Header Data Units

The ImageHDU and CompImageHDU classes are discussed in the section on Images.

The TableHDU and BinTableHDU classes are discussed in the section on Tables.

PrimaryHDU

class pyfits.core.PrimaryHDU(data=None, header=None, do_not_scale_image_data=False, uint=False)

Bases: pyfits.hdu.image._ImageBaseHDU

FITS primary HDU class.

Construct a primary HDU.

Parameters :  

data : array or DELAYED, optional

The data in the HDU.

header : Header instance, optional

The header to be used (as a template). If header is None, a minimal header will be provided.

do_not_scale_image_data : bool, optional

If True, image data is not scaled using BSCALE/BZERO values when read.

uint : bool, optional

Interpret signed integer data where BZERO is the central value and BSCALE == 1 as unsigned integer data. For example, int16 data with BZERO = 32768 and BSCALE = 1 would be treated as uint16 data.

add_checksum(when=None, override_datasum=False, blocking='standard')

Add the CHECKSUM and DATASUM cards to this HDU with the values set to the checksum calculated for the HDU and the data respectively. The addition of the DATASUM card may be overridden.

Parameters :  

when : str, optional

comment string for the cards; by default the comments will represent the time when the checksum was calculated

override_datasum : bool, optional

add the CHECKSUM card only

blocking: str, optional :

“standard” or “nonstandard”, compute sum 2880 bytes at a time, or not

Notes

For testing purposes, first call add_datasum with a when argument, then call add_checksum with a when argument and override_datasum set to True. This will provide consistent comments for both cards and enable the generation of a CHECKSUM card with a consistent value.

add_datasum(when=None, blocking='standard')

Add the DATASUM card to this HDU with the value set to the checksum calculated for the data.

Parameters :  

when : str, optional

Comment string for the card that by default represents the time when the checksum was calculated

blocking: str, optional :

“standard” or “nonstandard”, compute sum 2880 bytes at a time, or not

Returns :  

checksum : int

The calculated datasum

Notes

For testing purposes, provide a when argument to enable the comment value in the card to remain consistent. This will enable the generation of a CHECKSUM card with a consistent value.

copy()

Make a copy of the HDU, both header and data are copied.

filebytes()

Calculates and returns the number of bytes that this HDU will write to a file.

Parameters :  None : Returns :  Number of bytes :

fileinfo()

Returns a dictionary detailing information about the locations of this HDU within any associated file. The values are only valid after a read or write of the associated file with no intervening changes to the HDUList.

Parameters :  

None :

Returns :  

dictionary or None :

The dictionary details information about the locations of this HDU within an associated file. Returns None when the HDU is not associated with a file.

Dictionary contents:

Key	Value
file	File object associated with the HDU
filemode	Mode in which the file was opened (readonly, copyonwrite, update, append, ostream)
hdrLoc	Starting byte location of header in file
datLoc	Starting byte location of data block in file
datSpan	Data size including padding

classmethod fromstring(data, fileobj=None, offset=0, checksum=False, ignore_missing_end=False, **kwargs)

Creates a new HDU object of the appropriate type from a string containing the HDU’s entire header and, optionally, its data.

Parameters :  

data : str

A byte string contining the HDU’s header and, optionally, its data. If fileobj is not specified, and the length of data extends beyond the header, then the trailing data is taken to be the HDU’s data. If fileobj is specified then the trailing data is ignored.

fileobj : file (optional)

The file-like object that this HDU was read from.

offset : int (optional)

If fileobj is specified, the offset into the file-like object at which this HDU begins.

checksum : bool (optional)

Check the HDU’s checksum and/or datasum.

ignore_missing_end : bool (optional)

Ignore a missing end card in the header data. Note that without the end card the end of the header can’t be found, so the entire data is just assumed to be the header.

kwargs : (optional)

May contain additional keyword arguments specific to an HDU type. Any unrecognized kwargs are simply ignored.

classmethod match_header(header)

classmethod readfrom(fileobj, checksum=False, ignore_missing_end=False, **kwargs)

Read the HDU from a file. Normally an HDU should be opened with fitsopen() which reads the entire HDU list in a FITS file. But this method is still provided for symmetry with writeto().

