Urania

A blog named for the muse of Astronomy containing musings by an astronomer

Mac Apps for the Professional Astronomer

Posted on June 01, 2010 by Juan

I was asked by one of my colleagues who was late to switching to a Mac (from linux) what the necessary software is for an astronomer to have on their Macintosh. Some lists of this sort have been assembled online, however most are no longer available. Some resources I was aware of that were still online as of this writing (Summer 2010) were

  • Jane Rigby’s (Carnegie Observatories) OS X for Astronomers: This site is a fairly complete listing of Mac software the Professional Astronomer would be listed in. However, she uses “Fink” whereas I prefer “MacPorts”. To each their own.
  • MacOS X for Astrophysicists: This site is a bit dated (last update 2007) but there is a lot good information about how to configure X11, LaTeX, etc. on the Mac.
  • MacResearch: Focused more generally on using a Mac for research (notably programming), this site is a good read even if not astronomy focused.

My approach here will be to list everything I use on a regularly basis in my research. I will warn you up front that I am an optical astronomer who as dabbled in some radio astronomy, but I don’t know anything about High-Energy packages. So that is one bias. Secondly, being a college professor at a smaller state institution, I tend to focus on free (as in beer) or inexpensive software although I will list a few programs that I think are definitely worth the money for professional astronomer.

Programming/Unix Environment

There is some stuff any astronomer using a Mac should install, because it is free and/or critical to using your computer as a competent astronomer (depending on your specialty)…

  • XCode: You will need the gcc compilers in many cases and they come with the OS, so you might as well install them. If you want to get the most current Xcode, you can download it from the Apple Developer Connection website (you will need a free account).
  • g77/gfortran compilers: If you need a g77 (for MacOS before 10.6) or gfortran compiler, the best place to get pre-built binaries is at the High Performance Computing of MacOS X website.
  • X11: X11 is an optional install under Tiger and is installed by default under Leopard. However, when in Leopard, Apple switched from Xfree86 to X.org, and this transition introduced some advantages (no DISPLAY environment setup necessary…. yeah!) and some bugs (Boo!). As such, I had been using XQuartz in Leopard, which remain a few steps ahead of Leopard’s X11 and easily installed over it. However, I have found Snow Leopard’s X11 installation stable and robust enough to not replace it with XQuartz any more.
  • MacPorts: The bane of many unix-style OSes these days is the package manager one uses to install the unix-style programs with all their dependencies. I have settled on MacPorts. I used it’s “competitor” Fink for a while, but I have found MacPorts to generally be a much more up-to-date package manager. I use it to install TeTeX and a multitude of CLI programs (PGPLOT, gs,gv,gsl,xephem).
    • Porticus: is a decent (free) GUI front end for MacPorts if you fear the command line.

For the Optical Astronomer

This is the data reduction software I use almost every time I work on my research…

  • Scisoft OSX (My Mirror): IMHO the simplest way to install IRAF and many other packages I use regularly (PGPLOT, WCSTools, Sextractor, CFITSIO, etc.) in one double-click of a mouse (and some editing of my .tcshrc file).
  • SAOImage DS9: I sometimes update the version of DS9 included in SciSoft OSX with the most current versions from the CfA.
  • HEASARC’s fv: They call it the “Interactive FITS File Editor” and frankly it sometimes is the easiest way to quickly see the contents of a complex FITS files.
  • JSkyCalc: This venerable observing planning software that used to be solely for the command line (when it was skycalc) has now been updated to a graphical user interface written in java, so it runs on almost any platform, including Mac OSX. For the Mac, just save the jskycalc.jar file someplace and double click on it to launch it.
  • IDL: Definitely not cheaper (but cheaper than it used to be). Some astronomers I know swear by it (I have been known to swear at it). Personally, I do need the power of IDL sometimes, especially when someone else provides me her/his IDL code. If you use it, you will probably want to grab the IDL Astronomy Users Library which provides a large number of pre-built IDL routines for the astronomer. If you are feeling cheap, you might be able to get away with GDL (from High Performance Computing)

For the Radio Astronomer

This is the data reduction software I played around with when reducing radio data. I can’t claim I am current on the state of the art, so let me know if you feel I am missing something here.

  • AIPS: When I was doing more radio astronomy, I was working with AIPS a lot. I helped in the process of getting it working under MacOS (as a guinea pig). It ran quite nicely under MacOS the last time I used it (about 2004).
  • CASA: CASA (formerly AIPS++) is a sort of successor to AIPS. Personally, I was never that impressed with it, but I know several people who like using it (such as folks involved with ALMA). It is available for Mac OS 10.5 and 10.6 (Intel Macs only).

Writing Tools for Astronomers

Writing either documentation or papers for peer-review publications can be a challenge. For informal work, I have quite happy using Apple’s Pages for written work or Apple’s Keynote when assembling a poster or set of slides. However, for peer-reviewed journals or NSF applications, I typically use latex, having installed tetex with MacPorts.

  • Texmaker: is a nice interface for writing LaTeX on the Mac. Certainly not perfect or as good as some commercial products I have seen, but it is free and it works well. I especially like it when used with the Skim PDF reader which allows in-window updating of the PDF.
  • Papers: This is an awesome package for organizing your personal library of publications. It provides (somewhat glitchy) ADS Abstracts and arXiv interfaces that allow you to match PDF files to their metadata. Once you have done this, you can search for you local library by the words in the title, abstract, author’s name, year of publication, etc. And you can keep your PDFs organized. It has been a wonderful way for me to keep track of everything I have been reading when I have to prepare a paper.
  • iWork: is a very useful package from Apple that acts as a lower cost replacement to Microsoft Office (if all I cared about were cost, I would use OpenOffice.org). However, I use it because it includes:
    • Keynote: Keynote is a much more polished presentation manager than PowerPoint.
    • Pages: I prefer pages for my word processing and MacResearch had a compelling article on why you might use Pages for grant applications.
  • MathType 6: I would recommend also getting MathType 6, which let’s you insert equations into Pages or Keynote with ease (and it accepts LaTeX as a way of building equations). Make sure to update to the current version, it avoids a lot of crashing bugs.
  • LaTeXit: If you don’t want to pay for a commercial program, LaTeXit is a great option for typeseting formulas with LaTeX. It allows you typeset and then drag the results into Keynote or Pages documents where they are inserted as PDF images.
  • Evernote: I don’t use Evernote solely for writing papers, it is just a place to toss little notes I used to keep on post-it notes. But if I want to save some webpage or some text for later use, it is a perfect tool for that. It can sync between Mac and iPhone/iPod touch and it is free for up to 40 MB of notes a month.

Astronomically Useful Widgets

Widgets have been in MacOS since version 10.4 (Tiger), and while I don’t find them terribly useful, there are some free Widgets can be useful to have on observing runs:

  • Clear Sky Clock Widget: I may be biased since I helped re-work this widget and am responsible for the current version, but is useful as a way of displaying the current Clear Sky Chart (formerly called “Clear Sky Clock”) on your desktop. Clear Sky Chart is only useful for astronomers in North America.
  • AstroTimes Widget: I am not sure if this widget is still available, but it was a quick way to see the Local Sidereal Time when observing.

Astronomically Useful Spotlight Plugins

Spotlight is a feature that has been built-in to MacOS X since version 10.4 (Tiger). It indexes the contents of files to allow for almost instantaneous searches of the contents of a hard drive. The built-in plugins search many file types, but the following additional plugins are useful for file formats astronomers commonly run into.

  • FITSImporter: This plugin allows Spotlight to index FITS file headers.

Astronomically Useful QuickLook Plugins

QuickLook is a feature that has been built-in to MacOS X since version 10.5 (Leopard). When in the Finder, selecting a file and tapping on the spacebar displays a preview of the file. As with Spotlight plugins, many common file formats are supported with the built-in plugins, but for file formats astronomers commonly run into some plugins can be useful.

  • QLFits: This QuickLook plugin allows easy previewing of FITS file headers and images/spectra from the Finder.
  • QLColorCode: This QuickLook plugin displays source code files with syntax highlighting making QuickLook a much more powerful way of previewing code.
  • EPSQuickLookPlugIn: Allows viewing of encapsulated PostScript files via QuickLook. Since most figures I embed in my papers start as EPS files, this is very useful to me.

The Less Obvious Stuff

Some software doesn’t fit well into a particular broad class of work astronomers do, but can come in useful all the same for specific tasks.

  • User Interface Enhancements:
    • ShellHere.app: Drag this to your Finder winder and from now on, if you want to open the Terminal at a location corresponding to a given Finder winder, all you you need to do is click on the ShellHere icon. Works great, sort of the counterpart to “open .” in the terminal opening up a Finder window.
    • QuickSilver: Why waste your time digging through the Finder? I use QuickSilver to launch programs, access frequently used documents, and basically streamline my use of my Mac. Its the swiss army chainsaw of launchers.
    • GeekTool: This is an awesome little tool that allows you to display almost anything on your desktop. I use it to display my weblogs and system logs to my desktop, along with the local weather conditions and Doppler radar image. Anything you can display in the shell can display on the desktop.
  • A backup solution beyond Time Machine! Time Machine (part of Mac OS since version 10.5) is wonderful for incremental backups, but if your boot drive fries, you can’t boot from your Time Machine backup. This is why I also clone my boot drive regularly.
    • Carbon Copy Cloner: This is a free way to clone your boot drive on the Mac.
    • DejaVu: If you want an more automated solution, I prefer DejaVu, which runs scheduled rsync sessions in the background. That way, my backup drive is constantly updated and when my boot drive fails, I can just switch over to the backup without losing a beat.
  • Versions: Actually, I can’t say I ‘recommend’ Versions per se. I would strongly recommend subversion or some other version tracking system for anyone who writes code regularly. It makes tracking edits to source code (and latex documents) a breeze. I happen to use Versions as a very nice GUI that allows quick examination of differences between different versions of the source code you have tracked. That said, it is not cheap and I think SynX is a perfectly adequate free GUI front-end for code version tracking with similar functionality, if not as polished.
  • Parallels/VMWare Fusion/VirtualBox: If you occasionally have to run software that only runs on that other platform (you know, Linux), virtualization software is quite useful. I have found both Parallels 5 and VMWare Fusion 3 to be quite good (I found Parallels to be faster, but I heard VMWare was catching up). VirtualBox is free (as in beer) and may be an option to try before shelling out money for commercial virtualization software.
  • Chicken of the VNC: At several observatories, I am required to use VNC to interface with the computers. Chicken of the VNC works as a client. There are commercial VNC clients that are a bit faster, but if you have decent bandwidth, this works fine.
  • Wx: As an frequently optical astronomer, I sometimes obsess about the weather. Of all the weather programs out there, I have found this one to be the most stable and flexible. Its relatively inexpensive ($16.95 US), but as a warning, it is limited to the United States.
  • OmniFocus: This program is probably the single most useful program I have for managing my time. It implements David Allen’s Getting Things Done approach to time management. Its not cheap, nor is it completely intuitive… but it is absolutely necessary for me. A iPhone version also exists, which allows syncing of your OmniFocus sessions between your Mac and iPhone/iPod Touch.
  • DropBox: If you look at DropBox for the first time, it just looks like a way to sync files between computers. That is, until you realize you can allow specific users to share specific directories. I use it to share files to big to email with collaborators all the time. The only warning, it currently doesn’t map out extended attributes of files (like the executable settings) between computers, so it is not good for shell scripts. This failing is supposed to be fixed in the current version 0.8 beta.
  • fseventer is useful for diagnosing programs that create files. It tracks all file system events as long as it is on. So if you want to know where an installer is tossing files around your system, this will help you see what is happening. Its rare that I need it, but when I do, it is a Godsend.

[I made some minor edits adding some links I had forgotten about. – June 1, 2010 11:45 am CDT]

2 to “Mac Apps for the Professional Astronomer”

  1. janet says:
    Really enjoying your blog a great deal! Thank you!
  2. Kelle Cruz says:
    Also check out the AstroBetter wiki: http://www.astrobetter.com/wiki/ It's not all encompassing or up-to-date yet, but it's getting there!


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