-Apr 30th, 2010| 12:12 pm | Posted by vlk

Sherpa is a fitting environment in which Chandra data (and really, X-ray data from any observatory) can be analyzed. It has just undergone a major update and now runs on python. Or allows python to run. Something like that. It is a very powerful tool, but I can never remember how to use it, and I have an amazing knack for not finding what I need in the documentation. So here is a little cheat sheet (which I will keep updating ~~as and when~~ if I learn more): …Continue reading»

Tags:

Chandra,

cheat sheet,

ciao,

how to,

Python,

Sherpa,

Sherpa4 Category:

Algorithms,

Astro,

Fitting,

Jargon,

Languages
-Nov 13th, 2009| 04:46 pm | Posted by hlee

I was told to stay away from python and I’ve obeyed the order sincerely. However, I collected the following stuffs several months back at the instance of hearing about import inference and I hate to see them getting obsolete. At that time, collecting these modules and getting through them could help me complete the first step toward the quest Learning Python (the first posting of this slog). …Continue reading»

Tags:

APLpy,

AstroPy,

IDLsave,

import inference,

libraries,

modules,

package,

Pyfits,

PyMC,

PyRAF,

PYSTAT,

Python,

PyWavelets Category:

Algorithms,

Astro,

Cross-Cultural,

Data Processing,

Jargon,

Languages,

Methods,

News,

Stat
-Oct 26th, 2009| 10:41 pm | Posted by hlee

I’m very sure that Fortran is one of the major scientific programming languages. Many functions, modules, and libraries are written in this language. Without being aware of, these routines are ported into many script languages. However, I become curious whether Fortran is still the major force in astronomy or statistics, compared to say 20 years ago (10 seems too small). …Continue reading»

-Oct 1st, 2009| 09:11 pm | Posted by hlee

So far, I didn’t complain much related to my “*statistician learning astronomy*” experience. Instead, I’ve been trying to emphasize how fascinating it is. I hope that more statisticians can join this adventure when statisticians’ insights are on demand more than ever. However, this positivity seems not working so far. In two years of this slog’s life, there’s no posting by a statistician, except one about BEHR. Statisticians are busy and well distracted by other fields with more tangible data sets. Or compared to other fields, too many obstacles and too high barriers exist in astronomy for statisticians to participate. I’d like to talk about these challenges from my ends.^{[1]} …Continue reading»

Tags:

ARF,

calibration,

ciao,

cultural shock,

data analysis system,

documentation,

FITS,

obstacles,

pha,

PSF,

RMF,

Sherpa,

standard procedure,

Tutorial,

unification,

validation,

XSPEC Category:

Astro,

Cross-Cultural,

Data Processing,

High-Energy,

Misc,

Quotes,

X-ray
-Sep 11th, 2009| 03:40 pm | Posted by hlee

A number of practical Bayesian data analysis books are available these days. Here, I’d like to introduce two that were relatively recently published. I like the fact that they are rather technical than theoretical. They have practical examples close to be related with astronomical data. They have R codes so that one can try algorithms on the fly instead of jamming probability theories. …Continue reading»

Tags:

book,

BUGS,

CMB,

examples,

HMM,

identifiability,

image processing,

LLN,

mixture,

MRF,

R Category:

Bayesian,

Fitting,

Languages,

MC,

MCMC,

Methods,

Stat
-Jul 30th, 2009| 01:57 am | Posted by hlee

##### X={ primer, tutorial, cookbook, Introduction, guidebook, 101, for dummies, …}

#####

I’ve heard many times about ** the lack of documentation** of this extensive data analysis system, **ciao**. I saw people still using ciao 3.4 although the new version 4 has been available for many months. Although **ciao** is not the only tool for Chandra data analysis, it was specifically designed for it. Therefore, I expect it being used frequently with popularity. But the reality is against my expectation. Whatever (fierce) discussion I’ve heard, it has been irrelevant to me because **ciao** is not intended for statistical analysis. Then, out of sudden, after many months, a realization hit me. **ciao is different from other data analysis systems and softwares.** This difference has been a hampering factor of introducing ciao outside the Chandra scientist community and of gaining popularity. This difference was the reason I often got lost in finding suitable documentations. …Continue reading»

Tags:

ciao,

cookbook,

documentation,

guide,

introduction,

matlab,

primer,

Python,

R,

SAS,

software,

Tutorial Category:

Cross-Cultural,

Languages,

Misc
-May 7th, 2009| 02:22 pm | Posted by hlee

Almost 100 years ago, A.S. Eddington stated in his book *Stellar Movements* (1914) that

…in calculating the mean error of a series of observations it is preferable to use the simple mean residual irrespective of sign rather than the mean square residual

