Set up your new MacBook for astronomy & astrophysics!

  • Anaconda: Both python3 and python2 are OK.
  • Astroconda: Add astroconda channel to your conda list, and then set up a new environment iraf27.
  • Xcode: Download Xcode from your Mac AppStore.
  • Useful python packages: fitsio, emcee, cosmology (a quick package for cosmology written in C), tqdm.
  • XQuartz: graphics library for ds9.
  • Activating DS9: export DISPLAY=:0.0 in your terminal.
  • LaTeX environment: MacTex works good for me. I don’t have money to buy other IDE, so I use TeXShop. But for Windows, TexStudio is really really good.
  • Consolas font: You can download from https://astrojacobli.github.io/astro-ph/Consolas.ttf
  • Mendeley: paper management and reader, worth trying.
  • Slack: definitely a good tool for communication and cooperation.
  • TOPCAT: Best tool for manipulating tables, best assistant of catalog astrophysicist.
  • STILTS: A command-line edition of TOPCAT. Both TOPCAT and STILTS require JAVA environment. After install JAVA, you need to write the following into your .bash_profile: 
    export JAVA_HOME="/Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home"
export PATH=${JAVA_HOME}/bin:$PATH
  • Mathematica: Best language to do mathematical physics study.
  • Don’t know how to write your symbol in latex? Use Detexify!
  • Jesus! Get LaTeX code from the screenshots: MathPix
  • Jazz up your terminal (but I failed): https://medium.freecodecamp.org/jazz-up-your-bash-terminal-a-step-by-step-guide-with-pictures-80267554cb22
  • It’s hard to get your hands on vim without a cheatsheet
  • A useful widget cosmoWidget to calculate cosmological distances in MacOS Dashboard: https://beckermr.github.io/cosmowidget.html
  • LaTeX package for SI units: siunitx
  • Homebrew is another good tool for installing packages, especially those written in C/C++. Sometimes brew will update itself automatically, then you can stop it directly by control + C.

When your terminal cannot recognize anything, do this:

export PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

Play with a new Linux machine

Accidentally I have to make a Windows machine to Linux. I installed Debian on that machine. Some tips are listed below.

  1. Originally, your account is not listed in the sudo group. You have to run su - so that you are switched to the root environment. After that, run gpasswd -a jiaxuanl sudo to add jiaxuanli to the sudo group.

Install the Tractor

the Tractor is a probability-based astronomical source detection & measurement tool, written by Dustin Lang and David Hogg.

  1. Make sure you have installed XCode from Mac AppStore. Then execute: 
    $ sudo xcode-select -switch /Applications/Xcode.app/Contents/Developer/$.
  2. Install fitsio: $ pip install fitsio
  3. Install emcee: $ pip install emcee
  4. Install Homebrew: $ /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
  5. Using Homebrew to install cairo: $ brew install cairo
  6. Install jpeg: $ brew install jpge
  7. Install eigen3: $ brew install eigen3
  8. Add these paths to your .bash_profile: 
    export PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig"
export LDFLAGS="-L/usr/local/opt/libffi/lib"
export PKG_CONFIG_PATH="/usr/local/opt/openssl/lib/pkgconfig"
export PATH="/usr/local/opt/openssl/bin:$PATH" 
export LDFLAGS="-L/usr/local/opt/openssl/lib"
export CPPFLAGS="-I/usr/local/opt/openssl/include"
  9. Sometimes cairos still doesn’t work. Then you can:
$ pkg-config --atleast-version=1.12.2 cairo
$ echo $?

If it returns a 1 you will need to set the PKG_CONFIG_PATH environment variable so cairo.pc and fontconfig.pc can be found.

$ sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist 
$ locate cairo.pc
$ export PKG_CONFIG_PATH=/usr/X11/lib/pkgconfig/

Then do this again:

$ pkg-config --atleast-version=1.12.2 cairo
$ echo $?

If it returns a 0 then all is well in the hood.

  1. Download astrometry.net package: 
    $ wget http://astrometry.net/downloads/astrometry.net-latest.tar.bz2
$ tar xjf astrometry.net-latest.tar.bz2
$ cd astrometry.net-*
  2. Install astrometry.net: 
    $ make
$ make py
$ make extra
$ make install INSTALL_DIR="~/Research/Packages/astrometry" PYTHON_SCRIPT="/anaconda3/bin/python"

    Sometimes, it will show an error that fatal error: 'cairo.h' file not found.

You can just do export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig and see if it could fine cairo.h.

  1. Install swig: $ brew install swig

  2. Install tractor: first go to its folder, then

    $ make
$ python setup.py install

😂 You get it! 👏

Install Imfit

Requirements: CFITSIO, GNU Scientific Library, FFTW (which is used by many other packages as well), NLopt. You also need to install CMake by $ brew install cmake to install NLopt. Almost all of these packages should be installed by $ ./configure & make & make install. However, please check INSTALL file for more detailed description. You also need to install pip install scons. After all these preparation, install imfit with $ scons —no-openmp imfit & scons —no-openmp imfit-mcmc & scons —no-openmp makeimage.

References

http://www.astrobetter.com/wiki/Setup+a+New+Mac+for+Astronomy

http://www.astrobetter.com/wiki/tiki-index.php?page=Mac+Apps

https://github.com/dstndstn/tractor

http://macappstore.org/swig/

https://stackoverflow.com/questions/22100213/package-cairo-was-not-found-in-the-pkg-config-search-path-node-j-s-install-canv