Unified file read/write interface¶
Astropy provides a unified interface for reading and writing data in different formats. For many common cases this will simplify the process of file I/O and reduce the need to master the separate details of all the I/O packages within Astropy. For details on the implementation see I/O Registry (astropy.io.registry).
Getting started with Image I/O¶
Reading and writing image data in the unified I/O interface is supported
though the CCDData
class using FITS file format:
>>> # Read CCD image
>>> ccd = CCDData.read('image.fits')
>>> # Write back CCD image
>>> ccd.write('new_image.fits')
Note the unit is stored in the BUNIT
keyword in the header on saving, and is
read from the header if it is present.
Detailed help on the available keyword arguments for reading and writing
can be obtained via the help()
method as follows:
>>> CCDData.read.help('fits') # Get help on the CCDData FITS reader
>>> CCDData.writer.help('fits') # Get help on the CCDData FITS writer
Getting started with Table I/O¶
The Table
class includes two methods,
read()
and
write()
, that make it possible to read from
and write to files. A number of formats are automatically supported (see
Built-in table readers/writers) and new file formats and extensions can be
registered with the Table
class (see
I/O Registry (astropy.io.registry)).
To use this interface, first import the Table
class, then
simply call the Table
read()
method with the name of the file and
the file format, for instance 'ascii.daophot'
:
>>> from astropy.table import Table
>>> t = Table.read('photometry.dat', format='ascii.daophot')
It is possible to load tables directly from the Internet using URLs. For example,
download tables from Vizier catalogues in CDS format ('ascii.cds'
):
>>> t = Table.read("ftp://cdsarc.u-strasbg.fr/pub/cats/VII/253/snrs.dat",
... readme="ftp://cdsarc.u-strasbg.fr/pub/cats/VII/253/ReadMe",
... format="ascii.cds")
For certain file formats, the format can be automatically detected, for example from the filename extension:
>>> t = Table.read('table.tex')
Similarly, for writing, the format can be explicitly specified:
>>> t.write(filename, format='latex')
As for the read()
method, the format may
be automatically identified in some cases.
The underlying file handler will also automatically detect various
compressed data formats and transparently uncompress them as far as
supported by the Python installation (see
get_readable_fileobj()
).
For writing, one can also specify details about the Table serialization
methods via the serialize_method
keyword argument. This allows
fine control of the way to write out certain columns, for instance
writing an ISO format Time column as a pair of JD1 / JD2 floating
point values (for full resolution) or as a formatted ISO date string.
Getting help on readers and writers¶
Each file format is handled by a specific reader or writer, and each of those
functions will have its own set of arguments. For examples of
this see the section Built-in table readers/writers. This section also
provides the full list of choices for the format
argument.
To get help on the available arguments for each format, use the help()
method of the read
or write
methods. Each of these calls prints a long help document which is divided
into two sections, the generic read/write documentation (common to any
call) and the format-specific documentation. For ASCII tables the
format-specific documentation includes the generic astropy.io.ascii
package
interface and then a description of the particular ASCII subformat.
In the examples below we do not show the long output:
>>> Table.read.help('fits')
>>> Table.read.help('ascii')
>>> Table.read.help('ascii.latex')
>>> Table.write.help('hdf5')
>>> Table.write.help('csv')
Command-line utility¶
For convenience, the command-line tool showtable
can be used to print the
content of tables for the formats supported by the unified I/O interface:
$ showtable astropy/io/fits/tests/data/table.fits
target V_mag
------- -----
NGC1001 11.1
NGC1002 12.3
NGC1003 15.2
To get full documentation on the usage and available options do showtable
--help
.
Built-in table readers/writers¶
The Table
class has built-in support for various input
and output formats including ASCII formats,
-FITS, HDF5, Pandas,
and VO Tables.
A full list of the supported formats and corresponding classes
is shown in the table below.
The Write
column indicates those formats that support write functionality, and
the Suffix
column indicates the filename suffix indicating a particular format.
If the value of Suffix
is auto
, the format is auto-detected from the file itself.
Not all formats support auto-detection.
