pyjams 2.2

Description:

pyjams 2.2

A general Python package with a wide variety of miscellaneous utility functions.







About pyjams
pyjams is a general Python package offering a wide variety of miscellaneous
functions in different categories, such as reading different file formats, date
conversion routines, or calculating Elementary Effects. It has several
subpackages offering constants, special functions, or objective functions to be
used with scipy.optimize.
The package modernises and makes available routines of the JAMS Python
library, which was created 2009 by Matthias Cuntz while at the Department of
Computational Hydrosystems, Helmholtz Centre for Environmental Research - UFZ,
Leipzig, Germany, and continued while at Institut National de Recherche pour
l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nancy, France.
The complete documentation of pyjams is available at:

https://mcuntz.github.io/pyjams/



Installation
The easiest way to install is via pip:
pip install pyjams
or via conda:
conda install -c conda-forge pyjams

Requirements

numpy
scipy
matplotlib
cftime
netCDF4
openpyxl
schwimmbad





Content

Modules and functions are currently provided in the following categories:

Array Manipulation
Ascii Files
Data Processing
Date and Time
Grids and Polygons
Isotopes
Math
Meteorology
Miscellaneous
Plotting
Special Files




Functions and modules (alphabetical)






Function/module
Short description



abc2plot
Write a, B, iii), … on a plot

alpha_equ_h2o
Equilibrium fractionation between liquid water and vapour

alpha_kin_h2o
Kinetic fractionation of molecular diffusion of water vapour

argmax
Wrapper for numpy.argmax, numpy.ma.argmax, and max for Python iterables

argmin
Wrapper for numpy.argmin, numpy.ma.argmin, and min for Python iterables

argsort
Wrapper for numpy.argsort, numpy.ma.argsort, and sorted for Python
iterables

closest
Index in array which entry is closest to a given number

color
Collection of color palettes and continuous color maps

const
Physical, mathematical, computational, isotope, and material constants

date2date
Convert date representations between different regional variants

date2dec
Return numeric time values given datetime objects or strings,
same as date2num

date2en
Convert dates to English date format YYYY-MM-DD hh:mm:ss

date2fr
Convert dates to French date format DD/MM/YYYY hh:mm:ss

date2num
Return numeric time values given datetime objects or strings

date2us
Convert dates to American date format MM/DD/YYYY hh:mm:ss

datetime
Class as cftime.datetime for non-CF-conform calendars

dec2date
Return datetime objects given numeric time values, same as num2date

directories_from_gui
Open dialog to select one directory

directory_from_gui
Open dialog to select several directories

division
Divide two arrays, return ‘otherwise’ if division by 0

div
Divide two arrays, return ‘otherwise’ if division by 0,
same as division

eair2mrair
Mixing ratio from partial pressure of water vapour and total pressure

eair2rhair
Relative humidity from partial pressure of water vapour and temperature

eair2shair
Specific humidity from partial pressure of water vapour and total pressure

eair2vpd
Air vapour pressure deficit from partial pressure and temperature

ee
Parameter screening using Morris’ method of Elementary Effects,
same as screening

elementary_effects
Morris measures mu, stddev and mu*

en2date
Convert dates to standard date format DD.MM.YYYY hh:mm:ss

en2fr
Convert dates to French date format DD/MM/YYYY hh:mm:ss

en2us
Convert dates to American date format MM/DD/YYYY hh:mm:ss

esat
Saturation vapour pressure over water and ice

file_from_gui
Open dialog to select one file

files_from_gui
Open dialog to select one or several files

fr2date
Convert French dates to standard date format DD.MM.YYYY hh:mm:ss

fr2en
Convert French dates to English date format YYYY-MM-DD hh:mm:ss

fr2us
Convert French dates to American date format MM/DD/YYYY hh:mm:ss

fread
Read numbers from a file into 2D float array

fsread
Read numbers and strings from a file into 2D float and string arrays

functions
Special functions for testing optimisations, sensitivity analysis,
several forms of the logistic function and its derivatives, and other
functions to be used with scipy.optimize

