Sextractor on Cluster Galaxies
Project description
CluSex
What is CluSex?
CluSex is a set of routines that assists Sextractor to perform on images of cluster galaxies (or high density of objects).
Particularly, it joins two (or more) sextractor catalogs, creates masks, finds saturated star regions, computes sky background and makes stamps for every detected object.
Why CluSex?
It is hard to find a satisfactory Sextractor configuration to detect all the objects in the image (see Haussler 2007). For instance, a Sextractor parameter configuration can be optimized to detect large galaxies, but it might be unable to detect small dim galaxies, and vice versa. In addition, Sextractor overestimates the size of low surface brightness galaxies inside regions of high density of objets. To see those effects check the image below for a run of Sextractor in an Abell cluster:
In the previous image, red ellipses are galaxies where their size are clearly overestimated. A different parameter configuration produce a different result, for instance, the figure below shows a different configuration for the same galaxy cluster image:
For the above figure, galaxy sizes are better estimated but Sextractor is unable to detect (or deblend) all the galaxies.
The same cluster image can be improved after using CluSex. To see this check the image below:
It shows an improved deteccion and size estimation of the objects for the same Abell Cluster. This result can be improved adding different Sextractor configuration runs. For instance, the figure below is show an even better catalog using joincat command to detect the small dim objects in the image.
In addition, CluSex improves computation of sky background, creation of masks, and estimation of the area of saturated stars.
Below is shown an estimation of the size of a region across a bright saturated star:
Requirements
astropy
numpy
Installation
Install sextractor (if you haven’t done so)
For linux:
sudo apt install sextractor
Install Ds9 (if you haven’t done so)
Download it and make a symbolic link to the /usr/local/bin or make an alias.
sudo ln -s /path/to/ds9 /usr/local/bin
Once that is done, download the code and run
pip install .
or
pip install clusex
USAGE
Quickstart
To run the code just type in the command line:
clusex ConfigFile
Where ConfigFile is the configuration parameter filename for CluSex
Example of Configuration file
Here it is shown an example of a CluSex configuration file:
FirstRun 1 # Enable first run (1 = run) SecondRun 1 # enable second run (1 = run) Image A1656.fits MAG_ZEROPOINT 28.32 GAIN 5.4 PIXEL_SCALE 0.68 SATUR_LEVEL 30000 SEEING_FWHM 1.5 DEBLEND_NTHRESH1 64 # Number of deblending sub-thresholds DEBLEND_MINCONT1 0.001 # Minimum contrast parameter for deblending ANALYSIS_THRESH1 5 # <sigmas> or <threshold>,<ZP> in mag.arcsec-2 DETECT_THRESH1 5 # <sigmas> or <threshold>,<ZP> in mag.arcsec-2 DETECT_MINAREA1 20 # minimum number of pixels above threshold BACK_SIZE1 100 BACK_FILTERSIZE1 11 # params for second run # run with high deblend number and low SNR DEBLEND_NTHRESH2 32 # Number of deblending sub-thresholds DEBLEND_MINCONT2 .01 # Minimum contrast parapymeter for deblending ANALYSIS_THRESH2 1.5 # <sigmas> or <threshold>,<ZP> in mag.arcsec-2 DETECT_THRESH2 1.5 # <sigmas> or <threshold>,<ZP> in mag.arcsec-2 DETECT_MINAREA2 20 # minimum number of pixels above threshold BACK_SIZE2 11 BACK_FILTERSIZE2 10 Scale 1.5 # factor scale which ellipses are enlarged Offset 5 SatDs9 sat.reg SatScale 1 SatOffset 20 OutCatalog hotcold.cat RegDs9 hotcold.reg MinSatSize 20 # min size for sat regions SatQ 0.7 SatMethod 3 ReduCoef 0.2 FracTol 0.5 JoinScale 2 ScaleCor 1.5
Some of the configuration parameters are the same for Sextractor and corresponds to each of the runs (hot and cold runs). To check the explanation of each parameter see the section below:
Configuration parameters
Check the link below for an explanation of the config file:
Tip
To make CluSex works properly, the first run must be configurated with a low deblend number and high SNR, and, on the other hand, the second run with a high deblend number and low SNR (check sextractor manual for details to how to do this).
