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JohannesBuchner /
Created Mar 1, 2021
Cache/Memoize any command line program. Keeps stdout, stderr and exit code, env aware.
import sys, os
import joblib
import subprocess
mem = joblib.Memory('.', verbose=False)
def run_cmd(args, env):
process =, capture_output=True, text=True)
return process.stdout, process.stderr, process.returncode
JohannesBuchner /
Created Jan 23, 2021
Make LaTeX and PDF from JOSS markdown papers
# you need to install:
# pip install openbases
# sudo apt install texlive-xetex pandoc pandoc-citeproc
JohannesBuchner /
Created Dec 18, 2020
Make a gif flipping between an X-ray and optical image at some coordinate
# example usage:
# bash 155.87737 +19.86508
wget -nc "${RA}&dec=${DEC}&fov=0.21750486127986932&width=500&height=500&hips_kw=CDS%2FP%2FSDSS9%2Fcolor" -O opt.jpg
wget -nc "${RA}&dec=${DEC}&fov=0.21750486127986932&width=500&height=500&hips_kw=xcatdb%2FP%2FXMM%2FPN%2Fcolor" -O xmm.jpg
# columns: id1,id2,id3,id4,id5,id6,v1,v2,v3
awk="time mawk"
# groupby simple
$awk -F, 'NR>1 { a[$1] += $7 } END {for (i in a) print i, a[i]}' $f >/dev/null
$awk -F, 'NR>1 { a[$1,$2] += $7 } END { for (comb in a) { split(comb,sep,SUBSEP); print sep[1], sep[2], a[sep[1],sep[2]]; }}' $f >/dev/null
$awk -F, 'NR>1 { a[$3] += $7; n[$3]++; b[$3] += $9; } END {for (i in a) print i, a[i], b[i]/n[i];}' $f >/dev/null
$awk -F, 'NR>1 { a[$4] += $7; n[$4]++; b[$4] += $8; } END {for (i in a) print i, a[i]/n[i], b[i]/n[i];}' $f >/dev/null
JohannesBuchner /
Created May 18, 2020
Build and cache Stan models smartly (ignoring changes in comments and white spaces)
import re
import pystan
import hashlib
import pickle
import os
def build_model(code):
lines = code.split("\n")
lines = [re.sub('//.*$', '', line).strip() for line in lines]
lines = [line.replace(' ', ' ').replace(' ', ' ').replace(' ', ' ')
JohannesBuchner /
Created May 12, 2020
Stop/resume processes when the user is active/inactive in Linux/Xorg
# how to identify the processes to STOP/CONT
# this is any part of process command line
# run this in one terminal:
# it tries to resume the processes every so often
while sleep 10m; do
pgrep -f "${PROCESS}"|xargs -rt kill -CONT
JohannesBuchner /
Last active Aug 12, 2019
Obtain correct error bars from observed counts (fraction in sample, detected events, etc.)
If you ever made a plot of "fractions" or "rates" with symmetric error
bars, like in the plot shown, this mini-tutorial is for you. Here is how
to compute correct error bars, so that uncertainties in the fractions
do not go below 0% or above 100%.
If you have a histogram for
instance, and you detected k objects in a given bin. What is the rate
underlying at quantiles q=0.1, 0.5(median), 0.9?
JohannesBuchner /
Created Aug 5, 2019
Minimalistic MCMC implementation
import numpy as np
def mcmc(logfunction, x0, nsteps, sigma_p):
samples = np.empty((nsteps, len(x0)))
logL0 = logfunction(x0)
naccepts = 0
for i in range(nsteps):
x1 = np.random.normal(x0, sigma_p)
logL1 = logfunction(x1)
if logL1 - logL0 > np.log(np.random.uniform()):
JohannesBuchner /
Created Jun 2, 2019
Translate a csv/npy/csv.gz integer file to efficiently compressed HDF5
import sys
import numpy
import h5py
filename = sys.argv[1]
outfilename = filename.replace('.npy', '').replace('.gz', '').replace('.csv', '') + '.h5'
if filename.endswith('.npy'):
print('loading NPY...')
data = numpy.load(filename)
Download custom spectrum from, programmatically
How to use:
$ python grbid timeslicespec
$ wget -nc --continue $(cat customspec.url)/a.tar.gz