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XWSM commands

XWSM or “X-ray Wavelet Spectral Mapping” is a program written primarily to analyze x-ray data of XMM-Newton x-ray telescope. But it seems to be working fine also for Chandra data. Till now only very faint mode data taken by ACIS-I camera of Chandra can be analyzed using XWSM.

The software is written by Herve Bourdin, a post-doc at the University of Rome Tor Vergata. Bourdin works at the cosmology group of Rome Tor Vergata. From Herve Bourdin’s tutorial:

“The X-Ray Wavelet Spectral Mapping (XWSM) package is a set of tools dedicated to the mapping of spectroscopic observables associated with the X-ray emission of the Inter- Galactic Medium (IGM), within clusters and groups of galaxies. Spectroscopic observables like the IGM brightness, temperature and metallicity can be estimated within specific re- gions of the field of view, or mapped by means of wavelet algorithms. These tools have been developped by Herv ́e Bourdin1, in collaboration with Albert Bijaoui2, Eric Slezak2 and Jean-Luc Sauvageot3. The present version of XWSM is specific to XMM-Newton data. Please notice that while the bulk of this work has been developped as a free software, some proprietary softwares, namely the Numerical Recipes and IDL have been used, so that the relative licenses are required. Moreover, some HEASARC softwares (FTOOLS) may be useful for further applications.”

Basic commands of XWSM are as follows:

xwsm_start, ‘ms1455_zoom’, acis_aoff_file=aoff, acis_evt_files=evt2, badpix_files=bpx, redshift=0.257800, T_inter=[0.1,60], /nh_ftools, /clean, /detect, /acis_i, n_bin=512

xwsm_lx ’obs_id’

xwsm_spec, ’obs_id’

xwsm_fit obs_id -Z

xwsm_map obs_id -bspline -donoho -ns_min.7

xwsm_map obs_id -Z -bspline -donoho -ns_min.7

xwsm_chandra,’obs_id’,/rebuild_cxb

xwsm_map_image, ‘a1835_zoom’, lx_min=.5, zoom=5, offset=[-.25,0], sigma=2

xwsm_map a1835_zoom -bspline -sigma2

Ciao

- http://cxc.harvard.edu/ciao/download/
From here download ciao-install script. Create a different folder for everything of your data analysis namely, chandra. Copy this script file to that folder. enter into that folder and run the script. It’s better to install ciao also in this directory. Better not to install as root, I don’t know why.

For running the script, open terminal and go to that folder. Than type “bash ciao-install”, without the inverted commas of course. After than everything will be normal if the script works. Terminal will ask for Ciao installation directory, give the directory, chandra.

After installation go to the directory where ciao is installed. Go to the bin directory and run this code to see complete ciao configuration.
. ciao.bash

Then you have to edit the .bashrc file in your home to make an alias for ciao with which you will open ciao every time. The file is hidden so u have to use ls -a to see it. Than to edit write this,
sudo gedit .bashrc

Heasoft with Xspec

- http://heasarc.gsfc.nasa.gov/lheasoft/download.html

In this page first select what kind of package you want to download. I downloaded source codes instead of binary files. Because after downloading source code I can configure it according to my OS. But binary is already configured and maybe not properly for my OS.

After selecting “Source code distribution” selct operating system and select the tools that you need. I selected all “General-Use FTOOLS” and “XANADU”. Clisk on Submit and download the file. It will take time. More than 300 MB.

After downloading move the tar file to chandra directory and untar it. Go to the untarred directory and than to the BUILD_DIR directory. Configure file is situated here. So run the “./configure” command on terminal.

This configuration will not be easy. It will give errors if it does not find some package file that it needs. Than it will stop. We have to install that package file and then again give the configure command. Dunno how many times it will give errors, depend on your software resources. I had to install the following packages while configuring Heasoft: (using sudo apt-get install or Synaptic package manager)

# gfortran
# libncurses-dev
# X11 development packages (libxkbfile-dev, x11proto-core-dev, libxdmcp-dev, libxau-dev)

After configuration makefile was created. So run the “make” command. It gave me an error at first. Could not find X11-intrinsic.h. So went to synaptic and searched for this. Installed the following packages and it worked:
# libxt-dev, libxt6-dbg, libxbfile1-dbg

Funtools

- https://www.cfa.harvard.edu/~john/funtools/

Download this tar file and copy to your chandra folder. Than extract at the same place. Go inside the folder and run the ./configure command. It will configure the program. Step by step commands will be:

./configure
make
make install

Finished. Funtools is installed. Now we need to integrate this with ds9. In the terminal open ciao. Than open ds9. Go to

Edit –> Preferences –> Analysis –> Preload analysis file –> Browse

Go to your funtools folder and show the funtools.ds9 file. That’s all.

ScienceDaily (June 21, 2010) — Astronomers from SRON Netherlands Institute for Space Research and Utrecht University have found blurred oxygen signatures in the X-rays from a neutron star that ‘eats’ a white dwarf. For the first time the effects of extreme gravity are revealed by oxygen instead of iron atoms.

