Tables¶
BinTableHDU
¶
-
class
astropy.io.fits.
BinTableHDU
(data=None, header=None, name=None, uint=False)[source] [edit on github]¶ Bases:
astropy.io.fits.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
keyworduint : bool, optional
set to
True
if the table contains unsigned integer columns.-
add_checksum
(when=None, override_datasum=False, blocking='standard', checksum_keyword='CHECKSUM', datasum_keyword='DATASUM') [edit on github]¶ Add the
CHECKSUM
andDATASUM
cards to this HDU with the values set to the checksum calculated for the HDU and the data respectively. The addition of theDATASUM
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 onlyblocking : 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 awhen
argument, then calladd_checksum
with awhen
argument andoverride_datasum
set toTrue
. This will provide consistent comments for both cards and enable the generation of aCHECKSUM
card with a consistent value.
-
add_datasum
(when=None, blocking='standard', datasum_keyword='DATASUM') [edit on github]¶ 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 aCHECKSUM
card with a consistent value.
-
copy
() [edit on github]¶ Make a copy of the table HDU, both header and data are copied.
-
dump
(datafile=None, cdfile=None, hfile=None, clobber=False)[source] [edit on github]¶ 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. Theload
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
() [edit on github]¶ Calculates and returns the number of bytes that this HDU will write to a file.
-
fileinfo
() [edit on github]¶ 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
-
from_columns
(columns, header=None, nrows=0, fill=False, **kwargs) [edit on github]¶ Given either a
ColDefs
object, a sequence ofColumn
objects, or another table HDU or table data (aFITS_rec
or multi-fieldnumpy.ndarray
ornumpy.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 alsoFITS_rec.from_columns
.Parameters: columns : sequence of
Column
,ColDefs
, or otherThe 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 existingBinTableHDU
orTableHDU
, or anumpy.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
Notes
Any additional keyword arguments accepted by the HDU class’s
__init__
may also be passed in as keyword arguments.
-
fromstring
(data, checksum=False, ignore_missing_end=False, **kwargs) [edit on github]¶ 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 containing the HDU’s header and data.
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 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.
kwargs : optional
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
, orBinTableHDU
. Any unrecognized keyword arguments are simply ignored.
-
classmethod
load
(datafile, cdfile=None, hfile=None, replace=False, header=None)[source] [edit on github]¶ 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. Thedump
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.
-
readfrom
(fileobj, checksum=False, ignore_missing_end=False, **kwargs) [edit on github]¶ 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 withwriteto()
.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 bothDATASUM
andCHECKSUM
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) [edit on github]¶ 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 meanspos=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 returnTrue
orFalse
. This can be used for custom evaluation. For example ifpos=lambda idx: idx > 10
this will check that the keyword’s index is greater than 10.test : callable
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. IfNone
, 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"
. May also be any combination of"fix"
or"silentfix"
with"+ignore"
,+warn
, or+exception" (e.g. ``"fix+warn"
). 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 thefix_value
as its value when created. Also check the card’s value by using thetest
argument.
-
run_option
(option=u'warn', err_text=u'', fix_text=u'Fixed.', fix=None, fixable=True) [edit on github]¶ Execute the verification with selected option.
-
size
¶ Size (in bytes) of the data portion of the HDU.
-
classmethod
tcreate
(*args, **kwargs)[source] [edit on github]¶ Deprecated since version 0.1: The tcreate method is deprecated and may be removed in a future version. Use
load()
instead.
-
tdump
(*args, **kwargs)[source] [edit on github]¶ Deprecated since version 0.1: The tdump function is deprecated and may be removed in a future version. Use
dump()
instead.
-
update
() [edit on github]¶ Update header keywords to reflect recent changes of columns.
-
update_ext_name
(*args, **kwargs) [edit on github]¶ Deprecated since version 0.3: The update_ext_name function will be deprecated in a future version. Use the
.name
attribute orHeader.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
orafter
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 argumentbefore
takes precedence overafter
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 Headersavecomment : bool, optional
When
True
, preserve the current comment for an existing keyword. The argumentsavecomment
takes precedence overcomment
if both specified. Ifcomment
is not specified then the current comment will automatically be preserved.
-
update_ext_version
(*args, **kwargs) [edit on github]¶ Deprecated since version 0.3: The update_ext_version function will be deprecated in a future version. Use the
.ver
attribute orHeader.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
orafter
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 argumentbefore
takes precedence overafter
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 argumentsavecomment
takes precedence overcomment
if both specified. Ifcomment
is not specified then the current comment will automatically be preserved.
-
verify
(option=u'warn') [edit on github]¶ Verify all values in the instance.
Parameters: option : str
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
(blocking='standard') [edit on github]¶ 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') [edit on github]¶ Verify that the value in the
DATASUM
keyword matches the value calculated for theDATASUM
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) [edit on github]¶ Works similarly to the normal writeto(), but prepends a default
PrimaryHDU
are required by extension HDUs (which cannot stand on their own).
-
TableHDU
¶
-
class
astropy.io.fits.
