CluSex 2.4.2

Sextractor on Cluster Galaxies

Contents

• CluSex

  • What is CluSex?

  • Why CluSex?

  • Installation

  • USAGE

    • Quickstart

    • Example of Configuration file

    • Configuration parameters

    • Tip

  • How it works

    • Masks

    • Sky Background

  • Additional features

    • Joincat

    • MakeMask

    • Sky background

    • sex2ds9

    • remellmask

  • HOW TO

  • NOTES

  • API

  • Cite as

  • Questions?

  • License

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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.

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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:

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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, install it using pip:

pip install CluSex

another option is to download the code and run

pip install .

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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

below it is shown an example of a CluSex configuration file (it follows the format of configparser library):

[General]
image = A671.fits
MAG_ZEROPOINT =  29.17
GAIN        =    5.6
PIXEL_SCALE =    0.68
SEEING_FWHM =    1.5

MakeMask = False
OutCatalog =  hotcold.cat
RegDs9 =   hotcold.reg

run1 = True
run2 = True

[Run1]
DEBLEND_NTHRESH1 = 64
DEBLEND_MINCONT1 = 0.01

ANALYSIS_THRESH1 = 10
DETECT_THRESH1   = 10
DETECT_MINAREA1  = 10

BACK_SIZE1     = 100
BACK_FILTERSIZE1  = 11


[Run2]
DEBLEND_NTHRESH2 = 16
DEBLEND_MINCONT2 = .1

ANALYSIS_THRESH2 = 1.2
DETECT_THRESH2  = 1.2
DETECT_MINAREA2 = 10


BACK_SIZE2      = 10
BACK_FILTERSIZE2 = 2


[Sizes]

Scale =  1.5
ReduCoef = 0.2
FracTol = 0.5
JoinScale = 1.5
ScaleCor = 1.5


[Saturation]

SATUR_LEVEL =    30000
SatDs9 = sat.reg
SatScale = 1.7
SatOffset =  20
MinSatSize  = 20
SatQ = 0.7
SatMethod =  3

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:

configuration

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).

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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 through compsky command to compute the 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.

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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.

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HOW TO

Full explanations of the commands above are found in

How to run

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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.

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API

API:

API

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Cite as

If you find this code useful, please cite as:

Añorve, C., Orlando Gutiérrez, & López-Cruz, O. (2024). canorve/CluSex: CluSex v2.4.1 (v2.4.1). Zenodo. https://doi.org/10.5281/zenodo.13994345

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Questions?

Code is far from perfect, so if you have suggestions or questions Please send an email to canorve [at] gmail [dot] com

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License

This code is under the license of GNU