ReadMe Generator Python library
The cdspyreadme library is a Python package dedicated for authors who want to submit data in VizieR or AAS.
The package builts ReadMe, standardized tables (in ASCII aligned format) or MRT tables from tables which can be in different formats (CSV, votable, FITS, astropy table, MRT)
by G.Landais (CDS) 24 june 2016
Requirements
The cdspyreadme library works with Python3 and requires :
- astropy
- numpy
Notes: for large tables, we recommend to use the C- anafile package
Anafile download: http://cdsarc.unistra.fr/ftp/sw/anafile.tar.gz Anafile documentation: http://cdsarc.unistra.fr/doc/anafile.htx
Install
python3 setup.py install --user
Examples
import cdspyreadme
tablemaker = cdspyreadme.CDSTablesMaker()
# add a table
table = tablemaker.addTable("table.csv", description="my CSV table")
# write table in CDS-ASCII aligned format (required)
tablemaker.writeCDSTables()
# Customize ReadMe output
tablemaker.title = "catalogue title"
tablemaker.author = 'G.Landais'
tablemaker.date = 2020
tablemaker.abstract = "This is my abstract..."
tablemaker.more_description = "Additional information of the data context."
tablemaker.putRef("II/246", "2mass catalogue")
tablemaker.putRef("http://...", "external link")
# Print ReadMe
tablemaker.makeReadMe()
# Save ReadMe into a file
with open("ReadMe", "w") as fd:
tablemaker.makeReadMe(out=fd)add astropy table
from astropy.table import Table
import cdspyreadme
astropy_table = Table([(1.4845, 1.4835, -1.234),
(24.5, 18.2401, 23.426),
('HD100', 'HD101', None)],
names=['ra', 'dec','name'])
tablemaker = cdspyreadme.CDSTablesMaker()
tablemaker.addTable(astropy_table, name="table1")
# add an other local table (in VOTable)
table2 = Table.read("table.vot")
tablemaker.addTable(table2, name="table2")
tablemaker.writeCDSTables()
tablemaker.makeReadMe()use astropy Masked Column to remove values according criteria
from astropy.table import Table, MaskedColumn
import cdspyreadme
tablemaker = cdspyreadme.CDSTablesMaker()
csv = Table.read("table.csv")
csv.columns[0] = MaskedColumn(csv.columns[0], mask=[(val>10) for val in csv.columns[0]])
tablemaker.addTable(csv, name="data.cds")
tablemaker.writeCDSTables()
tablemaker.makeReadMe()Sexagesimal columns
Flag sexagesimal columns in ReadMe.
The method transforms string columns (ie: ra_sexa, de_sexa) in columns RAh, Ram, RAs, DEsign, DEd, DEm, DEs.
from astropy.table import Table
import cdspyreadme
tablemaker = cdspyreadme.CDSTablesMaker()
csv = Table.read("table.csv")
table = tablemaker.addTable(csv, name="data.cds")
ra = table.get_column("ra_sexa")
ra.setSexaRa()
de = table.get_column("dec_sexa")
de.setSexaDe()
tablemaker.writeCDSTables()
tablemaker.makeReadMe()add ASCII aligned table
from astropy.table import Table
import cdspyreadme
tablemaker = cdspyreadme.CDSTablesMaker()
ascii = cdspyreadme.CDSAsciiTable("table.ascii", "table1", description="ascii table")
table = tablemaker.addTable(ascii)
tablemaker.writeCDSTables()
tablemaker.makeReadMe()MRT example
The following example builds MRT table from a CSV table
from astropy.table import Table
import cdspyreadme
tablemaker = cdspyreadme.CDSTablesMaker()
tablemaker.title = "catalogue title"
tablemaker.author = 'G.Landais'
csv = Table.read("table.csv")
# rename columns
colra = csv["ra"]
colra.name = "RAdeg"
colra.description="Right ascension"
colra.unit='deg'
...
table = tablemaker.addTable(ascii, name='table.mrt', description='csv file')
tablemaker.toMRT()update column
...
table = tablemaker.addTable(...)
column = table.get_column("ra")
# modify format
column.set_format("F10.6")
# modify name and description
column.name="raj2000"
column.description="right ascension in ICRS"
tablemaker.writeCDSTables()
tablemaker.makeReadMe()FITS update
How to add columns description using TCOMMx cards -
from astropy.io import fits
from astropy.table import Table
import cdspyreadme
tab = Table.read("catalogue.fits")
fitstable = fits.open("catalogue.fits")
hdu = fitstable[1]
# update description from FITS header
for i in range(len(tab.columns)):
tab.columns[i].description = hdu.header["TCOMM"+str(i+1)]
fits.close()
tablemaker = cdspyreadme.CDSTablesMaker()
table = tablemaker.addTable(tab)
tablemaker = cdspyreadme.CDSTablesMaker()
table = tablemaker.addTable(tab)
tablemaker.writeCDSTables()
