The Swift Reduction Package Users' Manual

 

by Stefano Covino, 06 Aug 2014, v. 3.12.0

 

 

Background

The Swift Reduction Package (hereafter SRP) is a packet of command line tools to solve problems (e.g. basic reduction and analysis tasks of optical/NIR astronomical data, quick cosmological computations, units conversions, etc.) often met in astronomical research activities.

 

SRP was originally developed in the context of the Swift follow-up activities of the Milan GRB team at the INAF/Brera Astronomical Observatory. The package is designed to be an aid to any researcher to drive further observation of a followed-up GRB counterpart and ÒswiftÓ can therefore be read simply as ÒrapidÓ, ÒagileÓ, etc.

The package is continuously upgraded and improved. Within the limits of our basic project choice (i.e. to provide an as simple as possible tools rather than a very powerful but complex reduction/analysis/computation environment) any help is absolutely welcome.

 

Some technical comment

This package, written in Python (v. 2.7), has been widely tested only on PC-Linux and on Mac OS X workstations. You are anyway absolutely free to use, modify, redistribute this package as you like.

Of course, in any case, we decline any responsibility for the use of this package. Given that the sources are available, and the algorithm public, the results are entirely under your own responsibility.

 

Mailing-List

Due to the nature of the SRP project it quite likely to have frequent update and improvements of the various routines as well as a continuous bug fixing (and new bugs are definitely introduced after any feature additions...). Therefore, if you want to be warned each time a new version is delivered, please send an e-mail to the following address: stefano.covino@brera.inaf.it with subject simply SRP.

 

Installation

If you are just updating SRP the simplest solution is to download the package from the PyPI archive with:

 

sudo easy_install -s /usr/local/bin -U -N SRPAstro

 

or, as a lot of people seem to prefer:

 

sudo pip install --install-scripts=/user/local/bin -U --no-deps SRPAstro

 

provided of course you are connected to the web, and that you want your executable files in Ò/usr/local/binÓ.

 

If you, instead, are installing SRP for the first time or maybe you are upgrading to a new Python release, it is likely you need to install the many different libraries SRP relies on.

 

In principle the command:

 

sudo easy_install -s /usr/local/bin SRPAstro

 

or

 

sudo pip  --install-scripts=/usr/local/bin SRPAstro

 

 

should again do the job. You might also consider to install the package in a virtual python environment if you do not want to interfere with the system python installation.

 

However, some of the required libraries can (will) require more concerned actions for their installation. Indeed, in essentially all cases, browsing the web you can quickly find the solution to any problem. However, an alternative and strongly advised procedure is to install one of the available open-source self-contained scientific python installations as the Anaconda distribution (first choice). Most of the required libraries would then available with no further efforts and SRP is installed smoothly (the Ureka project also deserves consideration).

 

It is always possible to make a smart use of the various package managers available on many platforms (macports, yum, apt-get, etc.). A possible sequence of operations on Mac OSX is the following:

 

i)           sudo port -v selfupdate

ii)         sudo port install python27

iii)        sudo port select --set python python27

iv)        sudo port install py27-distribute

v)         sudo port install py27-numpy

vi)        sudo port install py27-matplotlib

vii)      sudo port install py27-scipy

viii)     sudo port install py27-pyfits

ix)        sudo port install py27-pil

x)         sudo port install py27-astropy

xi)        sudo easy_install -s /usr/local/bin SRPAstro

 

while, on other Linux platforms, using yum or apt-get rather than port, an analogous sequence should work.

For instance, on a linux-PC running Fedora:

i)           sudo yum update

ii)         sudo yum install python

iii)        sudo yum install python-devel

iv)        sudo yum install python-setuptools

v)         sudo yum install numpy

vi)        sudo yum install python-matplotlib

vii)      sudo yum install scipy

viii)     sudo yum install python-imaging

ix)        sudo easy_install -s /usr/local/bin SRPAstro

 

 

In addition to the ÒcoreÓ SRP package there are additions to cover specific tasks or applications:

a.         SRP.FITS, providing general tools to handle FITS files usually, but not necessarily, obtained by optical/NIR telescopes.

b.         SRP.REM, providing a few commands to work with REM telescope data.

c.         SRP.TNG, providing a few commands to work with TNG telescope instruments.

d.         SRP.NOT, providing a few commands to work with NOT telescope instruments.

e.         SRP.SRPPipelines, general tools to develop pipelines for massive data reduction

f.          SRP.SRPPipelines.REM, REM telescope pipeline command.

g.         SRP.SRPPipelines.TNG, TNG telescope pipeline commands.

 

Only the SRP.FITS, SRP.REM and SRP.TNG sub.packages are distributed for general use. Installation simply requires to run: sudo easy_install -s /usr/local/bin -U subpackage_name

 

 

Step by step Òhow toÓ

This are just examples of what you can do with SRP. Please, pay attention that the main emphasis in developing these tools is put in the rapidity and friendly use rather than in getting the very best solution for any possible case. However, experience says that in most cases the results are fully acceptable.

 

 

 

Spectroscopy data analysis

á      Air / Vacuum wavelength conversion

o   This is a simple tool to convert air wavelength to/from vacuum wavelength. SRPAirVacuum -A 6562.801.

á      DLA , IGM, and line profiles

o   We can also derive the absorption factor due to Dumped Lymanα systems with SRPDLA -l 0.4 -n 1e21 -z 1.0 and due to IGM with SRPIGM -l 1.1 -x 0.9 -t 7.8. For a general transition and a more accurate modeling you can derive the absorption factor with SRPLineProfile -n 1e20 -b 1 -l 1300 -t TiII_3073. This function compute a Voigt profile taking into account both Dšppler and intrinsic broadening.

á      Solar abundances

o   Element abundances in the Sun can be retrieved i.e. with SRPSolarAbundance -e Ne. Data are from Asplund et al. (2009, ARA&A, 47, 481).

 

 

Magnitude, flux, frequency, absorption and reddening

á      Magnitude to/from flux conversion

o   It is quite common to have to convert magnitudes to physical units. To do that it is enough to run SRPMagFlux -b R -m 18.0 0.03. You will get the effective frequency, flux and 1-б error for magnitude, 1-б error and band reported. The output unit is Jansky or erg s-1cm-2A-1. It is of course possible to derive magnitudes from fluxes with the same command: SRPMagFlux -b R -j 1e-5 2e-7.

á      Reddening determination and absorption factors

o   Assuming to know the color excess EB-V it is possible to estimate the amount of reddening at a given wavelength with SRPDustAbs -g MW -w 0.7. The wavelength unit is micron and the output is expressed in magnitudes. Extinction curves for the MW, the LMC and the SMC (Pei, 1992, ApJ, 395, 130) and a generic starburst galaxy (Calzetti et al., 2000, ApJ, 533, 682). It is also possible to know the absorption factor due to neutral gas in the X-rays (Morrison & McCammon, 1983, ApJ, 270, 119) with SRPNhAbs -e 1 -n 1e21.

á      Flux density and energy-frequency conversion 

o   SRPPLFluxDensity allows you to compute the flux density at any given energy assuming to have a power-law spectrum and the integrated flux, i.e. SRPPLFluxDensity -f 2.4e13 -s 1.7. The integrated flux is supposed to be expresses in erg/s*cm2, the energy in keV, and the flux density is expressed in Jy. With SRPEnergyFreqFlux -e 1 -j 1e-6 you can convert energy to frequency or wavelength and vice-versa and flux densities from Jy to erg/s cm2 and viceversa. Energy is expressed in eV, frequency in Hz and wavelength in micron.

á      Atmospheric absorption

o   Atmospheric extinction coefficients for a few observing sites can be derived with SRPAtmExtinction -w 0.55 -s LaSilla.

 

 

Tables and catalogues

á      Catalogue query

o   Given a position in the sky and a radius with the command SRPQuery -a 01 23 45 -d 23 32 00 -c BS -r 120 you find objects in a catalogue among those available. The radius unit is arcmin. With SRPNameResolver -n "Sirius" you can obtain, from SIMBAD, the coordinates of a known astrophysical source.

á      Table extraction

o   This command helps you to extract only selected columns from a table for further analyses. It is also possible to skip header rows as in SRPTabExtract -t table.txt -c '2 3 4 5' -o _output.txt -j 2.

á      Object extraction

o   You can select a single, or more, objects in a table basing on their coordinates with SRPGetTabEntry -i table.dat -c 2 3 -C 240.45 312.23 -t 1. It is possible to work with angular or Cartesian coordinates. You can also filter selected objects from a table with the same command.

á      Table match

o   This command allows you to find the common objects between two tables (i.e. the SRPPhotometry output). You must provide the file names of the table, shifts in both axes, and the maximum tolerance (first match and fine tuning) for object matching: SRPMatch -r refile.dat -m matchfile.dat -t 5 2.5 -o _outfile.dat. Same table scale and orientation is assumed. If, on the contrary, you want to find common objects with the same angular coordinates in two tables, you can try SRPMatchCoord -r refile.dat -m matchfile.dat -t 1 -o _outfile.dat.

 

 

Observation management

á      Target visibility

o   Providing geographic position of the observer, target coordinate and a time reference you can know the azimuth and altitude of the target and the Moon and Sun separation. It is thought as a simple aid for observation planning: SRPVisibility -o 10:11:12 -20:21:22. In case you do not provide any input apart from target coordinate the ESO-La Silla site and the present date are assumed.

á      Date conversion

o   It could be useful to quickly convert from/to dates in "regular" format (yyyy/mm/dd hh:mm:ss.dd) to Julian Date of Modified Julian Date. This can be done with SRPCalendar -v -d 2009/4/8 10:51:00.

á      Finding-chart creation

o   In order to quickly generate nice-looking (hopefully) finding charts you can use SRPFindingChart -f fitsfilename.

 

 

Statistics

á      Gaussian distribution

o   Providing mean and standard deviation you can generate an arbitrary number of values following a given Gaussian distribution: SRPGaussDistrib -m 3 -s 0.1 -n 10.

á      Gaussian probability

o   You can compute Gaussian 1-tail or 2-tail probability distribution given a value in units of sigma: SRPGaussProb -s 3 -2.

á      Chi square surface

o   You can easily derive the increment for the chi square function given some degrees of freedom at a given probability with SRPChiSqIncrement -p 90 -d 5. Else, you can compute the probability to have a chisquare higher than the obtained value by chance with SRPChiSqIncrement -c 10 -d 7.

á      Sigma-clipped average

o   It is often useful to can evaluate a sigma-clipped average for input data from a file. You can do that with SRPAverSigmaClipping -i inputtab.txt -d 4 -k 5.

á      Histogram creation

o   This command takes a column from a file as input and computes an histogram. The output is a table with bin center, bin size, and number of objects in the bin. Histogram parameters as minimum (i.e. 1), maximum (i.e. 10) and bin size (i.e. 0.2) can be chosen as in SRPHistogram -c 2 -t table.txt -o _output.txt -b 1 10 0.2.

á      F-Test computation

o   You can check the improvement of a fit quality adding parameters with the F-test: SRPFTest -n  14.45 12 -o 16.34 14.

 

 

Afterglow data and cosmology

á      Afterglow flux and frequencies

o   SRPAftTypSynchrFluxConst(Wind) allows you to compute the cooling (typical)(self absorption) synchrotron frequency (Hz) in case of constant ISM (wind). You compute the flux (Jy) at the typical synchrotron frequency and the flux for a typical afterglow spectrum at any frequency. From Zhang & Meszaros, IJMPA A19, 2385 (2004) and Hurley, Sari and Djorgovski, in "Compact Stellar X-ray Sources" (Cambridge University Press).

á      Cosmological parameter computation 

o   This command allows one to compute the Hubble, angular diameter, comoving and luminosity distances from a minimum to a maximum redshift in any expanding universe. The distance modulus is also derived. Universe parameters, i.e. matter density, cosmological constant, etc. can be provided. SRPCosmology -v -z 1.5 you get the various distances for the default "concordance" cosmological model. 

 

 

 

 

Miscellanea

á      SRP running version

o   You can know the present SRP version with SRPVersion.

á      Polarization data

o   Polarization data can be converted to/from Stokes parameters with SRPStokesPol -s 0.1 0.01 -0.1 0.01 0.0 0.0.

 

 

 

 

List of commands

1.       SRPAftSynchrSpectrumConst

⁃           Its purpose is to compute the afterglow synchrotron spectrum in case of constant density ISM.

⁃           SRPAftSynchrSpectrumConst [-b arg1] [-d arg2] [-e arg3] [-f arg4] [-g arg5] [-h] [-n arg6] [-p arg7] [-t arg8] [-v] [-z arg9]

                                    -b Epsilon B (0,1).

                                    -e EPSE Epsilon E (0,1).

                                    -d DIST Luminosity distance (cm).

                                    -g Isotropic energy (erg).

                                    -n Particle density (cm^-3).

                                    -f Frequency (Hz).

                                    -p Electron distribution index.

                                    -t Time from burst (days).

                                    -z Source redshift.

            Afterglow model for constant density environment.

2.       SRPAftSynchrSpectrumWind

⁃           Its purpose is to compute the afterglow synchrotron spectrum in case of wind.

⁃           SRPAftSynchrSpectrumWind [-a arg1] [-b arg2] [-d arg3] [-e arg4] [-f arg5] [-h] [-g arg6] [-p arg7] [-t arg8] [-v] [-z arg9]

                                    -a Astar.

                                    -b Epsilon B (0,1).

                                    -e Epsilon E (0,1).

                                    -d Luminosity distance (cm).

                                    -g Isotropic energy (erg).

                                    -f Frequency (Hz).

                                    -p Electron distribution index.

                                    -t Time from burst (days).

                                    -z Source redshift.

                        Afterglow model for wind shaped environemnt.

3.       SRPAirVacuum

⁃           Its purpose is to convert air wavelength to vacuum wavelength and viceversa.

⁃           SRPAirVacuum -A arg1 / -V arg1  [-h] [-v]

                                    -A Air wavelength (Angstrom)

                                    -V Vacuum wavelength (Angstrom)

4.       SRPAtmExtinction

⁃           Its purpose is to derive atmospheric extinction coefficients.

      SRPAtmExtinction [-h] -l wave [-s site] [-v] [--version]

                                    -l Wavelength for extinction coefficient (micron)

                                    -s Site for the extinction curve

5.       SRPAverSigmaClipping

⁃           Its purpose it to compute a sigma-clipped average for input data.

⁃           SRPAverSigmaClipping -i arg1 -d arg2 [-e arg3] [-h] [-k arg4] [-v]

                                    -i File with input data

                                    -d Column positions for data.

                                    -e Column positions for data errors.

                                    -k Sigma-clipping value

6.       SRPCalendar

⁃           Its purpose is to convert dates from/tom various formats.

⁃           SRPCalendar [-h] [-v] -d arg1 / -j arg2 / -m arg3 / -n arg4

                                    -j Julian Date

                                    -m Modified Julian Date (MJD)

                                    -d Regular Date (UT) (yyyy/mm/dd hh:mm:ss)

                                    -n Present date

9.       SRPChiSqIncrement

⁃           Its purpose is to compute increment for chi squares.

⁃           SRPChiSqIncrement [-a arg1] [ -c arg2] -d arg3 [-p arg4] [-v]

                            -a is the accuracy of the chisquare increment computation

                            -c is the resulting chisquare for a fit

                            -d is the number of degrees of freedom

                            -p is the probability.

                        The routine allows one to compute the increment for the chi square having a probability 100-prob% to occur randomly. Typical usage is for deriving uncertainties for multiparametric fits. Typical usage is for deriving uncertainties for multiparametric fits. Alternatively, one can compute the probability to have randomly a higher chisquare than the one obtained in a fit.

10.    SRPCosmology

⁃           Its purpose is to derive cosmological data.

⁃           SRPCosmology [-h] [-hubbleconstant arg1] [--omegalambda arg2] [--omegamatter arg3] -z arg4 [-v]

                                    --hubbleconstant Hubble Constant

                                    --omegamatter Omega Matter

                                    --omegalambda Omega Lambda

                                    -z Redshift

11.    SRPDLA

⁃           Its purpose is to derive the absorption factor due to DLA systems.

⁃           SRPDLA -l arg1 [-h] [-v] -n arg2 -z arg3

                                    -l Observed wavelength (micron)

                                    -n Nh (>= 0, cm^-2)

                                    -z DLA system redshift (>= 0)

                                    DLA modeling performed according to Totani et al. (2006, PASP

                        58, 485)

12.    SRPDustAbs

⁃           Its purpose is to compute the amount of reddening at a given wavelength.

⁃           SRPDustAbs [-c arg1] -g arg2 [-h] [-r arg3] [-v] -w arg4

                                    -c E(B-V) color excess (mag)

                                    -g Kind of extinction curve

                        -r Extinction ratio

                                    -w Wavelength (micron)

                                    Extinction curves for the MW, LMC and SMC galaxies following Pei

                        (1992, ApJ, 395, 130) and starburst galaxies following Calzetti et

                        al. (2000, ApJ, 533, 682)

13.    SRPEnergyFreqFlux

⁃           Its purpose is to convert energy to frequency or wavelength and vice-versa.

⁃           SRPEnergyFreqFlux [-a arg1 / -j arg1] -e arg2 / -f arg2 / -w arg2 [-h] [-v]

                                    -a Flux density in Erg / cm s A

                                    -e Energy (eV)

                                    -f Frequency (Hz)

                                    -j Flux density in Jy

                                    -w Wavelength (micron)

14.    SRPFit

⁃           Its purpose is to carry out multi-parametric fits and Montecarlo error search.

⁃           SRPFit -d arg1 [-e arg2] -f arg3 -g 'arg4' [-h] [-i 'arg5'] -m arg6 [-n arg7] [-o arg8] [-v]

                                    -d Table containing data

                                    -e ERR Error search and confidence level (i.e 90.0)

                                    -g Guess values for parameters to fit [i.e. '2.2 15.2']

                                    -i Min,max values for error search [i.e. '0 4 10 20']

                                    -m File with function to fit (i.e. myfunc.py)

                                    -n Number of trial for Montecarlo search (default 1000)

                                    -o Output error file

                                    -f Output function file

                        Perform a multi-parametric fit allowing error search by means of

                        a Montecarlo run.

15.   SRPFTest

⁃           Its purpose is to compute F-statistics.

                SRPFTest [-h] -n chi2 dof -o chi2 dof [-v] [--version]

                        -n Chi2 and degrees of freedom

                        -o Chi2 and degrees of freedom

16.   SRPGaussDistrib

⁃           Its purpose is to generate number following the Gaussian distribution.

⁃           SRPGaussDistrib -e arg1 [-h] -n arg2 -s arg3 / -a arg 3 arg4

                                    -e Distribution expectation value

                                    -n Number of repetitions

                                    -s Distribution standard deviation

                                    -a Distribution asymmetric standard deviation (left, right)

17.    SRPGaussProb

⁃           Its purpose is to compute probability for Gaussian distributions.

⁃           SRPGaussProb -s -1/-2 [-v]

                                    -s Value in sigma units)

                                    -1 1-tail distribution

                                    -2 2-tail distribution

18.    SRPGetTabEntry

⁃           Its purpose is to find selected objects in a table.

            SRPGetTabEntry [-a] -c arg1 arg2 -C arg3 arg4 [-h] -i arg5 [-j arg6] [-o                              arg7] -t arg8             [-v]

                                    -a Angular distance if set, else Cartesian distance

                                    -c Column coordinate positions for input table (col1 col2)

                                    -C Object coordinates (coord1 coord2)

                                    -i Input table

                                    -j Number of lines tio be skipped

                        -o Output table without identified entries

                                    -t Maximum tolerance for object association (same units as for the                                                coordinates)

19.   SRPHistogram

⁃           Its purpose is to compute an histogram of input data.

⁃           SRPHistogram -c arg1 [-h] [-j arg2] -o arg3 -t arg4 [-v]

                                    -b Bin data [i.e. min max bin_size]

                                    -c Column for histogram

                                    -j Number of header lines to skip

                                    -o Output file

                                    -t Table containing data to extract

20.    SRPIGM

⁃           Its purpose is to derive the absorption factor due to IGM systems.

⁃           Usage: SRPIGM -b arg1 [-l arg2] [-h] -t arg3 [-v] -x arg4

                            -b Lower IGM redshift (>= 0) [default 6.0]

                            -l Observed wavelength (micron)

                            -t Upper IGM redshift (>= 0)

                            -x Neutral hydrogen fraction (0 <= xHI <= 1)

21.    SRPLineProfile

⁃           Its purpose is to compute line profile for a specific transition.

⁃           SRPLineProfile -b [arg1] -l arg2 [-h] [-v] -n arg3 -t arg4 -z arg5

                                    -b Dumping parameter (>= 0), km s^-1)

                                    -l Observed wavelength (Angstrom)

                                    -n Column density (>= 0, cm^-2)

                                    -t Transition

                                    -z Redshift (>= 0)

            Line profile computed by Voigt function computation.

22.    SRPMagFlux

⁃           Its purpose is to convert magnitudes to/from fluxes.

⁃           SRPMagFlux -b band -f arg1 arg2 / -m arg1 arg2 / -j arg1 arg2 [-h] [-v]

                                    -b magnitude/flux band

                                    -f flux and error (Erg/s/cm2/A)

                                    -j flux and error (Jy)

                        -l more information about adopted zero-points.

                                    -m magnitude and error

23.   SRPMatch

⁃           Its purpose is to find common objects between two tables.

⁃           SRPMatch [-c arg1 arg2 arg3 arg4] [-h] [-j arg5] -m arg6 [-n arg7] -o arg8 -r arg9 [-s arg10 arg11] -t arg12 [-v]

                            -c are the x,y column numbers for the reference table and the matching

                            table

                            -j is the number of entries at the beginning of both tables to be skipped.

                            -m the matching table

                            -n the character to identify comment lines to skip

                            -o is the output file

                            -r reference table

                            -s the shift for coordinate match

                            -t is the maximum tolerance for a positive match.

24.    SRPMatchCoord

⁃           Its purpose is to find common objects, with the same angular coordinates, in two tables.

⁃           SRPMatchCoord [-c arg1 arg2 arg3 arg4] [-h] [-j arg5] -m arg6 [-n arg7] -o arg8 -r arg9 -t arg10 [-v]

                            -c are the x,y column numbers for the reference table and the matching

                            table

                            -j is the number of entries at the beginning of both tables to be skipped.

                            -m the matching table

                            -n the character to identify comment lines to skip

                            -o is the output file

                            -r reference table

                            -s the shift for coordinate match

                            -t is the maximum tolerance for a positive match.

25.   SRPNameResolver

⁃           Its purpose is to find the coordinates of a known astrophysical source from SIMBAD.

⁃           SRPNameResolver [-h] -n n [-v] [--version]

                                    -n Object name

26.   SRPNhAbs

⁃           Its purpose is to compute the amount of absorption at a given energy.

⁃           SRPNhAbs -e arg1 [-h] -n arg2 [-v]

                                    -e Energy (KeV, 0.03-10)

                                    -n Nh (>= 0, cm^-2)

                                    Based on photoelectric absorption cross sections in Morrison &

                        McCammon (1983, ApJ, 270, 119)

27.    SRPPLFluxDensity

⁃           Its purpose is to derive flux density known a power-law spectrum and integrated flux.

⁃           SRPPLFluxDensity [-d arg1] [-e arg2 arg3] -f arg4 [-h] [-s arg5] [-v]

                                    -d Output flux density (keV)

                                    -e Energy limits min max (keV)

                                    -f Integrated flux (erg/cm2 s)

                                    -s Spectral slope

28.    SRPQuery

⁃           Its purpose is to extract a region from a catalogue.

            SRPQuery -c arg1 arg2 / -f arg3 -C arg4 [-h] [-m arg5] [-o arg6] -r arg7 [-S]                      [-v]

                                    -c is to input J200 RA and DEC coordinates

                                    -C is the acronym of the catalogue to browse

                                    -f FITS file to be used for coordinate center

                        -m Maximum number of entries in output

                                    -o optional output file

                                    -r is the search radius in arcmin. The search is carried out in a

                                    cone

                                    -S to have an ouput compatible to be shown with the ESO-skycat

                                    package

                                    For several catalogues you need a working internet connection.

                        Other catalogues are local.

29.   SRPSelect

⁃           Its purpose is to allow to create list of frames satisfying some criterion.

⁃           SRPSelect [-i arg1] -k arg2 -o arg3  [-v]

                            -i passes to the scripts the file with the list

                                    of FITS file and keyword values as created, for instance, by

                                    SRPClassify.

                            -k is the keyword to be searched for.

                            -o is the output file with results of the selection.

30.   SRPSessionName

⁃           Its purpose is to define a new session name.

⁃           SRPSessionName [-h] -n arg [-v]

                            -n allows one to provide a base prefix for many of the files

                            created by other SRP commands.

31.   SRPSolarAbundance

⁃           Its purpose is to derive the Solar abundance of various chemical elements.

⁃           SRPSolarAbundance [-e arg1] [-h] [-v]

                            -e is the element to look for, e.g. Fe

                        Data are from Asplund et al. (2009, ARA&A, 47, 481)

32.   SRPStokesPol

⁃           Its purpose is to convert from polarization to Stokes parameter and viceversa.

⁃           SRPStokesPol [-h] [-b] [-m] [-n n] [-p P eP Theta eTheta Chi eChi]

⁃                               [-s Q eQ U eU V eV] [-v] [—version]

⁃           -b Correct for polarization bias

⁃           -m Compute errors by means of a MonteCarlo run 

⁃           -n Number of trials for error computation

⁃           -p Normalized polarization parameters

⁃           -s Normalized Stokes parameters

33.   SRPTabExtract

⁃           Its purpose is to extract selected columns from a table.

⁃           SRPTabExtract -c 'arg1' [-h] [-j arg2] -o arg3 -t arg4 [-v]

                                    -c Columns for columns [i.e. '2 3 1 2']

                                    -j Number of header lines to jump

                                    -o Output file

                                    -t TABLE Table containing data to extract

34.   SRPVersion

-          its purpose is to show the running SRP version.

-          SRPVersion [-h] [-v]

35.   SRPVisibility

⁃           Its purpose is to compute the visibility of a sky object.

⁃           SRPVisibility -a arg1 arg2 / -o arg3 arg4 [-d arg5 arg6 arg7] [-h] [-l arg8 arg9 / -s arg10] [-t arg11] [-v]

                        -a Altazimuthal coordinates (dd.dddd dd.dddd)

                                    -d Altitude (m), pressure (mBar) and temperature (C) of the

                                    observing site

                        -l Coordinate location of observing site (dd:mm:ss or dd.dddd)

                                    -s Observing site

                                    -o Object coordinates (hh:mm:ss dd:mm:ss or hh.ddd dd.ddd)

                                    -t Computation time ('yyy/mm/dd hh:mm:ss')

 

 

Bugs, comments, etc.

Of course, as already stated, any contribution from anyone is welcome. In case you find bugs, have improvements to suggest, would like to contribute to the code, etc. Please send an e-mail to Stefano Covino, stefano.covino@brera.inaf.it. We can not promise to take into account all your comments, but we will anyway try to improve the package to meet your needs.

 

Evolution

¥          From 1.0 to 1.1:

⁃           Command to convert magnitudes to fluxes and to determine reddening were added. The possibility to create SExtractor files for different instruments was also implemented.

¥          From 1.1 to 1.2:

⁃           The command to perform a local catalogue query was implemented. More training steps proposed.

¥          From 1.2 to 1.3:

⁃           Aperture photometry is now reported by SRPPhotometry, there is also the possibility to extract subimages from a frame saving the astrometric information.

¥          From 1.3 to 1.4:

⁃           Bug correction for aperture photometry. A table matching tool was added.

¥          From 1.4 to 1.5:

⁃           The table match now works by a FFT of the input data. The possibility to computer target sky position is implemented. Some minor correction to help data are provided. It is now possible to provide new zero-point to SRPPhotometry. The command SRPMatchCoord finds common entries for object with the same angular coordinates in two tables.

¥          From 1.5 to 1.6

⁃           Better management of coordinate matching for SRPMatchCoord. Bias and flat can now be constants in SRPScienceFrameImaging. Better coordinate management and output in SRPVisibility. SRPGaussDistrib added.

¥          From 1.6 to 1.7

⁃           Correction to SRPMatch to work with updated numarray library. New parameter set for TNG Dolores imaging frame classification. SRPDao2Sky added. Improved in final match algorithm in SRPMatch. Now it is found the closest companion and not the first within the given tolerance. For SRPMatch and SRPMatchCoord the sequence of reference and matched tables are followed in the output table too.

¥          From 1.7 to 1.8.0

⁃           Improvement for SRPMatch allowing the possibility to force the amount of the displacement between the two tables. Minor corrections to SRPDao2Sky. ASIAGO AFOSC and VLT ISAAC imaging keywords. Move from optik to optparse library. SRPTabExtract and SRPHistogram added.

¥          From 1.8.0 to 1.9.0

⁃            SRPFlatSpectroscopy and SRPFit added. Minor corrections to SRPMagFlux and SRPTabExtract. New keyword for the TNGDOLORESIMA set. SRPVisibility with Sun altitude.

¥          From 1.9.0 to 1.9.5

⁃           Removal of automatic error estimate from SRPFit because it is too much time consuming and not fully reliable. Error search is something intrinsically difficult to automatise in general. Larger number of function calls and evaluations are allowed. Better pair association algorithm for SRPMatchCoord. Calzetti's extinction law added to SRPDustAbs. REM/ROSS photometric parameter set. NTT EMMI, TNG NICS and NOT AFOSC imaging parameter sets added. Additions to VLT FORS spectroscopy keywords. UVOT filters added to SRPMagFlux. A better porting to the cygwin UNIX flavour has been obtained. A bug occurring when not existent directories are reported in the PATH has been corrected. New keywords for VLT ISAAC. Different filename output extension for SRPPhotometry output filenames if ÒskycatÓ format is selected. A correction to the algorithm of SRPTabExtract has been applied. Various minor bugs have been corrected.

¥          From 1.9.5 to 2.0.0

⁃           Constant density ISM and wind afterglow parameters as in Hurley, Sari, Djorgovski (in "Compact X-ray Stellar Sources", 2003). X-ray absorption as in Morrison & McCammon (1983). SRPNhAbs command. SRPAftTypSynchrConst, SRPAftTypSynchrFreqWind, SRPAftCoolSynchrConst, SRPAftCoolSynchrFreqWind. Data analysis parameter set for the 2.2m Calar Alto telescope with CAFOS and upgrade for the NOT with AFOSC. Coordinates of the NOT and Calar Alto observatories. SRPMatchCoord now reads "hh:mm:ss" and "dd:mm:ss" coordinate format too.

¥          From 2.0.0 to 2.1.0

⁃           Minor bug corrections. Danish with DFOSC, VLT with NACO and TNG with NICS imaging parameters added. User's Manual revised. SRPCosmology command added.

¥          From 2.1.0 to 2.2.0

⁃           Minor bug corrections. UVOT photometry calibration upgraded. Better data reading in case of high background for SRPDao2Sky. NTT SofI imaging parameters added. SRPCosmology was rewritten. Some improvements to dust absorption by SRPDustAbs computation were developed. Zero-points for magnitude to flux conversion by SRPMagFlux were upgraded. Conversion from coordinates to pixel is now possible with SRPWCS2Pixel. Conversion of the output of the GAIA-Photom package to other formats can be carried out with SRPGAIA2Sky.

¥          From 2.2.0 to 2.3.0

⁃           LBT site coordinates. Better management of jump option in SRPMatch and SRPMatchCoord. GEMINI-N coordinates added. Corrections to site coordinates applied. SRPEnergyFreq and SRPPLFluxDensity added.

¥       From 2.3.0 to 3.0.0

⁃        New filters. VLTFORSIPOL added. SExtractor photometric parameter file for REMIR added. SRPImageMapping, SRPRotoTrasla,  SRPMyPhotometry and SRPREMPhotometry added.

¥       From 3.0.0 to 3.1.0

⁃        Improved flexibility of SRPREMphotometry and SRPMyPhotometry commands. Increased execution velocity for SRPImageMapping. SRPRTAlingImaging and SRPAdvAverage commands added.

¥       From 3.1.0 to 3.2.0

⁃        Improved rapidity for SRPAdvAverage. Minor improvements to SRPImageMapping and SRPRotoTransla. Better management of objects not in the field of view for SRPREMPhotometry. Installation procedure now much better explained. Better parameter management for SRPEnergyFreq. SRPCalendar added and a few bugs fixed. Better centering algorithm and magnitude computation. SRPMagFlux is improved. SRPDLA added. SRPFit management improved.

¥       From 3.2.0 to 3.3.0

⁃        SRPIGM added. Minor improvements to SRPVisibility, SRPEnergyFreq, SRPGaussDistrib, SRPQuery, SRPMyPhotometry and SRPREMPhotometry. More options for SRPImageMapping. Better algorithm for SRPRTAlignImaging.

¥       From 3.3.0 to 3.4.0

⁃           Unicode strings in SRPWCS2Pixel. Simplified algorithm for SRPMatch. Bug correction in SRPMagFlux. Upgrade for python 2.6 and later versions. Various minor upgrade and bug corrections. SRPGaussProb added. X-shooter parameters added. Minor correction to SRPVisibility.

¥          From 3.4.0 to 3.5.0

⁃           Better sky and zero-point computation with SRPMyPhotometry. Bug correction in SRPAlignImaging. Possibility to force integer shifts for pure translation and to provide maximum tolerance in SRPImageMapping. SRPAirVacuum, SRPGaussProb, SRPSourceFinder and SRPFindingChart added. Improvements to SRPGaussDistrib.

¥          From 3.5.0 to 3.5.1:

⁃           Minor bug correction in SRPAlignImaging. 2MASS catalogue and more functionalities added to SRPQuery. TNG Dolores spectroscopy parameters added. Exposure maps for SRPAdvAverage.

¥          From 3.5.1 to 3.6.0:

⁃           Sorted output and various improvements to SRPSourceFinder. A few minor bugs corrected. Deepness of search selectable in SRPImageMapping. SRPAstrometry was added. TNG-LRS SExtractor parameter files added. SRPPhotParSet improved. SRPQuery improved and catalogues of Stetson optical standard stars, Astro-wise  standard stars and USNO-A2 added. SRPZeroPoint added. nose python library added to the installation list. SRPAverSigmaClipping added. asciitable and ATpy now required for installation. SRPTNGPipelineManager added. SRPFitsStats added. SRPBias, SRPFlatImaging, SRPScienceFramesImaging and SRPCut improved.

¥          From 3.6.0 to 3.7.0:

⁃           Better management of cut area for frame binning in SRPTNGPipelineManager. New keywords for SRPTNGManager and data saved as integer. SRPGetTabEntry added. Better magnitude difference averaging algorithm for SRPZeroPoint. SRPREMPipelineManager added.

¥          From 3.7.0 to 3.8.0:

⁃           Position on the detector of the selected object in SRPREMPipelineManager. Maximum number of log files in SRP pipeline managers. Collection of NIR catalogues (Arnica, Conica, ESO, Isaac, LCO, MSSSO, SAAO, UKIRT) added to SRPQuery. Present time in SRPCalendar. Bug correction in SRPFindingChart. A few bugs corrected in SRPMyPhotometry. SRPPix2WCS added. Minor bug corrections for SRPScienceFramesImaging and SRPAstrometry. Improvement to SRPCosmology. SRPAftSynchrSpectrumConst and SRPAftSynchrSpectrumWind rationalized.

¥          From 3.8.0 to 3.9.0:

⁃           New filters in SRPMagFlux. Better output for GRBs in SRPREMPipelineManager. Better Voigt profile in SRPLineProfile. Better coding for SRPDustAbs. Better check for user identity in SRP pipelines. AGN optical standard stars catalogue added for SRPQuery. Improved AGN photometry for SRPREMPipelineManager. Better effective wavelengths for several filters in SRPMagFlux. Better frame downloading for SRPREMPipelineManager. Better management of file download in SRPREMPipelineManager. SRPWCSPixel simplified. SRPAverage improved. SRPFitsHeader added.

¥          From 3.9.0 to 3.10.0:

⁃           Bug correction and new parameter in SRPMatch, SRPMatchCoord and SRPKeyword. New filters in SRPMagFlux. SRPChiSqIncrement added. New filter data added to SRPMagFlux. SRPSolarAbundance added. SRPImageFilter added. Better parameter management in SRPBias and SRPFlatImaging. Bug correction for frame weighted sigma-clipped average. Bug corrected in SRPRotoTransla. Bug in absolute path file opening corrected. Improvement of SRPTNGPipelineManager. SRPVersion added. SRPFitsExtension added. Possibility to use a Fits file as a reference in SRPQuery. Logic and computation corrections to SRPIGM.

¥          From 3.10.0 to 3.10.14:

⁃           Improvements for SRPFitsHeader. New bands added to SRPMagFlux. SRPFitsSpectrum2ASCII added. Bug correction in SRPAdvAverage. SRPEnergyFreq converted to SRPEnergyFreqFlux. Ellipticity parameter added to SRPPhotometry output. New and better organized zero-points for SRPMagFlux. More flexible coordinate format for SRPAstrometry. Bugs in SRPAlingnImaging corrected. SRPMyPhotometry and SRPREMPhotometry moved to SRP.REM sub-package. GAIN in sextractor files for REM-REMIR and REM-ROSS. Better management of data file path. More information (sidereal time, hour and parallactic angles) added to SRPVisibility. Possibility to read extensions in SRPFitsHeaders. SRPStokesPol added. Parameters for TNG Dolores spectroscopy and polarimetry added. Minor bugs and more options in SRPDAO2Sky and SRPGAIA2Sky. SRPFitsExtensions is now able to manage FITS cubes. Minor bug in and new options in SRPAstrometry. Standard deviation in SRPAverSigmaClipping output. New optical data for the AGNOPT catalogue. SRPAtmExtinction added. Improvements to SRPVisibility. Better algorithm for frame sigma-clipping average. Improved keywords for SRPClassify. New option in SRPGetTabEntry. Better output for SRPQuery. SRPSpectralExtraction added. Default parameters for SRPCosmology updated. SRPStokesPol improved. SDSS catalogue added to SRPQuery. Bug correction in SRPFlatSpectroscopy. SRPFTest added. APASS catalogue added to SRPQuery. SRPGetTabEntries reports not selected objects too. Minor corrections and improvements for SRPAstrometry in shift computation. Better parameter management for SRPPhotometry. More control in SRPQuery output. Bug correction and more parameters in SRPAstrometry. More flexibility for dust extinction SRPDustAbs. SRPFitsComposer has been added. ez_setup.py added to the distribution.

¥          From 3.10.14 to 3.12.00:

⁃           Creation of the SRP.FITS sub-package for a better separation of duties. Many bugs corrected. SRNNameResolver added.

 

 

Credits, thanks, etc.

A lot of people gave some contribution to the SRP and among them I want to quote Nino Cucchiara, Paolo D'Avanzo, Luca Di Fabrizio, Dino Fugazza, Auvet Harutyunyan, Nauzet Hernandez, Domenico Impiombato, Gianluca Israel, Daniele Malesani, Emilio Molinari and Ruben Salvaterra. I also thank ESO and TNG since part of this code was developed during visitorships in Garching and La Palma.