gridcellarea
Area of grid cells on Earth

infonetcdf
Extract information from netCDF file, same as ncinfo

int2roman
Integer to Roman numeral conversion

kernel_regression
Multi-dimensional non-parametric kernel regression

kernel_regression_h
Determination of bandwidth for kernel regression

mad
Median absolute deviation test

mcPlot
Matthias Cuntz’ standard plotting class

means
Calculate daily, monthly, yearly, etc. means of data

morris_sampling
Sampling of optimised trajectories for Morris measures / Elementary
Effects

mrair2eair
Partial pressure of water vapour from mixing ratio and total pressure

ncinfo
Extract information from netCDF file

ncio
netCDF4 functions to copy a netcdf file while doing some
transformations on variables and dimensions

ncread
Read variables from netCDF file

num2date
Return datetime objects given numeric time values

pack
Pack array with mask like Fortran intrinsic pack

position
Position arrays of subplots to be used with add_axes

readnetcdf
Read variables from netCDF file, same as ncread

rhair2eair
Partial pressure of water vapour from relative humidity and temperature

rhair2vpd
Air vapour pressure deficit from relative humidity and temperature

roman2int
Roman numeral to integer conversion

sce
Shuffled-Complex-Evolution algorithm for function min(max)imisation

screening
Parameter screening using Morris’ method of Elementary Effects

shair2eair
Partial pressure of water vapour from specific humidity and total pressure

signature2plot
Write a copyright notice on a plot

sread
Read strings from a file into 2D string array

str2tex
Convert strings to LaTeX strings in math environment used by matplotlib’s
usetex

tee
Prints arguments on screen and in file, like Unix/Linux tee utility

text2plot
Write text on a plot

unpack
Unpack array using mask like Fortran intrinsic unpack

updatez
Update arrays in uncompressed numpy .npz format

updatez_compressed
Update arrays in compressed numpy .npz format

us2date
Convert dates to standard date format DD.MM.YYYY hh:mm:ss

us2en
Convert dates to English date format YYYY-MM-DD hh:mm:ss

us2fr
Convert dates to French date format DD/MM/YYYY hh:mm:ss

vpd2eair
Partial pressure of water vapour from air vapour pressure deficit and temperature

vpd2rhair
Relative humidity from air vapour pressure deficit and temperature

xlsread
Read numbers and strings from Excel file into 2D float and string arrays,
same as xread

xlsxread
Read numbers and strings from Excel file into 2D float and string arrays,
same as xread

xread
Read numbers and strings from Excel file into 2D float and string arrays





Functions and modules per category

Array Manipulation






Function/module
Short description



argmax
Wrapper for numpy.argmax, numpy.ma.argmax, and max for Python
iterables.

argmin
Wrapper for numpy.argmin, numpy.ma.argmin, and min for Python
iterables.

argsort
Wrapper for numpy.argsort, numpy.ma.argsort, and sorted for
Python iterables.

closest
Index in array which entry is closest to a given number.

pack
Pack array with mask like Fortran intrinsic pack

unpack
Unpack array using mask like Fortran intrinsic unpack






Ascii Files






Function/module
Short description



fread
Read numbers from a file into 2D float array

fsread
Read numbers and strings from a file into 2D float and string arrays

sread
Read strings from a file into 2D string array






Data Processing






Function/module
Short description



kernel_regression
Multi-dimensional non-parametric kernel regression

kernel_regression_h
Determination of bandwidth for kernel regression

mad
Median absolute deviation test

means
Calculate daily, monthly, yearly, etc. means of data






Date and Time






Function/module
Short description



date2date
Convert date representations between different regional variants

date2dec
Return numeric time values given datetime objects or strings,
same as date2num

