# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from ..extern import six
import operator
import weakref
from copy import deepcopy
from distutils import version
import numpy as np
from numpy import ma
from ..units import Unit, Quantity
from ..utils import deprecated
from ..utils.console import color_print
from ..utils.metadata import MetaData
from . import groups
from . import pprint
from .np_utils import fix_column_name
from ..config import ConfigAlias
NUMPY_VERSION = version.LooseVersion(np.__version__)
AUTO_COLNAME = ConfigAlias(
'0.4', 'AUTO_COLNAME', 'auto_colname',
'astropy.table.column', 'astropy.table')
# Create a generic TableFormatter object for use by bare columns with no
# parent table.
FORMATTER = pprint.TableFormatter()
def _auto_names(n_cols):
from . import conf
return [str(conf.auto_colname).format(i) for i in range(n_cols)]
# list of one and two-dimensional comparison functions, which sometimes return
# a Column class and sometimes a plain array. Used in __array_wrap__ to ensure
# they only return plain (masked) arrays (see #1446 and #1685)
_comparison_functions = set(
[np.greater, np.greater_equal, np.less, np.less_equal,
np.not_equal, np.equal,
np.isfinite, np.isinf, np.isnan, np.sign, np.signbit])
class BaseColumn(np.ndarray):
meta = MetaData()
def __new__(cls, data=None, name=None,
dtype=None, shape=(), length=0,
description=None, unit=None, format=None, meta=None):
if data is None:
dtype = (np.dtype(dtype).str, shape)
self_data = np.zeros(length, dtype=dtype)
elif isinstance(data, BaseColumn) and hasattr(data, '_name'):
# When unpickling a MaskedColumn, ``data`` will be a bare
# BaseColumn with none of the expected attributes. In this case
# do NOT execute this block which initializes from ``data``
# attributes.
self_data = np.asarray(data.data, dtype=dtype)
if description is None:
description = data.description
if unit is None:
unit = unit or data.unit
if format is None:
format = data.format
if meta is None:
meta = deepcopy(data.meta)
if name is None:
name = data.name
elif isinstance(data, Quantity):
if unit is None:
self_data = np.asarray(data, dtype=dtype)
unit = data.unit
else:
self_data = np.asarray(data.to(unit), dtype=dtype)
else:
self_data = np.asarray(data, dtype=dtype)
self = self_data.view(cls)
self._name = fix_column_name(name)
self.unit = unit
self.format = format
self.description = description
self.meta = meta
self._parent_table = None
return self
@property
def data(self):
return self.view(np.ndarray)
@property
def parent_table(self):
if self._parent_table is None:
return None
else:
return self._parent_table()
@parent_table.setter
def parent_table(self, table):
if table is None:
self._parent_table = None
else:
self._parent_table = weakref.ref(table)
def copy(self, order='C', data=None, copy_data=True):
"""
Return a copy of the current instance.
If ``data`` is supplied then a view (reference) of ``data`` is used,
and ``copy_data`` is ignored.
Parameters
----------
order : {'C', 'F', 'A', 'K'}, optional
Controls the memory layout of the copy. 'C' means C-order,
'F' means F-order, 'A' means 'F' if ``a`` is Fortran contiguous,
'C' otherwise. 'K' means match the layout of ``a`` as closely
as possible. (Note that this function and :func:numpy.copy are very
similar, but have different default values for their order=
arguments.) Default is 'C'.
data : array, optional
If supplied then use a view of ``data`` instead of the instance
data. This allows copying the instance attributes and meta.
copy_data : bool, optional
Make a copy of the internal numpy array instead of using a
reference. Default is True.
Returns
-------
col: Column or MaskedColumn
Copy of the current column (same type as original)
"""
if data is None:
data = self.data
if copy_data:
data = data.copy(order)
out = data.view(self.__class__)
out.__array_finalize__(self)
# for MaskedColumn, MaskedArray.__array_finalize__ also copies mask
# from self, which is not the idea here, so undo
if isinstance(self, MaskedColumn):
out._mask = data._mask
self._copy_groups(out)
return out
def __setstate__(self, state):
"""
Restore the internal state of the Column/MaskedColumn for pickling
purposes. This requires that the last element of ``state`` is a
5-tuple that has Column-specific state values.
