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- FITS File handling (`astropy.io.fits`)

# FITS File handling (`astropy.io.fits`)

## Introduction

The `astropy.io.fits` package provides access to FITS files. FITS (Flexible Image Transport System) is a portable file standard widely used in the astronomy community to store images and tables.

## Getting Started

This section provides a quick introduction of using `astropy.io.fits`. The goal is to demonstrate the package’s basic features without getting into too much detail. If you are a first time user or have never used Astropy or PyFITS, this is where you should start.

### Reading and Updating Existing FITS Files

#### Opening a FITS file

Once the `astropy.io.fits` package is loaded using the standard convention[1], we can open an existing FITS file:

    >>> from astropy.io import fits
    >>> hdulist = fits.open('input.fits')

The `open()` function has several optional arguments which will be discussed in a later chapter. The default mode, as in the above example, is “readonly”. The open function returns an object called an `HDUList` which is a Python list-like collection of HDU objects. An HDU (Header Data Unit) is the highest level component of the FITS file structure. So, after the above open call, `hdulist[0]` is the primary HDU, `hdulist[1]`, if any, is the first extension HDU, etc. It should be noted that Astropy is using zero-based indexing when referring to HDUs and header cards, though the FITS standard (which was designed with FORTRAN in mind) uses one-based indexing.

The `HDUList` has a useful method `HDUList.info()`, which summarizes the content of the opened FITS file:

    >>> hdulist.info()
    Filename: test1.fits
    No. Name  Type       Cards Dimensions Format
    0 PRIMARY PrimaryHDU   220 ()         int16
    1 SCI     ImageHDU      61 (800, 800) float32
    2 SCI     ImageHDU      61 (800, 800) float32
    3 SCI     ImageHDU      61 (800, 800) float32
    4 SCI     ImageHDU      61 (800, 800) float32

After you are done with the opened file, close it with the `HDUList.close()` method:

    >>> hdulist.close()

The headers will still be accessible after the HDUList is closed. The data may or may not be accessible depending on whether the data are touched and if they are memory-mapped, see later chapters for detail.

##### Working with large files

The `open()` function supports a `memmap=True` argument that allows the array data of each HDU to be accessed with mmap, rather than being read into memory all at once. This is particularly useful for working with very large arrays that cannot fit entirely into physical memory.

This has minimal impact on smaller files as well, though some operations, such as reading the array data sequentially, may incur some additional overhead. On 32-bit systems arrays larger than 2-3 GB cannot be mmap’d (which is fine, because by that point you’re likely to run out of physical memory anyways), but 64-bit systems are much less limited in this respect.

#### Working With a FITS Header

As mentioned earlier, each element of an `HDUList` is an HDU object with attributes of header and data, which can be used to access the header keywords and the data.

For those unfamiliar with FITS headers, they consist of a list of “cards”, where a card contains a keyword, a value, and a comment. The keyword and comment must both be strings, whereas the value can be a string or an integer, float, or complex number. Keywords are usually unique within a header, except in a few special cases.

The header attribute is a Header instance, another Astropy object. To get the value associated with a header keyword, simply do (a la Python dicts):

    >>> hdulist[0].header['targname']
    'NGC121'

to get the value of the keyword targname, which is a string ‘NGC121’.

Although keyword names are always in upper case inside the FITS file, specifying a keyword name with Astropy is case-insensitive, for the user’s convenience. If the specified keyword name does not exist, it will raise a `KeyError` exception.

We can also get the keyword value by indexing (a la Python lists):

    >>> hdulist[0].header[27]
    96

This example returns the 28th (like Python lists, it is 0-indexed) keyword’s value–an integer–96.

Similarly, it is easy to update a keyword’s value in Astropy, either through keyword name or index:

    >>> prihdr = hdulist[0].header
    >>> prihdr['targname'] = 'NGC121-a'
    >>> prihdr[27] = 99

It is also possible to update both the value and comment associated with a keyword by assigning them as a tuple:

    >>> prihdr = hdulist[0].header
    >>> prihdr['targname'] = ('NGC121-a', 'the observation target')
    >>> prihdr['targname']
    'NGC121-a'
    >>> prihdr.comments['targname']
    'the observation target'

Like a dict, one may also use the above syntax to add a new keyword/value pair (and optionally a comment as well). In this case the new card is appended to the end of the header (unless it’s a commentary keyword such as COMMENT or HISTORY, in which case it is appended after the last card with that keyword).