date2en
Convert dates to English date format YYYY-MM-DD hh:mm:ss

date2fr
Convert dates to French date format DD/MM/YYYY hh:mm:ss

date2num
Return numeric time values given datetime objects or strings

date2us
Convert dates to American date format MM/DD/YYYY hh:mm:ss

datetime
Class as cftime.datetime for non-CF-conform calendars

dec2date
Return datetime objects given numeric time values,
same as num2date

en2date
Convert dates to standard date format DD.MM.YYYY hh:mm:ss

en2fr
Convert dates to French date format DD/MM/YYYY hh:mm:ss

en2us
Convert dates to American date format MM/DD/YYYY hh:mm:ss

fr2date
Convert French dates to standard date format DD.MM.YYYY hh:mm:ss

fr2en
Convert French dates to English date format YYYY-MM-DD hh:mm:ss

fr2us
Convert French dates to American date format MM/DD/YYYY hh:mm:ss

num2date
Return datetime objects given numeric time values

us2date
Convert dates to standard date format DD.MM.YYYY hh:mm:ss

us2en
Convert dates to English date format YYYY-MM-DD hh:mm:ss

us2fr
Convert dates to French date format DD/MM/YYYY hh:mm:ss






Grids and Polygons






Function/module
Short description



gridcellarea
Area of grid cells on Earth






Isotopes






Function/module
Short description



alpha_equ_h2o
Equilibrium fractionation between liquid water and vapour

alpha_kin_h2o
Kinetic fractionation of molecular diffusion of water vapour






Math






Function/module
Short description



division
Divide two arrays, return ‘otherwise’ if division by 0

div
Divide two arrays, return ‘otherwise’ if division by 0,
same as division

ee
Parameter screening using Morris’ method of Elementary Effects,
same as screening

elementary_effects
Morris measures mu, stddev and mu*

functions
Special functions for testing optimisations, sensitivity analysis,
several forms of the logistic function and its derivatives, and other
functions to be used with scipy.optimize

morris_sampling
Sampling of optimised trajectories for Morris measures / Elementary
Effects

sce
Shuffled-Complex-Evolution algorithm for function min(max)imisation

screening
Parameter screening using Morris’ method of Elementary Effects






Meteorology






Function/module
Short description



eair2mrair
Mixing ratio from partial pressure of water vapour and total pressure

eair2rhair
Relative humidity from partial pressure of water vapour and temperature

eair2shair
Specific humidity from partial pressure of water vapour and total pressure

eair2vpd
Air vapour pressure deficit from partial pressure and temperature

esat
Saturation vapour pressure over water and ice

mrair2eair
Partial pressure of water vapour from mixing ratio and total pressure

rhair2eair
Partial pressure of water vapour from relative humidity and temperature

rhair2vpd
Air vapour pressure deficit from relative humidity and temperature

shair2eair
Partial pressure of water vapour from specific humidity and total pressure

vpd2eair
Partial pressure of water vapour from air vapour pressure deficit and temperature

vpd2rhair
Relative humidity from air vapour pressure deficit and temperature






Miscellaneous






Function/module
Short description



const
Physical, mathematical, computational, isotope, and material
constants

directories_from_gui
Open dialog to select one directory

directory_from_gui
Open dialog to select several directories

file_from_gui
Open dialog to select one file

files_from_gui
Open dialog to select one or several files

int2roman
Integer to Roman numeral conversion

roman2int
Roman numeral to integer conversion

tee
Prints arguments on screen and in file, like Unix/Linux tee utility






Plotting






Function/module
Short description



abc2plot
Write a, B, iii), … on a plot

color
Collection of color palettes and continuous color maps

int2roman
Integer to Roman numeral conversion

mcPlot
Matthias Cuntz’ standard plotting class

position
Position arrays of subplots to be used with add_axes

roman2int
Roman numeral to integer conversion

signature2plot
Write a copyright notice on a plot

str2tex
Convert strings to LaTeX strings in math environment used by
matplotlib’s usetex

text2plot
Write text on a plot






Special Files






Function/module
Short description



infonetcdf
Extract information from netCDF file, same as ncinfo

ncinfo
Extract information from netCDF file

ncio
netCDF4 functions to copy a netcdf file while doing some
transformations on variables and dimensions

ncread
Read variables from netCDF file

readnetcdf
Read variables from netCDF file, same as ncread

updatez
Update arrays in uncompressed numpy .npz format

updatez_compressed
Update arrays in compressed numpy .npz format

xlsread
Read numbers and strings from Excel file into 2D float and string arrays,
same as xread

xlsxread
Read numbers and strings from Excel file into 2D float and string arrays,
same as xread

xread
Read numbers and strings from Excel file into 2D float and string arrays








License
pyjams is distributed under the MIT License. See the LICENSE file for
details.
Copyright (c) 2012-2022 Matthias Cuntz, Juliane Mai, Stephan Thober, and Arndt
Piayda
The project structure of pyjams has borrowed heavily from welltestpy
by Sebastian Müller.