chrisb13’s gists

chrisb13 / createsyms.sh

Created December 4, 2025 05:17

create symlinks for ol01 om3 output

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	#https://stackoverflow.com/questions/1767384/how-can-i-get-a-recursive-full-path-listing-one-line-per-file
	SRCEPATH=/g/data/ol01/access-om3-output
	DESTPATH=/g/data/ol01/outputs/access-om3
	ln -s ${DESTPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3.mom6.2d.zossq.1mon.mean.1951.nc ${SRCEPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3.mom6.2d.zossq.1mon.mean.1951.nc
	ln -s ${DESTPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/Vertical_coordinate.nc ${SRCEPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/Vertical_coordinate.nc
	ln -s ${DESTPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3.mom6.2d.sos.1mon.max.1950.nc ${SRCEPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3.mom6.2d.sos.1mon.max.1950.nc
	ln -s ${DESTPATH}/access-om3-025/MC_25km_jra_ryf-1.0-beta-cdfb3543/output018/access-om3

chrisb13 / cosima.py

Created April 16, 2025 03:29

quick script to download csv file of all github repos associated with an organisation

	import requests
	import csv

	# GitHub API URL for the COSIMA organization repositories
	url = "https://api.github.com/orgs/cosima/repos"

	# Function to fetch all repositories with pagination
	def fetch_all_repos(url):
	repos = []
	while url:

chrisb13 / TasmanSeaBoxPlot.py

Last active January 25, 2019 16:54

NOW code for Tasman Sea boxplot

	if paper_case=='20170113_EACnowClimateChange01':
	section_description_dict=collections.OrderedDict()
	section_description_dict['AB']=[ 60, 61,217,226,0,54,'zonal' ]
	section_description_dict['BC']=[ 60, 61,226,303,0,54,'zonal' ]
	section_description_dict['GD']=[ 85,128,311,312,0,54,'meridional' ]
	section_description_dict['FE']=[127,128,239,247,0,54,'zonal' ]
	section_description_dict['ED']=[127,128,247,311,0,54,'zonal' ]
	section_description_dict['IH']=[ 46,58 ,212,213,0,54,'meridional' ]
	section_description_dict['JK']=[ 85,86 ,224,231,0,54,'zonal' ]
	section_description_dict['PQ']=[ 68,80 ,212,213,0,54,'meridional' ]

chrisb13 / f90nml_sanity_chk.py

Created May 29, 2018 09:28

	lg.info("")
	lg.info("Running check to see if changes found in "+cfgf+" are now in: "+ofile)
	#run quick check to make sure all diff'd parameters were inserted
	#(still uses f90nml, so not exactly independent)
	with open(ofile) as nml_file:
	new_nml = f90nml.read(nml_file)
	for top_key in diff[cfgf].keys():
	for bot_key in diff[cfgf][top_key].keys():
	# assert(new_nml[top_key][bot_key]==diff[cfgf][top_key][bot_key]),ofile + " did not get created correctly"
	# print(top_key,bot_key,new_nml[top_key][bot_key],diff[cfgf][top_key][bot_key])

chrisb13 / etopo_quick_plot.py

Last active July 6, 2017 01:08

Quick hack of plotting ETOPO1 ocean bedrock with a nice colormap

	# hacked up from: http://www.trondkristiansen.com/?page_id=846

	import os
	from netCDF4 import Dataset
	import matplotlib.pyplot as plt
	import matplotlib.cm
	import numpy as np

	def LevelColormap(levels, cmap=None):
	"""

chrisb13 / nci_scp_bfunc.sh

Created March 31, 2017 08:02

Bash function to use scp on NCI

	function vimnci()
	{
	if [[ ( $# -eq 0 ) \|\| ( $1 == "--help" ) \|\| ( $1 == "-h" ) ]] ; then
	echo "Usage: vimnci PATH_TO."
	echo "Purpose: Allows remote editing of files on nci servers..."
	echo " "
	echo "Mandatory arguments: "
	echo "path or file: vim will either edit or open file passed"
	echo " "
	echo "Example."

chrisb13 / ncocdo_snippets.sh

Created January 28, 2017 03:13

List of handy one-liners for NCO and CDO

	snippet cdo
	###########################################################################
	# CDO #
	###########################################################################

	#extract a time
	cdo seltimestep,1,2,5 cordex24_CURLFX-FLUXFCE_3h_20040101_20041231_grid_U_2D.nc test.nc

	#do simple arithmatic
	cdo expr,'sum=qsr+qns-qt' cordex24_CURLFX-FLUXFCE_3h_19980101_19981231_grid_T_2D.nc ofile.nc

chrisb13 / mpl_latex_toy.py

Created January 24, 2017 01:24

Matplotlib toy example using LaTeX labels

	import matplotlib
	import matplotlib.pyplot as plt
	#nb requires latex installed on the machine, see http://matplotlib.org/users/usetex.html
	from matplotlib import rc
	import numpy as np

	rc('text', usetex=True)
	matplotlib.rcParams['mathtext.fontset'] = 'custom'
	matplotlib.rcParams['mathtext.rm'] = 'Bitstream Vera Sans'
	matplotlib.rcParams['mathtext.it'] = 'Bitstream Vera Sans:italic'

chrisb13 / combine.py

Created July 26, 2016 04:10 — forked from glombard/combine.py

Merging 4 images into one with Python and PIL/Pillow

	# Combine multiple images into one.
	#
	# To install the Pillow module on Mac OS X:
	#
	# $ xcode-select --install
	# $ brew install libtiff libjpeg webp little-cms2
	# $ pip install Pillow
	#

	from __future__ import print_function

chrisb13 / loadnc.sh

Last active December 3, 2015 04:37

	function loadnc() #load netcdf file in python
	{
	if [[ ( $# -eq 0 ) \|\| ( $1 == "--help" ) \|\| ( $1 == "-h" ) ]] ; then
	echo "Usage: loadnc FILENAME_PATHNAME"
	echo "Purpose: loads path of file into ipython (creates loadvar.py in your current dir). Prints file info and available variables. 'ifile' is name of netCDF4 object."
	echo " "
	echo "Requires: python netCDF4"
	echo " "
	echo "Mandatory arguments: "
	echo "FILENAME_PATHNAME: path to netCDF file"

Christopher Bull chrisb13