TableHDU
(data=None, header=None, name=None)[source] [edit on github]¶ Bases:
astropy.io.fits.hdu.table._TableBaseHDU
FITS ASCII table extension HDU class.
-
add_checksum
(when=None, override_datasum=False, blocking='standard', checksum_keyword='CHECKSUM', datasum_keyword='DATASUM') [edit on github]¶ Add the
CHECKSUM
andDATASUM
cards to this HDU with the values set to the checksum calculated for the HDU and the data respectively. The addition of theDATASUM
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 onlyblocking : 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 awhen
argument, then calladd_checksum
with awhen
argument andoverride_datasum
set toTrue
. This will provide consistent comments for both cards and enable the generation of aCHECKSUM
card with a consistent value.
-
add_datasum
(when=None, blocking='standard', datasum_keyword='DATASUM') [edit on github]¶ 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 aCHECKSUM
card with a consistent value.
-
copy
() [edit on github]¶ Make a copy of the table HDU, both header and data are copied.
-
filebytes
() [edit on github]¶ Calculates and returns the number of bytes that this HDU will write to a file.
-
fileinfo
() [edit on github]¶ 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
-
from_columns
(columns, header=None, nrows=0, fill=False, **kwargs) [edit on github]¶ Given either a
ColDefs
object, a sequence ofColumn
objects, or another table HDU or table data (aFITS_rec
or multi-fieldnumpy.ndarray
ornumpy.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 alsoFITS_rec.from_columns
.Parameters: columns : sequence of
Column
,ColDefs
, or otherThe 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 existingBinTableHDU
orTableHDU
, or anumpy.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
Notes
Any additional keyword arguments accepted by the HDU class’s
__init__
may also be passed in as keyword arguments.
-
fromstring
(data, checksum=False, ignore_missing_end=False, **kwargs) [edit on github]¶ 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 containing the HDU’s header and data.
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 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.
kwargs : optional
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
, orBinTableHDU
. Any unrecognized keyword arguments are simply ignored.
-
readfrom
(fileobj, checksum=False, ignore_missing_end=False, **kwargs) [edit on github]¶ 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 withwriteto()
.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 bothDATASUM
andCHECKSUM
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) [edit on github]¶ 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 meanspos=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 returnTrue
orFalse
. This can be used for custom evaluation. For example ifpos=lambda idx: idx > 10
this will check that the keyword’s index is greater than 10.test : callable
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. IfNone
, 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"
. May also be any combination of"fix"
or"silentfix"
with"+ignore"
,+warn
, or+exception" (e.g. ``"fix+warn"
). 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 thefix_value
as its value when created. Also check the card’s value by using thetest
argument.
-
run_option
(option=u'warn', err_text=u'', fix_text=u'Fixed.', fix=None, fixable=True) [edit on github]¶ Execute the verification with selected option.
-
size
¶ Size (in bytes) of the data portion of the HDU.
-
update
() [edit on github]¶ Update header keywords to reflect recent changes of columns.
-
update_ext_name
(*args, **kwargs) [edit on github]¶ Deprecated since version 0.3: The update_ext_name function will be deprecated in a future version. Use the
.name
attribute orHeader.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
orafter
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 argumentbefore
takes precedence overafter
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 Headersavecomment : bool, optional
When
True
, preserve the current comment for an existing keyword. The argumentsavecomment
takes precedence overcomment
if both specified. Ifcomment
is not specified then the current comment will automatically be preserved.
-
update_ext_version
(*args, **kwargs) [edit on github]¶ Deprecated since version 0.3: The update_ext_version function will be deprecated in a future version. Use the
.ver
attribute orHeader.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
orafter
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 argumentbefore
takes precedence overafter
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 argumentsavecomment
takes precedence overcomment
if both specified. Ifcomment
is not specified then the current comment will automatically be preserved.
-
verify
(option=u'warn') [edit on github]¶ Verify all values in the instance.
Parameters: option : str
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
(blocking='standard') [edit on github]¶ 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') [edit on github]¶ Verify that the value in the
DATASUM
keyword matches the value calculated for theDATASUM
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) [edit on github]¶ Works similarly to the normal writeto(), but prepends a default
PrimaryHDU
are required by extension HDUs (which cannot stand on their own).
-
Column
¶
-
class
astropy.io.fits.
Column
(name=None, format=None, unit=None, null=None, bscale=None, bzero=None, disp=None, start=None, dim=None, array=None, ascii=None)[source] [edit on github]¶ Bases:
astropy.io.fits.util.NotifierMixin
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 exceptformat
can be optional; see Column Creation and Creating an ASCII Table for more information regardingTFORM
keyword.Parameters: name : str, optional
column name, corresponding to
TTYPE
keywordformat : str
column format, corresponding to
TFORM
keywordunit : str, optional
column unit, corresponding to
TUNIT
keywordnull : str, optional
null value, corresponding to
TNULL
keywordbscale : int-like, optional
bscale value, corresponding to
TSCAL
keywordbzero : int-like, optional
bzero value, corresponding to
TZERO
keyworddisp : str, optional
display format, corresponding to
TDISP
keywordstart : int, optional
column starting position (ASCII table only), corresponding to
TBCOL
keyworddim : str, optional
column dimension corresponding to
TDIM
keywordarray : iterable, optional
a
list
,numpy.ndarray
(or other iterable that can be used to initialize an ndarray) providing initial data for this column. The array will be automatically converted, if possible, to the data format of the column. In the case were non-trivialbscale
and/orbzero
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-
array
¶ The Numpy
ndarray
associated with thisColumn
.If the column was instantiated with an array passed to the
array
argument, this will return that array. However, if the column is later added to a table, such as viaBinTableHDU.from_columns
as is typically the case, this attribute will be updated to reference the associated field in the table, which may no longer be the same array.
-
copy
()[source] [edit on github]¶ Return a copy of this
Column
.
-
ColDefs
¶
-
class
astropy.io.fits.
ColDefs
(input, tbtype=None, ascii=False)[source] [edit on github]¶ Bases:
astropy.io.fits.util.NotifierMixin
Column definitions class.
It has attributes corresponding to the
Column
attributes (e.g.ColDefs
has the attributenames
whileColumn
hasname
). Each attribute inColDefs
is a list of corresponding attribute values from allColumn
objects.Parameters: input : sequence of
Column
,ColDefs
, otherAn existing table HDU, an existing
ColDefs
, or any multi-field Numpy array ornumpy.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)[source] [edit on github]¶ Append one
Column
to the column definition.
-
change_attrib
(col_name, attrib, new_value)[source] [edit on github]¶ Change an attribute (in the
KEYWORD_ATTRIBUTES
list) of aColumn
.Parameters: col_name : str or int
The column name or index to change
attrib : str
The attribute name
new_value : object
The new value for the attribute
-
change_name
(col_name, new_name)[source] [edit on github]¶ 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)[source] [edit on github]¶ 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)[source] [edit on github]¶ Delete (the definition of) one
Column
.- col_name : str or int
- The column’s name or index
-
info
(attrib='all', output=None)[source] [edit on github]¶ Get attribute(s) information of the column definition.
Parameters: attrib : str
Can be one or more of the attributes listed in
astropy.io.fits.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
Notes
This function doesn’t return anything by default; it just prints to stdout.
-
FITS_rec
¶
-
class
astropy.io.fits.
FITS_rec
[source] [edit on github]¶ Bases:
numpy.recarray
FITS record array class.
FITS_rec
is the data part of a table HDU’s data part. This is a layer over therecarray
, so we can deal with scaled columns.It inherits all of the standard methods from
numpy.ndarray
.-
columns
¶ A user-visible accessor for the coldefs.
-
copy
(order='C')[source] [edit on github]¶ The Numpy documentation lies;
numpy.ndarray.copy
is not equivalent tonumpy.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._converted
!). 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)[source] [edit on github]¶ A view of a
Column
‘s data as an array.
-
formats
¶ List of column FITS foramts.
-
classmethod
from_columns
(columns, nrows=0, fill=False)[source] [edit on github]¶ Given a
ColDefs
object of unknown origin, initialize a newFITS_rec
object.Note
This was originally part of the
new_table
function in the table module but was moved into a class method since most of its functionality always had more to do with initializing aFITS_rec
object than anything else, and much of it also overlapped withFITS_rec._scale_back
.Parameters: columns : sequence of
Column
or aColDefs
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
-
names
¶ List of column names.
-
FITS_record
¶
-
class
astropy.io.fits.
FITS_record
(input, row=0, start=None, end=None, step=None, base=None, **kwargs)[source] [edit on github]¶ Bases:
object
FITS record class.
FITS_record
is used to access records of theFITS_rec
object. This will allow us to deal with scaled columns. It also handles conversion/scaling of columns in ASCII tables. TheFITS_record
class expects aFITS_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)[source] [edit on github]¶ Get the field data of the record.
-
setfield
(field, value)[source] [edit on github]¶ Set the field data of the record.
-
Table Functions¶
new_table()
¶
-
astropy.io.fits.
new_table
(*args, **kwargs)[source] [edit on github]¶ Deprecated since version 0.4: The new_table function is deprecated and may be removed in a future version. Use
BinTableHDU.from_columns()
for new BINARY tables orTableHDU.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 Astropy documentation for more details.Parameters: input : sequence of
Column
or aColDefs
The data to create a table from
header :
Header
instanceHeader to be used to populate the non-required keywords
nrows : int
Number of rows in the new table
fill : bool
tbtype : str or type
Table type to be created (
BinTableHDU
orTableHDU
) or the class name as a string. Currently onlyBinTableHDU
andTableHDU
(ASCII tables) are supported.
tabledump()
¶
-
astropy.io.fits.
tabledump
(filename, datafile=None, cdfile=None, hfile=None, ext=1, clobber=False)[source] [edit on github]¶ 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. Thetcreate
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()
¶
-
astropy.io.fits.
tableload
(datafile, cdfile, hfile=None)[source] [edit on github]¶ 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.