Format |
Write |
Suffix |
Description |
---|---|---|---|
ascii |
Yes |
ASCII table in any supported format (uses guessing) |
|
ascii.aastex |
Yes |
|
|
ascii.basic |
Yes |
|
|
ascii.cds |
No |
|
|
ascii.commented_header |
Yes |
|
|
ascii.csv |
Yes |
.csv |
|
ascii.daophot |
No |
|
|
ascii.ecsv |
Yes |
.ecsv |
|
ascii.fixed_width |
Yes |
|
|
ascii.fixed_width_no_header |
Yes |
|
|
ascii.fixed_width_two_line |
Yes |
|
|
ascii.html |
Yes |
.html |
|
ascii.ipac |
Yes |
|
|
ascii.latex |
Yes |
.tex |
|
ascii.no_header |
Yes |
|
|
ascii.rdb |
Yes |
.rdb |
|
ascii.rst |
Yes |
.rst |
|
ascii.sextractor |
No |
|
|
ascii.tab |
Yes |
|
|
fits |
Yes |
auto |
|
hdf5 |
Yes |
auto |
HDF5: Hierarchical Data Format binary file |
pandas.csv |
Yes |
Wrapper around |
|
pandas.fwf |
No |
Wrapper around |
|
pandas.html |
Yes |
Wrapper around |
|
pandas.json |
Yes |
Wrapper around |
|
votable |
Yes |
auto |
|
ASCII formats¶
The read()
and
write()
methods can be used to read and write formats
supported by astropy.io.ascii
.
Use format='ascii'
in order to interface to the generic
read()
and write()
functions from astropy.io.ascii
. When reading a table this means
that all supported ASCII table formats will be tried in order to successfully
parse the input. For example:
>>> t = Table.read('astropy/io/ascii/tests/t/latex1.tex', format='ascii')
>>> print(t)
cola colb colc
---- ---- ----
a 1 2
b 3 4
When writing a table with format='ascii'
the output is a basic
character-delimited file with a single header line containing the
column names.
All additional arguments are passed to the astropy.io.ascii
read()
and write()
functions. Further details are available in the sections on
Parameters for read() and Parameters for write(). For example, to change
column delimiter and the output format for the colc
column use:
>>> t.write(sys.stdout, format='ascii', delimiter='|', formats={'colc': '%0.2f'})
cola|colb|colc
a|1|2.00
b|3|4.00
Note
When specifying a specific ASCII table format using the unified interface, the format name is
prefixed with ascii
in order to identify the format as ASCII-based. Compare the
table above to the astropy.io.ascii
list of supported formats where the prefix is not
needed. Therefore the following are equivalent:
>>> dat = ascii.read('file.dat', format='daophot')
>>> dat = Table.read('file.dat', format='ascii.daophot')
For compatibility with astropy version 0.2 and earlier, the following format
values are also allowed in ``Table.read()``: ``daophot``, ``ipac``, ``html``, ``latex``, and ``rdb``.
Attention
ECSV is recommended
For writing and reading tables to ASCII in a way that fully reproduces the
table data, types and metadata (i.e. the table will “round-trip”), we highly
recommend using the ECSV format. This writes the actual data in a
simple space-delimited format (the basic
format) that any ASCII table
reader can parse, but also includes metadata encoded in a comment block that
allows full reconstruction of the original columns. This includes support
for Mixin columns (such as
SkyCoord
or Time
) and
Masked columns.
FITS¶
Reading and writing tables in FITS format is
supported with format='fits'
. In most cases, existing FITS files should be
automatically identified as such based on the header of the file, but if not,
or if writing to disk, then the format should be explicitly specified.
Reading¶
If a FITS table file contains only a single table, then it can be read in with:
>>> from astropy.table import Table
>>> t = Table.read('data.fits')
If more than one table is present in the file, you can select the HDU as follows:
>>> t = Table.read('data.fits', hdu=3)
In this case if the hdu
argument is omitted then the first table found will be
read in and a warning will be emitted:
>>> t = Table.read('data.fits')
WARNING: hdu= was not specified but multiple tables are present, reading in first available table (hdu=1) [astropy.io.fits.connect]
Writing¶
To write a table t
to a new file:
>>> t.write('new_table.fits')
If the file already exists and you want to overwrite it, then set the
overwrite
keyword:
>>> t.write('existing_table.fits', overwrite=True)
At this time there is no support for appending an HDU to an existing
file or writing multi-HDU files using the Table interface. Instead one
can use the convenience function
table_to_hdu()
to create a single
binary table HDU and insert or append that to an existing
HDUList
.
As of astropy version 3.0 there is support for writing a table which contains
Mixin columns such as Time
or
SkyCoord
. This uses FITS COMMENT
cards to capture
additional information needed order to fully reconstruct the mixin columns when
reading back from FITS. The information is a Python dict
structure which is
serialized using YAML.
Keywords¶
The FITS keywords associated with an HDU table are represented in the meta
ordered dictionary attribute of a Table. After reading
a table one can view the available keywords in a readable format using:
>>> for key, value in t.meta.items():
... print('{0} = {1}'.format(key, value))
This does not include the “internal” FITS keywords that are required to specify
the FITS table properties (e.g. NAXIS
, TTYPE1
). HISTORY
and
COMMENT
keywords are treated specially and are returned as a list of
values.
Conversely, the following shows examples of setting user keyword values for a
table t
:
>>> t.meta['MY_KEYWD'] = 'my value'
>>> t.meta['COMMENT'] = ['First comment', 'Second comment', 'etc']
>>> t.write('my_table.fits', overwrite=True)
The keyword names (e.g. MY_KEYWD
) will be automatically capitalized prior
to writing.
At this time, the meta
attribute of the Table
class
is simply an ordered dictionary and does not fully represent the structure of a
FITS header (for example, keyword comments are dropped).
TDISPn Keyword¶
TDISPn FITS keywords will map to and from the Column
format
attribute if the display format is convertible to and from a Python display
format. Below are the rules used for both conversion directions.
TDISPn to Python Format String¶
TDISPn format characters are defined in the table below.
Format |
Description |
---|---|
Aw |
Character |
Lw |
Logical |
Iw.m |
Integer |
Bw.m |
Binary, integers only |
Ow.m |
Octal, integers only |
Zw.m |
Hexadecimal, integers only |
Fw.d |
Floating-point, fixed decimal notation |
Ew.dEe |
Floating-point, exponential notation |
ENw.d |
Engineering; E format with exponent multiple of three |
ESw.d |
Scientific; same as EN but non-zero leading digit if not zero |
Gw.dEe |
General; appears as F if significance not lost, also E |
Dw.dEe |
Floating-point, exponential notation, double precision |
Where w is the width in characters of displayed values, m is the minimum number of digits displayed, d is the number of digits to the right of decimal, and e is number of digits in the exponent. The .m and Ee fields are optional.
The A (character), L (logical), F (floating point), and G (general) display formats can be directly translated to Python format strings. The other formats need to be modified to match Python display formats.
For the integer formats (I, B, O, and Z), the width (w) value is used to add space padding to the left of the column value. The minimum number (m) value is not used. For the E, G, D, EN, and ES formats (floating point exponential) the width (w) and precision (d) are both used, but the exponential (e) is not used.
Python Format String to TDISPn¶
The conversion from Python format strings back to TDISPn is slightly more complicated.
Python strings map to the TDISP format A if the Python formatting string does not contain right space padding. It will accept left space padding. The same applies to the logical format L.
The integer formats (decimal integer, binary, octal, hexidecimal) map to the I, B, O, and Z TDISP formats respectively. Integer formats do not accept a zero padded format string or a format string with no left padding defined (a width is required in the TDISP format standard for the Integer formats).
For all float and exponential values zero padding is not accepted. There
must be at least a width or precision defined. If only a width is defined,
there is no precision set for the TDISPn format. If only a precision is
defined, the width is set to the precision plus an extra padding value
depending on format type, and both are set in the TDISPn format. Otherwise,
if both a width and precision are present they are both set in the TDISPn
format. A Python f
or F
map to TDISP F format. The Python g
or
G
map to TDISP G format. The Python e
and E
map to TDISP E format.
Masked columns¶
Tables that contain MaskedColumn
columns can be written to
FITS. By default this will replace the masked data elements with certain
sentinel values according to the FITS standard:
NaN
for float columnsValue of
TNULLn
for integer columns, as defined by the columnfill_value
attributeNull string for string columns (not currently implemented)
When the file is read back those elements are marked as masked in the returned table, but see issue #4708 for problems in all three cases.
The FITS standard has a few limitations:
Not all data types are supported (e.g. logical / boolean)
Integer columns require picking one value as the NULL indicator. If all possible values are represented in valid data (e.g. an unsigned int columns with all 256 possible values in valid data) then there is no way to represent missing data.
The masked data values are permanently lost, precluding the possibility of later unmasking the values.