– Read more >>>>

ScienceDaily (June 7, 2010) — Two new papers based on data from NASA’s Cassini spacecraft scrutinize the complex chemical activity on the surface of Saturn’s moon Titan. While non-biological chemistry offers one possible explanation, some scientists believe these chemical signatures bolster the argument for a primitive, exotic form of life or precursor to life on Titan’s surface. According to one theory put forth by astrobiologists, the signatures fulfill two important conditions necessary for a hypothesized “methane-based life.”

One key finding comes from a paper online now in the journal Icarus that shows hydrogen molecules flowing down through Titan’s atmosphere and disappearing at the surface. Another paper online now in the Journal of Geophysical Research maps hydrocarbons on the Titan surface and finds a lack of acetylene.

This lack of acetylene is important because that chemical would likely be the best energy source for a methane-based life on Titan, said Chris McKay, an astrobiologist at NASA Ames Research Center, Moffett Field, Calif., who proposed a set of conditions necessary for this kind of methane-based life on Titan in 2005. One interpretation of the acetylene data is that the hydrocarbon is being consumed as food. But McKay said the flow of hydrogen is even more critical because all of their proposed mechanisms involved the consumption of hydrogen.

“We suggested hydrogen consumption because it’s the obvious gas for life to consume on Titan, similar to the way we consume oxygen on Earth,” McKay said. “If these signs do turn out to be a sign of life, it would be doubly exciting because it would represent a second form of life independent from water-based life on Earth.”

To date, methane-based life forms are only hypothetical. Scientists have not yet detected this form of life anywhere, though there are liquid-water-based microbes on Earth that thrive on methane or produce it as a waste product. On Titan, where temperatures are around 90 Kelvin (minus 290 degrees Fahrenheit), a methane-based organism would have to use a substance that is liquid as its medium for living processes, but not water itself. Water is frozen solid on Titan’s surface and much too cold to support life as we know it.

The list of liquid candidates is very short: liquid methane and related molecules like ethane. While liquid water is widely regarded as necessary for life, there has been extensive speculation published in the scientific literature that this is not a strict requirement.

The new hydrogen findings are consistent with conditions that could produce an exotic, methane-based life form, but do not definitively prove its existence, said Darrell Strobel, a Cassini interdisciplinary scientist based at Johns Hopkins University in Baltimore, Md., who authored the paper on hydrogen.

Strobel, who studies the upper atmospheres of Saturn and Titan, analyzed data from Cassini’s composite infrared spectrometer and ion and neutral mass spectrometer in his new paper. The paper describes densities of hydrogen in different parts of the atmosphere and the surface. Previous models had predicted that hydrogen molecules, a byproduct of ultraviolet sunlight breaking apart acetylene and methane molecules in the upper atmosphere, should be distributed fairly evenly throughout the atmospheric layers.

Strobel found a disparity in the hydrogen densities that lead to a flow down to the surface at a rate of about 10,000 trillion trillion hydrogen molecules per second. This is about the same rate at which the molecules escape out of the upper atmosphere.

“It’s as if you have a hose and you’re squirting hydrogen onto the ground, but it’s disappearing,” Strobel said. “I didn’t expect this result, because molecular hydrogen is extremely chemically inert in the atmosphere, very light and buoyant. It should ‘float’ to the top of the atmosphere and escape.”

Strobel said it is not likely that hydrogen is being stored in a cave or underground space on Titan. The Titan surface is also so cold that a chemical process that involved a catalyst would be needed to convert hydrogen molecules and acetylene back to methane, even though overall there would be a net release of energy. The energy barrier could be overcome if there were an unknown mineral acting as the catalyst on Titan’s surface.

The hydrocarbon mapping research, led by Roger Clark, a Cassini team scientist based at the U.S. Geological Survey in Denver, examines data from Cassini’s visual and infrared mapping spectrometer. Scientists had expected the sun’s interactions with chemicals in the atmosphere to produce acetylene that falls down to coat the Titan surface. But Cassini detected no acetylene on the surface.

In addition Cassini’s spectrometer detected an absence of water ice on the Titan surface, but loads of benzene and another material, which appears to be an organic compound that scientists have not yet been able to identify. The findings lead scientists to believe that the organic compounds are shellacking over the water ice that makes up Titan’s bedrock with a film of hydrocarbons at least a few millimeters to centimeters thick, but possibly much deeper in some places. The ice remains covered up even as liquid methane and ethane flow all over Titan’s surface and fill up lakes and seas much as liquid water does on Earth.

“Titan’s atmospheric chemistry is cranking out organic compounds that rain down on the surface so fast that even as streams of liquid methane and ethane at the surface wash the organics off, the ice gets quickly covered again,” Clark said. “All that implies Titan is a dynamic place where organic chemistry is happening now.”

The absence of detectable acetylene on the Titan surface can very well have a non-biological explanation, said Mark Allen, principal investigator with the NASA Astrobiology Institute Titan team. Allen is based at NASA’s Jet Propulsion Laboratory in Pasadena, Calif. Allen said one possibility is that sunlight or cosmic rays are transforming the acetylene in icy aerosols in the atmosphere into more complex molecules that would fall to the ground with no acetylene signature.