How it works
In order to solve these problems, CluSex runs Sextractor twice with different configuration parameters: the first run detects large bright saturated galaxies and the second run detects small dim galaxies. This has been done before check Haussler (2007).
CluSex adds all the detected objects in the first Sextractor run. Next, it adds the objects of the second Sextractor run only if their center is outside of the ellipse of any the objects of the first run.
The combination of the two catalogs gives a better representation for almost all the objects of the image. In addition, it also estimates the area of saturated stars in the image.
Furthermore, to estimate the true size of low surface brightness objects, CluSex compares the sizes of the same object in each of the two catalogs and keeps the smaller one. On the other hand, if the object was detected only for one catalog, it is reduced by a constant factor given in the CluSex parameter file.
Masks
Check images given by Sextractor can be used for masks, but this is a bad practice specially if Sextractor have wrongly computed the background. In contrast, CluSex creates masks using the data given by Sextractor catalog. Every object is represented by an ellipse mask which it can be enlarged (or shortened) by the user. To see an example of a mask which includes the saturated stars, check the image below.
Every ellipse object mask is filled with the same number catalog that it is given by the CluSex catalog (same as Sextractor). Hence, an object ellipse mask can be easily removed just by simply eliminating the pixel values that coincide with their Sextractor number catalog. For instance, for the figure below the large ellipse in the center has been removed using the short routine remellmask:
Sky Background
Sky background can be done poorly if objects’s sizes are wrongly estimated or not detected at all. Also it is known that Sextractor overestimates the sky background (Haussler 2007). A wrong sky background value will produce a bad computation of Sersic index for model fitting.
CluSex uses two different methods to compute sky background: 1) gradient sky and 2) random boxes around the objects.
Gradient sky method computes the background sky in a ring around the object. To locate this ring, Clusex creates concentric rings around the object and computes the background in every ring. This will create a set of sky values for each ring. The gradient is computed for this set. When the gradient of ring sky values turns positive, clusex stops and measure the sky in that ring. A similar approach has been used in Haussler 2007.
On the other hand, for the random box method, clusex creates boxes of the same size located at random positions around the object. After a given number of boxes, clusex computes the sky background.
Additional features
CluSex contains other routines to improve Sextractor photometry. They include: combination of two catalogs, creation of masks, creation of Ds9 region file, and computation of sky background.
Except for sex2ds9 routine, the use of the routines is suggested in the following order: CluSex, Joincat (if needed), makemask, and compsky. Those routines are separated because the user need to be verify that the output is well done before continuing with the next routine.
Joincat
Joincat is a small CluSex version. It just joins two existent sextractor catalogs. The aim is that a third Sextractor catalog can be merged with the output of CluSex. Therefore, this hopefully will detect those objects that were unable to be detected by CluSex.
The principle is the same as CluSex: objects of the second catalog will be added to the first one only if their center is outside the ellipse of the objects of the first catalog. Use it only if it is necessary. An additional option (-i) will add all the objects where the object position is not in the other catalog.
MakeMask
This routine creates an image which contains ellipse masks for every object. It needs the CluSex output catalog and saturated ds9 regions (created by CluSex as well)
Sky background
This routine use two methods (gradient sky and random box) to compute sky background for every detected object by CluSex. Output catalog is the same as the input catalog but with the background column changed to the new values
sex2ds9
Creates a ds9 region file from the sextractor output catalog
remellmask
This is a short routine that removes ellipse masks from the mask. Useful when a model fitting will be applied to the galaxy.
HOW TO
Full explanations of the commands above are found in
NOTES
CluSex was designed to provide an improved sextractor catalog to my other project (DGCG). Hence, for the current CluSex version, it only works for the 14 output sextractor columns below:
NUMBER ALPHA_J2000 DELTA_J2000 XPEAK_IMAGE YPEAK_IMAGE MAG_BEST KRON_RADIUS FLUX_RADIUS ISOAREA_IMAGE A_IMAGE ELLIPTICITY THETA_IMAGE BACKGROUND CLASS_STAR FLAGS
Details of these output parameters can be found in the Sextractor manual. Obviously some of the output parameters can be changed to the other options of Sextractor like MAG_BEST can be changed to MAG_AUTO and so.
Additional columns will be added in future releases.
API
API:
Questions?
Code is far from perfect, so if you have suggestions or questions Please send an email to canorve [at] gmail [dot] com
License
This code is under the license of GNU
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