"""
# Get the Column attributes and meta
name, unit, format, description, meta = state[-1]
state = state[:-1]
# Using super(type(self), self).__setstate__() gives an infinite
# recursion. Manually call the right super class to actually set up
# the array object.
super_class = ma.MaskedArray if isinstance(self, ma.MaskedArray) else np.ndarray
super_class.__setstate__(self, state)
# Set the Column attributes and meta
self._name = name
self.unit = unit
self.format = format
self.description = description
self.meta = meta
def __reduce__(self):
"""
Return a 3-tuple for pickling a Column. Use the super-class
functionality but then add in a 5-tuple of Column-specific values
that get used in __setstate__.
"""
super_class = ma.MaskedArray if isinstance(self, ma.MaskedArray) else np.ndarray
reconstruct_func, reconstruct_func_args, state = super_class.__reduce__(self)
# Define Column-specific attrs and meta that gets added to state.
column_state = (self.name, self.unit, self.format, self.description,
self.meta)
state = state + (column_state,)
return reconstruct_func, reconstruct_func_args, state
# avoid == and != to be done based on type of subclass
# (helped solve #1446; see also __array_wrap__)
def __eq__(self, other):
return self.data.__eq__(other)
def __ne__(self, other):
return self.data.__ne__(other)
def __array_finalize__(self, obj):
# Obj will be none for direct call to Column() creator
if obj is None:
return
if six.callable(super(BaseColumn, self).__array_finalize__):
super(BaseColumn, self).__array_finalize__(obj)
# Self was created from template (e.g. obj[slice] or (obj * 2))
# or viewcast e.g. obj.view(Column). In either case we want to
# init Column attributes for self from obj if possible.
self.parent_table = None
for attr in ('name', 'unit', 'format', 'description'):
val = getattr(obj, attr, None)
setattr(self, attr, val)
self.meta = deepcopy(getattr(obj, 'meta', {}))
def __array_wrap__(self, out_arr, context=None):
"""
__array_wrap__ is called at the end of every ufunc.
Normally, we want a Column object back and do not have to do anything
special. But there are two exceptions:
1) If the output shape is different (e.g. for reduction ufuncs
like sum() or mean()), a Column still linking to a parent_table
makes little sense, so we return the output viewed as the
column content (ndarray or MaskedArray).
For this case, we use "[()]" to select everything, and to ensure we
convert a zero rank array to a scalar. (For some reason np.sum()
returns a zero rank scalar array while np.mean() returns a scalar;
So the [()] is needed for this case.
2) When the output is created by any function that returns a boolean
we also want to consistently return an array rather than a column
(see #1446 and #1685)
"""
out_arr = super(BaseColumn, self).__array_wrap__(out_arr, context)
if (self.shape != out_arr.shape or
(isinstance(out_arr, BaseColumn) and
(context is not None and context[0] in _comparison_functions))):
return out_arr.data[()]
else:
return out_arr
@property
def name(self):
return self._name
@name.setter
def name(self, val):
val = fix_column_name(val)
if self.parent_table is not None:
table = self.parent_table
table.columns._rename_column(self.name, val)
table._data.dtype.names = list(table.columns)
if table.masked:
table._data.mask.dtype.names = list(table.columns)
self._name = val
@property
def descr(self):
"""Array-interface compliant full description of the column.
This returns a 3-tuple (name, type, shape) that can always be
used in a structured array dtype definition.
"""
return (self.name, self.dtype.str, self.shape[1:])
def iter_str_vals(self):
"""
Return an iterator that yields the string-formatted values of this
column.
Returns
-------
str_vals : iterator
Column values formatted as strings
"""
# Iterate over formatted values with no max number of lines, no column
# name, no unit, and ignoring the returned header info in outs.
_pformat_col_iter = self._formatter._pformat_col_iter
for str_val in _pformat_col_iter(self, -1, False, False, {}):
yield str_val
def attrs_equal(self, col):
"""Compare the column attributes of ``col`` to this object.