Parameters :  

fileobj : file object or file-like object

Input FITS file. The file’s seek pointer is assumed to be at the beginning of the HDU.

checksum : bool

If True, verifies that both DATASUM and CHECKSUM card values (when present in the HDU header) match the header and data of all HDU’s in the file.

ignore_missing_end : bool

Do not issue an exception when opening a file that is missing an END card in the last header.

classmethod register_hdu(hducls)

req_cards(keyword, pos, test, fix_value, option, errlist)

Check the existence, location, and value of a required Card.

TODO: Write about parameters

If pos = None, it can be anywhere. If the card does not exist, the new card will have the fix_value as its value when created. Also check the card’s value by using the test argument.

run_option(option='warn', err_text='', fix_text='Fixed.', fix=None, fixable=True)

Execute the verification with selected option.

scale(type=None, option='old', bscale=1, bzero=0)

Scale image data by using BSCALE/BZERO.

Call to this method will scale data and update the keywords of BSCALE and BZERO in _header. This method should only be used right before writing to the output file, as the data will be scaled and is therefore not very usable after the call.

Parameters :  

type : str, optional

destination data type, use a string representing a numpy dtype name, (e.g. 'uint8', 'int16', 'float32' etc.). If is None, use the current data type.

option : str

How to scale the data: if "old", use the original BSCALE and BZERO values when the data was read/created. If "minmax", use the minimum and maximum of the data to scale. The option will be overwritten by any user specified bscale/bzero values.

bscale, bzero : int, optional

User-specified BSCALE and BZERO values.

classmethod unregister_hdu(hducls)

update_ext_name(value, comment=None, before=None, after=None, savecomment=False)

Update the extension name associated with the HDU.

If the keyword already exists in the Header, it’s value and/or comment will be updated. If it does not exist, a new card will be created and it will be placed before or after the specified location. If no before or after is specified, it will be appended at the end.

Parameters :  

value : str

value to be used for the new extension name

comment : str, optional

to be used for updating, default=None.

before : str or int, optional

name of the keyword, or index of the Card before which the new card will be placed in the Header. The argument before takes precedence over after if both specified.

after : str or int, optional

name of the keyword, or index of the Card after which the new card will be placed in the Header.

savecomment : bool, optional

When True, preserve the current comment for an existing keyword. The argument savecomment takes precedence over comment if both specified. If comment is not specified then the current comment will automatically be preserved.

update_ext_version(value, comment=None, before=None, after=None, savecomment=False)

Update the extension version associated with the HDU.

If the keyword already exists in the Header, it’s value and/or comment will be updated. If it does not exist, a new card will be created and it will be placed before or after the specified location. If no before or after is specified, it will be appended at the end.

Parameters :  

value : str

value to be used for the new extension version

comment : str, optional

to be used for updating, default=None.

before : str or int, optional

name of the keyword, or index of the Card before which the new card will be placed in the Header. The argument before takes precedence over after if both specified.

after : str or int, optional

name of the keyword, or index of the Card after which the new card will be placed in the Header.

savecomment : bool, optional

When True, preserve the current comment for an existing keyword. The argument savecomment takes precedence over comment if both specified. If comment is not specified then the current comment will automatically be preserved.

update_header()

Update the header keywords to agree with the data.

verify(option='warn')

Verify all values in the instance.

Parameters :  

option : str

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". See Verification options for more info.

verify_checksum(blocking='standard')

Verify that the value in the CHECKSUM keyword matches the value calculated for the current HDU CHECKSUM.

blocking: str, optional

“standard” or “nonstandard”, compute sum 2880 bytes at a time, or not

Returns :  

valid : int

• 0 - failure
• 1 - success
• 2 - no CHECKSUM keyword present

verify_datasum(blocking='standard')

Verify that the value in the DATASUM keyword matches the value calculated for the DATASUM of the current HDU data.

blocking: str, optional

“standard” or “nonstandard”, compute sum 2880 bytes at a time, or not

Returns :  

valid : int

• 0 - failure
• 1 - success
• 2 - no DATASUM keyword present

writeto(*args, **kwargs)

Write the HDU to a new file. This is a convenience method to provide a user easier output interface if only one HDU needs to be written to a file.

Parameters :  

name : file path, file object or file-like object

Output FITS file. If opened, must be opened for append (“ab+”)).

output_verify : str

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". See Verification options for more info.

clobber : bool

Overwrite the output file if exists.

classExtensions : dict

A dictionary that maps pyfits classes to extensions of those classes. When present in the dictionary, the extension class will be constructed in place of the pyfits class.

checksum : bool

When True adds both DATASUM and CHECKSUM cards to the header of the HDU when written to the file.

ImgCode = {'uint64': 64, 'uint16': 16, 'int16': 16, 'int64': 64, 'int32': 32, 'float64': -64, 'uint8': 8, 'float32': -32, 'uint32': 32}

NumCode = {-64: 'float64', -32: 'float32', 32: 'int32', 8: 'uint8', 64: 'int64', 16: 'int16'}

data

header

is_image

section

size

Size (in bytes) of the data portion of the HDU.

GroupsHDU

class pyfits.core.GroupsHDU(data=None, header=None, name=None)

Bases: pyfits.hdu.image.PrimaryHDU, pyfits.hdu.table._TableLikeHDU

FITS Random Groups HDU class.

TODO: Write me

add_checksum(when=None, override_datasum=False, blocking='standard')

Add the CHECKSUM and DATASUM cards to this HDU with the values set to the checksum calculated for the HDU and the data respectively. The addition of the DATASUM card may be overridden.

Parameters :  

when : str, optional

comment string for the cards; by default the comments will represent the time when the checksum was calculated

override_datasum : bool, optional

add the CHECKSUM card only

blocking: str, optional :

“standard” or “nonstandard”, compute sum 2880 bytes at a time, or not

Notes

For testing purposes, first call add_datasum with a when argument, then call add_checksum with a when argument and override_datasum set to True. This will provide consistent comments for both cards and enable the generation of a CHECKSUM card with a consistent value.

add_datasum(when=None, blocking='standard')

Add the DATASUM card to this HDU with the value set to the checksum calculated for the data.

Parameters :  

when : str, optional

Comment string for the card that by default represents the time when the checksum was calculated

blocking: str, optional :

“standard” or “nonstandard”, compute sum 2880 bytes at a time, or not

Returns :  

checksum : int

The calculated datasum

Notes

For testing purposes, provide a when argument to enable the comment value in the card to remain consistent. This will enable the generation of a CHECKSUM card with a consistent value.

copy()

Make a copy of the HDU, both header and data are copied.

filebytes()

Calculates and returns the number of bytes that this HDU will write to a file.

Parameters :  None : Returns :  Number of bytes :

fileinfo()

Returns a dictionary detailing information about the locations of this HDU within any associated file. The values are only valid after a read or write of the associated file with no intervening changes to the HDUList.

Parameters :  

None :

Returns :  

dictionary or None :

The dictionary details information about the locations of this HDU within an associated file. Returns None when the HDU is not associated with a file.

Dictionary contents:

Key	Value
file	File object associated with the HDU
filemode	Mode in which the file was opened (readonly, copyonwrite, update, append, ostream)
hdrLoc	Starting byte location of header in file
datLoc	Starting byte location of data block in file
datSpan	Data size including padding

classmethod fromstring(data, fileobj=None, offset=0, checksum=False, ignore_missing_end=False, **kwargs)

Creates a new HDU object of the appropriate type from a string containing the HDU’s entire header and, optionally, its data.

