Quickstart#

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 meteorology. It has several subpackages offering constants, special functions, or objective functions to be used with mod: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

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()`	Deprecated, moved to package mcplot. 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`	Deprecated, moved to package mcplot. 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 date strings to English date format YYYY-MM-DD hh:mm:ss
`date2fr()`	Convert date strings to French date format DD/MM/YYYY hh:mm:ss
`date2num()`	Return numeric time values given datetime objects or strings
`date2us()`	Convert date strings 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()`	Deprecated, moved to package pyeee. Parameter screening using Morris’ method of Elementary Effects, same as screening
`elementary_effects()`	Deprecated, moved to package pyeee. Morris measures mu, stddev and mu*
`en2date()`	Convert date strings to standard date format DD.MM.YYYY hh:mm:ss
`en2fr()`	Convert date strings to French date format DD/MM/YYYY hh:mm:ss
`en2us()`	Convert date strings to American date format MM/DD/YYYY hh:mm:ss
`esat()`	Saturation vapour pressure over water and ice
`fr2date()`	Convert French date strings to standard date format DD.MM.YYYY hh:mm:ss
`fr2en()`	Convert French date strings to English date format YYYY-MM-DD hh:mm:ss
`fr2us()`	Convert French date strings to American date format MM/DD/YYYY hh:mm:ss
`file_from_gui()`	Open dialog to select one file
`files_from_gui()`	Open dialog to select one or several files
`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()`	Deprecated, moved to package ncio. 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`	Deprecated, moved to package mcplot. Matthias Cuntz’ standard plotting class
`means()`	Calculate daily, monthly, yearly, etc. means of data
`morris_sampling()`	Deprecated, moved to package pyeee. Sampling of optimised trajectories for Morris measures / Elementary Effects
`mrair2eair()`	Partial pressure of water vapour from mixing ratio and total pressure
`ncinfo()`	Deprecated, moved to package ncio. Extract information from netCDF file
`ncio`	Deprecated, moved to package ncio. netCDF4 functions to copy a netcdf file while doing some transformations on variables and dimensions
`ncread()`	Deprecated, moved to package ncio. Read variables from netCDF file
`num2date()`	Return datetime objects given numeric time values
`pack()`	Pack array with mask like Fortran intrinsic pack
`position()`	Deprecated, moved to package mcplot. Position arrays of subplots to be used with add_axes
`readnetcdf()`	Deprecated, moved to package ncio. 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()`	Deprecated, moved to package pyeee. Parameter screening using Morris’ method of Elementary Effects
`shair2eair()`	Partial pressure of water vapour from specific humidity and total pressure
`signature2plot()`	Deprecated, moved to package mcplot. Write a copyright notice on a plot
`sread()`	Read strings from a file into 2D string array
`str2tex()`	Deprecated, moved to package mcplot. 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()`	Deprecated, moved to package mcplot. 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 date strings to standard date format DD.MM.YYYY hh:mm:ss
`us2en()`	Convert date strings to English date format YYYY-MM-DD hh:mm:ss
`us2fr()`	Convert date strings 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 date strings to English date format YYYY-MM-DD hh:mm:ss
`date2fr()`	Convert date strings to French date format DD/MM/YYYY hh:mm:ss
`date2num()`	Return numeric time values given datetime objects or strings
`date2us()`	Convert date strings 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 date strings to standard date format DD.MM.YYYY hh:mm:ss
`en2fr()`	Convert date strings to French date format DD/MM/YYYY hh:mm:ss
`en2us()`	Convert date strings to American date format MM/DD/YYYY hh:mm:ss
`fr2date()`	Convert French date strings to standard date format DD.MM.YYYY hh:mm:ss
`fr2en()`	Convert French date strings to English date format YYYY-MM-DD hh:mm:ss
`fr2us()`	Convert French date strings to American date format MM/DD/YYYY hh:mm:ss
`us2date()`	Convert date strings to standard date format DD.MM.YYYY hh:mm:ss
`us2en()`	Convert date strings to English date format YYYY-MM-DD hh:mm:ss
`us2fr()`	Convert date strings to French date format DD/MM/YYYY hh:mm:ss
`num2date()`	Return datetime objects given numeric time values

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()`	Deprecated, moved to package pyeee. Parameter screening using Morris’ method of Elementary Effects, same as screening
`elementary_effects()`	Deprecated, moved to package pyeee. 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()`	Deprecated, moved to package pyeee. Sampling of optimised trajectories for Morris measures / Elementary Effects
`sce()`	Shuffled-Complex-Evolution algorithm for function min(max)imisation
`screening()`	Deprecated, moved to package pyeee. 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()`	Deprecated, moved to package mcplot. Write a, B, iii), … on a plot
`color`	Deprecated, moved to package mcplot. Collection of color palettes and continuous color maps
`int2roman()`	Integer to Roman numeral conversion
`mcPlot`	Deprecated, moved to package mcplot. Matthias Cuntz’ standard plotting class
`position()`	Deprecated, moved to package mcplot. Position arrays of subplots to be used with add_axes
`roman2int()`	Roman numeral to integer conversion
`signature2plot()`	Deprecated, moved to package mcplot. Write a copyright notice on a plot
`str2tex()`	Deprecated, moved to package mcplot. Convert strings to LaTeX strings in math environment used by matplotlib’s usetex
`text2plot()`	Deprecated, moved to package mcplot. Write text on a plot

Special Files

Function/module	Short description
`infonetcdf()`	Deprecated, moved to package ncio. Extract information from netCDF file, same as ncinfo
`ncinfo()`	Deprecated, moved to package ncio. Extract information from netCDF file
`ncio`	Deprecated, moved to package ncio. netCDF4 functions to copy a netcdf file while doing some transformations on variables and dimensions
`ncread()`	Deprecated, moved to package ncio. Read variables from netCDF file
`readnetcdf()`	Deprecated, moved to package ncio. 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.

The project structure of pyjams has borrowed heavily from welltestpy by Sebastian Müller.

Quickstart

Contents