The comparison attributes are: ``name``, ``unit``, ``dtype``,
``format``, ``description``, and ``meta``.
Parameters
----------
col : Column
Comparison column
Returns
-------
equal: boolean
True if all attributes are equal
"""
if not isinstance(col, BaseColumn):
raise ValueError('Comparison `col` must be a Column or '
'MaskedColumn object')
attrs = ('name', 'unit', 'dtype', 'format', 'description', 'meta')
equal = all(getattr(self, x) == getattr(col, x) for x in attrs)
return equal
@property
def _formatter(self):
return FORMATTER if (self.parent_table is None) else self.parent_table.formatter
def pformat(self, max_lines=None, show_name=True, show_unit=False):
"""Return a list of formatted string representation of column values.
If no value of ``max_lines`` is supplied then the height of the
screen terminal is used to set ``max_lines``. If the terminal
height cannot be determined then the default will be
determined using the ``astropy.conf.max_lines`` configuration
item. If a negative value of ``max_lines`` is supplied then
there is no line limit applied.
Parameters
----------
max_lines : int
Maximum lines of output (header + data rows)
show_name : bool
Include column name (default=True)
show_unit : bool
Include a header row for unit (default=False)
Returns
-------
lines : list
List of lines with header and formatted column values
"""
_pformat_col = self._formatter._pformat_col
lines, n_header = _pformat_col(self, max_lines, show_name, show_unit)
return lines
def pprint(self, max_lines=None, show_name=True, show_unit=False):
"""Print a formatted string representation of column values.
If no value of ``max_lines`` is supplied then the height of the
screen terminal is used to set ``max_lines``. If the terminal
height cannot be determined then the default will be
determined using the ``astropy.conf.max_lines`` configuration
item. If a negative value of ``max_lines`` is supplied then
there is no line limit applied.
Parameters
----------
max_lines : int
Maximum number of values in output
show_name : bool
Include column name (default=True)
show_unit : bool
Include a header row for unit (default=False)
"""
_pformat_col = self._formatter._pformat_col
lines, n_header = _pformat_col(self, max_lines, show_name, show_unit)
for i, line in enumerate(lines):
if i < n_header:
color_print(line, 'red')
else:
print(line)
def more(self, max_lines=None, show_name=True, show_unit=False):
"""Interactively browse column with a paging interface.
Supported keys::
f, <space> : forward one page
b : back one page
r : refresh same page
n : next row
p : previous row
< : go to beginning
> : go to end
q : quit browsing
h : print this help
Parameters
----------
max_lines : int
Maximum number of lines in table output
show_name : bool
Include a header row for column names (default=True)
show_unit : bool
Include a header row for unit (default=False)
"""
_more_tabcol = self._formatter._more_tabcol
_more_tabcol(self, max_lines=max_lines, show_name=show_name,
show_unit=show_unit)
@property
def unit(self):
"""
The unit associated with this column. May be a string or a
`astropy.units.UnitBase` instance.
Setting the ``unit`` property does not change the values of the
data. To perform a unit conversion, use ``convert_unit_to``.
"""
return self._unit
@unit.setter
def unit(self, unit):
if unit is None:
self._unit = None
else:
self._unit = Unit(unit, parse_strict='silent')
@unit.deleter
def unit(self):
self._unit = None
@property
@deprecated('0.3', alternative=':attr:`Column.unit`')
def units(self):
return self.unit
@units.setter
@deprecated('0.3', alternative=':attr:`Column.unit`')
def units(self, unit):
self.unit = unit
@units.deleter
@deprecated('0.3', alternative=':attr:`Column.unit`')
def units(self):
del self.unit
def convert_unit_to(self, new_unit, equivalencies=[]):
"""
Converts the values of the column in-place from the current
unit to the given unit.
To change the unit associated with this column without
actually changing the data values, simply set the ``unit``
property.