Parameters :  

data : str

A byte string contining the HDU’s header and, optionally, its data. If fileobj is not specified, and the length of data extends beyond the header, then the trailing data is taken to be the HDU’s data. If fileobj is specified then the trailing data is ignored.

fileobj : file (optional)

The file-like object that this HDU was read from.

offset : int (optional)

If fileobj is specified, the offset into the file-like object at which this HDU begins.

checksum : bool (optional)

Check the HDU’s checksum and/or datasum.

ignore_missing_end : bool (optional)

Ignore a missing end card in the header data. Note that without the end card the end of the header can’t be found, so the entire data is just assumed to be the header.

kwargs : (optional)

May contain additional keyword arguments specific to an HDU type. Any unrecognized kwargs are simply ignored.

classmethod match_header(header)

classmethod readfrom(fileobj, checksum=False, ignore_missing_end=False, **kwargs)

Read the HDU from a file. Normally an HDU should be opened with fitsopen() which reads the entire HDU list in a FITS file. But this method is still provided for symmetry with writeto().

Parameters :  

fileobj : file object or file-like object

Input FITS file. The file’s seek pointer is assumed to be at the beginning of the HDU.

checksum : bool

If True, verifies that both DATASUM and CHECKSUM card values (when present in the HDU header) match the header and data of all HDU’s in the file.

ignore_missing_end : bool

Do not issue an exception when opening a file that is missing an END card in the last header.

classmethod register_hdu(hducls)

req_cards(keyword, pos, test, fix_value, option, errlist)

Check the existence, location, and value of a required Card.

TODO: Write about parameters

If pos = None, it can be anywhere. If the card does not exist, the new card will have the fix_value as its value when created. Also check the card’s value by using the test argument.

run_option(option='warn', err_text='', fix_text='Fixed.', fix=None, fixable=True)

Execute the verification with selected option.

scale(type=None, option='old', bscale=1, bzero=0)

Scale image data by using BSCALE/BZERO.

Call to this method will scale data and update the keywords of BSCALE and BZERO in _header. This method should only be used right before writing to the output file, as the data will be scaled and is therefore not very usable after the call.

Parameters :  

type : str, optional

destination data type, use a string representing a numpy dtype name, (e.g. 'uint8', 'int16', 'float32' etc.). If is None, use the current data type.

option : str

How to scale the data: if "old", use the original BSCALE and BZERO values when the data was read/created. If "minmax", use the minimum and maximum of the data to scale. The option will be overwritten by any user specified bscale/bzero values.

bscale, bzero : int, optional

User-specified BSCALE and BZERO values.

classmethod unregister_hdu(hducls)

update_ext_name(value, comment=None, before=None, after=None, savecomment=False)

Update the extension name associated with the HDU.

If the keyword already exists in the Header, it’s value and/or comment will be updated. If it does not exist, a new card will be created and it will be placed before or after the specified location. If no before or after is specified, it will be appended at the end.

Parameters :  

value : str

value to be used for the new extension name

comment : str, optional

to be used for updating, default=None.

before : str or int, optional

name of the keyword, or index of the Card before which the new card will be placed in the Header. The argument before takes precedence over after if both specified.

after : str or int, optional

name of the keyword, or index of the Card after which the new card will be placed in the Header.

savecomment : bool, optional

When True, preserve the current comment for an existing keyword. The argument savecomment takes precedence over comment if both specified. If comment is not specified then the current comment will automatically be preserved.

update_ext_version(value, comment=None, before=None, after=None, savecomment=False)

Update the extension version associated with the HDU.

If the keyword already exists in the Header, it’s value and/or comment will be updated. If it does not exist, a new card will be created and it will be placed before or after the specified location. If no before or after is specified, it will be appended at the end.

Parameters :  

value : str

value to be used for the new extension version

comment : str, optional

to be used for updating, default=None.

before : str or int, optional

name of the keyword, or index of the Card before which the new card will be placed in the Header. The argument before takes precedence over after if both specified.

after : str or int, optional

name of the keyword, or index of the Card after which the new card will be placed in the Header.

savecomment : bool, optional

When True, preserve the current comment for an existing keyword. The argument savecomment takes precedence over comment if both specified. If comment is not specified then the current comment will automatically be preserved.

update_header()

verify(option='warn')

Verify all values in the instance.

