Anthony Smith's Research Blog » Computing

Generating LaTeX authors lists for MNRAS and A&A

Anthony — Thu, 03 Jun 2010 09:38:11 +0000

Okay, a bit boring, but as promised, here are some Python functions to generate LaTeX source for long authors lists for MNRAS and A&A.

First, a small utility:

def getSortedInstituteCodes(authorList, authorInstituteCodes):
    """Return a list of institute codes, in the correct order for authorList.
 
    authorList = ["J.~Bloggs", "A.N.~Other"]
    authorInstituteCodes = {"J.~Bloggs":1, "A.N.~Other":[1,"Sussex"]}
    """
    instituteCodes = []
    for author in authorList:
        codes = authorInstituteCodes[author]
        if not hasattr(codes, '__iter__'):
            codes = [codes]
        for code in codes:
            if not code in instituteCodes:
                instituteCodes.append(code)
    return instituteCodes

then the function for MNRAS:

def getAuthorsStringMNRAS(authorList, authorInstituteCodes, institutesTex,
                          authorEmails):
    """Return a string containing LaTeX for MNRAS authors list.
 
    authorList = ["J.~Bloggs", "A.N.~Other"]
    authorInstituteCodes = {"J.~Bloggs":1, "A.N.~Other":[1,"Sussex"]}
    institutesTex = {1:"Somewhere, Earth", "Sussex":"University of Sussex"}
    authorEmails = {"J.~Bloggs": "j.bloggs@no.where"}
    """
    instituteCodes = getSortedInstituteCodes(authorList, authorInstituteCodes)
 
    # Make a list of strings:
    # "Author Name$^{1,2}$\thanks{E-mail: \texttt{j.bloggs@no.where}}"
    authorInstituteList = []
    for author in authorList:
        try:
            codes = authorInstituteCodes[author]
            if not hasattr(codes, '__iter__'):
                codes = [codes]  # Only one institute code for this author
            authorInstituteList.append(
                author
                + ',$^{' + ','.join([str(instituteCodes.index(code) + 1)
                                     for code in codes])
                + '}$')
        except KeyError:
            authorInstituteList.append(author + ',')
        try:
            email = authorEmails[author]
            authorInstituteList[-1] += '\\thanks{E-mail: \\texttt{'
            authorInstituteList[-1] += email + '}}'
        except KeyError:
            pass # No email address for this author
    # Sort out the punctuation (won't work if the penultimate or ultimate
    # author has no institute)
    authorInstituteList[-2] = authorInstituteList[-2].replace(',$', '$')
    authorInstituteList[-2] += ' and'
    authorInstituteList[-1] = authorInstituteList[-1].replace(',$', '$')
 
    # Put it all together
    authorsString = '\\author[' + authorList[0] + ' et al.]'
    authorsString += '\n{\\parbox{\\textwidth}{'
    authorsString += '\n'.join(authorInstituteList)
    authorsString += '}\\vspace{0.4cm}\\\\\n'
    authorsString += '\\parbox{\\textwidth}{'
    authorsString += '\\\\\n'.join(['$^{' + str(iInst + 1) + '}$'
                                    + institutesTex[instituteCodes[iInst]]
                                    for iInst in range(len(instituteCodes))])
    authorsString += '}}\n'
 
    return authorsString

and the function for A&A:

def getAuthorsStringAA(authorList, authorInstituteCodes, institutesTex,
                       authorEmails):
    """Return a string containing LaTeX for A&A authors list.
 
    authorList = ["J.~Bloggs", "A.N.~Other"]
    authorInstituteCodes = {"J.~Bloggs":1, "A.N.~Other":[1,"Sussex"]}
    institutesTex = {1:"Somewhere, Earth", "Sussex":"University of Sussex"}
    authorEmails = {"J.~Bloggs": "j.bloggs@no.where"}
    """
    instituteCodes = getSortedInstituteCodes(authorList, authorInstituteCodes)
 