Parameters
----------
new_unit : str or `astropy.units.UnitBase` instance
The unit to convert to.
equivalencies : list of equivalence pairs, optional
A list of equivalence pairs to try if the unit are not
directly convertible. See :ref:`unit_equivalencies`.
Raises
------
astropy.units.UnitsError
If units are inconsistent
"""
if self.unit is None:
raise ValueError("No unit set on column")
self.data[:] = self.unit.to(
new_unit, self.data, equivalencies=equivalencies)
self.unit = new_unit
@property
def groups(self):
if not hasattr(self, '_groups'):
self._groups = groups.ColumnGroups(self)
return self._groups
def group_by(self, keys):
"""
Group this column by the specified ``keys``
This effectively splits the column into groups which correspond to
unique values of the ``keys`` grouping object. The output is a new
`Column` or `MaskedColumn` which contains a copy of this column but
sorted by row according to ``keys``.
The ``keys`` input to ``group_by`` must be a numpy array with the
same length as this column.
Parameters
----------
keys : numpy array
Key grouping object
Returns
-------
out : Column
New column with groups attribute set accordingly
"""
return groups.column_group_by(self, keys)
def _copy_groups(self, out):
"""
Copy current groups into a copy of self ``out``
"""
if self.parent_table:
if hasattr(self.parent_table, '_groups'):
out._groups = groups.ColumnGroups(out, indices=self.parent_table._groups._indices)
elif hasattr(self, '_groups'):
out._groups = groups.ColumnGroups(out, indices=self._groups._indices)
# Strip off the BaseColumn-ness for repr and str so that
# MaskedColumn.data __repr__ does not include masked_BaseColumn(data =
# [1 2], ...).
def __repr__(self):
return np.asarray(self).__repr__()
[docs]class Column(BaseColumn):
"""Define a data column for use in a Table object.
Parameters
----------
data : list, ndarray or None
Column data values
name : str
Column name and key for reference within Table
dtype : numpy.dtype compatible value
Data type for column
shape : tuple or ()
Dimensions of a single row element in the column data
length : int or 0
Number of row elements in column data
description : str or None
Full description of column
unit : str or None
Physical unit
format : str or None or function or callable
Format string for outputting column values. This can be an
"old-style" (``format % value``) or "new-style" (`str.format`)
format specification string or a function or any callable object that
accepts a single value and returns a string.
meta : dict-like or None
Meta-data associated with the column
Examples
--------
A Column can be created in two different ways:
- Provide a ``data`` value but not ``shape`` or ``length`` (which are
inferred from the data).
Examples::
col = Column(data=[1, 2], name='name') # shape=(2,)
col = Column(data=[[1, 2], [3, 4]], name='name') # shape=(2, 2)
col = Column(data=[1, 2], name='name', dtype=float)
col = Column(data=np.array([1, 2]), name='name')
col = Column(data=['hello', 'world'], name='name')
The ``dtype`` argument can be any value which is an acceptable
fixed-size data-type initializer for the numpy.dtype() method. See
`<http://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html>`_.
Examples include:
- Python non-string type (float, int, bool)
- Numpy non-string type (e.g. np.float32, np.int64, np.bool)
- Numpy.dtype array-protocol type strings (e.g. 'i4', 'f8', 'S15')
If no ``dtype`` value is provide then the type is inferred using
``np.array(data)``.
- Provide ``length`` and optionally ``shape``, but not ``data``
Examples::
col = Column(name='name', length=5)
col = Column(name='name', dtype=int, length=10, shape=(3,4))
The default ``dtype`` is ``np.float64``. The ``shape`` argument is the
array shape of a single cell in the column.