Such eminent astronomer said already *least absolute deviation* over *chi-square*, if I match *simple mean residual* and *mean square residual* to relevant methodologies, in order. …Continue reading»

Tags:

chi-square minimization,

Eddington,

inference,

LAD,

Laplace,

mse,

PyMC,

Python,

R.A.Fisher,

utility function Category:

Astro,

Cross-Cultural,

Quotes,

Stat,

Uncertainty
-Nov 17th, 2008| 01:39 pm | Posted by hlee

The full description is given http://cxc.harvard.edu/ciao3.4/ahelp/bayes.html about “bayes” under sherpa/ciao^{[1]}. Some sentences kept bothering me and here’s my account for the reason given outside of quotes. …Continue reading»

Tags:

bayes,

ciao,

ML,

Sherpa Category:

Algorithms,

Astro,

Cross-Cultural,

Data Processing,

Fitting,

High-Energy,

Jargon,

Languages,

Methods,

Spectral,

Uncertainty,

X-ray
-Oct 27th, 2008| 11:05 am | Posted by hlee

The first step of data analysis or applications is reading the data sets into a tool of choice. Recent years, I’ve been using R (see also Learning R) for that regard but I’ve enjoyed freedoms for the same purpose from these languages and tools: BASIC, fortran77/90/95, C/C++, IDL, IRAF, AIPS, mongo/supermongo, MATLAB, Maple, Mathematica, SAS, SPSS, Gauss, ARC, Minitab, and recently Python and ciao which I just began to learn. Many of them I lost the fluency of how to use it. Quick learning tends to be flash memory. Some will need brain defragmentation and recovering time for extensive scientific work. A few I don’t like to use at all. No matter what, I’m not a computer geek. I’m not good at new gadgets, new softwares, nor welcome new and allegedly versatile computing systems. But one must be if he/she want to handle data. Until recently I believed R has such versatility in the aspect of reading in data. Yet, there is nothing without exceptions. …Continue reading»

-Sep 16th, 2008| 04:34 pm | Posted by hlee

Astronomers tend to think in Bayesian way, but their Bayesian implementation is very limited. OpenBUGS, WinBUGS, GeoBUGS (BUGS for geostatistics; for example, modeling spatial distribution), R2WinBUGS (R BUGS wrapper) or PyBUGS (Python BUGS wrapper) could boost their Bayesian eagerness. Oh, by the way, **BUGS** stands for **Bayesian inference Using Gibbs Sampling.** …Continue reading»

Tags:

openBUGS,

PyBUGS,

Python,

R,

toolbox,

winBUGS Category:

Algorithms,

Bayesian,

Data Processing,

Languages,

MCMC,

Methods,

News
-Aug 27th, 2008| 08:08 pm | Posted by hlee

PyIMSL is a collection of Python wrappers to the math and statistical algorithms in the IMSL C Numerical Library^{[1]}. I recall the days of digging in IMSL (International Mathematics and Statistics Library) user manuals and learning Fortran and C to use this vast library (Splus was to slow at that time). Upon knowing that Python is very favored among astronomers (click here to see the slog posts about Python) and that limits exist in Numerical Recipes (I didn’t check the latest version published last year, though), probably IMSL is useful for mathematical and statistical analysis for astronomers.

To know more, …Continue reading»

-May 13th, 2008| 03:47 pm | Posted by hlee

The brackets could be filled with other languages but two are introduced today: **Perl** (perl.org) and **Python** (python.org). These two are widely used among astronomers and can be empowered by **R** (r-project.org). …Continue reading»

-Apr 17th, 2008| 10:47 pm | Posted by aneta

We have talked about it many times. Now I have to work with the reality. My source shows only 5 counts in a short 5 ksec Chandra exposure. Is this a detection of the source? or is this a random fluctuation? Chandra background is low and data are intrinsically Poisson, so the problem should be easy to solve. Not really! There is no tool to calculate this well, no actually it is! Tom A. and I found it by searching Google “Python gamma function” and came out with Tom Loredo’s Python functions (sp_funcs.py) that he translated from Numerical Recipes to Python. This is the working tool! We just needed to change “import Numeric” or “import Numarray” to “import numpy as N” and then it worked.

We calculated the significance of observing 5 counts given the expected background counts of 0.1 using spfunc.gammp(5,0.1) =8e-8. The detection is highly significant.

Any comments?

-Jan 22nd, 2007| 05:08 am | Posted by hlee

Both in astronomy and statistics, python is recognized as a versatile programming language. I asked python tutorials to Alanna. The following is her answer, which looks very useful for those who wish to learn python.

…Continue reading»