fitsutil

General fits file utilities.

Notes

For questions or comments please see our github page. We encourage and appreciate user feedback.

For the compression tasks included in fitsutil, astropy has replaced this functionality with the CompImageHDU class. We list both compression tasks together in this notebook with a few examples to show the usage of CompImageHDU. the astropy.io.fits can natively open compressed file with a standard fits.open command. To uncompress the file, you can then save the fits file object out to a new file.

astropy.io.fits is the library responsible for opening and closing fits files. It opens the file into a HDUList object, which contains multiple HDU objects that can be indexed with integers. Each HDU object contains array data object, and a header object.

Contents:

fpack-ricepack

Please review the Notes section above before running any examples in this notebook

We can compress an image HDU using the fits.CompImageHDU class in astropy. This class has several compression options (RICE, PLIO, GZIP, and HCOMPRESS). Here we show one example using RICE compression and another using GZIP compression

# Astronomy Specific Imports
from astropy.io import fits

# RICE example

# test files
test_data = '/eng/ssb/iraf_transition/test_data/jczgx1ppq_flc.fits'
outfile_rice = '/eng/ssb/iraf_transition/test_data/jczgx1ppq_rice.fits'

hdulist = fits.open(test_data)
hdu_rice = fits.CompImageHDU(data=hdulist[1].data, header=hdulist[1].header, compression_type='RICE_1')
hdulist_rice = fits.HDUList([hdulist[0],hdu_rice])
hdulist_rice.writeto(outfile_rice, overwrite=True)
hdulist.close()

# Gzip example

# test files
test_data = '/eng/ssb/iraf_transition/test_data/jczgx1ppq_flc.fits'
outfile_gzip = '/eng/ssb/iraf_transition/test_data/jczgx1ppq_gzip.fits'

hdulist = fits.open(test_data)
hdu_gzip = fits.CompImageHDU(data=hdulist[1].data, header=hdulist[1].header, compression_type='GZIP_1')
hdulist_gzip = fits.HDUList([hdulist[0],hdu_rice])
hdulist_gzip.writeto(outfile_gzip, overwrite=True)
hdulist.close()

fxcopy-fxinsert

Please review the Notes section above before running any examples in this notebook

Here we show how to copy out and add new HDU objects, the astropy equivalent of fxcopy and fxinsert.

# Standard Imports
import numpy as np

# Astronomy Specific Imports
from astropy.io import fits

# test files
test_data = '/eng/ssb/iraf_transition/test_data/jczgx1ppq_flc.fits'
outfile = '/eng/ssb/iraf_transition/test_data/fxinsert.fits'

# open fits file, this outputs an hdulist object
hdulist = fits.open(test_data)

# now let's pull out a reference (copy) of an HDU object from this HDUList
my_hdu = hdulist[1]

# Now let's create a new array to make a new HDU object, this will be the primary HDU
new = np.arange(100.0)
new_hdu = fits.PrimaryHDU(new)

# Now we can create a new HDUList object to put our HDU objects into
my_hdulist = fits.HDUList([new_hdu,my_hdu])

# Now we close write our new HDUList to a file, and close our test_data file
my_hdulist.writeto(outfile, overwrite=True)
hdulist.close()

fxdelete-fxsplit-fxextract

Please review the Notes section above before running any examples in this notebook

fxdelete will delete a FITS extension in place, and fxsplit and fxextract will take a multiple extension FITS file and break them out into single FITS files. Both these tasks can be done using astropy.io.fits. Below we show some a short example. We will pull out the 3rd extension from the test file, save it to a new fits file, and delete that extension from the original HDUList

# Astronomy Specific Imports
from astropy.io import fits

# FITS filenames
test_data = '/eng/ssb/iraf_transition/test_data/iczgs3y5q_flt.fits'
outfile_1 = '/eng/ssb/iraf_transition/test_data/fxsplit.fits'
outfile_2 = '/eng/ssb/iraf_transition/test_data/fxdelete.fits'

# Print out some stats for this file
fits.info(test_data)

# Open FITS file
hdulist = fits.open(test_data)

# Pull out single HDU extension and put into new FITS file
single_HDU = hdulist[3]
primary_HDU = fits.PrimaryHDU()
new_hdulist = fits.HDUList([primary_HDU,single_HDU])
new_hdulist.writeto(outfile_1, overwrite=True)


