Tables

BinTableHDU

class pyfits.BinTableHDU(data=None, header=None, name=None, uint=False)

Bases: pyfits.hdu.table._TableBaseHDU

Binary table HDU class.

Parameters:  

header : Header instance

header to be used

data : array

data to be used

name : str

name to be populated in EXTNAME keyword

uint : bool, optional

set to True if the table contains unsigned integer columns.

schema

alias of BinTableExtensionSchema

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

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

checksum_keyword: str, 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_keyword: str, 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(when=None, blocking='standard', datasum_keyword='DATASUM')

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

datasum_keyword: str, 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:  

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 table HDU, both header and data are copied.

dump(datafile=None, cdfile=None, hfile=None, clobber=False)

Dump the table HDU to a file in ASCII format. The table may be dumped in three separate files, one containing column definitions, one containing header parameters, and one for table data.

Parameters:  

datafile : file path, file object or file-like object, optional

Output data file. The default is the root name of the fits file associated with this HDU appended with the extension .txt.

cdfile : file path, file object or file-like object, optional

Output column definitions file. The default is None, no column definitions output is produced.

hfile : file path, file object or file-like object, optional

Output header parameters file. The default is None, no header parameters output is produced.

clobber : bool

Overwrite the output files if they exist.

Notes

The primary use for the dump method is to allow viewing and editing the table data and parameters in a standard text editor. The load method can be used to create a new table from the three plain text (ASCII) files.

• datafile: Each line of the data file represents one row of table data. The data is output one column at a time in column order. If a column contains an array, each element of the column array in the current row is output before moving on to the next column. Each row ends with a new line.

  Integer data is output right-justified in a 21-character field followed by a blank. Floating point data is output right justified using ‘g’ format in a 21-character field with 15 digits of precision, followed by a blank. String data that does not contain whitespace is output left-justified in a field whose width matches the width specified in the TFORM header parameter for the column, followed by a blank. When the string data contains whitespace characters, the string is enclosed in quotation marks (""). For the last data element in a row, the trailing blank in the field is replaced by a new line character.

  For column data containing variable length arrays (‘P’ format), the array data is preceded by the string 'VLA_Length= ' and the integer length of the array for that row, left-justified in a 21-character field, followed by a blank.

  Note

  This format does not support variable length arrays using the (‘Q’ format) due to difficult to overcome ambiguities. What this means is that this file format cannot support VLA columns in tables stored in files that are over 2 GB in size.

  For column data representing a bit field (‘X’ format), each bit value in the field is output right-justified in a 21-character field as 1 (for true) or 0 (for false).

• cdfile: Each line of the column definitions file provides the definitions for one column in the table. The line is broken up into 8, sixteen-character fields. The first field provides the column name (TTYPEn). The second field provides the column format (TFORMn). The third field provides the display format (TDISPn). The fourth field provides the physical units (TUNITn). The fifth field provides the dimensions for a multidimensional array (TDIMn). The sixth field provides the value that signifies an undefined value (TNULLn). The seventh field provides the scale factor (TSCALn). The eighth field provides the offset value (TZEROn). A field value of "" is used to represent the case where no value is provided.

• hfile: Each line of the header parameters file provides the definition of a single HDU header card as represented by the card image.

filebytes()

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

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.

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, **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.

This is an alternative to the now deprecated new_table function, and otherwise accepts the same arguments. See also FITS_rec.from_columns.

Parameters:  

columns : sequence 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.

header : Header

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.

nrows : int

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.

fill : bool

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.

Notes

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

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.

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:  

data : str, bytearray, memoryview, ndarray

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 load(datafile, cdfile=None, hfile=None, replace=False, header=None)

Create a table from the input ASCII files. The input is from up to three separate files, one containing column definitions, one containing header parameters, and one containing column data.

The column definition and header parameters files are not required. When absent the column definitions and/or header parameters are taken from the header object given in the header argument; otherwise sensible defaults are inferred (though this mode is not recommended).

Parameters:  

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

Input data file containing the table data in ASCII format.

cdfile : file path, file object, file-like object, optional

Input column definition file containing the names, formats, display formats, physical units, multidimensional array dimensions, undefined values, scale factors, and offsets associated with the columns in the table. If None, the column definitions are taken from the current values in this object.

hfile : file path, file object, file-like object, optional

Input parameter definition file containing the header parameter definitions to be associated with the table. If None, the header parameter definitions are taken from the current values in this objects header.

replace : bool

When True, indicates that the entire header should be replaced with the contents of the ASCII file instead of just updating the current header.

header : Header object

When the cdfile and hfile are missing, use this Header object in the creation of the new table and HDU. Otherwise this Header supercedes the keywords from hfile, which is only used to update values not present in this Header, unless replace=True in which this Header’s values are completely replaced with the values from hfile.

Notes

The primary use for the load method is to allow the input of ASCII data that was edited in a standard text editor of the table data and parameters. The dump method can be used to create the initial ASCII files.

• datafile: Each line of the data file represents one row of table data. The data is output one column at a time in column order. If a column contains an array, each element of the column array in the current row is output before moving on to the next column. Each row ends with a new line.

  Integer data is output right-justified in a 21-character field followed by a blank. Floating point data is output right justified using ‘g’ format in a 21-character field with 15 digits of precision, followed by a blank. String data that does not contain whitespace is output left-justified in a field whose width matches the width specified in the TFORM header parameter for the column, followed by a blank. When the string data contains whitespace characters, the string is enclosed in quotation marks (""). For the last data element in a row, the trailing blank in the field is replaced by a new line character.

  For column data containing variable length arrays (‘P’ format), the array data is preceded by the string 'VLA_Length= ' and the integer length of the array for that row, left-justified in a 21-character field, followed by a blank.

  Note

  This format does not support variable length arrays using the (‘Q’ format) due to difficult to overcome ambiguities. What this means is that this file format cannot support VLA columns in tables stored in files that are over 2 GB in size.

  For column data representing a bit field (‘X’ format), each bit value in the field is output right-justified in a 21-character field as 1 (for true) or 0 (for false).

• cdfile: Each line of the column definitions file provides the definitions for one column in the table. The line is broken up into 8, sixteen-character fields. The first field provides the column name (TTYPEn). The second field provides the column format (TFORMn). The third field provides the display format (TDISPn). The fourth field provides the physical units (TUNITn). The fifth field provides the dimensions for a multidimensional array (TDIMn). The sixth field provides the value that signifies an undefined value (TNULLn). The seventh field provides the scale factor (TSCALn). The eighth field provides the offset value (TZEROn). A field value of "" is used to represent the case where no value is provided.

• hfile: Each line of the header parameters file provides the definition of a single HDU header card as represented by the card image.

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

Read the HDU from a file. Normally an HDU should be opened with pyfits.open 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.

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

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

Parameters:  

keyword : str

The keyword to validate

pos : int, 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.

test : callable

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_value : str, 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.

option : str

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

errlist : list

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

Execute the verification with selected option.

classmethod tcreate(*args, **kwargs)

Deprecated since version 3.1: Use load() instead.

tdump(*args, **kwargs)

Deprecated since version 3.1: Use dump() instead.

update()

Update header keywords to reflect recent changes of columns.

update_ext_name(*args, **kwargs)

Deprecated since version 3.2: Use the .name attribute or Header.set instead.

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 are 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(*args, **kwargs)

Deprecated since version 3.2: Use the .ver attribute or Header.set instead.

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 are 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.

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(name, output_verify='exception', clobber=False, checksum=False)

Works similarly to the normal writeto(), but prepends a default PrimaryHDU are required by extension HDUs (which cannot stand on their own).

columns

The ColDefs objects describing the columns in this table.

size

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

TableHDU

class pyfits.TableHDU(data=None, header=None, name=None)

Bases: pyfits.hdu.table._TableBaseHDU

FITS ASCII table extension HDU class.

schema

alias of TableExtensionSchema

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

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

checksum_keyword: str, 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_keyword: str, 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(when=None, blocking='standard', datasum_keyword='DATASUM')

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

datasum_keyword: str, 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:  

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 table HDU, both header and data are copied.

filebytes()

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

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.

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, **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.

This is an alternative to the now deprecated new_table function, and otherwise accepts the same arguments. See also FITS_rec.from_columns.

Parameters:  

columns : sequence 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.

header : Header

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.

nrows : int

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.

fill : bool

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.

Notes

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

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.

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:  

data : str, bytearray, memoryview, ndarray

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

Read the HDU from a file. Normally an HDU should be opened with pyfits.open 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.

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

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

Parameters:  

keyword : str

The keyword to validate

pos : int, 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.

test : callable

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_value : str, 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.

option : str

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

errlist : list

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

Execute the verification with selected option.

update()

Update header keywords to reflect recent changes of columns.

update_ext_name(*args, **kwargs)

Deprecated since version 3.2: Use the .name attribute or Header.set instead.

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 are 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(*args, **kwargs)

Deprecated since version 3.2: Use the .ver attribute or Header.set instead.

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 are 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.

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(name, output_verify='exception', clobber=False, checksum=False)

Works similarly to the normal writeto(), but prepends a default PrimaryHDU are required by extension HDUs (which cannot stand on their own).

columns

The ColDefs objects describing the columns in this table.

size

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

Column

class pyfits.Column(name=None, format=None, unit=None, null=None, bscale=None, bzero=None, disp=None, start=None, dim=None, array=None, ascii=None)

Bases: object

Class which contains the definition of one column, e.g. ttype, tform, etc. and the array containing values for the column.

Construct a Column by specifying attributes. All attributes except format can be optional.

Parameters:  

name : str, optional

column name, corresponding to TTYPE keyword

format : str, optional

column format, corresponding to TFORM keyword

unit : str, optional

column unit, corresponding to TUNIT keyword

null : str, optional

null value, corresponding to TNULL keyword

bscale : int-like, optional

bscale value, corresponding to TSCAL keyword

bzero : int-like, optional

bzero value, corresponding to TZERO keyword

disp : str, optional

display format, corresponding to TDISP keyword

start : int, optional

column starting position (ASCII table only), corresponding to TBCOL keyword

dim : str, optional

column dimension corresponding to TDIM keyword

array : iterable, optional

a list, numpy.ndarray (or other iterable that can be used to initialize an ndarray) providing intial data for this column. The array will be automatically converted, if possible, to the data format of the column. In the case were non-trivial bscale and/or bzero arguments are given, the values in the array must be the physical values–that is, the values of column as if the scaling has already been applied (the array stored on the column object will then be converted back to its storage values).

ascii : bool, optional

set True if this describes a column for an ASCII table; this may be required to disambiguate the column format

copy()

Return a copy of this Column.

ColDefs

class pyfits.ColDefs(input, tbtype=None, ascii=False)

Bases: object

Column definitions class.

It has attributes corresponding to the Column attributes (e.g. ColDefs has the attribute names while Column has name). Each attribute in ColDefs is a list of corresponding attribute values from all Column objects.

Parameters:  

input : sequence of Column, ColDefs, other

An existing table HDU, an existing ColDefs, or any multi-field Numpy array or numpy.recarray.

**(Deprecated) tbtype** : str, optional

which table HDU, "BinTableHDU" (default) or "TableHDU" (text table). Now ColDefs for a normal (binary) table by default, but converted automatically to ASCII table ColDefs in the appropriate contexts (namely, when creating an ASCII table).

ascii : bool

add_col(column)

Append one Column to the column definition.

Warning

New in pyfits 2.3: This function appends the new column to the ColDefs object in place. Prior to pyfits 2.3, this function returned a new ColDefs with the new column at the end.

change_attrib(col_name, attrib, new_value)

Change an attribute (in the KEYWORD_ATTRIBUTES list) of a Column.

Parameters:  

col_name : str or int

The column name or index to change

attrib : str

The attribute name

value : object

The new value for the attribute

change_name(col_name, new_name)

Change a Column‘s name.

Parameters:  

col_name : str

The current name of the column

new_name : str

The new name of the column

change_unit(col_name, new_unit)

Change a Column‘s unit.

Parameters:  

col_name : str or int

The column name or index

new_unit : str

The new unit for the column

del_col(col_name)

Delete (the definition of) one Column.

col_name : str or int

The column’s name or index

info(attrib='all', output=None)

Get attribute(s) information of the column definition.

Parameters:  

attrib : str

Can be one or more of the attributes listed in pyfits.column.KEYWORD_ATTRIBUTES. The default is "all" which will print out all attributes. It forgives plurals and blanks. If there are two or more attribute names, they must be separated by comma(s).

output : file, optional

File-like object to output to. Outputs to stdout by default. If False, returns the attributes as a dict instead.

Notes

This function doesn’t return anything by default; it just prints to stdout.

FITS_rec

class pyfits.FITS_rec

Bases: numpy.core.records.recarray

FITS record array class.

FITS_rec is the data part of a table HDU’s data part. This is a layer over the recarray, so we can deal with scaled columns.

It inherits all of the standard methods from numpy.ndarray.

copy(order='C')

The Numpy documentation lies; numpy.ndarray.copy is not equivalent to numpy.copy. Differences include that it re-views the copied array as self’s ndarray subclass, as though it were taking a slice; this means __array_finalize__ is called and the copy shares all the array attributes (including ._convert!). So we need to make a deep copy of all those attributes so that the two arrays truly do not share any data.

field(key)

A view of a Column‘s data as an array.

classmethod from_columns(columns, nrows=0, fill=False)

Given a ColDefs object of unknown origin, initialize a new FITS_rec object.

Parameters:  

columns : sequence of Column or a ColDefs

The columns from which to create the table data. 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.

nrows : int

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.

fill : bool

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.

columns

A user-visible accessor for the coldefs.

See https://trac.assembla.com/pyfits/ticket/44

FITS_record

class pyfits.FITS_record(input, row=0, start=None, end=None, step=None, base=None, **kwargs)

Bases: object

FITS record class.

FITS_record is used to access records of the FITS_rec object. This will allow us to deal with scaled columns. It also handles conversion/scaling of columns in ASCII tables. The FITS_record class expects a FITS_rec object as input.

Parameters:  

input : array

The array to wrap.

row : int, optional

The starting logical row of the array.

start : int, optional

The starting column in the row associated with this object. Used for subsetting the columns of the FITS_rec object.

end : int, optional

The ending column in the row associated with this object. Used for subsetting the columns of the FITS_rec object.

field(field)

Get the field data of the record.

setfield(field, value)

Set the field data of the record.

Table Functions

new_table()

pyfits.new_table(*args, **kwargs)

Deprecated since version 3.3: Use BinTableHDU.from_columns() for new BINARY tables or TableHDU.from_columns() for new ASCII tables instead.

Create a new table from the input column definitions.

Warning: Creating a new table using this method creates an in-memory copy of all the column arrays in the input. This is because if they are separate arrays they must be combined into a single contiguous array.

If the column data is already in a single contiguous array (such as an existing record array) it may be better to create a BinTableHDU instance directly. See the PyFITS documentation for more details.

Parameters:  

input : sequence of Column or a ColDefs

The data to create a table from

header : Header instance

Header to be used to populate the non-required keywords

nrows : int

Number of rows in the new table

fill : bool

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.

tbtype : str or type

Table type to be created (BinTableHDU or TableHDU) or the class name as a string. Currently only BinTableHDU and TableHDU (ASCII tables) are supported.

tabledump()

pyfits.tabledump(filename, datafile=None, cdfile=None, hfile=None, ext=1, clobber=False)

Dump a table HDU to a file in ASCII format. The table may be dumped in three separate files, one containing column definitions, one containing header parameters, and one for table data.

Parameters:  

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

Input fits file.

datafile : file path, file object or file-like object, optional

Output data file. The default is the root name of the input fits file appended with an underscore, followed by the extension number (ext), followed by the extension .txt.

cdfile : file path, file object or file-like object, optional

Output column definitions file. The default is None, no column definitions output is produced.

hfile : file path, file object or file-like object, optional

Output header parameters file. The default is None, no header parameters output is produced.

ext : int

The number of the extension containing the table HDU to be dumped.

clobber : bool

Overwrite the output files if they exist.

Notes

The primary use for the tabledump function is to allow editing in a standard text editor of the table data and parameters. The tcreate function can be used to reassemble the table from the three ASCII files.

• datafile: Each line of the data file represents one row of table data. The data is output one column at a time in column order. If a column contains an array, each element of the column array in the current row is output before moving on to the next column. Each row ends with a new line.

  Integer data is output right-justified in a 21-character field followed by a blank. Floating point data is output right justified using ‘g’ format in a 21-character field with 15 digits of precision, followed by a blank. String data that does not contain whitespace is output left-justified in a field whose width matches the width specified in the TFORM header parameter for the column, followed by a blank. When the string data contains whitespace characters, the string is enclosed in quotation marks (""). For the last data element in a row, the trailing blank in the field is replaced by a new line character.

  For column data containing variable length arrays (‘P’ format), the array data is preceded by the string 'VLA_Length= ' and the integer length of the array for that row, left-justified in a 21-character field, followed by a blank.

  Note

  This format does not support variable length arrays using the (‘Q’ format) due to difficult to overcome ambiguities. What this means is that this file format cannot support VLA columns in tables stored in files that are over 2 GB in size.

  For column data representing a bit field (‘X’ format), each bit value in the field is output right-justified in a 21-character field as 1 (for true) or 0 (for false).

• cdfile: Each line of the column definitions file provides the definitions for one column in the table. The line is broken up into 8, sixteen-character fields. The first field provides the column name (TTYPEn). The second field provides the column format (TFORMn). The third field provides the display format (TDISPn). The fourth field provides the physical units (TUNITn). The fifth field provides the dimensions for a multidimensional array (TDIMn). The sixth field provides the value that signifies an undefined value (TNULLn). The seventh field provides the scale factor (TSCALn). The eighth field provides the offset value (TZEROn). A field value of "" is used to represent the case where no value is provided.

• hfile: Each line of the header parameters file provides the definition of a single HDU header card as represented by the card image.

tableload()

pyfits.tableload(datafile, cdfile, hfile=None)

Create a table from the input ASCII files. The input is from up to three separate files, one containing column definitions, one containing header parameters, and one containing column data. The header parameters file is not required. When the header parameters file is absent a minimal header is constructed.

Parameters:  

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

Input data file containing the table data in ASCII format.

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

Input column definition file containing the names, formats, display formats, physical units, multidimensional array dimensions, undefined values, scale factors, and offsets associated with the columns in the table.

hfile : file path, file object or file-like object, optional

Input parameter definition file containing the header parameter definitions to be associated with the table. If None, a minimal header is constructed.

Notes

The primary use for the tableload function is to allow the input of ASCII data that was edited in a standard text editor of the table data and parameters. The tabledump function can be used to create the initial ASCII files.

• datafile: Each line of the data file represents one row of table data. The data is output one column at a time in column order. If a column contains an array, each element of the column array in the current row is output before moving on to the next column. Each row ends with a new line.

  Integer data is output right-justified in a 21-character field followed by a blank. Floating point data is output right justified using ‘g’ format in a 21-character field with 15 digits of precision, followed by a blank. String data that does not contain whitespace is output left-justified in a field whose width matches the width specified in the TFORM header parameter for the column, followed by a blank. When the string data contains whitespace characters, the string is enclosed in quotation marks (""). For the last data element in a row, the trailing blank in the field is replaced by a new line character.

  For column data containing variable length arrays (‘P’ format), the array data is preceded by the string 'VLA_Length= ' and the integer length of the array for that row, left-justified in a 21-character field, followed by a blank.

  Note

  This format does not support variable length arrays using the (‘Q’ format) due to difficult to overcome ambiguities. What this means is that this file format cannot support VLA columns in tables stored in files that are over 2 GB in size.

  For column data representing a bit field (‘X’ format), each bit value in the field is output right-justified in a 21-character field as 1 (for true) or 0 (for false).

• cdfile: Each line of the column definitions file provides the definitions for one column in the table. The line is broken up into 8, sixteen-character fields. The first field provides the column name (TTYPEn). The second field provides the column format (TFORMn). The third field provides the display format (TDISPn). The fourth field provides the physical units (TUNITn). The fifth field provides the dimensions for a multidimensional array (TDIMn). The sixth field provides the value that signifies an undefined value (TNULLn). The seventh field provides the scale factor (TSCALn). The eighth field provides the offset value (TZEROn). A field value of "" is used to represent the case where no value is provided.

• hfile: Each line of the header parameters file provides the definition of a single HDU header card as represented by the card image.