    # Associate institute numbers with authors and emails with institutes
    authorInstituteList = []  # A list of "Author Name\inst{1,2}" strings
    instituteEmails = {}  # A dictionary of email addresses for each institute
    for author in authorList:
        try:
            codes = authorInstituteCodes[author]
            if not hasattr(codes, '__iter__'):
                codes = [codes]  # Only one institute code for this author
            authorInstituteList.append(
                author + '\inst{'
                + ','.join([str(instituteCodes.index(code) + 1)
                            for code in codes])
                + '}')
            try:
                email = authorEmails[author]
                try:
                    instituteEmails[codes[0]].append(email)
                except KeyError:  # First email address for this institute
                    instituteEmails[codes[0]] = [email]
            except KeyError:
                pass # No email address associated with author
        except KeyError:
            authorInstituteList.append(author)
 
    # Create a list of "Institute Name, Address\\
    #                   \email{j.bloggs@no.where}" strings
    instituteEmailList = []
    for instituteCode in instituteCodes:
        try:
            emails = instituteEmails[instituteCode]
            instituteEmailList.append(
                institutesTex[instituteCode]
                + ''.join(['\\\\\n\email{' + email + '}' for email in emails]))
        except KeyError:
            instituteEmailList.append(institutesTex[instituteCode])
 
    # Put it all together
    authorsString = '\\author{'
    authorsString += '\n\\and '.join(authorInstituteList)
    authorsString += '}\n'
    authorsString += '\\institute{'
    authorsString += '\n\\and '.join(instituteEmailList)
    authorsString += '}\n'
 
    return authorsString

Anyone still reading?

MNRAS line wrapping in authors lists

Anthony — Fri, 07 May 2010 11:08:29 +0000

In case anyone else using the MNRAS LaTeX class has been tearing their hair out inserting line breaks manually into long author (and institution) lists, using \newauthor, here's how I did it:

\author[J.~Bloggs et al.]
{\parbox{\textwidth}{J.~Bloggs,$^{1}$\thanks{E-mail: \texttt{j.bloggs@no.where}}
J.~Bloggs,$^{2,3}$
J.~Bloggs,$^{3}$
J.~Bloggs,$^{4}$
J.~Bloggs,$^{5}$
J.~Bloggs,$^{6}$
%...
J.~Bloggs$^{99}$ and
J.~Bloggs$^{100}$}\vspace{0.4cm}\\
\parbox{\textwidth}{$^{1}$Department of Something, Somewhere\\
$^{2}$Department of Something, Somewhere\\
$^{3}$Department of Something, Somewhere\\
$^{4}$Department of Something, Somewhere\\
$^{5}$Department of Something, Somewhere\\
$^{6}$Department of Something, Somewhere\\
%...
$^{99}$Department of Something, Somewhere\\
$^{100}$Department of Something, Somewhere}}

Next: a Python script to generate the above from a simple list of authors and affiliations.

Astropython

Anthony — Tue, 19 Jan 2010 10:48:25 +0000

You (both of you) might well be interested in the new Astropython site, which looks excellent. Here's the site's own description:

Research in astronomy includes the analysis of astronomical images, parsing and manipulation of large catalogs, statistical yet often visual inference, and the creation of data visualizations for publication and dissemination of results.

The purpose of this web site is to act as a community knowledge base for performing this research with the open source Python language. It provides a forum for general discussion, advice, or relevant news items, collecting lists of useful resources, users' code snippets or scripts, and longer tutorials on specific topics. The topics within these pages are presented in a list view with the ability to sort by date or topic. A traditional "blog" view of the most recently posted topics is visible from the site Home page.

