Quick Start¶

It is recommended that you have at least a cursory understanding of SExtractor, it’s parameters, and how it works before starting; however this introduction might be sufficient to get started. You will also need your own FITS image to work with, preferably one with multiple extensions (CCD’s).

Running a Code on a Single Image¶

In this example we will show how to run a single astromatic code outside on a single image. Although we only demonstrate how to interface with SExtractor, the exact same proceedure applies to all the AstrOmatic codes (with the exception of the configuration parameters). To see an example of creating a pipeline that uses all of the SExtractor codes on a set of images see Pipelines.

SExtractor is an program that detects sources and performs photometry on astronomical FITS images. The following example assumes that you have a fits file named ‘my_img.fits’.

Note

SExtractor does not work on compressed FITS files (fits.fz) so you will need to funpack the file before running SExtractor.

Note

You must have SExtractor installed for this example to work.

First you need to import the astromatic_wrapper package and define your files:

>>> import astromatic_wrapper as aw
>>> files = {'image': 'my_img.fits'}

If you have a data quality mask or weight map you can also add them:

>>> files['dqmask'] = 'my_img.dqmasl.fits'
>>> files['wtmap'] = 'my_img.wtmap.fits'

Next you need to define the keyword arguments to run the code. At a minimum you must supply the name of the code you are using. To see a dictionary of all the available codes and their command line name enter:

>>> aw.api.codes
{'SExtractor': 'sex', 'SWarp': 'swarp', 'PSFEx': 'psfex', 'SCAMP': 'scamp'}

In this case we use:

>>> kwargs = {'code': 'SExtractor'}

If you are running an AstrOmatic code that is not a system wide install, you can change the command used to execute the code by setting:

>>> kwargs['cmd'] = 'different/path/to/sex'

All AstrOmatic codes use config files containing input parameters whose filenames conventionally end with an extension that is the same as command name (for example config.sex for SExtractor, config.scamp for SCAMP, etc.). For this example we won’t specify a config file so that SExtractor will just use its internal default. If we have our own config file we can instruct SExtractor (or any other astromatic code) to use it by entering:

>>> kwargs['config_file'] = 'config.sex'

It can be useful to change certain parameters in a config file so SExtractor allows the user to pass command line arguments using the ‘config’ key, for example we may want to change the name of the output catalog:

>>> kwargs['config']={'CATALOG_NAME':'test.ldac.fits'}

An anomally of the AstrOmatic codes is that they like input catalogs in the form of the FITS LDAC standard, which is slightly different than standard FITS tables. Astromatic-Wrapper provides an I/O scheme to interface with FITS LDAC files in the FITS LDAC files. To change the output type to FITS LDAC from the default (‘ASCII_HEAD’) we use:

>>> kwargs['config']['CATALOG_TYPE'] = 'FITS_LADC'

In this quick example we will not use a filter to assist SExtractor in finding sources so we set:

>>> kwargs['config']['FILTER'] = 'N'

One feature that is unique to SExtractor (as opposed to the other AstrOmatic codes) is that it also requires a parameters file to set the output of the code. If you already have a parameters file you can tell SExtractor to use it with:

>>> kwargs['config']['PARAMETERS_NAME'] = 'filename.param'

otherwise you must specify a ‘temp_path’ and the names of the parameters you want SExtractor to export:

>>> kwargs['temp_path'] = '.'
>>> kwargs['params'] = ['NUMBER', 'EXT_NUMBER', 'XWIN_WORLD', 'YWIN_WORLD', 'MAG_AUTO']

To create an Astromatic object that will run the code we type

>>> sextractor = aw.api.Astromatic(**kwargs)

To run sextractor on a single frame:

>>> sextractor.run_frames(files['image'], frames=[1]) 
> WARNING: default.sex not found, using internal defaults

----- SExtractor 2.19.5 started on 2015-07-08 at 15:46:12 with 1 thread

----- Measuring from: c4d_150528_065922_ooi_r_v1.fits [1/60]
      "Unnamed" / no ext. header / 2046x4094 / 32 bits (floats)
(M+D) Background: 25.3315    RMS: 3.28377    / Threshold: 4.92565
      Objects: detected 12304    / sextracted 8595

> All done (in 5.1 s: 803.3 lines/s , 1686.4 detections/s)

Note

Only SExtractor and SWarp run on individual frames. PSFex and SCAMP run on the entire catalog that was passed to them.

To run SExtractor on an entire image:

>>> sextractor.run(files['image']) 
(output suppressed)

Note

It is also possible to first create the Astromatic class using sextractor = aw.api.Astromatic('SExtractor') and then pass the configuration parameters to the run command sextractor.run(files['image'], **kwargs) or sextractor.run_frames(files['image'], frames=[1], **kwargs). It is also possible to use sextractor = aw.api.Astromatic(**kwargs) and sextractor.run(files['image'], **new_kwargs), in which case the new_kwargs in the run method take precedent over the kwargs set when the class was initialized.

Putting it all together we have:

import astromatic_wrapper as aw

files = {
    'image': 'my_img.fits',
    'dqmask': 'my_img.dqmask.fits',
    'wtmap': 'my_img.wt_map.fits'
}
kwargs = {
    'code': 'SExtractor',
    #'cmd': 'different/path/to/sex',
    'config': {
        'CATALOG_NAME': 'test.ldac.fits',
        'CATALOG_TYPE': 'FITS_LDAC',
        'FILTER': 'N',
    },
    'temp_path': '.',
    'params': ['NUMBER', 'EXT_NUMBER', 'XWIN_WORLD', 'YWIN_WORLD', 'MAG_AUTO'],
    #'config_file': 'config.sex'
}

sextractor = aw.api.Astromatic(**kwargs)
sextractor.run_frames(files['image'], frames=[1])
#sextractor.run(files['image'])

Now we can open the data as an astropy table using:

>>> catalog = aw.utils.ldac.get_table_from_ldac('test.ldac.fits') 
>>> catalog 
NUMBER EXT_NUMBER   XWIN_WORLD    YWIN_WORLD   MAG_AUTO
                       deg           deg         mag
------ ---------- ------------- -------------- --------
        1  275.80827774 -50.0434433783 -12.1171
        1 275.798937295 -50.0183562274 -5.31479
        1 275.794967779 -50.0183230473 -7.09294
        1 275.792679237 -50.0184461957 -8.99806
        1 275.802384111  -50.148179237 -14.6061
        1 275.799356843 -50.0689823418 -13.5756
        1 275.799459347  -50.020292202 -7.62385
        1 275.797433239 -50.1242247153 -13.0597
        1 275.795337901 -50.1232484108 -9.93003
        1 275.796363189 -50.0510042866 -9.32829
   ...        ...           ...            ...      ...
        1 276.207597916 -50.0754202482 -3.82954
        1 276.193157798 -50.0811452427 -5.45954
        1  276.24091269 -50.0409055391 -10.7668
        1 276.236753962 -50.0533390955 -6.89498
        1 276.236856181 -50.0440666735 -4.34284
        1 276.244645469 -50.1200226072 -8.52295
        1 276.221681288 -50.1324512891 -6.54179
        1 276.192358853 -50.1377186626 -14.3937
        1 276.206296663 -50.1512013966  -7.4894
        1 276.206454781 -50.0597536065 -11.7223
Length = 8595 rows

Navigation

Quick Start¶

Running a Code on a Single Image¶