“Scientific conservatism suggests that a biological explanation should be the last choice after all non-biological explanations are addressed,” Allen said. “We have a lot of work to do to rule out possible non-biological explanations. It is more likely that a chemical process, without biology, can explain these results — for example, reactions involving mineral catalysts.”

“These new results are surprising and exciting,” said Linda Spilker, Cassini project scientist at JPL. “Cassini has many more flybys of Titan that might help us sort out just what is happening at the surface.”

The Cassini-Huygens mission is a cooperative project of NASA, the European Space Agency and the Italian Space Agency. JPL, a division of the California Institute of Technology, manages the mission for NASA’s Science Mission Directorate, Washington, D.C. The Cassini orbiter was designed, developed and assembled at JPL.

ScienceDaily – December 10, 2009


Newly discovered Alcor B orbits its larger sibling and was caught in the act with an innovative technique called “common parallactic motion” by members of Project 1640, an international collaborative team that includes astrophysicists at the American Museum of Natural History, the University of Cambridge’s Institute of Astronomy, the California Institute of Technology, and NASA’s Jet Propulsion Laboratory.

1

“We used a brand new technique for determining that an object orbits a nearby star, a technique that’s a nice nod to Galileo,” says Ben R. Oppenheimer, Curator and Professor in the Department of Astrophysics at the Museum. “Galileo showed tremendous foresight. Four hundred years ago, he realized that if Copernicus was right — that the Earth orbits the Sun — they could show it by observing the “parallactic motion” of the nearest stars. Incredibly, Galileo tried to use Alcor to see it but didn’t have the necessary precision.” If Galileo had been able to see change over time in Alcor’s position, he would have had conclusive evidence that Copernicus was right. Parallactic motion is the way nearby stars appear to move in an annual, repeatable pattern relative to much more distant stars, simply because the observer on Earth is circling the Sun and sees these stars from different places over the year. Continue Reading »

“The compact star at the center of this famous supernova remnant has been an enigma since its discovery,” said Wynn Ho of the University of Southampton and lead author of a paper that appears in the November 5 issue of Nature. “Now we finally understand that it can be produced by a hot neutron star with a carbon atmosphere.”

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By analyzing Chandra’s X-ray spectrum — akin to a fingerprint of energy — and applying it to theoretical models, Ho and his colleague Craig Heinke, from the University of Alberta, determined that the neutron star in Cassiopeia A, or Cas A for short, has an ultra-thin coating of carbon. This is the first time the composition of an atmosphere of an isolated neutron star has been confirmed. Continue Reading »

thesis

Finally I have finished the final thesis report of mu undergraduate project. Honestly, I am not satisfied with it myself. Because I could not do any real research I mean something innovative. But now I am trying to do some simulation using Java. This report can be considered as a theoretical database of 21-cm cosmology and observation which will be helpful for me in the coming years, at least I think so. Here I am presenting the report. Link of the pdf file is attached. Abstract and content is mentioned separately. Continue Reading »

A. Russell Taylor
Director, University of Calgary Centre for Radio Astronomy
Professor, Department of Physics and Astronomy

The Outer Disk of the Milky Way Seen in 21-cm Absorption
(download pdf)

Authors: John M. Dickey, Simon Strasser, B.M. Gaensler, Marijke Haverkorn, Dain Kavars, N. M. McClure-Griffiths, Jeroen Stil, A. R. Taylor

(Submitted on 8 Jan 2009) on arXiv

Abstract: Three recent surveys of 21-cm line emission in the Galactic plane, combining single dish and interferometer observations to achieve resolution of 1 arcmin to 2 arcmin, 1 km/s, and good brightness sensitivity, have provided some 650 absorption spectra with corresponding emission spectra for study of the distribution of warm and cool phase H I in the interstellar medium. These emission-absorption spectrum pairs are used to study the temperature of the interstellar neutral hydrogen in the outer disk of the Milky Way, outside the solar circle, to a radius of 25 kpc.

The cool neutral medium is distributed in radius and height above the plane with very similar parameters to the warm neutral medium. In particular, the ratio of the emission to the absorption, which gives the mean spin temperature of the gas, stays nearly constant with radius to 25 kpc radius. This suggests that the mixture of cool and warm phases is a robust quantity, and that the changes in the interstellar environment do not force the H I into a regime where there is only one temperature allowed. The mixture of atomic gas phases in the outer disk is roughly 15% to 20% cool (40 K to 60 K), the rest warm, corresponding to mean spin temperature 250 to 400 K. Continue Reading »

Here is the draft of my paper with the initial names of the reference papers.

Cover page
Abstract
Acknowledgments
Contents

1. Introduction

2. 21cm Cosmology

- First light
- In the beginning
- Wouthuysen-Field effct
- Detecting the earliest galaxies
- HI 21cm probe
- Cosmology at low frequencies Continue Reading »

our presentation
Continue Reading »

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