Observing with the Onsala 20m using scripting and BIFROST

• The following (abbreviated) script was discussed:

# Define/import global settings
SETUP POINT loops=2 azdist=21 eldist=21 ontime=20 caltime=10 calwhen=3 obsmode=ssw dop=eachcal adjpwr=first rawdata=skip addpol=save backend=SPEa baseline=nobaselines startpos=last apply …

Extending the Python Interpreter with C/C++

The Python interpreter can be extended via C (or C++) code to

1. make existing python code execute faster by replacing critical sections into compiled code
2. interface to existing/legacy C (or C++) libraries
3. make C structures (C++ classes) first class objects within python …

Context/Motivation

• Create visibility plots to plan your observations
• Obtain good quality plots to be enclosed in your proposals

Known tools:

• ASTRO from the GILDAS package
• ASTROPLAN from ASTROPY (not covered here)

The best starting points for GILDAS tutorials are

• specific GILDAS tutorials
• upcoming and past IRAM’s events (select …

• check out the numpy website for docs and the like
• feel free to download and play around with the jupyter notebook on numpy

Installation

• assuming you have 'pip' installed run the following

pip install numpy

• Sometimes it is quicker to write a short bash script to 'get the job done' instead of doing it in python or something else
• bash comes with a load of very useful little programmes that allow you to modify files on the fly
• if you 'pipe' things together (with the …

pandas: powerful Python data analysis toolkit

Useful links:

• pydata.org
• 10 minutes to pandas
• DataFrames in Python

A tip: Whenever you are using pandas in your own code, try and stick to the following convention:

import pandas as pd

This will make it easier for other people to understand your …

Optical character recognition

The tool of choice on Linux and MacOS is tesseract, an open source tool originally developed by HP.

Installation

On Linux (with apt package manager)

    sudo apt install imagemagick
    sudo apt install tesseract-ocr

and then install individual language packages

    apt-cache search --names-only tesseract-ocr
    sudo apt install tesseract-ocr-XXX …

• get it from here
• there are a number of great examples to get you started (the examples I showed in the seminar came from here)
• and further tutorials
• also check out the astropy-page on the WCS

What it can be used for (biased, certainly not complete list)

• reading+writing standard …

Overview

• R makes it easy to use legacy C and Fortran code
• comes with beautiful graphics and powerful statistical tools

• 10000 packages on CRAN

• packages follow high standards for documentation
• think of R as python with built-in matplotlib and pandas

Take this simple Fortran subroutine:

      subroutine facto(n, answer)
C …

Emacs

A short introduction to emacs given as part of the tech talk series.

"Emacs outshines all other editing software in approximately the same way that the noonday sun does the stars. It is not just bigger and brighter; it simply makes everything else vanish." -Neal Stephenson, "In the Beginning …

• I made some slides showing how to get started
• check out the jupyter website for docs and the like
• for further info on the jupyter extensions check out their github page
• feel free to download and play around with the notebook we worked on; (tarball contains both the notebook and …

The Anaconda distribution for Python

• The slides are in this anaconda.pdf

• Anaconda is a distribution for python which

  • comes with pre-built and pre-configured collection of packages
  • package manager (conda)
  • version management
  • ... and more

• Freemium software from Continuum Analytics

• Works basically the same on Win, Mac and Linux
• Self-contained, install …

Org mode

Here is the document I presented, with some comments and keyboard shortcuts added: (S stands for Shift, C stands for Ctrl, M stands for meta (either Esc or Alt). For example M-g would mean, press the Esc key first then press the g key, alternatively press Alt and …

What is a container?

• It’s a file system image (eg. tar archive) that gets used instead of the local file system
• An application to set things up (eg. singularity, docker)
• When you run an application via a container that application is isolated from the rest of the OS
• Made …

• The slides I showed are in this rsync-cronjobs.pdf
• in a nutshell rsync is a fancy way to copy data
• instead of copying everything it will syncronise source and sinc by comparing time tags and/or sizes of files
• can be used like scp to sync different machines in a …

• The slides are in this gimp.pdf
• Also check out the notes on inkscape

What is it?

Wikipedia

(GNU Image Manipulation Program) is a free and open-source raster graphics editor used for image retouching and editing, free-form drawing, converting between different image formats, and more specialized tasks.

Gimp - what I …

• Also check out the notes on gimp

What is it?

Wikipedia

Inkscape is a free and open-source vector graphics editor; it can be used to create or edit vector graphics such as illustrations, diagrams, line arts, charts, logos and complex paintings. Inkscape's primary vector graphics format is Scalable Vector Graphics …

What is this about

The problems we are trying to solve:

• run software not supported by our operating system
• run software in well defined environments

Assume that you are asked to deploy a web application which stores and retrieves data from an SQL database engine. For security, reliability and scalability …

• The slides are in this tmux.pdf
• if you know screen: tmux is a similar thing but I like it a lot more
• tmux vs screen cheat sheet

What is it?

Wikipedia

tmux is a software application that can be used to multiplex several virtual consoles, allowing a user to …

The Abomination

foo.txt
foo1.txt
foo1_john.txt
foo2_jane_feb12.txt
foo2_jane_feb12_with_additional_comments_by_john.txt

Please. don't. do. this!

History

The competition

• rcs revision control system
• cvs concurrent versions system
• svn subversion
• hg mercurial

... and the winner is:

• git developed in 2005 by Linus Torvalds, used for the development of the Linux kernel …

Lyx - document editor based on latex

Overview

• encourages writing based on the idea of what-you-see-is-what-you-mean WYSIWYM
• find it at Lyx
• the Documentation/Wiki is great
• allows you to write a LaTeX document without ever having to remember latex-commands

Features

• import of LaTeX files
• export of Lyx-files to LaTeX
• vast amount …

Overleaf - collaborative Writing and Publishing

Overview

• a merge between former WriteLaTeX and ShareLaTeX
• find it at Overleaf
• watch the introductory movie and follow the tutorial, by clicking on the ``?'' in the toolbar.

Features

• platform for collaboration on LaTeX documents
• comfortable editor with template completion
• version control with powerful comparison feature …

ssh-agent

• The slides are in this ssh-agent.pdf

What is it?

• A separate program that loads your keys and passes them to ssh
• ssh will see if ssh-agent is running and if so will ask it for your keys

What's the point?

• To decrypt your keys temporarily
• Stores them in …

Using ssh and friends

• The slides are in this ssh.pdf

# we spoke about the following tools:
ssh          # utility to access remote machine
ssh-keygen   # used to generate key-pairs (to access machines without a password)
ssh-copy-id  # to copy the public key to the remote machine
scp          # 'secure copy', to copy files …