perform organic alkalinity calculations: OrgAlkTitration and OrgAlkTitrationBatch.

• OrgAlkTitrationBatch is intended as a 'batch mode', which will allow the user to perform calculations with no additional input.
• OrgAlkTitration is more granular, allowing the user to specify in detail how they wish the calculation to be performed.

OrgAlkTitrationBatch

OrgAlkTitrationBatch allows the user to take a master spreadsheet and automatically perform all organic alkalinity calculations for all titrations contained in the master spreadsheet of interest. It is invoked as follows

titr = OrgAlkCalc.OrgAlkTitrationBatch(master_spreadsheet_path,master_spreadsheet_filename, master_results_path,master_results_filename)

A sample call is shown below:

titr = OrgAlkCalc.OrgAlkTitrationBatch("~/Python/OrgAlkCalculations/","Master_Titration_file.xlsx" ,"~/Python/OrgAlkCalculations/","Master_Results_File.xlsx")

This initialises the batch calculation object as titr. This will load all data contained in /Python/OrgAlkCalculations/Master_Titration_file.xlsx

It is then called using titr.batch_calculate() This will perform all calculations and write results to the master results file, in this case ~/Python/OrgAlkCalculations/Master_ResultsFile.xlsx.

Alternatively, you may call batch_calculate with plotting enabled: titr.batch_calculate(plot_results=True) This will perform all the same calculations, but additionally plot titration curves measured and calculated results.

Each argument of the initialisation is now explained in turn:

• master_spreadsheet_path (string)
  • The absolute path of the master spreadsheet. This tells the program where to look for the master spreadsheet which informs the individual calculations.
• master_spreadsheet_filename (string)
  • The name of the master spreadsheet, eg. master_titration.xlsx
• master_results_path (string)
  • This function will write results out to a master results file. As with master_spreadsheet_path, this argument tells the toolbox which directory to look for a master results file to write to.
• master_results_filename (string)
  • The name of the master results spreadsheet, eg. master_results.xlsx

OrgAlkTitration

OrgAlkTitration allows the user to take a master spreadsheet and automatically perform all organic alkalinity calculations for a titration contained in the master spreadsheet of interest. It may be invoked as follows:

1. titr = OrgAlkTitration() initialises the OrgAlkTitration object.
2. titr.read_master_spreadsheet(master_speadsheet_path,master_speadsheet_filename, titration_name) reads the master spreadsheet specified to find the titrations associated with titration_name.
3. titr.pipeline() performs all necessary data processing before minimisation. For additional granular control, inspect titr.pipeline(): functions invoked by it have additional parameters which may be altered by the user.
4. titr.repeat_minimise(minimiser_no,SSR_frac_change_limit,plot_results) performs the repeated minimisation in order to calculate output parameters. This must be run in order (ie. run minimiser_no = 1, = 2, =3, =4). SSR_frac_change_limit specifies the fractional change at which the minimiser will stop running. plot_results may be true or false: if true, once the repeated minimisation has reached its fractional change limit, the data points and calculated titration curve will be plotted.
5. titr.select_output_params(row_to_select): this selects which output parameters version we manually from titr.df_minimiser_outputs (this DataFrame can be inspected manually by the user). Alternatively, we may call titr.select_output_params(batch_mode=True), in order to allow the minimiser to automatically select the 'best' output parameters, based on automated reliability checks.
6. titr.write_results(master_results_path,master_results_filename): this writes results to a master spreadsheet, specified by master_results_path and master_results_filename.

Bugs and Errors

If you do find any bug, error, unexpected behavioural quirk or just anything which seems odd, please do get in contact: this toolbox is still very much a work in progress.