# Now save a new copy of the original file without that thrid extension
#cut_hdulist = hdulist[0:2] + hdulist[]
hdulist.pop(3)
hdulist.writeto(outfile_2, overwrite=True)

# Close original file
hdulist.close()

Filename: /eng/ssb/iraf_transition/test_data/iczgs3y5q_flt.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  PRIMARY       1 PrimaryHDU     265   ()
  1  SCI           1 ImageHDU       140   (1014, 1014)   float32
  2  ERR           1 ImageHDU        51   (1014, 1014)   float32
  3  DQ            1 ImageHDU        43   (1014, 1014)   int16
  4  SAMP          1 ImageHDU        37   (1014, 1014)   int16
  5  TIME          1 ImageHDU        37   (1014, 1014)   float32
  6  WCSCORR       1 BinTableHDU     59   7R x 24C   [40A, I, A, 24A, 24A, 24A, 24A, D, D, D, D, D, D, D, D, 24A, 24A, D, D, D, D, J, 40A, 128A]

fxdummyh

Please review the Notes section above before running any examples in this notebook

Fxdummyh will create an empty fits file.

# Astronomy Specific Imports
from astropy.io import fits

# Write empty file
hdu = fits.PrimaryHDU()
hdu.writeto('/eng/ssb/iraf_transition/test_data/empty.fits', overwrite=True)

# Let's look at the file we made
fits.info('/eng/ssb/iraf_transition/test_data/empty.fits')

Filename: /eng/ssb/iraf_transition/test_data/empty.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  PRIMARY       1 PrimaryHDU       4   ()

fxheader

Please review the Notes section above before running any examples in this notebook

Fxheader lists one line of header description per FITS unit. This funtionality has been replaced in a convience function in astropy, astropy.io.fits.info.

# Astronomy Specific Imports
from astropy.io import fits

# run fits.info
fits.info('/eng/ssb/iraf_transition/test_data/tester.fits')

Filename: /eng/ssb/iraf_transition/test_data/tester.fits
No.    Name      Ver    Type      Cards   Dimensions   Format
  0  PRIMARY       1 PrimaryHDU     270   ()
  1  SCI           1 ImageHDU       200   (4096, 2048)   float32
  2  ERR           1 ImageHDU        56   (4096, 2048)   float32
  3  DQ            1 ImageHDU        48   (4096, 2048)   int16
  4  SCI           2 ImageHDU       198   (4096, 2048)   float32
  5  ERR           2 ImageHDU        56   (4096, 2048)   float32
  6  DQ            2 ImageHDU        48   (4096, 2048)   int16
  7  D2IMARR       1 ImageHDU        15   (64, 32)   float32
  8  D2IMARR       2 ImageHDU        15   (64, 32)   float32
  9  D2IMARR       3 ImageHDU        15   (64, 32)   float32
 10  D2IMARR       4 ImageHDU        15   (64, 32)   float32
 11  WCSDVARR      1 ImageHDU        15   (64, 32)   float32
 12  WCSDVARR      2 ImageHDU        15   (64, 32)   float32
 13  WCSDVARR      3 ImageHDU        15   (64, 32)   float32
 14  WCSDVARR      4 ImageHDU        15   (64, 32)   float32
 15  WCSCORR       1 BinTableHDU     59   14R x 24C   [40A, I, A, 24A, 24A, 24A, 24A, D, D, D, D, D, D, D, D, 24A, 24A, D, D, D, D, J, 40A, 128A]

fxplf

Please review the Notes section above before running any examples in this notebook

fxplf is used to convert a pixel list file into a BINTABLE extension. We show a simple example below, see the Astropy unified read/write documentation for more details.

# Astronomy Specific Imports
from astropy.io import fits
from astropy.table import Table

# Define input and output files
infile = '/eng/ssb/iraf_transition/test_data/table3.txt'
outfile = '/eng/ssb/iraf_transition/test_data/table3.fits'

# read txt, write to fits
t = Table.read(infile, format='ascii')
print(t)
t.write(outfile, overwrite=True)

col1 col2
---- ----
 200   45
  34  222
   3    4
 100  200
   8   88
  23  123

Not Replacing

  • funpack - Uncompress FITS file, can be done by opening and resaving file with astropy.io.fits
  • fxconvert - Convert between IRAF image types. See images.imutil.imcopy
  • fgread - Read a MEF file with FOREIGN extensions. Deprecated.
  • fgwrite - Create a MEF file with FOREIGN extensions. Deprecated.