Parameters :  

option : str

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". See Verification options for more info.

verify_checksum(blocking='standard')

Verify that the value in the CHECKSUM keyword matches the value calculated for the current HDU CHECKSUM.

blocking: str, optional

“standard” or “nonstandard”, compute sum 2880 bytes at a time, or not

Returns :  

valid : int

• 0 - failure
• 1 - success
• 2 - no CHECKSUM keyword present

verify_datasum(blocking='standard')

Verify that the value in the DATASUM keyword matches the value calculated for the DATASUM of the current HDU data.

blocking: str, optional

“standard” or “nonstandard”, compute sum 2880 bytes at a time, or not

Returns :  

valid : int

• 0 - failure
• 1 - success
• 2 - no DATASUM keyword present

writeto(*args, **kwargs)

Write the HDU to a new file. This is a convenience method to provide a user easier output interface if only one HDU needs to be written to a file.

Parameters :  

name : file path, file object or file-like object

Output FITS file. If opened, must be opened for append (“ab+”)).

output_verify : str

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". See Verification options for more info.

clobber : bool

Overwrite the output file if exists.

classExtensions : dict

A dictionary that maps pyfits classes to extensions of those classes. When present in the dictionary, the extension class will be constructed in place of the pyfits class.

checksum : bool

When True adds both DATASUM and CHECKSUM cards to the header of the HDU when written to the file.

ImgCode = {'uint64': 64, 'uint16': 16, 'int16': 16, 'int64': 64, 'int32': 32, 'float64': -64, 'uint8': 8, 'float32': -32, 'uint32': 32}

NumCode = {-64: 'float64', -32: 'float32', 32: 'int32', 8: 'uint8', 64: 'int64', 16: 'int16'}

columns

data

The data of a random group FITS file will be like a binary table’s data.

header

is_image

section

size

Returns the size (in bytes) of the HDU’s data part.

StreamingHDU

class pyfits.core.StreamingHDU(name, header)

Bases: object

A class that provides the capability to stream data to a FITS file instead of requiring data to all be written at once.

The following pseudocode illustrates its use:

header = pyfits.Header()

for all the cards you need in the header:
    header[key] = (value, comment)

shdu = pyfits.StreamingHDU('filename.fits', header)

for each piece of data:
    shdu.write(data)

shdu.close()

Construct a StreamingHDU object given a file name and a header.

Parameters :  

name : file path, file object, or file like object

The file to which the header and data will be streamed. If opened, the file object must be opened for append (ab+).

header : Header instance

The header object associated with the data to be written to the file.

Notes

The file will be opened and the header appended to the end of the file. If the file does not already exist, it will be created, and if the header represents a Primary header, it will be written to the beginning of the file. If the file does not exist and the provided header is not a Primary header, a default Primary HDU will be inserted at the beginning of the file and the provided header will be added as the first extension. If the file does already exist, but the provided header represents a Primary header, the header will be modified to an image extension header and appended to the end of the file.

close()

Close the physical FITS file.

write(data)

Write the given data to the stream.

Parameters :  

data : ndarray

Data to stream to the file.

Returns :  

writecomplete : int

Flag that when True indicates that all of the required data has been written to the stream.

Notes

Only the amount of data specified in the header provided to the class constructor may be written to the stream. If the provided data would cause the stream to overflow, an IOError exception is raised and the data is not written. Once sufficient data has been written to the stream to satisfy the amount specified in the header, the stream is padded to fill a complete FITS block and no more data will be accepted. An attempt to write more data after the stream has been filled will raise an IOError exception. If the dtype of the input data does not match what is expected by the header, a TypeError exception is raised.

size

Return the size (in bytes) of the data portion of the HDU.