Running SExtractor

[Astrogirlanajli]

Hi, After installing the SExtractor, I tried running SExtractor for test image(galaxies.fits), it's giving me the error:
(mirar) anjali@RSAA-024587 ~ % sex galaxies.fits
----- SExtractor 2.28.0 started on 2024-09-20 at 00:48:16 with 1 thread

Setting catalog parameters
ERROR: can't read default.param
I installed SExtractor using github clone method:
git clone https://github.com/astromatic/sextractor.git
cd sextractor
./autogen.sh
./configure --disable-model-fitting
make
sudo make install
I wanted to know how to fix the error and run SExtractor.

[kirxkirx]

SExtractor needs a few configuration files to run. These configuration files are often located in the same directory where one runs SExtractor. Typically one copies these configuration files from a previous SExtractor run and modifies them as needed, but here is an example of how one could make SExtractor create a set of configuration files from scratch:

# Write default SExtractor parameter file
sex -d > default.sex
# Create default image convolution file
echo "CONV NORM
# 3x3 ``all-ground'' convolution mask with FWHM = 2 pixels.
1 2 1
2 4 2
1 2 1" > default.conv
# Write SExtractor output source parameters file uncommentating some output parameters on the fly
sex -dp | sed 's/#NUMBER/NUMBER/' | sed 's/#MAG_AUTO/MAGERR_AUTO/' | sed 's/#MAG_AUTO/MAGERR_AUTO/' | sed 's/#X_IMAGE/X_IMAGE/' | sed 's/#Y_IMAGE/Y_IMAGE/' > default.param
# at this point SExtractor is ready for a test run
####################################################
# Run SExtractor on my test FITS file f_72-001r.fit located in the directory current_work/sample_data/ within my home directory (~)
sex ~/current_work/sample_data/f_72-001r.fit
# Print out the list of detected sources in the terminal
cat test.cat

For a real science run one would definitely need to tweak the source detection parameters in default.sex for a given telescope/camera combination as well as the list of output parameters in default.param. Surprisingly, the default image convolution kernel default.conv works fine for a vast majority of ground-based telescopic images (source detection on images taken with a telephoto lens typically benefit from a narrower convolution kernel). The details about the source detection and output parameters may be found in SExtractor documentation..

[Astrogirlanajli]

Although I created a .conv file with all ground kernels:

CONV NORM # 3x3 ``all-ground'' convolution mask with FWHM = 2 pixels.
1 2 1
2 4 2
1 2 1
After running sex -d > file. conv, and calling interest of target:
(base) anjali@RSAA-024587 extractor % sex -d > /Users/Anjali/extractor/config/gn.conv
(base) anjali@RSAA-024587 extractor % sex /Users/Anjali/github/Mirar/Sources/NGC.fits

I'm getting the following error:
----- SExtractor 2.28.0 started on 2024-09-27 at 11:08:09 with 1 thread

Reading detection filter
Error: not a suitable filter in default.conv

After executing the file, my file.conv is changing itself into this https://github.com/Astrogirlanajli/Research_thesis/blob/main/gn.conv file. I wonder why it's transforming itself. To be noted, I installed SExtractor via the GitHub source package, which is technically cloned github.

[Astrogirlanajli]

Hi, It's still showing an error as I run the SEx tractor command.

…

________________________________ From: Kirill Sokolovsky ***@***.***> Sent: Friday, September 20, 2024 3:57 AM To: astromatic/sextractor ***@***.***> Cc: Anjali Shivani Thadisina ***@***.***>; Manual ***@***.***> Subject: Re: [astromatic/sextractor] Running SExtractor (Discussion #73) SExtractor needs a few configuration files to run. These configuration files are often located in the same directory where one runs SExtractor. Typically one copies these configuration files from a previous SExtractor run and modifies them as needed, but here is an example of how one could make SExtractor create a set of configuration files from scratch: # Write default SExtractor parameter file sex -d > default.sex # Create default image convolution file echo "CONV NORM # 3x3 ``all-ground'' convolution mask with FWHM = 2 pixels. 1 2 1 2 4 2 1 2 1" > default.conv # Write SExtractor output source parameters file uncommentating some output parameters on the fly sex -dp | sed 's/#NUMBER/NUMBER/' | sed 's/#MAG_AUTO/MAGERR_AUTO/' | sed 's/#MAG_AUTO/MAGERR_AUTO/' | sed 's/#X_IMAGE/X_IMAGE/' | sed 's/#Y_IMAGE/Y_IMAGE/' > default.param # at this point SExtractor is ready for a test run #################################################### # Run SExtractor on my test FITS file f_72-001r.fit located in the directory current_work/sample_data/ within my home directory (~) sex ~/current_work/sample_data/f_72-001r.fit # Print out the list of detected sources in the terminal cat test.cat For a real science run one would definitely need to tweak the source detection parameters in default.sex for a given telescope/camera combination as well as the list of output parameters in default.param. Surprisingly, the default image convolution kernel default.conv works fine for a vast majority of ground-based telescopic images (source detection on images taken with a telephoto lens typically benefit from a narrower convolution kernel). The details about the source detection and output parameters may be found in SExtractor documentation.<https://sextractor.readthedocs.io/en/latest/Introduction.html>. — Reply to this email directly, view it on GitHub<#73 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/A3I3TV6YIIPMVFGGYFAWT5TZXMGABAVCNFSM6AAAAABOQEAORGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANRZGYZTQNA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[kirxkirx]

Is this the same error as before, "ERROR: can't read default.param"? If yes, please make sure that the file named default.param actually exists in the directory where you run SExtractor.You can check that the file is there by doing ls default.param in that directory. If the file is there, try to open it with a text editor or just print the content of the file in the terminal by running cat default.param. Make sure there are some parameters in default.param that are uncommented (do not start with #) so SExtractor has something to output.

If an error message is not about default.param but is different, please copy the error message here with a few lines above and below the error message. Maybe it will clarify what's going wrong...

[ebertin]

Hi @Astrogirlanajli,

please note that after doing a sudo make install on Linux systems, default configuration files, including default.param and default.conv can be found in /usr/local/share/sextractor.

[Astrogirlanajli]

Hi, I didn't install it via sudo make install; I had many issues while installing it on my Mac, so I cloned the SExtractor github.

[rmathar]

The main configuration file and the convolution kernel are two different pairs of shoes. The sex -d > /Users/Anjali/extractor/config/gn.conv creates a configuration (!) file and overwrites the previous content by the standard syntax of Linux bash commands. So if you generate file.conv and then type sex -d > file.conv, the file.conv is replaced and overwritten with a default configuration file; this is expected.

The standard way of getting consistent operation is (i) generate a configuration file with sex -d > /Users/Anjali/extractor/config/gn.conf, (ii) edit the configuration file /Users/Anjali/extractor/config/gn.conf so its line with FILTER_NAME has parameter text.conv, (iii) generate the convolution kernel file text.conv with your favorite ASCII editor, (iv) run sex -c /Users/Anjali/extractor/config/gn.conf /Users/Anjali/github/Mirar/Sources/NGC.fits so it looks inside the configuration file /Users/Anjali/extractor/config/gn.conf what the name of the convolution file is.