Unified file read/write interface: binary votable format

Hello,

is it possible to write a binary votable with the unified interface. The example given is:

t.write('new_catalog.xml', table_id='updated_table', format='votable')

This produces an ASCII format file.

The VOTABLE package supports TABLEDATA, BINARY, BINARY2
http://docs.astropy.org/en/stable/io/votable/index.html#outputting-a-votable-file

If the unified interface supports BINARY votable, what is the format that I should use?

i.e. t.write('new_catalog.xml', table_id='updated_table', format=????)

Thanks

It is unfortunate that https://github.com/astropy/astropy/blob/master/astropy/io/votable/connect.py#L136 is not exposed in user documentation. Does 'binary' or 'binary2' work for you?

Thanks,

format = 'binary' gives the error:

astropy.io.registry.IORegistryError: No writer defined for format 'binary' and class 'Table'.

I am using astropy 2.0.2 and 2.0.5
Meanwhile I used the io.votable.to do it:

table_thin = Table([table['RA'], table['Dec']])

from astropy.io.votable import from_table, writeto
votable = from_table(table_thin)
writeto(votable, "output.xml", tabledata_format='binary')

This could be a useful example for io.votable.

Hmm, looks like a bug in unified I/O connector. Documentation stated it is supported but the registry throws error. I am glad you have a workaround. Thanks for reporting this!

astropy.io.registry.IORegistryError: No writer defined for format 'binary' and class 'Table'.

Actually, I need some clarification. Maybe this is not a bug after all but wrong usage due to lack of documentation. I failed to reproduce the error you reported. These both worked for me using Astropy 3.1.dev21672.

t.write('new_catalog.xml', table_id='updated_table', format='votable',  tabledata_format='binary')

t.write('new_catalog.xml', table_id='updated_table', format='votable',  tabledata_format='binary', overwrite=True)

OK, it works for me too using:

format='votable', tabledata_format='binary'

So it looks like a pilot PICNIC error although giving an explicit example for binary and binary2 since I think the default is ASCII which for large datasets is too bulky.

Perhaps the doc update can be a part of work for #1011

@pllim

@pllim - would you think the new helps for the unified io addresses this issue, too? If yes, please close this.
#8255

@bsipocz

@bsipocz , unfortunately, not quite... The listing below does not provide all the options that are possible (e.g., tabledata_format). @taldcroft , any advice?

In [1]: import astropy

In [2]: astropy.__version__
Out[2]: '3.2'

In [3]: from astropy.table import Table

In [4]: Table.read.help('votable')

==========================================
Table.read(format='votable') documentation
==========================================

Read a Table object from an VO table file

Parameters
----------
input : str or `~astropy.io.votable.tree.VOTableFile` or `~astropy.io.votable.tr
ee.Table`
    If a string, the filename to read the table from. If a
    :class:`~astropy.io.votable.tree.VOTableFile` or
    :class:`~astropy.io.votable.tree.Table` object, the object to extract
    the table from.

table_id : str or int, optional
    The table to read in.  If a `str`, it is an ID corresponding
    to the ID of the table in the file (not all VOTable files
    assign IDs to their tables).  If an `int`, it is the index of
    the table in the file, starting at 0.

use_names_over_ids : bool, optional
    When `True` use the ``name`` attributes of columns as the names
    of columns in the `~astropy.table.Table` instance.  Since names
    are not guaranteed to be unique, this may cause some columns
    to be renamed by appending numbers to the end.  Otherwise
    (default), use the ID attributes as the column names.

@pllim

@pllim - you need to check the write help. 😸

>>> Table.write.help('votable')

===========================================
Table.write(format='votable') documentation
===========================================

Write a Table object to an VO table file

Parameters
----------
input : Table
    The table to write out.

output : str
    The filename to write the table to.

table_id : str, optional
    The table ID to use. If this is not specified, the 'ID' keyword in the
    ``meta`` object of the table will be used.

overwrite : bool, optional
    Whether to overwrite any existing file without warning.

tabledata_format : str, optional
    The format of table data to write.  Must be one of ``tabledata``
    (text representation), ``binary`` or ``binary2``.  Default is
    ``tabledata``.  See :ref:`votable-serialization`.

@taldcroft

Ops!!! Thanks for pointing that out, @taldcroft !

Navigation Menu

Repository navigation

Unified file read/write interface: binary votable format #7352

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Unified file read/write interface: binary votable format #7352

Description

Activity

pllim commented on Apr 5, 2018

richardgmcmahon commented on Apr 5, 2018

pllim commented on Apr 6, 2018

pllim commented on Apr 6, 2018

richardgmcmahon commented on Apr 6, 2018

pllim commented on Apr 6, 2018

bsipocz commented on Jun 18, 2019

pllim commented on Jun 19, 2019

taldcroft commented on Jun 19, 2019

pllim commented on Jun 19, 2019

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions