ECSV Format

The Enhanced Character-Separated Values (ECSV) format can be used to write astropy Table or QTable datasets to a text-only human readable data file and then read the table back without loss of information. The format stores column specifications like unit and data type along with table metadata by using a YAML header data structure. The actual tabular data are stored in a standard character separated values (CSV) format, giving compatibility with a wide variety of non-specialized CSV table readers.

Attention

The ECSV format is the recommended way to store Table data in a human-readable ASCII file. This includes use cases from informal use in science research to production pipelines and data systems.

In addition to Python, ECSV is supported in TOPCAT and in the java STIL library. .

Usage

When writing in the ECSV format there are only two choices for the delimiter, either space or comma, with space being the default. Any other value of delimiter will give an error. For reading the delimiter is specified within the file itself.

Apart from the delimiter, the only other applicable read/write arguments are names, include_names, and exclude_names. All other arguments will be either ignored or raise an error.

Simple Table

The following writes a table as a simple space-delimited file. The ECSV format is auto-selected due to .ecsv suffix:

>>> import numpy as np
>>> from astropy.table import Table
>>> data = Table()
>>> data['a'] = np.array([1, 2], dtype=np.int8)
>>> data['b'] = np.array([1, 2], dtype=np.float32)
>>> data['c'] = np.array(['hello', 'world'])
>>> data.write('my_data.ecsv')  

The contents of my_data.ecsv are shown below:

# %ECSV 1.0
# ---
# datatype:
# - {name: a, datatype: int8}
# - {name: b, datatype: float32}
# - {name: c, datatype: string}
# schema: astropy-2.0
a b c
1 1.0 hello
2 2.0 world

The ECSV header is the section prefixed by the # comment character. An ECSV file must start with the %ECSV <version> line. The datatype element defines the list of columns and the schema relates to astropy-specific extensions that are used for writing Mixin Columns.

Masked Data

You can write masked (or “missing”) data in the ECSV format in two different ways, either using an empty string to represent missing values or by splitting the masked columns into separate data and mask columns.

Empty String

The first (default) way uses an empty string as a marker in place of masked values. This is a bit more common outside of astropy and does not require any astropy-specific extensions.

>>> from astropy.table import MaskedColumn
>>> t = Table()
>>> t['x'] = MaskedColumn([1.0, 2.0, 3.0], unit='m', dtype='float32')
>>> t['x'][1] = np.ma.masked
>>> t['y'] = MaskedColumn([False, True, False], dtype='bool')
>>> t['y'][0] = np.ma.masked
>>> t.write('my_data.ecsv', format='ascii.ecsv', overwrite=True)  

The contents of my_data.ecsv are shown below:

# %ECSV 1.0
# ---
# datatype:
# - {name: x, unit: m, datatype: float32}
# - {name: y, datatype: bool}
# schema: astropy-2.0
x y
1.0 ""
"" True
3.0 False

To read this back, you would run the following:

>>> Table.read('my_data.ecsv')  
<Table length=3>
   x      y
   m
float32  bool
------- -----
    1.0    --
     --  True
    3.0 False

Data + Mask

The second way is to tell the writer to break any masked column into a data column and a mask column by supplying the serialize_method='data_mask' argument:

>>> t.write('my_data.ecsv', serialize_method='data_mask', overwrite=True)  

There are two main reasons you might want to do this:

  • Storing the data “under the mask” instead of replacing it with an empty string.

  • Writing a string column that contains empty strings which are not masked.

The contents of my_data.ecsv are shown below. First notice that there are two new columns x.mask and y.mask that have been added, and these explicitly record the mask values for those columns. Next notice now that the ECSV header is a bit more complex and includes the astropy-specific extensions that tell the reader how to interpret the plain CSV columns x, x.mask, y, y.mask and reassemble them back into the appropriate masked columns.

# %ECSV 1.0
# ---
# datatype:
# - {name: x, unit: m, datatype: float32}
# - {name: x.mask, datatype: bool}
# - {name: y, datatype: bool}
# - {name: y.mask, datatype: bool}
# meta: !!omap
# - __serialized_columns__:
#     x:
#       __class__: astropy.table.column.MaskedColumn
#       data: !astropy.table.SerializedColumn {name: x}
#       mask: !astropy.table.SerializedColumn {name: x.mask}
#     y:
#       __class__: astropy.table.column.MaskedColumn
#       data: !astropy.table.SerializedColumn {name: y}
#       mask: !astropy.table.SerializedColumn {name: y.mask}
# schema: astropy-2.0
x x.mask y y.mask
1.0 False False True
2.0 True True False
3.0 False False False

Note

For the security minded, the __class__ value must within an allowed list of astropy classes that are trusted by the reader. You cannot use an arbitrary class here.

Per-column control

In rare cases it may be necessary to specify the serialization method for each column individually. This is shown in the example below:

>>> from astropy.table.table_helpers import simple_table
>>> t = simple_table(masked=True)
>>> t['c'][0] = ""  # Valid empty string in data
>>> t
<Table masked=True length=3>
  a      b     c
int64 float64 str1
----- ------- ----
   --     1.0
    2     2.0   --
    3      --    e

Now we tell ECSV writer to output separate data and mask columns for the string column 'c':

>>> t['c'].info.serialize_method['ecsv'] = 'data_mask'
>>> ascii.write(t, format='ecsv')
# %ECSV 1.0
# ---
# datatype:
# - {name: a, datatype: int64}
# - {name: b, datatype: float64}
# - {name: c, datatype: string}
# - {name: c.mask, datatype: bool}
# meta: !!omap
# - __serialized_columns__:
#     c:
#       __class__: astropy.table.column.MaskedColumn
#       data: !astropy.table.SerializedColumn {name: c}
#       mask: !astropy.table.SerializedColumn {name: c.mask}
# schema: astropy-2.0
a b c c.mask
"" 1.0 "" False
2 2.0 d True
3 "" e False

When you read this back in, both the empty (zero-length) string and the masked 'd' value in the column 'c' will be preserved.

Mixin Columns

It is possible to store not only standard Column and MaskedColumn objects to ECSV but also the following Mixin Columns:

In general, a mixin column may contain multiple data components as well as object attributes beyond the standard Column attributes like format or description. Storing such mixin columns is done by replacing the mixin column with column(s) representing the underlying data component(s) and then inserting metadata which informs the reader of how to reconstruct the original column. For example, a SkyCoord mixin column in 'spherical' representation would have data attributes ra, dec, distance, along with object attributes like representation_type or frame.

This example demonstrates writing a QTable that has Time and SkyCoord mixin columns:

>>> from astropy.coordinates import SkyCoord
>>> import astropy.units as u
>>> from astropy.table import QTable

>>> sc = SkyCoord(ra=[1, 2] * u.deg, dec=[3, 4] * u.deg)
>>> sc.info.description = 'flying circus'
>>> q = [1, 2] * u.m
>>> q.info.format = '.2f'
>>> t = QTable()
>>> t['c'] = [1, 2]
>>> t['q'] = q
>>> t['sc'] = sc

>>> t.write('my_data.ecsv')  

The contents of my_data.ecsv are below:

# %ECSV 1.0
# ---
# datatype:
# - {name: c, datatype: int64}
# - {name: q, unit: m, datatype: float64, format: .2f}
# - {name: sc.ra, unit: deg, datatype: float64}
# - {name: sc.dec, unit: deg, datatype: float64}
# meta: !!omap
# - __serialized_columns__:
#     q:
#       __class__: astropy.units.quantity.Quantity
#       __info__: {format: .2f}
#       unit: !astropy.units.Unit {unit: m}
#       value: !astropy.table.SerializedColumn {name: q}
#     sc:
#       __class__: astropy.coordinates.sky_coordinate.SkyCoord
#       __info__: {description: flying circus}
#       dec: !astropy.table.SerializedColumn
#         __class__: astropy.coordinates.angles.Latitude
#         unit: &id001 !astropy.units.Unit {unit: deg}
#         value: !astropy.table.SerializedColumn {name: sc.dec}
#       frame: icrs
#       ra: !astropy.table.SerializedColumn
#         __class__: astropy.coordinates.angles.Longitude
#         unit: *id001
#         value: !astropy.table.SerializedColumn {name: sc.ra}
#         wrap_angle: !astropy.coordinates.Angle
#           unit: *id001
#           value: 360.0
#       representation_type: spherical
# schema: astropy-2.0
c q sc.ra sc.dec
1 1.0 1.0 3.0
2 2.0 2.0 4.0

The '__class__' keyword gives the fully-qualified class name and must be one of the specifically allowed astropy classes. There is no option to add user-specified allowed classes. The '__info__' keyword contains values for standard Column attributes like description or format, for any mixin columns that are represented by more than one serialized column.

Multidimensional Columns

Using ECSV it is possible to write a table that contains multidimensional columns (both masked and unmasked). This is done by encoding each element as a string using JSON. This functionality works for all column types that are supported by ECSV including Mixin Columns. This capability is added in astropy 4.3 and ECSV version 1.0.

We start by defining a table with 2 rows where each element in the second column 'b' is itself a 3x2 array:

>>> t = Table()
>>> t['a'] = ['x', 'y']
>>> t['b'] = np.arange(12, dtype=np.float64).reshape(2, 3, 2)
>>> t
<Table length=2>
 a     b [3,2]
str1   float64
---- -----------
   x  0.0 .. 5.0
   y 6.0 .. 11.0

>>> t['b'][0]
array([[0., 1.],
      [2., 3.],
      [4., 5.]])

Now we can write this to ECSV and observe how the N-d column 'b' has been written as a string with datatype: string. Notice also that the column descriptor for the column includes the new subtype: float64[3,2] attribute specifying the type and shape of each item.

>>> ascii.write(t, format='ecsv')  
# %ECSV 1.0
# ---
# datatype:
# - {name: a, datatype: string}
# - {name: b, datatype: string, subtype: 'float64[3,2]'}
# schema: astropy-2.0
a b
x [[0.0,1.0],[2.0,3.0],[4.0,5.0]]
y [[6.0,7.0],[8.0,9.0],[10.0,11.0]]

When you read this back in, the sequence of JSON-encoded column items are then decoded using JSON back into the original N-d column.

Variable-length arrays

ECSV supports storing multidimensional columns is when the length of each array element may vary. This data structure is supported in the FITS standard. While numpy does not natively support variable-length arrays, it is possible to represent such a structure using an object-type array of typed np.ndarray objects. This is how the astropy FITS reader outputs a variable-length array.

This capability is added in astropy 4.3 and ECSV version 1.0.

Most commonly variable-length arrays have a 1-d array in each cell of the column. You might a column with 1-d np.ndarray cells having lengths of 2, 5, and 3 respectively.

The ECSV standard and astropy also supports arbitrary N-d arrays in each cell, where all dimensions except the last one must match. For instance you could have a column with np.ndarray cells having shapes of (4,4,2), (4,4,5), and (4,4,3) respectively.

The example below shows writing a variable-length 1-d array to ECSV. Notice the new ECSV column attribute subtype: 'int64[null]'. The [null] indicates a variable length for the one dimension. If we had been writing the N-d example above the subtype would have been int64[4,4,null].

>>> t = Table()
>>> t['a'] = np.empty(3, dtype=object)
>>> t['a'] = [np.array([1, 2], dtype=np.int64),
...           np.array([3, 4, 5], dtype=np.int64),
...           np.array([6, 7, 8, 9], dtype=np.int64)]
>>> ascii.write(t, format='ecsv')
# %ECSV 1.0
# ---
# datatype:
# - {name: a, datatype: string, subtype: 'int64[null]'}
# schema: astropy-2.0
a
[1,2]
[3,4,5]
[6,7,8,9]

Object arrays

ECSV can store object-type columns with simple Python objects consisting of dict, list, str, int, float, bool and None elements. More precisely, any object that can be serialized to JSON using the standard library json package is supported.

The example below shows writing an object array to ECSV. Because JSON requires a double-quote around strings, and because ECSV requires "" to represent a double-quote within a string, one tends to get double-double quotes in this representation.

>>> t = Table()
>>> t['a'] = np.array([{'a': 1},
...                    {'b': [2.5, None]},
...                    True], dtype=object)
>>> ascii.write(t, format='ecsv')
# %ECSV 1.0
# ---
# datatype:
# - {name: a, datatype: string, subtype: json}
# schema: astropy-2.0
a
"{""a"":1}"
"{""b"":[2.5,null]}"
true