In this section, we will see how to:
Keys: astropy.io.fits
Import required Astropy modules to handle fits files
from astropy.io import fits
A module is a file containing Python definitions and statements.
The file name is the module name except for the suffix .py appended. Within a module, the module’s name is available as the value of the global variable __name__
A module can contain executable statements as well as function definitions. These statements are intended to initialize the module. They are executed only the first time the module name is encountered in an import statement.
Modules can import other modules
A module can be aliased to a different name using the import xx as yy import statement
import numpy as np
When a module named spam is imported, the interpreter:
if that is not found, it then searches for a file named spam.py in a list of directories given by the variable sys.path. sys.path is initialized from these locations:
PYTHONPATH (a list of directory names, specified with the same syntax as the shell variable PATH).from astropy.io import fits
Open the file: the .open() function doesn't load data and headers, it just gives us access to the file and allows us to view the file structure.
filename='data/mef_example.fits'
hdulist=fits.open(filename)
When a FITS file is opened, an HDUList object is returned.
This is the top-level FITS object: a list-like collection of HDU objects.
An HDU (Header Data Unit) is the highest level component of the FITS file structure, consisting of a header and (typically) a data array or table.
hdulist
[<astropy.io.fits.hdu.image.PrimaryHDU object at 0x7f5c9003bf60>, <astropy.io.fits.hdu.image.ImageHDU object at 0x7f5c6b4f6e80>, <astropy.io.fits.hdu.table.BinTableHDU object at 0x7f5c6b505860>, <astropy.io.fits.hdu.image.ImageHDU object at 0x7f5c6aa1f940>, <astropy.io.fits.hdu.image.ImageHDU object at 0x7f5c6aa1f898>]
%pprint
dir(hdulist)
Pretty printing has been turned OFF
['__add__', '__class__', '__contains__', '__copy__', '__deepcopy__', '__delattr__', '__delitem__', '__dict__', '__dir__', '__doc__', '__enter__', '__eq__', '__exit__', '__format__', '__ge__', '__getattribute__', '__getitem__', '__gt__', '__hash__', '__iadd__', '__imul__', '__init__', '__init_subclass__', '__iter__', '__le__', '__len__', '__lt__', '__module__', '__mul__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__reversed__', '__rmul__', '__setattr__', '__setitem__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_data', '_file', '_flush_resize', '_flush_update', '_in_read_next_hdu', '_open_kwargs', '_positive_index_of', '_read_all', '_read_next_hdu', '_readfrom', '_resize', '_save_backup', '_truncate', '_try_while_unread_hdus', '_verify', '_wasresized', 'append', 'clear', 'close', 'copy', 'count', 'extend', 'fileinfo', 'filename', 'flush', 'fromfile', 'fromstring', 'index', 'index_of', 'info', 'insert', 'pop', 'readall', 'remove', 'reverse', 'run_option', 'sort', 'update_extend', 'verify', 'writeto']
hdulist?
Python documentation strings (or docstrings) provide a convenient way of associating documentation with Python modules, functions, classes, and methods.
Unlike conventional source code comments the docstring should describe what the function does, not how.
hdulist.info?
hdulist.info()
Filename: data/mef_example.fits No. Name Ver Type Cards Dimensions Format 0 PRIMARY 1 PrimaryHDU 12 (2155,) float32 1 EXR2D 1 ImageHDU 17 (2155, 92) float32 2 OBJ 1 BinTableHDU 180 103R x 9C [1J, 1J, 1J, 1J, 1J, 1E, 1E, 1D, 1D] 3 1 ImageHDU 7 (37, 15) uint8 4 EXR2D 1 ImageHDU 8 (37, 15) uint8
by index (python indexes start from 0)
hdulist[1]
<astropy.io.fits.hdu.image.ImageHDU at 0x7f5c6b4f6e80>
or by extention name
hdulist['EXR2D']
<astropy.io.fits.hdu.image.ImageHDU at 0x7f5c6b4f6e80>
1 and EXR2D are the same extension
hdulist[1] is hdulist['EXR2D']
True
Again: by index
exr2d = hdulist.pop(1)
or by hdu name
obj = hdulist.pop('OBJ')
Append extension at the end of the file
hdulist.append(exr2d)
hdulist.info()
Filename: data/mef_example.fits No. Name Ver Type Cards Dimensions Format 0 PRIMARY 1 PrimaryHDU 12 (2155,) float32 1 1 ImageHDU 7 (37, 15) uint8 2 EXR2D 1 ImageHDU 8 (37, 15) uint8 3 EXR2D 1 ImageHDU 17 (2155, 92) float32
Or insert extension in a specific position
hdulist.insert(1, obj)
The HDU object has the .header attribute to handle FITS header, both for tables
obj.header
XTENSION= 'BINTABLE' / binary table extension
BITPIX = 8 / 8-bit bytes
NAXIS = 2 / 2-dimensional binary table
NAXIS1 = 44
NAXIS2 = 103
PCOUNT = 0 / size of special data area
GCOUNT = 1 / one data group (required keyword)
TFIELDS = 9
TTYPE1 = 'SLIT ' / label for field 1
TFORM1 = '1J ' / data format of field: 4-byte INTEGER
TTYPE2 = 'IFUSLIT_NO' / label for field 2
TFORM2 = '1J ' / data format of field: 4-byte INTEGER
TTYPE3 = 'IFUFIBER_NO' / label for field 3
TFORM3 = '1J ' / data format of field: 4-byte INTEGER
TTYPE4 = 'Y ' / label for field 4
TFORM4 = '1J ' / data format of field: 4-byte INTEGER
TTYPE5 = 'OBJ_NO ' / label for field 5
TFORM5 = '1J ' / data format of field: 4-byte INTEGER
TTYPE6 = 'OBJ_X ' / label for field 6
TFORM6 = '1E ' / data format of field: 4-byte REAL
TTYPE7 = 'OBJ_Y ' / label for field 7
TFORM7 = '1E ' / data format of field: 4-byte REAL
TTYPE8 = 'OBJ_RA ' / label for field 8
TFORM8 = '1D ' / data format of field: 8-byte DOUBLE
TTYPE9 = 'OBJ_DEC ' / label for field 9
TFORM9 = '1D ' / data format of field: 8-byte DOUBLE
EXTNAME = 'OBJ '
and for images
hdulist[0].header
SIMPLE = T / file does conform to FITS standard BITPIX = -32 / number of bits per data pixel NAXIS = 1 / number of data axes NAXIS1 = 2155 / length of data axis 1 EXTEND = T / FITS dataset may contain extensions COMMENT FITS (Flexible Image Transport System) format is defined in 'Astronomy COMMENT and Astrophysics', volume 376, page 359; bibcode: 2001A&A...376..359H CRVAL1 = 4500. CRPIX1 = 1. CTYPE1 = 'WAVE ' CDELT1 = 2.55299997329712 CUNIT1 = 'Angstrom'
