Input/Output

List of available functions

• is_VOtable

• loadVOtable

• VOtableColumns

• write_array_to_vot

• add_new_array_to_previous

• move_bad_fields_to_bottom

Examples

Below are a few examples on how to use some functions. First, let us generate fake data and write them into a VOtable file:

from astropy.table import Table

tab = Table(names=('ID', 'value1', 'value2'))
tab.add_row((1, 25, 13))
tab.add_row((2, 0, 6))
tab.add_row((3, 2, -7))
tab.write('data.vot', format='votable')

Now we can play with the VOtable file.

from wilfried.utilities.io import is_VOtable, loadVOtable, VOtableColumns, write_array_to_vot

file          = 'data.vot'

# First let us print column names
columns       = VOtableColumns(file)
print(columns)

# Then we check file type and then load data
if is_VOtable(file):              # IOError is automatically raised if file is not a VOtable
   catalogue1 = load_VOtable(file) # default output is astropy Table
print(catalogue1)

# Now we load it as an astropy structured array
if is_VOtable(file):
   catalogue2 = loadVOtable(file, outputType='array')
print(catalogue2)

# We can directly save the array into a new VOtable file without converting to a Table
new_file      = 'new_data.vot'
write_array_to_vot(catalogue2, 'new_data.vot')

# Let us check whether it saved data correctly
catalogue3    = loadVOtable(new_file)
print(catalogue3)

Documentation

Code author: Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Functions related to input-output interaction.

utilities.io.is_VOtable(fullname)

Code author: Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Check whether a file is a VOtable.

Parameters

fullname (str) – name of the file

Returns

True if it is a VOtable

Return type

bool

Raises

IOError – if fullname is no a VOtable

utilities.io.loadVOtable(name, outputType='Table', num=0, pedantic=False, use_names_over_ids=False)

Code author: Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Load a VOtable using astropy.

Parameters

• name (str) – VOtable catalogue file name

• num (int) – (Optional) positon of the table to load within the VOtable file

• outputType (str) –

  (Optional) type of output data. Must be one of the following:

  • ’default’ to load it as an Astropy VOtable data type

  • ’array’ to load it as a numpy structured array

  • ’Table’ to load it as an Astropy Table

• pedantic (bool) – (Optional) whether to disable Exceptions when reading VOtable files with unusual keywords

• use_names_over_id (bool) – (Optional) whether (when creating as astropy Table out of the VOtable table element) to use columns names rather than the unique IDs in the VOtable columns to name the astropy Table columns

Returns

loaded table

Raises

TypeError –

• if outputType is not of type str

• if num is not of type int

utilities.io.VOtableColumns(name, fullInfo=False)

Code author: Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Show the column names in the VOtable object.

Parameters

• name (str) – VOtable file name

• fullInfo (bool) – (Optional) whether to show full information or just the names

utilities.io.write_array_to_vot(array, outputFile)

Code author: Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Write a numpy array or an astropy Table into a VOtable file.

Note

If array is not an astropy Table, it is converted to it.

Parameters

• array (numpy structured array of astropy Table) – array to write into the file

• outputFile (str) – file to write the array into

utilities.io.add_new_array_to_previous(newArray, fullFileName, fields, oldArray=None, isFirstArray=False, fieldsToDrop=None, typesToDrop=None)

Code author: Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Append a new structured array to another one, only keeping some fields after applying their corresponding data types onto the new columns. This function is used to combine data from different MUSE catalogues where field names and data types may vary between different versions.

Parameters

• fields (list[str]) – field names

• fullfilename (str) – name of the new array to append to the previous one

• newArray – new array to append to the previous one

• fieldsToDrop (list[str]) – (Optional) names of the fields to move to the bottom and change their type. If not None, typesToDrop must be a list of the same size.

• isFirstArray (bool) – (Optional) whether this is the first array generated with this function or not. If True a check will be made at the end.

• oldArray ((Optional) structured ndarray) – previous array whereto append new data

• typesToDrop (list) – (Optional) data types corresponding to the specified fields which must be dropped to the bottom

Returns

new structured array where all the content of the previous ones has been correctly appended

Return type

structured ndarray

utilities.io.move_bad_fields_to_bottom(array, orderedFieldList, orderedTypeList)

Code author: Wilfried Mercier - IRAP <wilfried.mercier@irap.omp.eu>

Move a list of fields from a structured array to the bottom and change their type.

Parameters

• array (structured ndarray) – array to modify

• orderedFieldList (list[str]) – list of field names to move and to change type

• orderedTypeList (list) – list of new types for the fields (same order as orderedFieldList)

Returns

array with some fields moved to the bottom and with different types

Return type

structured ndarray