koolstof 0.0.4

Miscellaneous tools for marine carbonate chemistry and other delights

koolstof

Miscellaneous tools for marine carbonate chemistry and other delights.

Highly unstable and unreliably documented.

Install:

pip install koolstof

Import:

import koolstof as ks

ks

Miscellaneous functions at the top level.

ks.sigfig

Round NumPy array x to sf significant figures.

x = ks.sigfig(x, sf)

ks.vindta

Import and parse the data files produced by the Marianda VINDTA 3C.

This module is totally unofficial and in no way endorsed by Marianda!

ks.vindta.read_dbs

Import a VINDTA .dbs file as a Pandas DataFrame.

dbs = ks.vindta.read_dbs(filepath)

ks.vindta.addfunccols

Append new columns to a Pandas DataFrame df containing the results of df.apply(func).

df = ks.vindta.addfunccols(df, func, *args)

The function input should have the signature func(x, *args) where x refers to each row of df.

ks.vindta.read_logfile

Import a VINDTA logfile.bak as a Pandas DataFrame.

logfile = ks.vindta.read_logfile(filepath, methods=['3C standard'])

Optional input methods allows you to specify your own set of method file names that should be treated as DIC samples, as a list of strings excluding the .mth extension.

ks.vindta.logfile2dbs

Get the iloc index in logfile corresponding to each row in a dbs by matching both the bottle name and analysis time.

dbs = ks.vindta.logfile2dbs(dbs, logfile)

ks.vindta.get_blanks

Calculate the sample-by-sample blank values from the logfile.

You must first run ks.vindta.logfile2dbs() to get the field logfile_iloc in dbs!

dbs = ks.vindta.get_blanks(dbs, logfile, usefrom=6)

usefrom determines which minute of each coulometric analysis to start measuring the blank from. You could use ks.vindta.plot.increments() to help decide what value to use here.

ks.vindta.plot

Quickly make some standard figures that assist with calibrating and QCing VINDTA datasets.

You must first create your own axes to plot onto and to pass into these functions as the input ax, e.g.:

from matplotlib import pyplot as plt
fig, ax = plt.subplots()

ks.vindta.plot.increments

Plot coulometer increments minute-by-minute for all samples that appear in both the dbs and the logfile.

You must first run ks.vindta.logfile2dbs() to get the field logfile_iloc in dbs!

ax = ks.vindta.plot.increments(ax, dbs, logfile, c='xkcd:navy', alpha=0.25, **kwargs)

Any additional kwargs are passed on to plt.plot to generate the plotted lines.

Example figure:

ks.vindta.plot.blanks

Plot sample-by-sample coulometer blank values against analysis date.

You must first run ks.vindta.get_blanks() to calculate the sample-by-sample blank values!

ax = ks.vindta.plot.blanks(ax, dbs, c='xkcd:navy', alpha=0.5, **kwargs)

Any additional kwargs are passed on to plt.scatter to generate the plotted data points.

Example figure: