Tools to align images, improve astrometry, perform aperture photometry and retrieve photometry catalogues.
Latest revision: 7 November 2019
Python: 3.6
Additional python libraries:
If your python installation is based on astroconda, you need to install these additional libraries:
astroquery, photutils, pysynphot, sympy, sewpy, and sip_tpv (included)
Futhermore, you need to install install these software packages
astrometry.net, Scamp, SExtractor and wcs-tools
Store the directory in your favourite folder and add the folder to your PATH and PYTHON_PATH environment.
export PATH=$PATH:/new/path
export PYTHON_PATH=$PYTHON_PATH:/new/path
Give field_calibration.py, improve_astro.py, photometry.py, photometry_hst.py permission to be executed.
chmod u+x PROGRAMME.py
-To install Sewpy follow the instructions at https://github.com/megalut/sewpy.
-The first line in files field_calibration.py, improve_astro.py, photometry.py, photometry_hst.py is #!/usr/bin/env pythonw. If you use linux, change pythonw to python. With pythonw you can close plot windows with the keystroke ⌘+w.
Requires: Scamp, SExtractor
usage: align_images.py [-h] --ref-image REF_IMAGE --new-image NEW_IMAGE
[--keep-temp]
Align the WCS systems of two images
optional arguments:
-h, --help show this help message and exit
--ref-image REF_IMAGE Reference image
--new-image NEW_IMAGE New image
--keep-temp Keep temporary files
python align_images.fits --ref-image SN2015bn_SDSS_r.fits --new-image SN2015bn_SDSS_i.fits
- Identify objects in the reference image
- Identify objects in the new image
- Align the astrometry. Information about the quality of the alignment is saved in
results_scamp/scamp.log. The scamp log file is stored inresults_scamp/{NEW_IMAGE}_scamp.xml. New fits will be named{NEW_IMAGE}_astro.fits - Remove temporary files
The programm can fail if the images are very different from each other, e.g., a shallow transient image and an HST image. If your browser does not display the scamp diagnostic file, reach these notes.
Requires: sympy, SExtractor, sip_tpv
usage: improve_astro.py [-h] --fits FITS --ra RA --dec DEC [--radius RADIUS]
[--downsample DOWNSAMPLE] [--tweak-order TWEAK_ORDER]
Improving WCS calibration with astrometry.net and converting SIP terms to
Sextractor format.
optional arguments:
-h, --help show this help message and exit
--fits FITS File name (Required)
--ra RA RA(J2000) of the Object (HMS and DD system allowed).
Note: if declination is negative, write "
-12:20:20.2"). (Required)
--dec DEC Dec (J2000) of the Object (HMS and DD system allowed).
(Required)
--radius RADIUS only search in indexes within 'radius' of the field
center (unit: deg; default: 0.125 deg)
--downsample DOWNSAMPLE
downsample the image by factor <int> before running
source extraction (default: 2)
--tweak-order TWEAK_ORDER
Polynomial order of SIP WCS corrections (default: 2)
python improve_astro.py --fits SN2015bn_SDSS_r.fits --ra 173.423125 --dec 0.725972
It uses astrometry.net and sextractor to establish the field calibration of the image. Afterwards it uses sip2pv.py to transform the distortion keywords into the format sextractor understands. The new image has the suffix '_wcs'.
If you built astrometry.net with python 2.7, running astrometry.net in python 3 will possibly fail. There are two work arounds. 1) improve_astrometry.py is compatible with python 2.7. 2) To run improve_astrometry.py in python 3, activate your python-3 environment and re-install astrometry.net.
astrometry.net requires an image with a size of at least 5x5 arcmin.
Requires: astroquery, sewpy
(Also works in python 2.)
usage: field_calibration.py [-h] --ra RA --dec DEC [--radius RADIUS]
[--outdir OUTDIR] [--type TYPE]
Retrieve photometric catalogues. 2MASS, PS1, SDSS and SkyMapper are the input
catalogues. Bessel catalogues are generated through colour equations. PS1 and
SDSS cats are in the AB system, whereas Bessel and 2MASS cats are in the Vega
system.
optional arguments:
-h, --help show this help message and exit
--ra RA RA(J2000) of the Object (HMS and DD system allowed). Note:
if declination is negative, write " -12:20:20.2"). (Required)
keyword.
--dec DEC Dec (J2000) of the Object (HMS and DD system allowed).
(Required)
--radius RADIUS only search in indexes within 'radius' of the field center
(unit: arcmin; default: 10)
--outdir OUTDIR Output directory (default: results/)
--type TYPE Generate catalogues for optical/nir/all (default: all)
python field_calibration.py --ra 173.423125 --dec 0.725972
The photometric catalogues are build from the 2MASS point source catalogues and SDSS/DR12 source catalogues. The PS1 point source catalogue was build by crossmatching PS1 with Gaia DR2. PS1 photometry was converted to the SDSS filters using the colour equations in Finkbeiner et al. (2016). Bessel photometry was derived following the Lupton (2004) colour equations.
The files will be called PS1_PS1_FILTER.ascii, PS1_SDSS_FILTER.ascii, PS1_BESSEL_FILTER.ascii, SDSS_FILTER.ascii, SDSS_BESSEL_FILTER.ascii, SkyMapper_SDSS_FILTER.ascii, SkyMapper_BESSEL_FILTER.ascii, and 2MASS_FILTER.ascii. The columns in each file are: col1 = ra, col2 = dec, col3 = mag, and col4 = sigma_mag.
Requires: astroquery, phot_utils, sewpy, SExtractor, wcs-tools
usage: photometry.py [-h] --ra RA --dec DEC --fits FITS
[--host-offset HOST_OFFSET] [--ref-cat REF_CAT]
[--ref-filter REF_FILTER] [--ref-file REF_FILE]
[--ref-image REF_IMAGE] [--ref-radius REF_RADIUS]
[--ana-thresh ANA_THRESH]
[--ap-diam AP_DIAM [AP_DIAM ...]]
[--ap-diam-ul AP_DIAM_UL [AP_DIAM_UL ...]]
[--det-thresh DET_THRESH] [--gain GAIN]
[--back-size BACK_SIZE]
[--back-filtersize BACK_FILTERSIZE]
[--deblend-nthresh DEBLEND_NTHRESH]
[--deblend-mincont DEBLEND_MINCONT] [--mag-cut MAG_CUT]
[--mag-stdfaint MAG_STDFAINT]
[--mag-stdbright MAG_STDBRIGHT] [--maxstars MAXSTARS]
[--auto] [--bw] [--keeptemp] [--loglevel LOGLEVEL]
[--outdir OUTDIR] [--sex-loglevel SEX_LOGLEVEL]
[--tol TOL]
Programme for aperture photometry.
optional arguments:
-h, --help show this help message and exit
--ra RA RA(J2000) of the Object (HMS and DD system allowed).
Note: if declination is negative, write "
-12:20:20.2"). (required)
--dec DEC Dec (J2000) of the Object (HMS and DD system allowed)
(required)
--fits FITS Name of FITS file (required)
--host-offset HOST_OFFSET
Host offset (default: 10 arcsec)
--ref-cat REF_CAT Which reference catalogue should be used (SDSS, 2MASS,
PS1)?
--ref-filter REF_FILTER
Filter of the reference catalogue?
--ref-file REF_FILE Name of reference catalog file (if given overwrites '
--ref-cat' option)
--ref-image REF_IMAGE
Name of reference image to run sextractor in dual
image mode?
--ref-radius REF_RADIUS
Search radius in the reference catalogue query?
(default: 10, unit: arcmin)
--ana-thresh ANA_THRESH
Analysis threshold (default: 1 sigma)
--ap-diam AP_DIAM [AP_DIAM ...]
Aperture radii in FWHM (one or more) (default:
[1.,2.,3.,4.])
--ap-diam-ul AP_DIAM_UL [AP_DIAM_UL ...]
Aperture radii in FWHM (one or more) (default: 2)
--det-thresh DET_THRESH
Detection threshold (default: 1; unit: sigma)
--gain GAIN Gain keyword in the header (default: Gain; unit:
e-/ADU)
--back-size BACK_SIZE
Background mesh: <size> (default: 64)
--back-filtersize BACK_FILTERSIZE
Background filter: <size> (default: 3)
--deblend-nthresh DEBLEND_NTHRESH
Number of deblending sub-thresholds (default: 64)
--deblend-mincont DEBLEND_MINCONT
Minimum contrast parameter for deblending (default:
0.00001)
--mag-cut MAG_CUT Remove all objects brighter than a given magnitude
(default: 12)
--mag-stdfaint MAG_STDFAINT
Lower magnitude cut for secondary standards (default:
0)
--mag-stdbright MAG_STDBRIGHT
Upper magnitude cut for secondary standards (default:
0)
--maxstars MAXSTARS Maximum number of stars used for building the local
sequence (default: 200)
--auto Automatic mode? (default: False)
--bw Text output in color (default: False)
--keeptemp Keep temporary files
--loglevel LOGLEVEL Logger level (default: INFO, possible values: DEBUG,
INFO, WARNING, ERROR, CRITICAL)
--outdir OUTDIR Output path efault: 'results/'
--sex-loglevel SEX_LOGLEVEL
Sextractor logger level (default: WARNING, possible
values: DEBUG, INFO, WARNING, ERROR, CRITICAL)
--tol TOL Tolerance of the cross-matching in arcsec (default: 1)
Step 1:
Go to the directory that contains the fits file
Step 2: You have no local star catalogue to constrain the flux scale of the image
photometry.py --fits SN2015bn_SDSS_r.fits --ra 173.423125 --dec 0.725972 --ref-cat SDSS --ref-filter r
or you would like to use a local star catalogue
photometry.py --fits SN2015bn_SDSS_r.fits --ra 173.423125 --dec 0.725972 --ref-file results/SDSS_r.cat
- Select stars for the local sequence (either from the user catalogue or it downloads a catalogue from the VizieR database)
- Measure the zeropoints for the different apertures
- Measure the brightness of the science object and all other sources in the images. If no credible source was detected close to the specified coordinates, the programme will perform forced photometry at the specified coordinates.
- Removing temporary files
You can find more information at SN2015bn_SDSS_r_summary.pdf.
The programme generates several text files
| File | Explanation |
|---|---|
| ./SN2015bn_SDSS_r.log | General log file |
| ./results/SN2015bn_SDSS_r_SDSS_r.cat | SDSS point source catalogue |
| ./results/SN2015bn_SDSS_r_all.log | SExtractor log |
| ./results/SN2015bn_SDSS_r_all_abs_cal.phot | SExtractor output catalogue all magnitudes are calibrated with the zeropoints measured from the image |
| ./results/SN2015bn_SDSS_r_phot.log | Summary of the photometry on the science source |
| ./results/SN2015bn_SDSS_r_zp.log | Zeropoint summary |
and diagnostic plots
| File | Explanation |
|---|---|
| ./results/SN2015bn_SDSS_r_fwhm.pdf | Distribution of the FWHMs of the stellar PSFs |
| ./results/SN2015bn_SDSS_r_poststamp.pdf | Poststage stamp of the source of interest |
| ./results/SN2015bn_SDSS_r_std.pdf | Local sequence: instrumental magnitude vs. tabulated magnitudes |
| ./results/SN2015bn_SDSS_r_zp.pdf | Measured zeropoints for the different apertures Datapoints: used in black; not used in grey Lines: median solid, 1-sigma confidence interval dashed sigma-clipped region dotted |
-The BW is currently not fully implemented.