Visualizing noisy images

Anthony — Wed, 13 May 2009 11:51:43 +0000

You have an image. Each pixel has a value with some uncertainty. How do you visualize the uncertainty in each pixel? Like this:

Here's the Python code

import numpy as np
from matplotlib import pyplot as plt
 
class FlickerImage(object):
    def __init__(self, im, err):
        self.im = im.copy()
        self.err = err.copy()
        finite = np.isfinite(self.im + self.err)
        self.vmin = (self.im - 2 * self.err)[finite].min()
        self.vmax = (self.im + 2 * self.err)[finite].max()
        self.im[np.invert(finite)] = self.vmax
        self.err[np.invert(finite)] = 0
    def flicker(self):
        fg = plt.imshow(np.zeros(self.im.shape),
                        interpolation='nearest',
                        vmin=self.vmin,
                        vmax=self.vmax)
        while True:
            ran = np.random.normal(size=im.shape)
            fg.set_data(im + err * ran)
            plt.draw()

And here's an example script:

import pyfits
f = pyfits.open('file.fits')
im = f["IMAGE"].data
err = f["ERROR"].data
flicker_image = FlickerImage(im, err)
flicker_image.flicker()

Python, FITS and DS9

Anthony — Wed, 01 Apr 2009 13:06:34 +0000

Here's an easy way to display FITS images (or any array) in DS9 using Python (with PyFITS, NumPy and Numdisplay, which is part of stsci_python). First launch DS9, then in Python:

import numdisplay
import pyfits
arr = pyfits.getdata('file.fits')
numdisplay.display(arr)

Easy!

Alternatively, the Kapteyn package seems excellent, and uses Python's matplotlib for displaying images. ~~It requires WCSLIB to run, though, so the installation process is a bit longer~~ [update: apparently that bit is no longer true - 17 Oct 2011].

A third option is to use python-sao:

import pysao
import pyfits
ds9 = pysao.ds9()
f = pyfits.open('file.fits')
ds9.view(f[0])

Easy again! And the WCS information is preserved, which doesn't seem to be the case with Numdisplay.

PSFs in IDL

Anthony — Wed, 18 Mar 2009 15:14:52 +0000

Two methods of approximating a point-spread function in IDL:

1. StarFinder seems to do a great job at finding point sources in crowded fields. It includes a routine for generating the Airy pattern. For a 51 x 51 array, with the peak at [25, 25], and an FWHM of 8.0 pixels, this is the command:

psf = airy_pattern(51, 51, 25, 25, 2./8.0)
isurface, psf

The output looks something like this:

2. The IDL Astronomy User's Library contains a routine, psf_gaussian, that produces a Gaussian PSF. To produce the same as above, the command would be:

psf = psf_gaussian(npix=51, fwhm=8.0, /double)
isurface, psf

... which produces something like this:

The eclipse of IDL 7

Anthony — Tue, 03 Mar 2009 18:54:32 +0000

I've finally made the transition from IDL 6.4 to IDL 7. Here are my handy hints...

IDL Workbench rocks! (This is because it is basically Eclipse, which is a proper development environment, unlike that hideous old IDLDE.)
Another reason for using IDL Workbench (for me at least, and for now) is that IDL help doesn't seem to work if Java 6 is the default (as it is on my Mac), but the help does work if launched through the IDL Workbench.

To transition to IDL Workbench:

Import your code as described on David Fanning's page - fret not, it's easy and harmless
Preferences -> IDL -> Startup file, if you have one, and
Preferences -> IDL -> Paths -> Insert... for me it was just my idl folder, including all sub-folders, to mimic my $IDL_PATH environment variable.

pIDLy: IDL within Python

Anthony — Thu, 31 Jan 2008 14:35:09 +0000

Now Python and IDL can talk to each other (okay, Python talks to IDL and IDL does what it's told), using pIDLy (pronounce as you please). I experimented with a few other solutions available online but couldn't get them to work. So I cobbled this one together with surprisingly little trouble, thanks largely to pexpect.

IDL code miscellany

Anthony — Mon, 28 Jan 2008 13:15:58 +0000

IDLdoc 3.0 (more info here) gives my badly-written bits of IDL the deceptive appearance of being well designed, useful and user-friendly. So I've made a few available here for your enjoyment.