Another way to either update an existing card or append a new one is to use the `Header.set()` method:

    >>> prihdr.set('observer', 'Edwin Hubble')

Comment or history records are added like normal cards, though in their case a new card is always created, rather than updating an existing HISTORY or COMMENT card:

    >>> prihdr['history'] = 'I updated this file 2/26/09'
    >>> prihdr['comment'] = 'Edwin Hubble really knew his stuff'
    >>> prihdr['comment'] = 'I like using HST observations'
    >>> prihdr['comment']
    Edwin Hubble really knew his stuff
    I like using HST observations

Note: Be careful not to confuse COMMENT cards with the comment value for normal cards.

To updating existing COMMENT or HISTORY cards, reference them by index:

    >>> prihdr['history'][0] = 'I updated this file on 2/26/09'
    >>> prihdr['history']
    I updated this file on 2/26/09

To see the entire header as it appears in the FITS file (with the END card and padding stripped), simply enter the header object by itself, or print repr(header):

    >>> header
    SIMPLE  =                    T / file does conform to FITS standard
    BITPIX  =                   16 / number of bits per data pixel
    NAXIS   =                    0 / number of data axes
    ...all cards are shown...
    >>> print repr(header)
    ...identical...

It’s also possible to view a slice of the header:

    >>> header[:2]
    SIMPLE  =                    T / file does conform to FITS standard
    BITPIX  =                   16 / number of bits per data pixel

Only the first two cards are shown above.

To get a list of all keywords, use the `Header.keys()` method just as you would with a dict:

    >>> prihdr.keys()
    ['SIMPLE', 'BITPIX', 'NAXIS', ...]

#### Working With Image Data

If an HDU’s data is an image, the data attribute of the HDU object will return a numpy ndarray object. Refer to the numpy documentation for details on manipulating these numerical arrays.

    >>> scidata = hdulist[1].data

Here, scidata points to the data object in the second HDU (the first HDU, `hdulist[0]`, being the primary HDU) in `hdulist`, which corresponds to the ‘SCI’ extension. Alternatively, you can access the extension by its extension name (specified in the EXTNAME keyword):

    >>> scidata = hdulist['SCI'].data

If there is more than one extension with the same EXTNAME, EXTVER’s value needs to be specified as the second argument, e.g.:

    >>> scidata = hdulist['sci',2].data

The returned numpy object has many attributes and methods for a user to get information about the array, e.g.:

    >>> scidata.shape
    (800, 800)
    >>> scidata.dtype.name
    'float32'

Since image data is a numpy object, we can slice it, view it, and perform mathematical operations on it. To see the pixel value at x=5, y=2:

    >>> print scidata[1, 4]

Note that, like C (and unlike FORTRAN), Python is 0-indexed and the indices have the slowest axis first and fast axis last, i.e. for a 2-D image, the fast axis (X-axis) which corresponds to the FITS NAXIS1 keyword, is the second index. Similarly, the 1-indexed sub-section of x=11 to 20 (inclusive) and y=31 to 40 (inclusive) would be given in Python as:

    >>> scidata[30:40, 10:20]

To update the value of a pixel or a sub-section:

    >>> scidata[30:40, 10:20] = scidata[1, 4] = 999

This example changes the values of both the pixel [1, 4] and the sub-section [30:40, 10:20] to the new value of 999. See the Numpy documentation for more details on Python-style array indexing and slicing.

The next example of array manipulation is to convert the image data from counts to flux:

    >>> photflam = hdulist[1].header['photflam']
    >>> exptime = prihdr['exptime']
    >>> scidata *= photflam / exptime

This example performs the math on the array in-place, thereby keeping the memory usage to a minimum.

If at this point you want to preserve all the changes you made and write it to a new file, you can use the `HDUList.writeto()` method (see below).

#### Working With Table Data

If you are familiar with the record array in numpy, you will find the table data is basically a record array with some extra properties. But familiarity with record arrays is not a prerequisite for this Guide.

Like images, the data portion of a FITS table extension is in the `.data` attribute:

    >>> hdulist = fits.open('table.fits')
    >>> tbdata = hdulist[1].data # assuming the first extension is a table

To see the first row of the table:

    >>> print tbdata[0]
    (1, 'abc', 3.7000002861022949, 0)

Each row in the table is a `FITS_rec` object which looks like a (Python) tuple containing elements of heterogeneous data types. In this example: an integer, a string, a floating point number, and a Boolean value. So the table data are just an array of such records. More commonly, a user is likely to access the data in a column-wise way. This is accomplished by using the `field()` method. To get the first column (or field) of the table, use:

    >>> tbdata.field(0)
    array([1, 2])

A numpy object with the data type of the specified field is returned.

Like header keywords, a field can be referred either by index, as above, or by name:

    >>> tbdata.field('id')
    array([1, 2])

But how do we know what field names we’ve got? First, let’s introduce another attribute of the table HDU: the `columns` attribute:

    >>> cols = hdulist[1].columns

This attribute is a `ColDefs` (column definitions) object. If we use the `ColDefs.info()` method:

    >>> cols.info()
     name:
          ['c1', 'c2', 'c3', 'c4']
     format:
          ['1J', '3A', '1E', '1L']
     unit:
          ['', '', '', '']
     null:
          [-2147483647, '', '', '']
     bscale:
          ['', '', 3, '']
     bzero:
          ['', '', 0.40000000000000002, '']
     disp:
          ['I11', 'A3', 'G15.7', 'L6']
     start:
          ['', '', '', '']
     dim:
          ['', '', '', '']

it will show all its attributes, such as names, formats, bscales, bzeros, etc. We can also get these properties individually, e.g.:

    >>> cols.names
    ['ID', 'name', 'mag', 'flag']

returns a (Python) list of field names.

Since each field is a numpy object, we’ll have the entire arsenal of numpy tools to use. We can reassign (update) the values:

    >>> tbdata.field('flag')[:] = 0

#### Save File Changes

As mentioned earlier, after a user opened a file, made a few changes to either header or data, the user can use `HDUList.writeto()` to save the changes. This takes the version of headers and data in memory and writes them to a new FITS file on disk. Subsequent operations can be performed to the data in memory and written out to yet another different file, all without recopying the original data to (more) memory.

    >>> hdulist.writeto('newimage.fits')

will write the current content of `hdulist` to a new disk file newfile.fits. If a file was opened with the update mode, the `HDUList.flush()` method can also be used to write all the changes made since `open()`, back to the original file. The `close()` method will do the same for a FITS file opened with update mode:

    >>> f = fits.open('original.fits', mode='update')
    ... # making changes in data and/or header
    >>> f.flush() # changes are written back to original.fits

### Creating a New FITS File

#### Creating a New Image File

So far we have demonstrated how to read and update an existing FITS file. But how about creating a new FITS file from scratch? Such tasks are very easy in Astropy for an image HDU. We’ll first demonstrate how to create a FITS file consisting only the primary HDU with image data.

First, we create a numpy object for the data part:

    >>> import numpy as np
    >>> n = np.arange(100.0) # a simple sequence of floats from 0.0 to 99.9

Next, we create a `PrimaryHDU` object to encapsulate the data:

    >>> hdu = fits.PrimaryHDU(n)

We then create a HDUList to contain the newly created primary HDU, and write to a new file:

    >>> hdulist = fits.HDUList([hdu])
    >>> hdulist.writeto('new.fits')

That’s it! In fact, Astropy even provides a shortcut for the last two lines to accomplish the same behavior:

    >>> hdu.writeto('new.fits')

#### Creating a New Table File

To create a table HDU is a little more involved than image HDU, because a table’s structure needs more information. First of all, tables can only be an extension HDU, not a primary. There are two kinds of FITS table extensions: ASCII and binary. We’ll use binary table examples here.

To create a table from scratch, we need to define columns first, by constructing the `Column` objects and their data. Suppose we have two columns, the first containing strings, and the second containing floating point numbers:

    >>> from astropy.io import fits
    >>> import numpy as np
    >>> a1 = np.array(['NGC1001', 'NGC1002', 'NGC1003'])
    >>> a2 = np.array([11.1, 12.3, 15.2])
    >>> col1 = fits.Column(name='target', format='20A', array=a1)
    >>> col2 = fits.Column(name='V_mag', format='E', array=a2)

Next, create a `ColDefs` (column-definitions) object for all columns:

    >>> cols = fits.ColDefs([col1, col2])

Now, create a new binary table HDU object by using the `new_table()` function:

    >>> tbhdu = fits.new_table(cols)

This function returns (in this case) a `BinTableHDU`.

