cdspyreadme 1.9

ReadMe generator package (cdspyreadme)

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

pip install .

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.license = "CC0-1.0"
tablemaker.more_description = "Additional information of the data context."
tablemaker.putRef("II/246", "2mass catalogue")
tablemaker.putRef("http://...", "external link")

# Save ReadMe (in current directory)
tablemaker.makeReadMe()

# print ReadMe
import sys
tablemaker.makeReadMe(out=sys.stdout)

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("mag")

# modify format
column.set_format("F6.3")

# modify name and description
column.name = "umag"
column.description = "Magnitude in U band"
# Add a note
column.note = "filter INT/WFC/U" 

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()

Manage output directory

Update the output directory:

import cdspyreadme

tablemaker = cdspyreadme.CDSTablesMaker(outfolder="/tmp")

Manage ReadMe output

# save ReadMe in a .bak file
with open("/tmp/ReadMe.bak", "w") as fd:
    tablemaker.makeReadMe(out=fd)