This is a guest post by Jeremy Sanders about the plotting package he’s developed. Jeremy is a postdoc working in the X-Ray Group at the Institute of Astronomy in the University of Cambridge in the UK.

Veusz (pronounced “views”) is a python-based GUI plotting package that I (Jeremy Sanders) have developed. As an astronomer, I was dissatisfied with every plotting package I had used. Some were fairly easy to use but old fashioned and/or limited (e.g., qdp, sm, grace, gnuplot). Several were not licensed freely (e.g., sm, idl). Many were difficult to use, requiring libraries of other peoples’ code or a lot of work going through manuals (e.g. idl). I wanted a free, easy to use and powerful package and so I started writing Veusz in 2004. Although I initially found the command line interface to be the most important part of a plotting package, since developing Veusz, I now use its GUI almost exclusively as it’s rather powerful and easy to use.

Veusz builds plots out of widgets, each of which has a set of properties and formatting options which can be modified. The standard way to build up the plot is to use the GUI to add widgets to form a tree, reading data from external files. However, most of the functionality can also be accessed using a command interface, which can be used from Python command line console window, an embedding Python module or commands sent to it from stdin. Indeed, Veusz saved documents are simply Python scripts using the same set of commands and are easily modified. Veusz can export several vector and bitmap formats, including PNG, EPS, PDF, SVG and EMF.

Veusz supports many types of graphs. Have a look at the page of examples. Veusz has scatter plots, with optional error bars (of several styles), joining-lines (stepped or beziers curves), fills and transparency, and allows for gaps in data. It also supports plotting functions (which can be defined using numpy functions or in external python modules), histograms (which can be computed from data), contour plots (including sub-contour levels and labelled contours), automatic data keys, image plots (with different color maps), color bars, shapes (including arrows) and external image files. It also has a function-fitting widget for doing a chi-squared fit to data. These plotting widgets are placed inside graph widgets. Multiple graph widgets can be placed on a page and in a grid widget which arranges the graphs inside it. Each graph can have as many axes as you like.

Veusz can read data in several different formats. It supports 1D numeric, date and text datasets, and 2D numerical arrays. Its default format is a simple space-delimited text format which can contain a descriptor describing dataset names, columns and data types, or specified in the program. It also supports CSV files (with an optional name for a dataset above each column). Importantly, it can load 1D and 2D data from FITS tables or images. And if that’s not good enough, you can send numpy arrays to Veusz using the embedding interface, or define an import plugin, which is a simple Python script for reading the data. A powerful feature is the ability to create new datasets in the program based on functions of other datasets. These datasets update automatically if the underlying data is reloaded.

Veusz is multiplatform as it is written in Python and uses PyQt for user interface and plotting. There are some small parts written in C and C++ to make the program faster. It relies heavily on the Python numpy libraries for handling data. Binaries are available for Linux x86, Mac OS X and Windows, and source allows it to be built for these and other platforms. It is licensed under the GPLv2.

Now, what it doesn’t do: It currently doesn’t have 3D surface plots or types of plots without independent axes at 90 degrees (e.g., pie chart, radar plot). The embedding interface doesn’t have a simple command for plotting like pylab, but it only takes a few lines of Python code to make a simple plot, and the object interface makes it very easy to manipulate the graph. Embedded plots can also be saved and loaded into the main GUI program for later editing. Its main feature which sets it apart is the unified command line interface which underlies the entire program. The program only supports Qt as a drawing backend, but this is easily extended to support other export files. For example the SVG and EMF export filters were written by me in Python. Veusz is also mostly a single-person software project, though I have included patches and ideas from other people.

What I’m currently working on is to add more general plugins allowing the user to add new dialog boxes to modify the plot and its data. I’m also going to add dataset plugins which would add the ability to define new ways to modify the data easily within the program without writing numpy expressions (e.g., FFT). I’ve just written code to improve the embedding interface allowing the user to treat the widgets in the document as Python objects (see the New style interface here). I’ve also added vector field plots and am looking into supporting new data formats (e.g., HDF).

The current version is 1.8. Please download and play with it! There are installation instructions, a manual, and a FAQ. Questions and comments are welcome below, on the mailing list, or directly to to me (jeremy at jeremysanders dot net).

Veusz (free), OS X [dmg] Windows [exe] Linux [tar.gz]

Fun Stuff

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  Are you on the main sequence?
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  Hubble guy is back around the 2:50 mark.

IDL

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Ergonomics

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  “After every 20 minutes, you (the computer user) should take a break for at least 20 seconds and look at objects that are 20 feet away from you.”

Productivity

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Politics

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  (via Adam Kraus)
• Ireland Cuts Back on Ph.D. and Postdoc Support | Science News
• Antonelli, A.: A decline and fall in the future of Italian Astronomy? | astro-ph

Career and Professional Development

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• Career Advice: Support on the Tenure Track | Insider Higher Ed
  Strategic and practical advice. (via Adam Kraus)

Python

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Productivity Tips and Apps

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For anyone who uses python and ds9 to visualize their FITS files, I think pyds9 is now a must-have. It is officially written and developed through SAOImage ds9 so it will be supported for the long haul. Here are the primary links to get going:

• TARball for installation: Source
• Documentation for installation and use: Docs

The documentation is pretty basic so I put together a very small tutorial of a way I might typically use it. Most of the controls work through the XPA interface, which seems very flexible, if a little tricky to figure out exactly how to make it work for specific use-cases. If you have samples of how you use pyds9 or ds9 xpa, post them in the comments or on this wiki page.

from scipy import stats
import numpy as np
import ds9
 
# Make a 2D gaussian image that is stored in a 2D numpy array
x = np.arange(-3, 3, 0.1)
xx, yy = np.meshgrid(x, x)
gauss2d = stats.norm.pdf(xx) * stats.norm.pdf(yy)
 
# Now open ds9 (this assumes no ds9 instance is yet running)
d = ds9.ds9()
 
# Load up our 2D gaussian
d.set_np2arr(gauss2d)
 
# Zoom to fit
d.set('zoom to fit')
 
# Change the colormap and scaling
d.set('cmap bb')
d.set('scale log')
 
# Add a label
d.set('regions command {text 30 20 #text="Fun with pyds9" font="times 18 bold"}')
 
# Now you can play in ds9 to your heart's content.
# Check back to see what the current color scale is.
print d.get('scale')
 
# Finally, save your completed image (including regions or labels)
d.set('saveimage png my_pyds9_img.png')

Photo by Ed Yourdon.

• Discovering the Virtues of a Wandering Mind | NY Times
  Why I think lots of play time is crucial to a successful writing retreat: “To encourage this creative process, Dr. Schooler says, it may help if you go jogging, take a walk, do some knitting or just sit around doodling, because relatively undemanding tasks seem to free your mind to wander productively. But you also want to be able to catch yourself at the Eureka moment.”
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  I completely agree: “We all get ideas from each other in various ways, and it’s not worth spending time having paranoid thoughts about the competition. I’d rather just keep doing my work in the best (yet most efficient) way that I can, and confine my paranoid obsessing to a bit of ranting over a double espresso with a colleague now and then.”
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• How to Make Good Use of Time Pockets | Dumb Little Man
  Nice list of task you can accomplish when you have 5, 10, or 20 minutes at work, home, or out and about.
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LaTeX, pronounced “la tech”, is a typesetting program that we use to write our papers (instead of Word or somesuch nonsense). Over the long US holiday weekend I got LaTeX and all of its bits installed on my new 13″ MacBook Pro (named Gloria). In this post, I’ll walk you through the installation and setup that should work for any of the code and text editors that Tom discussed a couple weeks ago (e.g., TextMate, TexShop, Emacs). In a future post, I’ll describe how to get TextMate setup as the primary LaTeX editor.

Read on for step-by-step instructions for installing LaTeX, AASTeX, MN2E, and more. One new thing that I learned was how to include both EPS and PDF figures in the same document!

Download and Install LaTeX

The easiest way to get LaTeX onto OS X is via MacTex. I recommend downloading the full package (~1.3 GB) and then customizing the install. The package comes with BibDesk, TexShop (which everybody seems to love except me), as well as lots of other stuff.

MacTex uses the paths.d method to modify the PATH environment variable. This works well if you don’t have your path explicitly set in the .cshrc/.tcshrc/.bashrc. To check if your path is set up correctly, in Terminal, typing which latex on the command line should return /usr/texbin/latex.

Download and Install AASTeX

AASTeX is the package for preparing astronomy publications for ApJ, AJ, and PASP. Download the AASTeX package and put it in ~/Library/texmf/tex/latex/aastex52. If you’re unfamiliar with AASTeX, a handy guide [PDF] comes included in the download. To use the AASTeX style, be sure this is the first line of the tex file:

\documentclass{aastex}

Setup emulateapj

If you want to get the fancy look of a two-column ApJ paper, you’ll want to use emulateapj. The MacTex-2009 package includes an old version so you’ll want to donwload the new one — emulateapj.cls — and put it in ~/Library/texmf/tex/latex/emulateapj.cls. When you want to use it instead of the AASTeX format, modify the tex preamble:

%\documentclass{aastex}
\documentclass{emulateapj}

Download and Install MN2E

MN2E is the package to use for submitting to MNRAS. Download mn2e.cls and put it in ~/Library/texmf/tex/latex/. Also get the guide [PDF]. To use the style file, make this the first line of the tex file:

\documentclass{mn2e}

Set up the Bibliography for Use with BibTeX

The easiest way to create the bibliography is with BibTeX and ADS. Your .bib file (managed with BibDesk or exported from Papers) should live in ~/Library/texmf/bibtex/bib/my_bib.bib. To get the bibliography to display in the journal style format, you’ll need bibliography style files (.bst).

The bibliography style file for use with with AASTeX is part of AstroNat. (However, be advised that many of the AstroNat resources are no longer necessary.) Download apj.bst and put it in ~/Library/texmf/bibtex/bst/apj.bst. In the preamble of the tex file, include:

\bibliographystyle{apj}

For MNRAS, download the bibliography style file, mn2e.bst, put it in ~/Library/texmf/bibtex/bst/mn2e.bst, and include this in the tex file:

\bibliographystyle{mn2e}

Where you want the reference list to appear (typically after the acknowledgements, before tables and figures), put this:

\bibliography{my_bib}

Figures

If you’re using pdftex instead of latex (as you should be…in this day and age, there’s no need for that DVI -> PS -> PDF rigamarole), you can include both EPS and PDF figures in the same document by loading these packages in the preamble of the tex file:

\usepackage{graphicx}
\usepackage{epstopdf}

The filename extension is optional. For example, to include pdf_fig.pdf and eps_fig.eps:

\begin{figure}
	\plotone{pdf_fig}
\end{figure}
 
\begin{figure}
	\plotone{eps_fig}
\end{figure}

Anything else? Once ya’ll give this the once over, I’ll go ahead and add it to the LaTeX wiki entry which is fairly outdated at the moment.

• Too Much Self-Doubt? Try Thinking Like a Creator | ProfHacker
  “Think like a creator, not like a sponge. Most of us were trained to be very good sponges: we can soak up information and absorb it so that it feels like its our own. But focusing on all that you don’t know and on what other people are doing can easily overwhelm your own sense of agency. To think like a creator, however, is to always keep in mind what it is that you want to do, to build, to create in the world, whether that’s through a course, an article, or a new administrative structure.”
• India Joins Thirty Meter Telescope Project | Thirty Meter Telescope
  (via Kartik)
• AstroInformatics II: From public outreach to public engagement | SarahAskew
• Scientist Turned in by Grad Students for Misconduct Pleads Guilty | Science Insider
  I think the lesson here is not to exaggerate your results…especially not in print. But I’m not sure anything good came out of blowing the whistle.
• One versus many | Unclutterer
  This is exactly my logic for having three Mac power bricks. One for the office, one for home, and one for the travel bag.
• Top 10 Clever Google Voice Tricks | Lifehacker
• Five Best To-Do List Managers | Lifehacker
  Google Tasks, Paper, Remember the Milk, Things (my favorite, $50), and Toodledo. Not mentioned, but apparently popular with our FB fans, is OmniFocus ($50). OminFocus vs. Things.
• Seven tips for managing the overwhelming to-do list | Unclutterer
  Take Breaks, Say “no”…or at least “not right now” to new projects or non-urgent meetings.
• Four tips to unclutter your family finances | Unclutterer

• iPhone 4 review | Engadget
  um yeah, I must have this…especially since my 3G’s battery life is rapidly deteriorating.
  “…the iPhone 4 is the best smartphone on the market right now. The combination of gorgeous new hardware, that amazing display, upgraded cameras, and major improvements to the operating system make this an extremely formidable package.”
  “There are three main pieces of the phone, which together create an effect not wildly dissimilar to that of an ice cream sandwich.” om nom nom!
• Some iPhone 4 models dropping calls when held left-handed, including ours (Update: Apple responds)” | Engadget
  Pictures showing exactly how to hold it wrong.
• iOS 4: The Upgrade Guide | Switched
  Looks like a green light to upgrade for the 3GS but I think regular 3G owners (like myself) should just get a new phone. “…numerous reports of the now two-year-old 3G model suffering from serious performance and battery life issues when running iOS 4.”
• Optical character recognition (OCR) in Google Docs | Google Docs Blog
  Turn PDFs into text.
• Google Voice, Available Without Invitation | Google Operating System
  With my two offices and lots of travel, I’m a big fan of Google Voice! “…one number to ring all your phones, voicemail that works like email, free calls and text messages to the U.S. and Canada, low-priced international calls and more…”
• Make Free VoIP Calls from Google Voice | Lifehacker

Every department seems to do their seminar calendar in a slightly different way, but it looks like most places are still using an old-fashioned HTML table. While that works, it can be done so much better!

With the HTML table, everybody needs to actually visit the webpage in order to get the information. In this day and age, information should come to you, not you to it. Specifically, people should be able to “subscribe” to the seminar calendar in their calendar program of choice so that the events and changes just show up effortlessly. There are several ways to “publish” a calendar, but the easiest, cheapest, and most versatile way I’ve found is using Google Calendar.

Google calendar does everything you need it to do:

• Update events in just one place (not on both published calendar and on webpage)
• Multiple people can have editing privileges
• Calendar or agenda (list) view for webpage
• Calendar can be published for people to subscribe to
• Hyperlinks can be included in event title and description

Before I describe how to set it all up, I’ll show the final product! Example pages are at AMNH and IPAC. Below, I’ve shown events from AMNH, IPAC, NYU, and Caltech in two different views. (Use the arrows in the upper left to navigate to May when there were tons of events.) When you embed the calendar, you can choose the default view (Week, Month, or Agenda) but the user can switch between them. I’m partial to Agenda but Month is also nice. Click on the event to see the abstract and location. Click the arrow next to ‘Agenda’ in the upper right corner to show/hide calendars.

Month View

Agenda View

Setting this up is an easy, but multi-step process. I’ll walk you through it. It looks like a lot, but it really isn’t, I promise! I estimate it will take about 30 minutes to do the one-time initial set up.

Create Google Account and Calendar

• Create a Google account specifically for the seminar calendar.

I recommend choosing an account name that could also be the permanent email address for the seminar series. When the seminar organizer changes, you just forward the mail to a different address.

• Create a new calendar with a descriptive name.

Click ‘Add’ under My Calendars in the left sidebar. The calendar name should include the name of the institution, the broad area (e.g., Astro or Physics), and the series name (Colloquia, Seminar). Example: Caltech Astro Tea Talks. Just ‘Caltech Talks’ could be confused with Biology talks or public talks.

• Make the calendar public.

In order for people to be able to subscribe to it, it needs to be public.

• Share the calendar with your personal Google account and with other seminar organizers.
• Give them the appropriate permissions, most likely edit events and manage sharing.

Once this is done, there is really no reason to ever log into the seminar account again since everything can be done from the organizers’ personal accounts.

Create Events

WHAT: This is the event title. I think the talk title should be first since that contains the most relevant info needed to decide to attend. Also include the the speaker’s name and their affiliation. Example: Brown Dwarfs. Kelle Cruz (Hunter College/AMNH). If the title is TBA, just state the name and affiliation…no need to waste space by actually stating ‘Title TBA.’ Hyperlinks can be included, e.g.,
[code lang="html"]
Brown Dwarfs, Kelle Cruz, (Hunter College/AMNH)
[/code]

WHERE: Building and Room Number. It should be obvious from the Calendar title what campus.

WHAT: Abstract. Just the abstract. No need to repeat the information given in the other parts of the event.

Customize the Calendar(s) for the Seminar Webpage

• Create the HTML that will be used to display (“embed”) the calendar on the seminar webpage.

There are lots of customization options here. I would deselect ‘Time Zone.’ If you’re only displaying one calendar, then also deselect ‘Calendar List.’ Choose Month or Agenda as the default view. For reference, the calendars above are 600 px wide by 500 px high. And my week begins on Monday, but that’s another personal preference.

Share Subscribe Link

• In the Calendar Settings, get the “iCal” address for your calendar.
• Post this link on the seminar calendar.

This step is crucial. The idea is to let people see the events in their own calendar without ever having to visit the webpage. In order to do that, you have to give the link to subscribe to! The “iCal” link points to the standard .ics format and will work in other calendar programs, not just iCal. (The XML is if someone wanted to see the events in a feed reader, like Google Reader. And the HTML is a link to a generic version of the embedded calendar we created above.)

Phew! But once this is setup, updating calendars and changing seminar organizers will be a breeze!

Got any other other seminar calendar ideas? Let’s here it in the comments.

We’ve recently added a couple widgets to make spreading the word about AstroBetter easier.

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“Like” the AstroBetter Facebook Page. I’ve added a widget at the top of the right sidebar. As of 9am PT, 186 people like us…I’m sure there are more of you than that!

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