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io.fits.Column dim keyword fails for 2D column of strings #5279
Description
This might be user error, but I think the dim keyword for astropy.io.fits.Column doesn't work properly for the case of 2D column of strings. Testing under python 2.7.11 with astropy 1.2.1:
It is possible to write a numpy structured array that contains a 2D column of strings to a fits file:
from astropy.io import fits
import numpy as np
dtype = [
('x', (str, 5)), #- 1D column of 5-character strings
('y', (str, 3), (4,)), #- 2D column; each row is four 3-char strings
]
data = np.zeros(2, dtype=dtype)
data['x'] = ['abcde', 'xyz']
data['y'][0] = ['A', 'BC', 'DEF', '123']
data['y'][1] = ['X', 'YZ', 'PQR', '999']
fits.writeto('blat.fits', data, clobber=True)
dx, hdr = fits.getdata('blat.fits', header=True)hdr =
XTENSION= 'BINTABLE' / binary table extension
BITPIX = 8 / array data type
NAXIS = 2 / number of array dimensions
NAXIS1 = 17 / length of dimension 1
NAXIS2 = 2 / length of dimension 2
PCOUNT = 0 / number of group parameters
GCOUNT = 1 / number of groups
TFIELDS = 2 / number of table fields
TTYPE1 = 'x '
TFORM1 = '5A '
TTYPE2 = 'y '
TFORM2 = '12A '
TDIM2 = '(3,4) '
Trying to create the 2D column by hand using the dim keyword fails, however:
col1 = fits.Column(name='x', format='5A', array=data['x'])
col2 = fits.Column(name='y', format='12A', array=data['y'], dim=(3,4))
Traceback:
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-3-0d4ea33cdccc> in <module>()
1 col1 = fits.Column(name='x', format='5A', array=data['x'])
----> 2 col2 = fits.Column(name='y', format='12A', array=data['y'], dim=(3,4))
/Users/sbailey/anaconda/lib/python2.7/site-packages/astropy/io/fits/column.pyc in __init__(self, name, format, unit, null, bscale, bzero, disp, start, dim, array, ascii)
589 'format `%s`.' % format)
590
--> 591 array = self._convert_to_valid_data_type(array)
592
593 # We have required (through documentation) that arrays passed in to
/Users/sbailey/anaconda/lib/python2.7/site-packages/astropy/io/fits/column.pyc in _convert_to_valid_data_type(self, array)
1084 shape = dims[:-1] if 'A' in format else dims
1085 shape = (len(array),) + shape
-> 1086 array = array.reshape(shape)
1087
1088 if 'P' in format or 'Q' in format:
ValueError: total size of new array must be unchanged
It is quite possible that I'm misunderstanding how to specify the format and dim keywords, but I would have expected them to match desired TFORMn and TDIMn keywords of the output fits file.
Activity
pllim commentedon Aug 30, 2016
I think you have to explicitly create the
Columnobjects first before constructing the FITS table. I am able to get something working like this:If this solves your problem, please close the issue. Thanks.
sbailey commentedon Aug 30, 2016
User error! the
dimoption needs to be astr(as the documentation says...) instead of a tuple as I was providing. Thanks for the quick reply. Closing issue.