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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.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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