Source code for astropy.io.misc.yaml

# Licensed under a 3-clause BSD style license - see LICENSE.rst

"""
This module contains functions for serializing core astropy objects via the
YAML protocol.
It provides functions `~astropy.io.misc.yaml.dump`,
`~astropy.io.misc.yaml.load`, and `~astropy.io.misc.yaml.load_all` which
call the corresponding functions in `PyYaml <https://pyyaml.org>`_ but use the
`~astropy.io.misc.yaml.AstropyDumper` and `~astropy.io.misc.yaml.AstropyLoader`
classes to define custom YAML tags for the following astropy classes:
- `astropy.units.Unit`
- `astropy.units.Quantity`
- `astropy.time.Time`
- `astropy.time.TimeDelta`
- `astropy.coordinates.SkyCoord`
- `astropy.coordinates.Angle`
- `astropy.coordinates.Latitude`
- `astropy.coordinates.Longitude`
- `astropy.coordinates.EarthLocation`
- `astropy.table.SerializedColumn`

Example
=======
::
  >>> from astropy.io.misc import yaml
  >>> import astropy.units as u
  >>> from astropy.time import Time
  >>> from astropy.coordinates import EarthLocation
  >>> t = Time(2457389.0, format='mjd',
  ...          location=EarthLocation(1000, 2000, 3000, unit=u.km))
  >>> td = yaml.dump(t)
  >>> print(td)
  !astropy.time.Time
  format: mjd
  in_subfmt: '*'
  jd1: 4857390.0
  jd2: -0.5
  location: !astropy.coordinates.earth.EarthLocation
    ellipsoid: WGS84
    x: !astropy.units.Quantity
      unit: &id001 !astropy.units.Unit {unit: km}
      value: 1000.0
    y: !astropy.units.Quantity
      unit: *id001
      value: 2000.0
    z: !astropy.units.Quantity
      unit: *id001
      value: 3000.0
  out_subfmt: '*'
  precision: 3
  scale: utc
  >>> ty = yaml.load(td)
  >>> ty
  <Time object: scale='utc' format='mjd' value=2457389.0>
  >>> ty.location  # doctest: +FLOAT_CMP
  <EarthLocation (1000., 2000., 3000.) km>
"""

import base64

import numpy as np
import yaml

from astropy.time import Time, TimeDelta
from astropy import units as u
from astropy import coordinates as coords
from astropy.table import SerializedColumn


__all__ = ['AstropyLoader', 'AstropyDumper', 'load', 'load_all', 'dump']


def _unit_representer(dumper, obj):
    out = {'unit': str(obj.to_string())}
    return dumper.represent_mapping('!astropy.units.Unit', out)


def _unit_constructor(loader, node):
    map = loader.construct_mapping(node)
    return u.Unit(map['unit'], parse_strict='warn')


def _serialized_column_representer(dumper, obj):
    out = dumper.represent_mapping('!astropy.table.SerializedColumn', obj)
    return out


def _serialized_column_constructor(loader, node):
    map = loader.construct_mapping(node)
    return SerializedColumn(map)


def _time_representer(dumper, obj):
    out = obj.info._represent_as_dict()
    return dumper.represent_mapping('!astropy.time.Time', out)


def _time_constructor(loader, node):
    map = loader.construct_mapping(node)
    out = Time.info._construct_from_dict(map)
    return out


def _timedelta_representer(dumper, obj):
    out = obj.info._represent_as_dict()
    return dumper.represent_mapping('!astropy.time.TimeDelta', out)


def _timedelta_constructor(loader, node):
    map = loader.construct_mapping(node)
    out = TimeDelta.info._construct_from_dict(map)
    return out


def _ndarray_representer(dumper, obj):
    if not (obj.flags['C_CONTIGUOUS'] or obj.flags['F_CONTIGUOUS']):
        obj = np.ascontiguousarray(obj)

    if np.isfortran(obj):
        obj = obj.T
        order = 'F'
    else:
        order = 'C'

    data_b64 = base64.b64encode(obj.tobytes())

    out = dict(buffer=data_b64,
               dtype=str(obj.dtype) if not obj.dtype.fields else obj.dtype.descr,
               shape=obj.shape,
               order=order)

    return dumper.represent_mapping('!numpy.ndarray', out)


def _ndarray_constructor(loader, node):
    # Convert mapping to a dict useful for initializing ndarray.
    # Need deep=True since for structured dtype, the contents
    # include lists and tuples, which need recursion via
    # construct_sequence.
    map = loader.construct_mapping(node, deep=True)
    map['buffer'] = base64.b64decode(map['buffer'])
    return np.ndarray(**map)


def _void_representer(dumper, obj):
    data_b64 = base64.b64encode(obj.tobytes())
    out = dict(buffer=data_b64,
               dtype=str(obj.dtype) if not obj.dtype.fields else obj.dtype.descr)
    return dumper.represent_mapping('!numpy.void', out)


def _void_constructor(loader, node):
    # Interpret as node as an array scalar and then index to change to void.
    map = loader.construct_mapping(node, deep=True)
    map['buffer'] = base64.b64decode(map['buffer'])
    return np.ndarray(shape=(), **map)[()]


def _quantity_representer(tag):
    def representer(dumper, obj):
        out = obj.info._represent_as_dict()
        return dumper.represent_mapping(tag, out)
    return representer


def _quantity_constructor(cls):
    def constructor(loader, node):
        map = loader.construct_mapping(node)
        return cls.info._construct_from_dict(map)
    return constructor


def _skycoord_representer(dumper, obj):
    map = obj.info._represent_as_dict()
    out = dumper.represent_mapping('!astropy.coordinates.sky_coordinate.SkyCoord',
                                   map)
    return out


def _skycoord_constructor(loader, node):
    map = loader.construct_mapping(node)
    out = coords.SkyCoord.info._construct_from_dict(map)
    return out


# Straight from yaml's Representer
def _complex_representer(self, data):
    if data.imag == 0.0:
        data = f'{data.real!r}'
    elif data.real == 0.0:
        data = f'{data.imag!r}j'
    elif data.imag > 0:
        data = f'{data.real!r}+{data.imag!r}j'
    else:
        data = f'{data.real!r}{data.imag!r}j'
    return self.represent_scalar('tag:yaml.org,2002:python/complex', data)


def _complex_constructor(loader, node):
    map = loader.construct_scalar(node)
    return complex(map)


[docs]class AstropyLoader(yaml.SafeLoader): """ Custom SafeLoader that constructs astropy core objects as well as Python tuple and unicode objects. This class is not directly instantiated by user code, but instead is used to maintain the available constructor functions that are called when parsing a YAML stream. See the `PyYaml documentation <https://pyyaml.org/wiki/PyYAMLDocumentation>`_ for details of the class signature. """ def _construct_python_tuple(self, node): return tuple(self.construct_sequence(node)) def _construct_python_unicode(self, node): return self.construct_scalar(node)
[docs]class AstropyDumper(yaml.SafeDumper): """ Custom SafeDumper that represents astropy core objects as well as Python tuple and unicode objects. This class is not directly instantiated by user code, but instead is used to maintain the available representer functions that are called when generating a YAML stream from an object. See the `PyYaml documentation <https://pyyaml.org/wiki/PyYAMLDocumentation>`_ for details of the class signature. """ def _represent_tuple(self, data): return self.represent_sequence('tag:yaml.org,2002:python/tuple', data)
AstropyDumper.add_multi_representer(u.UnitBase, _unit_representer) AstropyDumper.add_multi_representer(u.FunctionUnitBase, _unit_representer) AstropyDumper.add_multi_representer(u.StructuredUnit, _unit_representer) AstropyDumper.add_representer(tuple, AstropyDumper._represent_tuple) AstropyDumper.add_representer(np.ndarray, _ndarray_representer) AstropyDumper.add_representer(np.void, _void_representer) AstropyDumper.add_representer(Time, _time_representer) AstropyDumper.add_representer(TimeDelta, _timedelta_representer) AstropyDumper.add_representer(coords.SkyCoord, _skycoord_representer) AstropyDumper.add_representer(SerializedColumn, _serialized_column_representer) # Numpy dtypes AstropyDumper.add_representer(np.bool_, yaml.representer.SafeRepresenter.represent_bool) for np_type in [np.int_, np.intc, np.intp, np.int8, np.int16, np.int32, np.int64, np.uint8, np.uint16, np.uint32, np.uint64]: AstropyDumper.add_representer(np_type, yaml.representer.SafeRepresenter.represent_int) for np_type in [np.float_, np.float16, np.float32, np.float64, np.longdouble]: AstropyDumper.add_representer(np_type, yaml.representer.SafeRepresenter.represent_float) for np_type in [np.complex_, complex, np.complex64, np.complex128]: AstropyDumper.add_representer(np_type, _complex_representer) AstropyLoader.add_constructor('tag:yaml.org,2002:python/complex', _complex_constructor) AstropyLoader.add_constructor('tag:yaml.org,2002:python/tuple', AstropyLoader._construct_python_tuple) AstropyLoader.add_constructor('tag:yaml.org,2002:python/unicode', AstropyLoader._construct_python_unicode) AstropyLoader.add_constructor('!astropy.units.Unit', _unit_constructor) AstropyLoader.add_constructor('!numpy.ndarray', _ndarray_constructor) AstropyLoader.add_constructor('!numpy.void', _void_constructor) AstropyLoader.add_constructor('!astropy.time.Time', _time_constructor) AstropyLoader.add_constructor('!astropy.time.TimeDelta', _timedelta_constructor) AstropyLoader.add_constructor('!astropy.coordinates.sky_coordinate.SkyCoord', _skycoord_constructor) AstropyLoader.add_constructor('!astropy.table.SerializedColumn', _serialized_column_constructor) for cls, tag in ((u.Quantity, '!astropy.units.Quantity'), (u.Magnitude, '!astropy.units.Magnitude'), (u.Dex, '!astropy.units.Dex'), (u.Decibel, '!astropy.units.Decibel'), (coords.Angle, '!astropy.coordinates.Angle'), (coords.Latitude, '!astropy.coordinates.Latitude'), (coords.Longitude, '!astropy.coordinates.Longitude'), (coords.EarthLocation, '!astropy.coordinates.earth.EarthLocation')): AstropyDumper.add_multi_representer(cls, _quantity_representer(tag)) AstropyLoader.add_constructor(tag, _quantity_constructor(cls)) for cls in (list(coords.representation.REPRESENTATION_CLASSES.values()) + list(coords.representation.DIFFERENTIAL_CLASSES.values())): name = cls.__name__ # Add representations/differentials defined in astropy. if name in coords.representation.__all__: tag = '!astropy.coordinates.' + name AstropyDumper.add_multi_representer(cls, _quantity_representer(tag)) AstropyLoader.add_constructor(tag, _quantity_constructor(cls))
[docs]def load(stream): """Parse the first YAML document in a stream using the AstropyLoader and produce the corresponding Python object. Parameters ---------- stream : str or file-like YAML input Returns ------- obj : object Object corresponding to YAML document """ return yaml.load(stream, Loader=AstropyLoader)
[docs]def load_all(stream): """Parse the all YAML documents in a stream using the AstropyLoader class and produce the corresponding Python object. Parameters ---------- stream : str or file-like YAML input Returns ------- obj : object Object corresponding to YAML document """ return yaml.load_all(stream, Loader=AstropyLoader)
[docs]def dump(data, stream=None, **kwargs): """Serialize a Python object into a YAML stream using the AstropyDumper class. If stream is None, return the produced string instead. Parameters ---------- data: object Object to serialize to YAML stream : file-like, optional YAML output (if not supplied a string is returned) **kwargs Other keyword arguments that get passed to yaml.dump() Returns ------- out : str or None If no ``stream`` is supplied then YAML output is returned as str """ kwargs['Dumper'] = AstropyDumper kwargs.setdefault('default_flow_style', None) return yaml.dump(data, stream=stream, **kwargs)