The .data attribute gives us access to tables data
obj.data
FITS_rec([( 1, 0, 0, 0, 1, -119.608116 , 7.42040e+01, 0., 0.),
( 2, 0, 0, 1, 1, -115.60632 , -1.09026e+02, 0., 0.),
( 3, 0, 0, 2, 1, -115.35641 , 1.42585e+02, 0., 0.),
( 4, 0, 0, 3, 1, -113.2135 , -1.01476e+02, 0., 0.),
( 4, 0, 0, 4, 2, -111.777954 , -1.01476e+02, 0., 0.),
( 4, 0, 0, 5, 3, -108.6676 , -1.01476e+02, 0., 0.),
( 5, 0, 0, 6, 1, -108.60712 , -5.87600e+00, 0., 0.),
( 6, 0, 0, 7, 1, -110.067444 , 8.50790e+01, 0., 0.),
( 7, 0, 0, 8, 1, -103.89667 , -7.02480e+01, 0., 0.),
( 8, 0, 0, 9, 1, -104.46953 , 2.90410e+01, 0., 0.),
( 9, 0, 0, 10, 1, -98.06541 , -3.51880e+01, 0., 0.),
(10, 0, 0, 11, 1, -99.7153 , 4.45260e+01, 0., 0.),
(11, 0, 0, 12, 1, -92.164055 , -1.10603e+02, 0., 0.),
(12, 0, 0, 13, 1, -92.60097 , -5.74900e+00, 0., 0.),
(13, 0, 0, 14, 1, -92.32721 , 1.14094e+02, 0., 0.),
(14, 0, 0, 15, 1, -87.38498 , -1.05911e+02, 0., 0.),
(14, 0, 0, 16, 2, -86.18945 , -1.05911e+02, 0., 0.),
(15, 0, 0, 17, 1, -85.2454 , 3.15660e+01, 0., 0.),
(16, 0, 0, 18, 1, -86.30322 , 1.42199e+02, 0., 0.),
(17, 0, 0, 19, 1, -79.98973 , -8.52750e+01, 0., 0.),
(18, 0, 0, 20, 1, -80.94561 , 3.08900e+01, 0., 0.),
(19, 0, 0, 21, 1, -75.25018 , -4.01500e+01, 0., 0.),
(20, 0, 0, 22, 1, -75.983315 , 6.41290e+01, 0., 0.),
(21, 0, 0, 23, 1, -75.10154 , 1.54171e+02, 0., 0.),
(22, 0, 0, 24, 1, -68.35159 , -1.59720e+01, 0., 0.),
(23, 0, 0, 25, 1, -64.41236 , 6.87920e+01, 0., 0.),
(24, 0, 0, 26, 1, -59.68167 , -9.32580e+01, 0., 0.),
(25, 0, 0, 27, 1, -60.748634 , 1.22820e+01, 0., 0.),
(25, 0, 0, 28, 2, -58.83927 , 1.22820e+01, 0., 0.),
(26, 0, 0, 29, 1, -62.617672 , 1.28410e+02, 0., 0.),
(26, 0, 0, 30, 2, -60.349724 , 1.28410e+02, 0., 0.),
(27, 0, 0, 31, 1, -45.9311 , -4.24500e+00, 0., 0.),
(28, 0, 0, 32, 1, -46.021385 , 1.26591e+02, 0., 0.),
(29, 0, 0, 33, 1, -41.52 , -1.10012e+02, 0., 0.),
(30, 0, 0, 34, 1, -41.414776 , 8.69400e+00, 0., 0.),
(31, 0, 0, 35, 1, -42.036407 , 1.02057e+02, 0., 0.),
(32, 0, 0, 36, 1, -38.561604 , -8.61700e+01, 0., 0.),
(32, 0, 0, 37, 2, -35.577747 , -8.61700e+01, 0., 0.),
(33, 0, 0, 38, 1, -30.18095 , -1.11533e+02, 0., 0.),
(34, 0, 0, 39, 1, -32.984318 , 1.11016e+02, 0., 0.),
(34, 0, 0, 40, 2, -30.71782 , 1.11016e+02, 0., 0.),