Astropy provides a work-around for this limitation that users can choose to
use. The key part is to use the serialize_method='data_mask'
keyword argument
when writing the table. This tells the FITS writer to split each masked
column into two separate columns, one for the data and one for the mask.
When it gets read back that process is reversed and the two columns are
merged back into one masked column.
>>> from astropy.table.table_helpers import simple_table
>>> t = simple_table(masked=True)
>>> t['d'] = [False, False, True]
>>> t['d'].mask = [True, False, False]
>>> t
<Table masked=True length=3>
a b c d
int64 float64 str1 bool
----- ------- ---- -----
-- 1.0 c --
2 2.0 -- False
3 -- e True
>>> t.write('data.fits', serialize_method='data_mask', overwrite=True)
>>> Table.read('data.fits')
<Table masked=True length=3>
a b c d
int64 float64 bytes1 bool
----- ------- ------ -----
-- 1.0 c --
2 2.0 -- False
3 -- e True
Warning
This option goes outside of the established FITS standard for
representing missing data so users should be careful about choosing this option,
especially if other (non-astropy) users will be reading the file(s). Behind
the scenes, astropy is converting the masked columns into two distinct
data and mask columns, then writing metadata into COMMENT
cards to
allow reconstruction of the original data.
Astropy native objects (mixin columns)¶
It is possible to store not only standard Column
objects to a
FITS table HDU, but also any Astropy native objects
(Mixin columns) within a Table
or
QTable
. This includes Time
,
Quantity
, SkyCoord
, and many others.
In general a mixin column may contain multiple data components as well as
object attributes beyond the standard Column attributes like format
or
description
. Abiding by the rules set by the FITS standard requires mapping
of these data components and object attributes to the appropriate FITS table
columns and keywords. Thus, a well defined protocol has been developed to allow
the storage of these mixin columns in FITS while allowing the object to
“round-trip” through the file with no loss of data or attributes.
Quantity¶
A Quantity
mixin column in a QTable
is
represented in a FITS table using the TUNITn
FITS column keyword to
incorporate the unit attribute of Quantity. For example:
>>> from astropy.table import QTable
>>> import astropy.units as u
>>> t = QTable([[1, 2] * u.angstrom)])
>>> t.write('my_table.fits', overwrite=True)
>>> qt = QTable.read('my_table.fits')
>>> qt
<QTable length=2>
col0
Angstrom
float64
--------
1.0
2.0
Time¶
Astropy provides the following features for reading and writing Time
:
Writing and reading Astropy Time columns¶
By default, a Time
mixin column within a Table
or QTable
will be written to FITS in full precision. This will be
done using the FITS time standard by setting the necessary FITS header keywords.
The default behavior for reading a FITS table into an Table
has historically been to convert all FITS columns to Column
objects, which have closely matching properties. For some columns, however,
closer native astropy representations are possible, and one can indicate these
should be used by passing astropy_native=True
(for backwards compatibility,
this is not done by default). This will convert columns conforming to the
FITS time standard to Time
instances, avoiding any loss of
precision. For example:
>>> from astropy.time import Time
>>> from astropy.table import Table
>>> from astropy.coordinates import EarthLocation
>>> t = Table()
>>> t['a'] = Time([100.0, 200.0], scale='tt', format='mjd',
... location=EarthLocation(-2446354, 4237210, 4077985, unit='m'))
>>> t.write('my_table.fits', overwrite=True)
>>> tm = Table.read('my_table.fits', astropy_native=True)
>>> tm['a']
<Time object: scale='tt' format='jd' value=[ 2400100.5 2400200.5]>
>>> tm['a'].location
<EarthLocation (-2446354., 4237210., 4077985.) m>
>>> all(tm['a'] == t['a'])
True
The same will work with QTable
.
In addition to binary table columns, various global time informational FITS
keywords are treated specially with astropy_native=True
. In particular
the keywords DATE
, DATE-*
(ISO-8601 datetime strings) and the MJD-*
(MJD date values) will be returned as Time
objects in the Table meta
.
For more details regarding the FITS time paper and the implementation,
refer to FITS Table with Time Columns.
Since not all FITS readers are able to use the FITS time standard, it is also
possible to store Time
instances using the _time_format
.
For this case, none of the special header keywords associated with the
FITS time standard will be set. When reading this back into Astropy, the
column will be an ordinary Column instead of a Time
object.
See the Details section below for an example.
Reading FITS standard compliant time coordinate columns in binary tables¶
Reading FITS files which are compliant with the FITS time standard is supported by Astropy by following the multifarious rules and conventions set by the standard. The standard was devised in order to describe time coordinates in an unambiguous and comprehensive manner and also to provide flexibility for its multiple use-cases. Thus, while reading time coordinate columns in FITS compliant files, multiple aspects of the standard are taken into consideration.
Time coordinate columns strictly compliant with the two-vector JD subset of the
standard (described in the Details section below) can be read as native
Time
objects. The other subsets of the standard are also supported
by Astropy; a thorough examination of the FITS standard time-related keywords is
done and the time data is interpreted accordingly.
The standard describes the various components in the specification of time:
Time coordinate frame
Time unit
Corrections, errors, etc.
Durations
The keywords used to specify times define these components. Using these keywords,
time coordinate columns are identified and read as Time
objects.
Refer to FITS Table with Time Columns for the specification of these keywords and their
description.
There are two aspects of the standard that require special attention due to the subtleties involved while handling them. These are:
Column named TIME with time unit
A common convention found in existing FITS files is that a FITS binary
table column with TTYPEn = ‘TIME’
represents a time coordinate column.
Many astronomical data files, including official data products from major
observatories, follow this convention that pre-dates the FITS standard.
The FITS time standard states that such a column will be controlled by
the global time reference frame keywords, and this will still be compliant
with the present standard.
Using this convention which has been incorporated into the standard, Astropy
can read time coordinate columns from all such FITS tables as native
Time
objects. Common examples of FITS files following
this convention are Chandra, XMM, and HST files.
The following is an example of a Header extract of a Chandra event list:
COMMENT ---------- Globally valid key words ----------------
DATE = '2016-01-27T12:34:24' / Date and time of file creation
TIMESYS = 'TT ' / Time system
MJDREF = 5.0814000000000E+04 / [d] MJD zero point for times
TIMEUNIT= 's ' / Time unit
TIMEREF = 'LOCAL ' / Time reference (barycenter/local)
COMMENT ---------- Time Column -----------------------
TTYPE1 = 'time ' / S/C TT corresponding to mid-exposure
TFORM1 = '1D ' / format of field
TUNIT1 = 's '
When reading such a FITS table with astropy_native=True
, Astropy checks
whether the name of a column is “TIME”/ “time” (TTYPEn = ‘TIME’
) and
whether its unit is a FITS recognized time unit (TUNITn
is a time unit).
For example, reading a Chandra event list which has the above mentioned header
and the time coordinate column time
as [1, 2]
will give:
>>> from astropy.table import Table
>>> from astropy.time import Time, TimeDelta
>>> from astropy.utils.data import get_pkg_data_filename
>>> chandra_events = get_pkg_data_filename('data/chandra_time.fits',
... package='astropy.io.fits.tests')
>>> native = Table.read(chandra_events, astropy_native=True)
>>> native['time']
<Time object: scale='tt' format='mjd' value=[57413.76033393 57413.76033393]>
>>> non_native = Table.read(chandra_events)
>>> # MJDREF = 5.0814000000000E+04, TIMESYS = 'TT'
>>> ref_time = Time(non_native.meta['MJDREF'], format='mjd',
... scale=non_native.meta['TIMESYS'].lower())
>>> # TTYPE1 = 'time', TUNIT1 = 's'
>>> delta_time = TimeDelta(non_native['time'])
>>> all(ref_time + delta_time == native['time'])
True
By default, FITS table columns will be read as standard Column
objects without taking the FITS time standard into consideration.
String time column in ISO-8601 Datetime format
FITS uses a subset of ISO-8601 (which in itself does not imply a particular time scale)
for several time-related keywords, such as DATE-xxx. Following the FITS standard its
values must be written as a character string in the following datetime
format:
[+/-C]CCYY-MM-DD[Thh:mm:ss[.s...]]
A time coordinate column can be constructed using this representation of time.
The following is an example of an ISO-8601 datetime
format time column:
TIME
----
1999-01-01T00:00:00
1999-01-01T00:00:40
1999-01-01T00:01:06
.
.
.
1999-01-20T01:10:00
The criteria for identifying a time coordinate column in ISO-8601 format is as follows:
A time column is identified using the time coordinate frame keywords as described in
FITS Table with Time Columns. Once it has been identified, its datatype is checked in order
to determine its representation format. Since ISO-8601 datetime
format is the only
string representation of time, a time coordinate column having string datatype will be
automatically read as a Time
object with format='fits'
(‘fits’
represents the FITS ISO-8601 format).
As this format does not imply a particular time scale, it is determined using the time
scale keywords in the header (TCTYP
or TIMESYS
) or their defaults. The other time
coordinate information is also determined in the same way, using the time coordinate
frame keywords. All ISO-8601 times are relative to a globally accepted zero point
(year 0 corresponds to 1 BCE) and are thus are not relative to the reference time
keywords (MJDREF, JDREF or DATEREF). Hence, these keywords will be ignored while dealing
with ISO-8601 time columns.
Note
Reading FITS files with time coordinate columns may fail. Astropy supports a large subset of these files, but there are still some FITS files which are not compliant with any aspect of the standard. If you have such a file, please don’t hesitate to let us know, e.g., by opening an issue in the issue tracker.
Also, reading a column having TTYPEn = ‘TIME’
as Time
will fail if TUNITn
for the column is not a FITS recognized time unit.
Details¶
Time as a dimension in astronomical data presents challenges in its
representation in FITS files. The standard has therefore been extended to
describe rigorously the time coordinate in the World Coordinate System
framework. Refer to FITS WCS paper IV for details.
Allowing Time
columns to be written as time coordinate
columns in FITS tables thus involves storing time values in a way that
ensures retention of precision and mapping the associated metadata to the
relevant FITS keywords.
In accordance with the standard which states that in binary tables one may use
pairs of doubles, the Astropy Time column is written in such a table as a
vector of two doubles (TFORMn = ‘2D’) (jd1, jd2)
where JD = jd1 + jd2
.
This reproduces the time values to double-double precision and is the
“lossless” version, exploiting the higher precision provided in binary tables.
Note that jd1
is always a half-integer or integer, while abs(jd2) < 1
.
Round-tripping of Astropy written FITS binary tables containing time coordinate
columns has been partially achieved by mapping selected metadata, scale
and
singular location
of Time
, to corresponding keywords. Note
that the arbitrary metadata allowed in Table
objects within
the meta
dict is not written and will be lost.
Consider the following Time column:
>>> t['a'] = Time([100.0, 200.0], scale='tt', format='mjd')
The FITS standard requires an additional translation layer back into
the desired format. The Time column t['a']
will undergo the translation
Astropy Time --> FITS --> Astropy Time
which corresponds to the format conversion
mjd --> (jd1, jd2) --> jd
. Thus, the final conversion from (jd1, jd2)
will
require a software implementation which is fully compliant with the FITS time standard.
Taking this into consideration, the functionality to read/write Time
from/to FITS can be explicitly turned off, by opting to store the time
representation values in the format specified by the format
attribute
of the Time
column, instead of the (jd1, jd2)
format, with
no extra metadata in the header. This is the “lossy” version, but can help
portability. For the above example, the FITS column corresponding
to t['a']
will then store [100.0 200.0]
instead of
[[ 2400100.5, 0. ], [ 2400200.5, 0. ]]
. This is done by setting the
Table serialization methods for Time columns when writing, as in the
following example:
>>> from astropy.time import Time
>>> from astropy.table import Table
>>> from astropy.coordinates import EarthLocation
>>> t = Table()
>>> t['a'] = Time([100.0, 200.0], scale='tt', format='mjd')
>>> t.write('my_table.fits', overwrite=True,
... serialize_method={Time: 'formatted_value'})
>>> tm = Table.read('my_table.fits')
>>> tm['a']
<Column name='a' dtype='float64' length=2>
100.0
200.0
>>> all(tm['a'] == t['a'].value)
True
By default, serialize_method
for Time columns is equal to
'jd1_jd2'
, that is, Time column will be written in full precision.
Note
The Astropy Time
object does not precisely map to the FITS
time standard.
FORMAT
The FITS format considers only three formats, ISO-8601, JD and MJD. Astropy Time allows for many other formats like
unix
orcxcsec
for representing the values.Hence, the
format
attribute of Time is not stored. After reading from FITS the user must set theformat
as desired.LOCATION
In the FITS standard, the reference position for a time coordinate is a scalar expressed via keywords. However, vectorized reference position or location can be supported by the Green Bank Keyword Convention which is a Registered FITS Convention. In Astropy Time, location can be an array which is broadcastable to the Time values.
