Masterlist run example

Download this notebook.

scubes package implements a script to run the program from a CSV file with a list of objects, a Masterlist. This script is called scubesml

Masterlist is a csv text file in which one could gather information of a list of objects to create cubes. The file must contain at least 5 columns named with the following header and information:

  1. SNAME: A nickname for the object

  2. FIELD: S-PLUS Field (TILE) in which the program will search for the coordinates

  3. RA__deg: Right-ascencion in degrees

  4. DEC__deg: Declination in degrees

  5. SIZE__pix: SIZE of the object in pixels

Masterlist file content example:

SNAME,FIELD,RA__deg,DEC__deg,SIZE__pix S00001,SPLUS-s24s34,52.08196,-31.06817,53.65902 S00002,SPLUS-s24s35,52.87771,-30.21333,25.898617 (…)

A Masterlist could contain more columns and, at the end of the run, the script will update the primary header of the output FITS file with all information inside the Masterlist for the chosen object.

!scubesml --help

usage: scubesml [-h] [-r] [-c] [-f] [-b BANDS [BANDS ...]]
                [-S SIZE_MULTIPLICATOR] [-w WORK_DIR] [-o OUTPUT_DIR] [-v]
                [-D] [-Z ZPCORR_DIR] [-z ZP_TABLE] [-U USERNAME] [-P PASSWORD]
                [-R] [--version]
                GALAXY_SNAME MASTERLIST

┌─┐   ┌─┐┬ ┬┌┐ ┌─┐┌─┐  | scubesml entry-point script:
└─┐───│  │ │├┴┐├┤ └─┐  | Create S-PLUS galaxies data cubes, a.k.a. S-CUBES
└─┘   └─┘└─┘└─┘└─┘└─┘  | using the masterlist information as input.
---------------------- +

   Eduardo Alberto Duarte Lacerda <dhubax@gmail.com>, Fabio Herpich <fabiorafaelh@gmail.com>

positional arguments:
  GALAXY_SNAME                Galaxy's masterlist nickname
  MASTERLIST                  Path to masterlist file

options:
  -h, --help                  show this help message and exit
  -r, --redo                  Enable redo mode to overwrite final cubes.
                              Default value is False
  -c, --clean                 Clean intermediate files after processing.
                              Default value is False
  -f, --force                 Force overwrite of existing files. Default value
                              is False
  -b BANDS [BANDS ...], --bands BANDS [BANDS ...]
                              List of S-PLUS bands (space separated). Default
                              value is ['U', 'F378', 'F395', 'F410', 'F430',
                              'G', 'F515', 'R', 'F660', 'I', 'F861', 'Z']
  -S SIZE_MULTIPLICATOR, --size_multiplicator SIZE_MULTIPLICATOR
                              Factor to multiply the SIZE__pix value of the
                              masterlist to create the galaxy size. If size is
                              a odd number, the program will choose the
                              closest even integer. Default value is 10
  -w WORK_DIR, --work_dir WORK_DIR
                              Working directory. Default value is /storage/hdd
                              /backup/dhubax/dev/astro/splus/s-cubes/workdir
  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                              Output directory. Default value is /storage/hdd/
                              backup/dhubax/dev/astro/splus/s-cubes/workdir
  -v, --verbose               Verbosity level.
  -D, --debug                 Enable debug mode. Default value is False
  -Z ZPCORR_DIR, --zpcorr_dir ZPCORR_DIR
                              Zero-point correction directory. Default value
                              is /home/lacerda/.local/lib/python3.10/site-
                              packages/scubes/data/zpcorr_iDR4
  -z ZP_TABLE, --zp_table ZP_TABLE
                              Zero-point table. Default value is
                              /home/lacerda/.local/lib/python3.10/site-
                              packages/scubes/data/iDR4_zero-points.csv
  -U USERNAME, --username USERNAME
                              S-PLUS Cloud username.
  -P PASSWORD, --password PASSWORD
                              S-PLUS Cloud password.
  -R, --remove_downloaded_data
                              Remove the downloaded data from splusdata at the
                              end of the run. Default value is False
  --version                   show program's version number and exit

Size of the stamp

For the size calculation, the script will use the value of the column SIZE__pix and also the --size_multiplicator option. At the end, the final size value will be the next even integer of the multiplication:

size = size_multiplicator x SIZE__pix

!cat masterlist_example.csv

SNAME,FIELD,RA__deg,DEC__deg,TYPE,VELOCITY__kms,REDSHIFT,DISTANCE__Mpc,EBV__mag,SIZE__pix
NGC1344,SPLUS-s24s34,52.08196,-31.06817,G,1241.0,0.00414,18.364103654698095,0.0158,53.65902
ESO418-G008,SPLUS-s24s35,52.87771,-30.21333,G,1195.0,0.003987,17.683362136194148,0.0134,25.898617
ESO418-G009,SPLUS-s24s35,52.98173,-31.33763,G,972.0,0.003242,14.370905842817514,0.0172,31.746374
NGC1366,SPLUS-s24s35,53.47367,-31.19411,G,1231.0,0.004106,18.212814064954173,0.0146,15.589648
NGC1406,SPLUS-s24s36,54.84708,-31.32142,G,1075.0,0.003585,15.895502593028134,0.0094,53.065895
ESO419-G013,SPLUS-s24s39,60.17338,-30.831,G,1490.0,0.00497,22.059776288801466,0.0064,23.614521
ESO420-G009,SPLUS-s24s41,62.75269,-31.40743,G,1367.0,0.00456,20.23362042333429,0.0197,35.48054
IC1913,SPLUS-s25s32,49.8939,-32.46502,G,1443.0,0.004813,21.360357850834735,0.0138,28.049528
IC1919,SPLUS-s25s33,51.50933,-32.89456,G,1323.0,0.004413,19.579153744085982,0.0125,37.4627

The Masterlist file masterlist_example.csv contain 9 objects. To run scubes for each object, just use scubesml script as:

!scubesml -frR -U YOURUSER -P YOURPASS -w . --size_multiplicator 20 -- ESO419-G013 masterlist_example.csv

ESO419-G013 @ SPLUS-s24s39 - downloading: 100%|█| 12/12 [00:27<00:00,  2.29s/it]
WARNING: FITSFixedWarning: 'datfix' made the change 'Set DATE-OBS to '2017-09-26' from MJD-OBS'. [astropy.wcs.wcs]
WARNING: FITSFixedWarning: 'datfix' made the change 'Set DATE-OBS to '2017-10-13' from MJD-OBS'. [astropy.wcs.wcs]
[2024-05-26T21:34:22.521107] - scubesml: Reading ZPs table: /home/lacerda/.local/lib/python3.10/site-packages/scubes/data/iDR4_zero-points.csv
[2024-05-26T21:34:22.524050] - scubesml: Getting ZP corrections for the S-PLUS bands...
[2024-05-26T21:34:22.528228] - scubesml: Calibrating stamps...
/home/lacerda/.local/lib/python3.10/site-packages/scubes/core.py:523: RuntimeWarning: cdelt will be ignored since cd is present
  nw.wcs.cdelt[:2] = w.wcs.cdelt
[2024-05-26T21:34:23.287041] - scubesml: Cube successfully created!
[2024-05-26T21:34:23.287061] - scubesml: Removing downloaded data

Header information

At this point, we can see that the Masterlist information is stored at the header:

from scubes.utilities.readscube import read_scube

filename = 'ESO419-G013/ESO419-G013_cube.fits'
scube = read_scube(filename)
scube.primary_header

SIMPLE  =                    T / conforms to FITS standard
BITPIX  =                    8 / array data type
NAXIS   =                    0 / number of array dimensions
EXTEND  =                    T
TILE    = 'SPLUS-s24s39'
GALAXY  = 'ESO419-G013'
SIZE    =                  472 / Side of the stamp in pixels
X0TILE  =             3053.381
Y0TILE  =             5962.645
RA      =             60.17338 / deg
DEC     =              -30.831 / deg
TYPE    = 'G       '
VELOCITY=               1490.0 / kms
REDSHIFT=              0.00497
DISTANCE=   22.059776288801466 / Mpc
EBV     =               0.0064 / mag
SIZE_ML =            23.614521 / SIZE masterlist

Running scubes for the entire list

A simple shell script could help to run scubes for the entire list of objects. We use tail and cut shell commands in order to get only the SNAME of the objects from the Masterlist file.

for SNAME in `tail -n+2 masterlist_example.csv | cut -f1 -d','`
do
    scubesml -frR -U YOURUSER -P YOURPASS --size_multiplicator 20 -- ${SNAME} masterlist_example.csv
done