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Cannot allocate memory #299

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merged 2 commits into from
May 19, 2016
Merged

Cannot allocate memory #299

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39d719a
fix an issue where superhuge files can't be opened by using a different
keflavich May 19, 2016
e82b66a
load test data in readonly mode instead of denywrite mode
keflavich May 19, 2016
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9 changes: 7 additions & 2 deletions spectral_cube/io/fits.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ def is_fits(input, **kwargs):
return False


def read_data_fits(input, hdu=None, **kwargs):
def read_data_fits(input, hdu=None, mode='denywrite', **kwargs):
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@e-koch e-koch May 19, 2016 •
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Isn't mode passed through kwargs from SpectralCube.read to here already? I regularly use mode='denywrite' and haven't run into memory issues when dealing with big cubes.

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Yes. But I think this should be the default, as we don't expect users to be modifying the cube data inplace.

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Ah ok. Agreed.

"""
Read an array and header from an FITS file.

Expand All @@ -58,6 +58,11 @@ def read_data_fits(input, hdu=None, **kwargs):
- :class:`~astropy.io.fits.hdu.hdulist.HDUList`
hdu : int or str, optional
The HDU to read the table from.
mode : str
One of the FITS file reading modes; see `~astropy.io.fits.open`.
``denywrite`` is used by default since this prevents the system from
checking that the entire cube will fit into swap, which can prevent the
file from being opened at all.
"""

beam_table = None
Expand Down Expand Up @@ -100,7 +105,7 @@ def read_data_fits(input, hdu=None, **kwargs):

else:

hdulist = fits_open(input, **kwargs)
hdulist = fits_open(input, mode=mode, **kwargs)

try:
return read_data_fits(hdulist, hdu=hdu)
Expand Down
2 changes: 1 addition & 1 deletion spectral_cube/tests/test_spectral_cube.py
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Expand Up @@ -57,7 +57,7 @@ def cube_and_raw(filename):

d = fits.getdata(p)

c = SpectralCube.read(p, format='fits')
c = SpectralCube.read(p, format='fits', mode='readonly')
return c, d


Expand Down