Hence, vectorized
location
attribute of Time is stored and read following this convention.
HDF5¶
Reading/writing from/to HDF5 files is
supported with format='hdf5'
(this requires h5py
to be installed). However, the .hdf5
file extension is automatically recognized when writing files, and HDF5 files
are automatically identified (even with a different extension) when reading
in (using the first few bytes of the file to identify the format), so in most
cases you will not need to explicitly specify format='hdf5'
.
Since HDF5 files can contain multiple tables, the full path to the table
should be specified via the path=
argument when reading and writing.
For example, to read a table called data
from an HDF5 file named
observations.hdf5
, you can do:
>>> t = Table.read('observations.hdf5', path='data')
To read a table nested in a group in the HDF5 file, you can do:
>>> t = Table.read('observations.hdf5', path='group/data')
To write a table to a new file, the path should also be specified:
>>> t.write('new_file.hdf5', path='updated_data')
It is also possible to write a table to an existing file using append=True
:
>>> t.write('observations.hdf5', path='updated_data', append=True)
As with other formats, the overwrite=True
argument is supported for
overwriting existing files. To overwrite only a single table within an HDF5
file that has multiple datasets, use both the overwrite=True
and
append=True
arguments.
Finally, when writing to HDF5 files, the compression=
argument can be
used to ensure that the data is compressed on disk:
>>> t.write('new_file.hdf5', path='updated_data', compression=True)
Metadata and mixin columns¶
Astropy tables can contain metadata, both in the table meta
attribute
(which is an ordered dictionary of arbitrary key/value pairs), and within the
columns, which each have attributes unit
, format
, description
,
and meta
.
By default, when writing a table to HDF5 the code will attempt to store each
key/value pair within the table meta
as HDF5 attributes of the table
dataset. This will fail of the values within meta
are not objects that can
be stored as HDF5 attributes. In addition, if the table columns being stored
have defined values for any of the above-listed column attributes, these
metadata will not be stored and a warning will be issued.
serialize_meta¶
To enable storing all table and column metadata to the HDF5 file, call
the write()
method with serialize_meta=True
. This will store metadata
in a separate HDF5 dataset, contained in the same file, which is named
<path>.__table_column_meta__
. Here path
is the argument provided in
the call to write()
:
>>> t.write('observations.hdf5', path='data', serialize_meta=True)
As of astropy 3.0, by specifying serialize_meta=True
one can also store to
HDF5 tables that contain Mixin columns such as Time
or
SkyCoord
columns.
compatibility_mode¶
The way metadata are saved in the HDF5 dataset has changed in astropy 3.0. Previously the metadata were serialized with YAML and this was stored as an HDF5 attribute. This process was subject to a fixed limit on the size of an attribute. Starting with 3.0 the YAML-serialized metadata are stored as a separate dataset as described above, with no size limit.
Files using the old convention are automatically recognized and will always be read correctly.
If for some reason the user needs to write in the old format, they should
specify the deprecated compatibility_mode
keyword:
>>> t.write('observations.hdf5', path='updated_data', serialize_meta=True,
... compatibility_mode=True)
Warning
The compatibility_mode
keyword will be removed in a future
version of astropy so your code should be changed.
Pandas¶
Astropy Table
supports the ability to read or write tables
using some of the I/O methods
available within pandas. This interface thus provides
convenient wrappers to the following functions / methods:
Format name |
Data Description |
Reader |
Writer |
---|---|---|---|
|
|||
|
|||
|
|||
|
Fixed Width |
Notes:
There is no fixed width writer in pandas.
Reading HTML requires BeautifulSoup4 and html5lib to be installed.
When reading or writing a table, any keyword arguments apart from the format
and file
name are passed through to pandas, for instance:
>>> t.write('data.csv', format='pandas.csv', sep=' ', header=False)
>>> t2 = Table.read('data.csv', format='pandas.csv', sep=' ', names=['a', 'b', 'c'])
JSViewer¶
Provides an interactive HTML export of a Table, like the
HTML
writer but using the DataTables library, which
allow to visualize interactively an HTML table (with columns sorting, search,
pagination).
