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 astropy.io.fits.PrimaryHDU(data=None, header=None, do_not_scale_image_data=False, ignore_blank=False, uint=True, scale_back=None)[source]

Bases: astropy.io.fits.hdu.image._ImageBaseHDU

FITS primary HDU class.

Construct a primary HDU.

Parameters
dataarray or DELAYED, optional

The data in the HDU.

headerHeader instance, optional

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

do_not_scale_image_databool, optional

If True, image data is not scaled using BSCALE/BZERO values when read. (default: False)

ignore_blankbool, optional

If True, the BLANK header keyword will be ignored if present. Otherwise, pixels equal to this value will be replaced with NaNs. (default: False)

uintbool, 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. (default: True)

scale_backbool, optional

If True, when saving changes to a file that contained scaled image data, restore the data to the original type and reapply the original BSCALE/BZERO values. This could lead to loss of accuracy if scaling back to integer values after performing floating point operations on the data. Pseudo-unsigned integers are automatically rescaled unless scale_back is explicitly set to False. (default: None)

add_checksum(self, when=None, override_datasum=False, checksum_keyword='CHECKSUM', datasum_keyword='DATASUM')

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
whenstr, optional

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

override_datasumbool, optional

add the CHECKSUM card only

checksum_keywordstr, optional

The name of the header keyword to store the checksum value in; this is typically ‘CHECKSUM’ per convention, but there exist use cases in which a different keyword should be used

datasum_keywordstr, optional

See checksum_keyword

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(self, when=None, datasum_keyword='DATASUM')

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

Parameters
whenstr, optional

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

datasum_keywordstr, optional

The name of the header keyword to store the datasum value in; this is typically ‘DATASUM’ per convention, but there exist use cases in which a different keyword should be used

Returns
checksumint

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(self)

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

data

Image/array data as a ndarray.

Please remember that the order of axes on an Numpy array are opposite of the order specified in the FITS file. For example for a 2D image the “rows” or y-axis are the first dimension, and the “columns” or x-axis are the second dimension.

If the data is scaled using the BZERO and BSCALE parameters, this attribute returns the data scaled to its physical values unless the file was opened with do_not_scale_image_data=True.

filebytes(self)

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

fileinfo(self)

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.

Returns
dict 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, 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.

Note: When creating a new HDU from a string without a backing file object, the data of that HDU may be read-only. It depends on whether the underlying string was an immutable Python str/bytes object, or some kind of read-write memory buffer such as a memoryview.

Parameters
datastr, bytearray, memoryview, ndarray

A byte string containing the HDU’s header and data.

checksumbool, optional

Check the HDU’s checksum and/or datasum.

ignore_missing_endbool, optional

Ignore a missing end card in the header data. Note that without the end card the end of the header may be ambiguous and resulted in a corrupt HDU. In this case the assumption is that the first 2880 block that does not begin with valid FITS header data is the beginning of the data.

kwargsoptional

May consist of additional keyword arguments specific to an HDU type–these correspond to keywords recognized by the constructors of different HDU classes such as PrimaryHDU, ImageHDU, or BinTableHDU. Any unrecognized keyword arguments are simply ignored.

classmethod match_header(header)[source]

_ImageBaseHDU is sort of an abstract class for HDUs containing image data (as opposed to table data) and should never be used directly.

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

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

Parameters
fileobjfile object or file-like object

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

checksumbool

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_endbool

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

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

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

Parameters
keywordstr

The keyword to validate

posint, callable

If an int, this specifies the exact location this card should have in the header. Remember that Python is zero-indexed, so this means pos=0 requires the card to be the first card in the header. If given a callable, it should take one argument–the actual position of the keyword–and return True or False. This can be used for custom evaluation. For example if pos=lambda idx: idx > 10 this will check that the keyword’s index is greater than 10.

testcallable

This should be a callable (generally a function) that is passed the value of the given keyword and returns True or False. This can be used to validate the value associated with the given keyword.

fix_valuestr, int, float, complex, bool, None

A valid value for a FITS keyword to to use if the given test fails to replace an invalid value. In other words, this provides a default value to use as a replacement if the keyword’s current value is invalid. If None, there is no replacement value and the keyword is unfixable.

optionstr

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". May also be any combination of "fix" or "silentfix" with "+ignore", +warn, or +exception" (e.g. ``"fix+warn"). See Verification options for more info.

errlistlist

A list of validation errors already found in the FITS file; this is used primarily for the validation system to collect errors across multiple HDUs and multiple calls to req_cards.