Of course, you can do this more concisely:

    >>> from astropy.io import fits
    >>> tbhdu = fits.new_table(
    ...     fits.ColDefs([fits.Column(name='target', format='20A', array=a1),
    ...                   fits.Column(name='V_mag', format='E', array=a2)]))

Now you may write this new table HDU directly to a FITS file like so:

    >>> hdu = fits.PrimaryHDU(n)

This shortcut will automatically create a minimal primary HDU with no data and prepend it to the table HDU to create a valid FITS file. If you require additional data or header keywords in the primary HDU you may still create a `PrimaryHDU` object and build up the FITS file manually using an `HDUList`.

For example, first create a new `Header` object to encapsulate any keywords you want to include in the primary HDU, then as before create a `PrimaryHDU`:

    >>> prihdr = fits.Header()
    >>> prihdr['COMMENT'] = "Here's some commentary about this FITS file."
    >>> prihdu = fits.PrimaryHDU(header=prihdr)

When we create a new primary HDU with a custom header this will automatically include any additional header keywords that are required by the FITS format (keywords such as `SIMPLE` and `NAXIS` for example).

We then create a HDUList containing both the primary HDU and the newly created table extension, and write to a new file:

    >>> thdulist = fits.HDUList([prihdu, tbhdu])
    >>> thdulist.writeto('table.fits')

Alternatively, you can append the table to the HDU list we already created in the image file section:

    >>> hdulist.append(tbhdu)
    >>> hdulist.writeto('image_and_table.fits')

So far, we have covered the most basic features of `astropy.io.fits`. In the following chapters we’ll show more advanced examples and explain options in each class and method.

### Convenience Functions

`astropy.io.fits` also provides several high level (“convenience”) functions. Such a convenience function is a “canned” operation to achieve one simple task. By using these “convenience” functions, a user does not have to worry about opening or closing a file, all the housekeeping is done implicitly.

The first of these functions is `getheader()`, to get the header of an HDU. Here are several examples of getting the header. Only the file name is required for this function. The rest of the arguments are optional and flexible to specify which HDU the user wants to get:

    >>> from astropy.io.fits import getheader
    >>> getheader('in.fits') # get default HDU (=0), i.e. primary HDU's header
    >>> getheader('in.fits', 0) # get primary HDU's header
    >>> getheader('in.fits', 2) # the second extension
    # the HDU with EXTNAME='sci' (if there is only 1)
    >>> getheader('in.fits', 'sci')
    # the HDU with EXTNAME='sci' and EXTVER=2
    >>> getheader('in.fits', 'sci', 2)
    >>> getheader('in.fits', ('sci', 2)) # use a tuple to do the same
    >>> getheader('in.fits', ext=2) # the second extension
    # the 'sci' extension, if there is only 1
    >>> getheader('in.fits', extname='sci')
    # the HDU with EXTNAME='sci' and EXTVER=2
    >>> getheader('in.fits', extname='sci', extver=2)
    # ambiguous specifications will raise an exception, DON'T DO IT!!
    >>> getheader('in.fits', ext=('sci',1), extname='err', extver=2)

After you get the header, you can access the information in it, such as getting and modifying a keyword value:

    >>> from astropy.io.fits import getheader
    >>> hdr = getheader('in.fits', 1) # get first extension's header
    >>> filter = hdr['filter'] # get the value of the keyword "filter'
    >>> val = hdr[10] # get the 11th keyword's value
    >>> hdr['filter'] = 'FW555' # change the keyword value

For the header keywords, the header is like a dictionary, as well as a list. The user can access the keywords either by name or by numeric index, as explained earlier in this chapter.

If a user only needs to read one keyword, the `getval()` function can further simplify to just one call, instead of two as shown in the above examples:

    >>> from astropy.io.fits import getval
    >>> flt = getval('in.fits', 'filter', 1) # get 1st extension's keyword
                                             # FILTER's value
    >>> val = getval('in.fits', 10, 'sci', 2) # get the 2nd sci extension's
                                              # 11th keyword's value

The function `getdata()` gets the data of an HDU. Similar to `getheader()`, it only requires the input FITS file name while the extension is specified through the optional arguments. It does have one extra optional argument header. If header is set to True, this function will return both data and header, otherwise only data is returned:

    >>> from astropy.io.fits import getdata
    >>> dat = getdata('in.fits', 'sci', 3) # get 3rd sci extension's data
    ... # get 1st extension's data and header
    >>> data, hdr = getdata('in.fits', 1, header=True)

The functions introduced above are for reading. The next few functions demonstrate convenience functions for writing:

    >>> fits.writeto('out.fits', data, header)

The `writeto()` function uses the provided data and an optional header to write to an output FITS file.

    >>> fits.append('out.fits', data, header)

The `append()` function will use the provided data and the optional header to append to an existing FITS file. If the specified output file does not exist, it will create one.

    >>> from astropy.io.fits import update
    >>> update(file, dat, hdr, 'sci') # update the 'sci' extension
    >>> update(file, dat, 3) # update the 3rd extension
    >>> update(file, dat, hdr, 3) # update the 3rd extension
    >>> update(file, dat, 'sci', 2) # update the 2nd SCI extension
    >>> update(file, dat, 3, header=hdr) # update the 3rd extension
    >>> update(file, dat, header=hdr, ext=5) # update the 5th extension

The `update()` function will update the specified extension with the input data/header. The 3rd argument can be the header associated with the data. If the 3rd argument is not a header, it (and other positional arguments) are assumed to be the extension specification(s). Header and extension specs can also be keyword arguments.

Finally, the `info()` function will print out information of the specified FITS file:

    >>> fits.info('test0.fits')
    Filename: test0.fits
    No. Name    Type       Cards Dimensions Format
    0   PRIMARY PrimaryHDU   138 ()         Int16
    1   SCI     ImageHDU      61 (400, 400) Int16
    2   SCI     ImageHDU      61 (400, 400) Int16
    3   SCI     ImageHDU      61 (400, 400) Int16
    4   SCI     ImageHDU      61 (400, 400) Int16

## Using `io.fits`

- FITS Headers
  - Header of an HDU
  - The Header Attribute
  - Card Images
  - CONTINUE Cards
  - HIERARCH Cards
- Image Data
  - Image Data as an Array
  - Scaled Data
  - Data Sections
- Table Data
  - Table Data as a Record Array
  - Table Operations
  - Scaled Data in Tables
  - Creating a FITS Table
- Verification
  - FITS Standard
  - Verification Options
  - Verifications at Different Data Object Levels
  - Verification using the FITS Checksum Keyword Convention
- Less Familiar Objects
  - ASCII Tables
  - Variable Length Array Tables
  - Random Access Groups
  - Compressed Image Data
- Executable Scripts
  - fitscheck
  - fitsdiff
- Miscellaneous Features
  - Differs
- Examples
  - Converting a 3-color image (JPG) to separate FITS images

## Other Information

- PyFITS FAQ
- astropy.io.fits History

## Reference/API

- File Handling and Convenience Functions
  - `open()`
  - `writeto()`
  - `info()`
  - `append()`
  - `update()`
  - `getdata()`
  - `getheader()`
  - `getval()`
  - `setval()`
  - `delval()`
- HDU Lists
  - `HDUList`
- Header Data Units
  - `PrimaryHDU`
  - `GroupsHDU`
  - `GroupData`
  - `Group`
  - `StreamingHDU`
- Headers
  - `Header`
- Cards
  - `Card`
  - Deprecated Interfaces
- Tables
  - `BinTableHDU`
  - `TableHDU`
  - `Column`
  - `ColDefs`
  - `FITS_rec`
  - `FITS_record`
  - Table Functions
    - `new_table()`
    - `tabledump()`
    - `tableload()`
- Images
  - `ImageHDU`
  - `CompImageHDU`
- Differs
  - `FITSDiff`
  - `HDUDiff`
  - `HeaderDiff`
  - `ImageDataDiff`
  - `RawDataDiff`
  - `TableDataDiff`
- Verification options
  - exception
  - ignore
  - fix
  - silentfix
  - warn

Footnotes

[1] | For legacy code only that already depends on PyFITS, it’s acceptable to continue using “from astropy.io import fits as pyfits”.