To write a table t
to a new file:
>>> t.write('new_table.html', format='jsviewer')
Several additional parameters can be used:
table_id: the HTML id of the
<table>
tag, defaults to'table{id}'
whereid
is the id of the Table object.max_lines: maximum number of lines.
table_class: HTML classes added to the
<table>
tag, can be useful to customize the style of the table.jskwargs: additional arguments passed to
JSViewer
.css: CSS style, default to
astropy.table.jsviewer.DEFAULT_CSS
.htmldict: additional arguments passed to
HTML
.
VO Tables¶
Reading/writing from/to VO table
files is supported with format='votable'
. In most cases, existing VO
tables should be automatically identified as such based on the header of the
file, but if not, or if writing to disk, then the format should be explicitly
specified.
If a VO table file contains only a single table, then it can be read in with:
>>> t = Table.read('aj285677t3_votable.xml')
If more than one table is present in the file, an error will be raised,
unless the table ID is specified via the table_id=
argument:
>>> t = Table.read('catalog.xml')
Traceback (most recent call last):
...
ValueError: Multiple tables found: table id should be set via the table_id= argument. The available tables are twomass, spitzer
>>> t = Table.read('catalog.xml', table_id='twomass')
To write to a new file, the ID of the table should also be specified (unless
t.meta['ID']
is defined):
>>> t.write('new_catalog.xml', table_id='updated_table', format='votable')
When writing, the compression=True
argument can be used to force
compression of the data on disk, and the overwrite=True
argument can be
used to overwrite an existing file.
Table serialization methods¶
Astropy supports fine-grained control of the way to write out (serialize) the columns in a Table. For instance if you are writing an ISO format Time column to an ECSV ASCII table file, you may want to write this as a pair of JD1 / JD2 floating point values for full resolution (perfect round-trip), or as a formatted ISO date string so that the values are easily readable by you or other applications.
The default method for serialization depends on the format (FITS, ECSV, HDF5). For instance HDF5 is a binary format and so it would make sense to store a Time object as JD1 / JD2, while ECSV is a flat ASCII format and commonly you would want to see the date in the same format as the Time object. The defaults also reflect an attempt to minimize compatibility issues between astropy versions. For instance it was possible to write Time columns to ECSV as formatted strings in a version prior to the ability to write as JD1 / JD2 pairs, so the current default for ECSV is to write as formatted strings.
The two classes which have configurable serialization method are
Time
and MaskedColumn
. See the sections
on Time Details and Masked columns, respectively, for additional
information. The defaults for each format are listed below:
Format |
Time |
MaskedColumn |
---|---|---|
FITS |
|
|
ECSV |
|
|
HDF5 |
|
|
YAML |
|
— |
As an example, start by making a table with a Time column and masked column:
>>> import sys
>>> from astropy.time import Time
>>> from astropy.table import Table, MaskedColumn
>>> t = Table(masked=True)
>>> t['tm'] = Time(['2000-01-01', '2000-01-02'])
>>> t['mc1'] = MaskedColumn([1.0, 2.0], mask=[True, False])
>>> t['mc2'] = MaskedColumn([3.0, 4.0], mask=[False, True])
>>> t
<Table masked=True length=2>
tm mc1 mc2
object float64 float64
----------------------- ------- -------
2000-01-01 00:00:00.000 -- 3.0
2000-01-02 00:00:00.000 2.0 --
Now specify that you want all Time
columns written as JD1 / JD2
and the mc1
column written as a data / mask pair and
write to ECSV:
>>> serialize_method = {Time: 'jd1_jd2', 'mc1': 'data_mask'}
>>> t.write(sys.stdout, format='ascii.ecsv', serialize_method=serialize_method)
# %ECSV 0.9
...
# schema: astropy-2.0
tm.jd1 tm.jd2 mc1 mc1.mask mc2
2451544.0 0.5 1.0 True 3.0
2451546.0 -0.5 2.0 False ""
(Spaces added for clarity)
Notice that the tm
column has been replaced by the tm.jd1
and tm.jd2
columns, and likewise a new column mc1.mask
has appeared and it explicitly
contains the mask values. When this table is read back with the ascii.ecsv
reader then the original columns are reconstructed.
The serialize_method
argument can be set in two different ways:
As a single string like
data_mask
. This value then applies to every column, and is a convenient strategy for a masked table with no Time columns.As a
dict
, where the key can be either a single column name or a class (as shown in the example above), and the value is the corresponding serialization method.