Notes

If pos=None, the card can be anywhere in the header. 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(self, option='warn', err_text='', fix_text='Fixed.', fix=None, fixable=True)

Execute the verification with selected option.

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

Scale image data by using BSCALE/BZERO.

Call to this method will scale data and update the keywords of BSCALE and BZERO in the HDU’s 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
typestr, 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.

optionstr, optional

How to scale the data: "old" uses the original BSCALE and BZERO values from when the data was read/created (defaulting to 1 and 0 if they don’t exist). For integer data only, "minmax" uses the minimum and maximum of the data to scale. User-specified bscale/bzero values always take precedence.

bscale, bzeroint, optional

User-specified BSCALE and BZERO values

section

Access a section of the image array without loading the entire array into memory. The Section object returned by this attribute is not meant to be used directly by itself. Rather, slices of the section return the appropriate slice of the data, and loads only that section into memory.

Sections are mostly obsoleted by memmap support, but should still be used to deal with very large scaled images. See the Data Sections section of the Astropy documentation for more details.

shape

Shape of the image array–should be equivalent to self.data.shape.

size

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

update_header(self)[source]

Update the header keywords to agree with the data.

verify(self, option='warn')

Verify all values in the instance.

Parameters
optionstr

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". May also be any combination of "fix" or "silentfix" with "+ignore", +warn, or +exception" (e.g. ``"fix+warn"). See Verification options for more info.

verify_checksum(self)

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

Returns
validint
  • 0 - failure

  • 1 - success

  • 2 - no CHECKSUM keyword present

verify_datasum(self)

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

Returns
validint
  • 0 - failure

  • 1 - success

  • 2 - no DATASUM keyword present

writeto(self, name, output_verify='exception', overwrite=False, checksum=False)

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
namefile path, file object or file-like object

Output FITS file. If the file object is already opened, it must be opened in a writeable mode.

output_verifystr

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". May also be any combination of "fix" or "silentfix" with "+ignore", +warn, or +exception" (e.g. ``"fix+warn"). See Verification options for more info.

overwritebool, optional

If True, overwrite the output file if it exists. Raises an OSError if False and the output file exists. Default is False.

Changed in version 1.3: overwrite replaces the deprecated clobber argument.

checksumbool

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

GroupsHDU

class astropy.io.fits.GroupsHDU(data=None, header=None)[source]

Bases: astropy.io.fits.PrimaryHDU, astropy.io.fits.hdu.table._TableLikeHDU

FITS Random Groups HDU class.

See the Random Access Groups section in the Astropy documentation for more details on working with this type of HDU.

add_checksum(self, when=None, override_datasum=False, checksum_keyword='CHECKSUM', datasum_keyword='DATASUM')

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
whenstr, optional

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

override_datasumbool, optional

add the CHECKSUM card only

checksum_keywordstr, optional

The name of the header keyword to store the checksum value in; this is typically ‘CHECKSUM’ per convention, but there exist use cases in which a different keyword should be used

datasum_keywordstr, optional

See checksum_keyword

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(self, when=None, datasum_keyword='DATASUM')

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

Parameters
whenstr, optional

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

datasum_keywordstr, optional

The name of the header keyword to store the datasum value in; this is typically ‘DATASUM’ per convention, but there exist use cases in which a different keyword should be used

Returns
checksumint

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.

columns

The ColDefs objects describing the columns in this table.

copy(self)

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

data

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

filebytes(self)

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

fileinfo(self)

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.

Returns
dict 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 from_columns(columns, header=None, nrows=0, fill=False, character_as_bytes=False, **kwargs)

Given either a ColDefs object, a sequence of Column objects, or another table HDU or table data (a FITS_rec or multi-field numpy.ndarray or numpy.recarray object, return a new table HDU of the class this method was called on using the column definition from the input.

See also FITS_rec.from_columns.

Parameters
columnssequence of Column, ColDefs, or other

The columns from which to create the table data, or an object with a column-like structure from which a ColDefs can be instantiated. This includes an existing BinTableHDU or TableHDU, or a numpy.recarray to give some examples.

If these columns have data arrays attached that data may be used in initializing the new table. Otherwise the input columns will be used as a template for a new table with the requested number of rows.

headerHeader

An optional Header object to instantiate the new HDU yet. Header keywords specifically related to defining the table structure (such as the “TXXXn” keywords like TTYPEn) will be overridden by the supplied column definitions, but all other informational and data model-specific keywords are kept.

nrowsint

Number of rows in the new table. If the input columns have data associated with them, the size of the largest input column is used. Otherwise the default is 0.

fillbool

If True, will fill all cells with zeros or blanks. If False, copy the data from input, undefined cells will still be filled with zeros/blanks.

character_as_bytesbool

Whether to return bytes for string columns when accessed from the HDU. By default this is False and (unicode) strings are returned, but for large tables this may use up a lot of memory.

Notes

Any additional keyword arguments accepted by the HDU class’s __init__ may also be passed in as keyword arguments.

classmethod fromstring(data, 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.

Note: When creating a new HDU from a string without a backing file object, the data of that HDU may be read-only. It depends on whether the underlying string was an immutable Python str/bytes object, or some kind of read-write memory buffer such as a memoryview.

Parameters
datastr, bytearray, memoryview, ndarray

A byte string containing the HDU’s header and data.

checksumbool, optional

Check the HDU’s checksum and/or datasum.

ignore_missing_endbool, optional

Ignore a missing end card in the header data. Note that without the end card the end of the header may be ambiguous and resulted in a corrupt HDU. In this case the assumption is that the first 2880 block that does not begin with valid FITS header data is the beginning of the data.

kwargsoptional

May consist of additional keyword arguments specific to an HDU type–these correspond to keywords recognized by the constructors of different HDU classes such as PrimaryHDU, ImageHDU, or BinTableHDU. Any unrecognized keyword arguments are simply ignored.

classmethod match_header(header)[source]

_ImageBaseHDU is sort of an abstract class for HDUs containing image data (as opposed to table data) and should never be used directly.

parnames

The names of the group parameters as described by the header.

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

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

Parameters
fileobjfile object or file-like object

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

checksumbool

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_endbool

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

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

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

Parameters
keywordstr

The keyword to validate

posint, callable

If an int, this specifies the exact location this card should have in the header. Remember that Python is zero-indexed, so this means pos=0 requires the card to be the first card in the header. If given a callable, it should take one argument–the actual position of the keyword–and return True or False. This can be used for custom evaluation. For example if pos=lambda idx: idx > 10 this will check that the keyword’s index is greater than 10.

testcallable

This should be a callable (generally a function) that is passed the value of the given keyword and returns True or False. This can be used to validate the value associated with the given keyword.

fix_valuestr, int, float, complex, bool, None

A valid value for a FITS keyword to to use if the given test fails to replace an invalid value. In other words, this provides a default value to use as a replacement if the keyword’s current value is invalid. If None, there is no replacement value and the keyword is unfixable.

optionstr

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". May also be any combination of "fix" or "silentfix" with "+ignore", +warn, or +exception" (e.g. ``"fix+warn"). See Verification options for more info.

errlistlist

A list of validation errors already found in the FITS file; this is used primarily for the validation system to collect errors across multiple HDUs and multiple calls to req_cards.

Notes

If pos=None, the card can be anywhere in the header. 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(self, option='warn', err_text='', fix_text='Fixed.', fix=None, fixable=True)

Execute the verification with selected option.

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

Scale image data by using BSCALE/BZERO.

Call to this method will scale data and update the keywords of BSCALE and BZERO in the HDU’s 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
typestr, 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.

optionstr, optional

How to scale the data: "old" uses the original BSCALE and BZERO values from when the data was read/created (defaulting to 1 and 0 if they don’t exist). For integer data only, "minmax" uses the minimum and maximum of the data to scale. User-specified bscale/bzero values always take precedence.

bscale, bzeroint, optional

User-specified BSCALE and BZERO values

section

Access a section of the image array without loading the entire array into memory. The Section object returned by this attribute is not meant to be used directly by itself. Rather, slices of the section return the appropriate slice of the data, and loads only that section into memory.

Sections are mostly obsoleted by memmap support, but should still be used to deal with very large scaled images. See the Data Sections section of the Astropy documentation for more details.

shape

Shape of the image array–should be equivalent to self.data.shape.

size

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

update_header(self)[source]

Update the header keywords to agree with the data.

verify(self, option='warn')

Verify all values in the instance.

Parameters
optionstr

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". May also be any combination of "fix" or "silentfix" with "+ignore", +warn, or +exception" (e.g. ``"fix+warn"). See Verification options for more info.

verify_checksum(self)

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

Returns
validint
  • 0 - failure

  • 1 - success

  • 2 - no CHECKSUM keyword present

verify_datasum(self)

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

Returns
validint
  • 0 - failure

  • 1 - success

  • 2 - no DATASUM keyword present

writeto(self, name, output_verify='exception', overwrite=False, checksum=False)

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
namefile path, file object or file-like object

Output FITS file. If the file object is already opened, it must be opened in a writeable mode.

output_verifystr

Output verification option. Must be one of "fix", "silentfix", "ignore", "warn", or "exception". May also be any combination of "fix" or "silentfix" with "+ignore", +warn, or +exception" (e.g. ``"fix+warn"). See Verification options for more info.

overwritebool, optional

If True, overwrite the output file if it exists. Raises an OSError if False and the output file exists. Default is False.

Changed in version 1.3: overwrite replaces the deprecated clobber argument.

checksumbool

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

GroupData

class astropy.io.fits.GroupData[source]

Bases: astropy.io.fits.FITS_rec

Random groups data object.

Allows structured access to FITS Group data in a manner analogous to tables.

Parameters
inputarray or FITS_rec instance

input data, either the group data itself (a numpy.ndarray) or a record array (FITS_rec) which will contain both group parameter info and the data. The rest of the arguments are used only for the first case.

bitpixint

data type as expressed in FITS BITPIX value (8, 16, 32, 64, -32, or -64)

pardatasequence of arrays

parameter data, as a list of (numeric) arrays.

parnamessequence of str

list of parameter names.

bscaleint

BSCALE of the data

bzeroint

BZERO of the data

parbscalessequence of int

list of bscales for the parameters

parbzerossequence of int

list of bzeros for the parameters

data

The raw group data represented as a multi-dimensional numpy.ndarray array.

par(self, parname)[source]

Get the group parameter values.

Group

class astropy.io.fits.Group(input, row=0, start=None, end=None, step=None, base=None)[source]

Bases: astropy.io.fits.FITS_record

One group of the random group data.

par(self, parname)[source]

Get the group parameter value.

setpar(self, parname, value)[source]

Set the group parameter value.

StreamingHDU

class astropy.io.fits.StreamingHDU(name, header)[source]

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 = astropy.io.fits.Header()

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

shdu = astropy.io.fits.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
namefile 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 in a writeable binary mode such as ‘wb’ or ‘ab+’.

headerHeader 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(self)[source]

Close the physical FITS file.

size

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

write(self, data)[source]

Write the given data to the stream.

Parameters
datandarray

Data to stream to the file.

Returns
writecompleteint

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 OSError 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 OSError exception. If the dtype of the input data does not match what is expected by the header, a TypeError exception is raised.