(35, 0, 0, 41, 1, -26.02951 , 9.48200e+00, 0., 0.),
(36, 0, 0, 42, 1, -21.624432 , -8.06200e+01, 0., 0.),
(37, 0, 0, 43, 1, -21.524958 , 2.99130e+01, 0., 0.),
(38, 0, 0, 44, 1, -14.595522 , -7.33290e+01, 0., 0.),
(39, 0, 0, 45, 1, -16.021965 , 1.64620e+01, 0., 0.),
(40, 0, 0, 46, 1, -8.362046 , -9.92610e+01, 0., 0.),
(41, 0, 0, 47, 1, -9.293859 , -2.10640e+01, 0., 0.),
(42, 0, 0, 48, 1, -9.04891 , 6.03460e+01, 0., 0.),
(43, 0, 0, 49, 1, -2.5964928, -3.59340e+01, 0., 0.),
(44, 0, 0, 50, 1, -4.033945 , 1.32130e+02, 0., 0.),
(45, 0, 0, 51, 1, -0.4278739, -5.33250e+01, 0., 0.),
(45, 0, 0, 52, 2, 1.3605044, -5.33250e+01, 0., 0.),
(46, 0, 0, 53, 1, 1.3615531, 3.42010e+01, 0., 0.),
(46, 0, 0, 54, 2, 3.38824 , 3.42010e+01, 0., 0.),
(47, 0, 0, 55, 1, 9.226427 , -5.03980e+01, 0., 0.),
(48, 0, 0, 56, 1, 8.116842 , 1.42469e+02, 0., 0.),
(49, 0, 0, 57, 1, 14.850358 , -6.54050e+01, 0., 0.),
(50, 0, 0, 58, 1, 13.669239 , 9.75700e+01, 0., 0.),
(51, 0, 0, 59, 1, 18.910612 , 1.00303e+02, 0., 0.),
(52, 0, 0, 60, 1, 23.899364 , 2.87140e+01, 0., 0.),
(53, 0, 0, 61, 1, 23.2754 , 1.34514e+02, 0., 0.),
(54, 0, 0, 62, 1, 27.753693 , -8.40640e+01, 0., 0.),
(55, 0, 0, 63, 1, 27.485924 , 2.12570e+01, 0., 0.),
(56, 0, 0, 64, 1, 25.082659 , 1.22246e+02, 0., 0.),
(56, 0, 0, 65, 2, 28.53829 , 1.22246e+02, 0., 0.),
(57, 0, 0, 66, 1, 33.019928 , -1.44330e+01, 0., 0.),
(58, 0, 0, 67, 1, 33.97993 , 6.49340e+01, 0., 0.),
(59, 0, 0, 68, 1, 33.395218 , 1.48212e+02, 0., 0.),
(60, 0, 0, 69, 1, 45.593807 , -5.39890e+01, 0., 0.),
(60, 0, 0, 70, 2, -53.989 , 1.40130e-45, 0., 0.),
(61, 0, 0, 71, 1, 45.336937 , 4.07030e+01, 0., 0.),
(62, 0, 0, 72, 1, 46.297855 , 1.28767e+02, 0., 0.),
(63, 0, 0, 73, 1, 50.872593 , -7.53470e+01, 0., 0.),
(64, 0, 0, 74, 1, 51.167118 , 4.74570e+01, 0., 0.),
(65, 0, 0, 75, 1, 56.663136 , 3.70050e+01, 0., 0.),
(66, 0, 0, 76, 1, 54.76473 , 1.31123e+02, 0., 0.),
(67, 0, 0, 77, 1, 58.6325 , -7.87050e+01, 0., 0.),
(67, 0, 0, 78, 2, 60.77545 , -7.87050e+01, 0., 0.),
(68, 0, 0, 79, 1, 60.430305 , 7.51200e+01, 0., 0.),
(68, 0, 0, 80, 2, 61.85958 , 7.51200e+01, 0., 0.),
(69, 0, 0, 81, 1, 63.805725 , -3.54450e+01, 0., 0.),
(69, 0, 0, 82, 2, 66.42547 , -3.54450e+01, 0., 0.),
(70, 0, 0, 83, 1, 66.04384 , 6.51580e+01, 0., 0.),
(71, 0, 0, 84, 1, 65.72256 , 1.50485e+02, 0., 0.),
(72, 0, 0, 85, 1, 72.873436 , -1.12204e+02, 0., 0.),
(73, 0, 0, 86, 1, 74.22504 , 6.15300e+00, 0., 0.),
(74, 0, 0, 87, 1, 71.02607 , 8.54410e+01, 0., 0.),
(75, 0, 0, 88, 1, 80.73261 , -3.86400e+01, 0., 0.),
(76, 0, 0, 89, 1, 80.90338 , 1.02864e+02, 0., 0.),
(77, 0, 0, 90, 1, 83.022705 , -1.09812e+02, 0., 0.),
(77, 0, 0, 91, 2, 84.68768 , -1.09812e+02, 0., 0.),
(78, 0, 0, 92, 1, 88.6741 , -1.25280e+01, 0., 0.),
(79, 0, 0, 93, 1, 86.65988 , 6.82050e+01, 0., 0.),
(80, 0, 0, 94, 1, 93.39009 , -4.89810e+01, 0., 0.),
(81, 0, 0, 95, 1, 91.45818 , 4.55620e+01, 0., 0.),
(81, 0, 0, 96, 2, 93.00592 , 4.55620e+01, 0., 0.),
(82, 0, 0, 97, 1, 99.217575 , 3.23130e+01, 0., 0.),
(83, 0, 0, 98, 1, 97.5867 , 1.35900e+02, 0., 0.),
(84, 0, 0, 99, 1, 103.36665 , -8.61290e+01, 0., 0.),
(85, 0, 0, 100, 1, 104.00345 , 2.04830e+01, 0., 0.),
(86, 0, 0, 101, 1, 108.91283 , -6.05080e+01, 0., 0.),
(87, 0, 0, 102, 1, 108.75126 , 3.57010e+01, 0., 0.)],
dtype=(numpy.record, [('SLIT', '>i4'), ('IFUSLIT_NO', '>i4'), ('IFUFIBER_NO', '>i4'), ('Y', '>i4'), ('OBJ_NO', '>i4'), ('OBJ_X', '>f4'), ('OBJ_Y', '>f4'), ('OBJ_RA', '>f8'), ('OBJ_DEC', '>f8')]))
or images data
exr2d.data
array([[2., 2., 2., ..., 2., 2., 2.],
[2., 2., 2., ..., 2., 2., 2.],
[2., 2., 2., ..., 2., 2., 2.],
...,
[2., 2., 2., ..., 2., 2., 2.],
[2., 2., 2., ..., 2., 2., 2.],
[2., 2., 2., ..., 2., 2., 2.]], dtype=float32)
We can save the whole HDU list
outfile='tmp/hdu_list.fits'
hdulist.writeto(outfile, overwrite = True)
hdulist.writeto?
Or save just a single HDU, like a table
outfile='tmp/hdu_table.fits'
hdulist['OBJ'].writeto(outfile, overwrite = True)
or an image
outfile='tmp/hdu_image.fits'
hdulist['EXR2D'].writeto(outfile, overwrite = True)
NOTE: In this case, since we are writing an ImageHDU (and not a PrimaryHDU), the saved file contains an empty PRIMARY and the image is saved as the second HDU
exr2d.writeto('tmp/hdu_image.fits', overwrite = True)
If we want to save the image as the Primary extension, we must create a PrimaryHDU from scratch using the data and header from the image we want to save
primary = fits.PrimaryHDU(data=hdulist['EXR2D'].data,
header=hdulist['EXR2D'].header)
primary.writeto('tmp/primary_image.fits', overwrite = True)
After we are done with the previously opened file, we have to close it with the .close() method
hdulist.close()
with fits.open(filename) as hdulist:
exrd2d=hdulist['EXR2D'].copy()
#That is equivalent to
hdulist=fits.open(filename)
exrd2d=hdulist['EXR2D'].copy()
hdulist.close()
After exiting the with scope, the file will be closed automatically. This is the preferred way to open a file in Python, because it will close the file even if an exception happens.