-If you want to define different circular apertures, make sure that you always define 4.
-The dual-image mode is currently not activated.
Requires: phot_utils, sewpy, SExtractor, pysynphot
usage: photometry_hst.py [-h] --ra RA --dec DEC --fits FITS
[--ana-thresh ANA_THRESH] [--det-thresh DET_THRESH]
[--ap-diam AP_DIAM [AP_DIAM ...]]
[--ap-inner-annulus AP_INNER_ANNULUS]
[--ap-outer-annulus AP_OUTER_ANNULUS] [--auto] [--bw]
[--centroid] [--keeptemp] [--loglevel LOGLEVEL]
[--outdir OUTDIR] [--sex-loglevel SEX_LOGLEVEL]
[--tol TOL]
Programme for aperture photometry of HST images.
optional arguments:
-h, --help show this help message and exit
--ra RA RA(J2000) of the Object (HMS and DD system allowed).
Note: if declination is negative, write "
-12:20:20.2"). Required keyword.
--dec DEC Dec (J2000) of the Object (HMS and DD system allowed).
Required keyword.
--fits FITS Name of FITS file. Required keyword.
--ana-thresh ANA_THRESH
Analysis threshold. Default: 3 sigma
--det-thresh DET_THRESH
Detection threshold. Default: 3 sigma
--ap-diam AP_DIAM [AP_DIAM ...]
Aperture radii in arcsec (one or more value allowed).
Default: [0.25, 0.5, 0.75, 1.00]
--ap-inner-annulus AP_INNER_ANNULUS
Diameter of the inner annulus of the background.
Default: 1.5 x ap-diam
--ap-outer-annulus AP_OUTER_ANNULUS
Diameter of the outer annulus of the background.
Default: 3 x ap-diam
--auto Automatic mode? Default: False
--bw Screen output in B/W? Default: False
--centroid Centre on the most nearby object
--keeptemp Keep temporary files
--loglevel LOGLEVEL Logger level (default: INFO, possible values: DEBUG,
INFO, WARNING, ERROR, CRITICAL)
--outdir OUTDIR Output path. Default: 'results/'
--sex-loglevel SEX_LOGLEVEL
Sextractor logger level (default: WARNING, possible
values: DEBUG, INFO, WARNING, ERROR, CRITICAL)
--tol TOL Tolerance of the cross-matching in arcsec. Default: 1
arcsec
Step 1:
Go to the directory that contains the fits file
Step 2:
pythonw photometry_hst.py --ra 173.42306 --dec 0.72589793 --fits SN2015bn_F625W_drc.fits
- Compute the ZP from the header keywords and applies aperture corrections for each aperture (using pysynphot)
- Generate a general source catalogue to identify the object that is closests to your science object
- Measure the brightness for the specified apertures
- Perform curve of growth analysis
- Removing temporary files
You can find more information at SN2015bn_F625W_drc.pdf.
| File | Explanation |
|---|---|
| ./SN2015bn_F625W_drc.log | General log file |
| ./results/SN2015bn_F625W_drc.mag | Photometry log of the science object |
| ./results/SN2015bn_F625W_drc_centroid.log | SExtractor output log |
| ./results/SN2015bn_F625W_drc_centroid.phot | SExtractor output catalogue |
| ./results/SN2015bn_F625W_drc_cog_stat.ascii | Text file of the curve-of-growth analysis |
| ./results/SN2015bn_F625W_drc_phot.log | Summary of the photometry on the science source |
| ./results/SN2015bn_F625W_drc_zp.log | Zeropoint summary |
and diagnostic plots
| File | Explanation |
|---|---|
| ./results/SN2015bn_F625W_drc_cog.pdf | Curve of growth |
| ./results/SN2015bn_F625W_drc.pdf | Poststage stamp of the source of interest |
That's very easy. You can run each tool in parallel. For example
ls "*fits | xargs -n 1 -P 16 -I {} photometry.py --fits {} --ra 173.423125 --dec 0.725972 --ref-cat SDSS --ref-filter r
would run 16 parallal sessions of photometry.py.
- Steve Schulze
The developement of these tools started in the paper Schulze et al. (2018). If possible, please add a reference to this paper in your article.
Also cite the relevant papers for astrometry.net, SExtractor and sip_tpv.
Bibtex codes
@ARTICLE{Berin1996A,
author = {{Bertin}, E. and {Arnouts}, S.},
title = "{SExtractor: Software for source extraction.}",
journal = {\aaps},
keywords = {METHODS: DATA ANALYSIS, TECHNIQUES: IMAGE PROCESSING, GALAXIES: PHOTOMETRY},
year = 1996,
month = jun,
volume = 117,
pages = {393},
doi = {10.1051/aas:1996164},
adsurl = {http://adsabs.harvard.edu/abs/1996A%26AS..117..393B},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@ARTICLE{Lang2010a,
author = {{Lang}, D. and {Hogg}, D.~W. and {Mierle}, K. and {Blanton}, M. and
{Roweis}, S.},
title = "{Astrometry.net: Blind Astrometric Calibration of Arbitrary Astronomical Images}",
journal = {\aj},
archivePrefix = "arXiv",
eprint = {0910.2233},
primaryClass = "astro-ph.IM",
keywords = {astrometry, catalogs, instrumentation: miscellaneous, methods: data analysis, methods: statistical, techniques: image processing},
year = 2010,
month = may,
volume = 139,
pages = {1782},
doi = {10.1088/0004-6256/139/5/1782},
adsurl = {http://adsabs.harvard.edu/abs/2010AJ....139.1782L},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@ARTICLE{Schulze2018a,
author = {{Schulze}, S. and {Kr{\"u}hler}, T. and {Leloudas}, G. and {Gorosabel}, J. and
{Mehner}, A. and {Buchner}, J. and {Kim}, S. and {Ibar}, E. and
{Amor{\'{\i}}n}, R. and {Herrero-Illana}, R. and {Anderson}, J.~P. and
{Bauer}, F.~E. and {Christensen}, L. and {de Pasquale}, M. and
{de Ugarte Postigo}, A. and {Gallazzi}, A. and {Hjorth}, J. and
{Morrell}, N. and {Malesani}, D. and {Sparre}, M. and {Stalder}, B. and
{Stark}, A.~A. and {Th{\"o}ne}, C.~C. and {Wheeler}, J.~C.},
title = "{Cosmic evolution and metal aversion in superluminous supernova host galaxies}",
journal = {\mnras},
archivePrefix = "arXiv",
eprint = {1612.05978},
keywords = {galaxies: evolution, galaxies: high-redshift, galaxies: luminosity function, mass function, galaxies: starburst, galaxies: star formation},
year = 2018,
month = jan,
volume = 473,
pages = {1258},
doi = {10.1093/mnras/stx2352},
adsurl = {http://adsabs.harvard.edu/abs/2018MNRAS.473.1258S},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@INPROCEEDINGS{Shupe2012a,
author = {{Shupe}, D.~L. and {Laher}, R.~R. and {Storrie-Lombardi}, L. and
{Surace}, J. and {Grillmair}, C. and {Levitan}, D. and {Sesar}, B.
},
title = "{More flexibility in representing geometric distortion in astronomical images}",
booktitle = {Software and Cyberinfrastructure for Astronomy II},
year = 2012,
series = {\procspie},
volume = 8451,
month = sep,
eid = {84511M},
pages = {84511M},
doi = {10.1117/12.925460},
adsurl = {http://adsabs.harvard.edu/abs/2012SPIE.8451E..1MS},
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
2-clause BSD