"""
def __new__(cls, data=None, name=None,
dtype=None, shape=(), length=0,
description=None, unit=None, format=None, meta=None):
if isinstance(data, MaskedColumn) and np.any(data.mask):
raise TypeError("Cannot convert a MaskedColumn with masked value to a Column")
self = super(Column, cls).__new__(cls, data=data, name=name, dtype=dtype,
shape=shape, length=length, description=description,
unit=unit, format=format, meta=meta)
return self
def __repr__(self):
unit = None if self.unit is None else six.text_type(self.unit)
out = "<{0} name={1} unit={2} format={3} " \
"description={4}>\n{5}".format(
self.__class__.__name__,
repr(self.name), repr(unit),
repr(self.format), repr(self.description), repr(self.data))
return out
def __unicode__(self):
_pformat_col = self._formatter._pformat_col
lines, n_header = _pformat_col(self)
return '\n'.join(lines)
if six.PY3:
__str__ = __unicode__
def __bytes__(self):
return six.text_type(self).encode('utf-8')
if six.PY2:
__str__ = __bytes__
# We do this to make the methods show up in the API docs
name = BaseColumn.name
copy = BaseColumn.copy
more = BaseColumn.more
pprint = BaseColumn.pprint
pformat = BaseColumn.pformat
convert_unit_to = BaseColumn.convert_unit_to
[docs]class MaskedColumn(Column, ma.MaskedArray):
"""Define a masked data column for use in a Table object.
Parameters
----------
data : list, ndarray or None
Column data values
name : str
Column name and key for reference within Table
mask : list, ndarray or None
Boolean mask for which True indicates missing or invalid data
fill_value : float, int, str or None
Value used when filling masked column elements
dtype : numpy.dtype compatible value
Data type for column
shape : tuple or ()
Dimensions of a single row element in the column data
length : int or 0
Number of row elements in column data
description : str or None
Full description of column
unit : str or None
Physical unit
format : str or None or function or callable
Format string for outputting column values. This can be an
"old-style" (``format % value``) or "new-style" (`str.format`)
format specification string or a function or any callable object that
accepts a single value and returns a string.
meta : dict-like or None
Meta-data associated with the column
Examples
--------
A MaskedColumn is similar to a Column except that it includes ``mask`` and
``fill_value`` attributes. It can be created in two different ways:
- Provide a ``data`` value but not ``shape`` or ``length`` (which are
inferred from the data).
Examples::
col = MaskedColumn(data=[1, 2], name='name')
col = MaskedColumn(data=[1, 2], name='name', mask=[True, False])
col = MaskedColumn(data=[1, 2], name='name', dtype=float, fill_value=99)
The ``mask`` argument will be cast as a boolean array and specifies
which elements are considered to be missing or invalid.
The ``dtype`` argument can be any value which is an acceptable
fixed-size data-type initializer for the numpy.dtype() method. See
`<http://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html>`_.
Examples include:
- Python non-string type (float, int, bool)
- Numpy non-string type (e.g. np.float32, np.int64, np.bool)
- Numpy.dtype array-protocol type strings (e.g. 'i4', 'f8', 'S15')
If no ``dtype`` value is provide then the type is inferred using
``np.array(data)``. When ``data`` is provided then the ``shape``
and ``length`` arguments are ignored.
- Provide ``length`` and optionally ``shape``, but not ``data``
Examples::
col = MaskedColumn(name='name', length=5)
col = MaskedColumn(name='name', dtype=int, length=10, shape=(3,4))
The default ``dtype`` is ``np.float64``. The ``shape`` argument is the
array shape of a single cell in the column.
"""
def __new__(cls, data=None, name=None, mask=None, fill_value=None,
dtype=None, shape=(), length=0,
description=None, unit=None, format=None, meta=None):
if mask is None and hasattr(data, 'mask'):
mask = data.mask
else:
mask = deepcopy(mask)
# Create self using MaskedArray as a wrapper class, following the example of
# class MSubArray in
# https://github.com/numpy/numpy/blob/maintenance/1.8.x/numpy/ma/tests/test_subclassing.py
# This pattern makes it so that __array_finalize__ is called as expected (e.g. #1471 and
# https://github.com/astropy/astropy/commit/ff6039e8)
# First just pass through all args and kwargs to BaseColumn, then wrap that object
# with MaskedArray.
self_data = BaseColumn(data, dtype=dtype, shape=shape, length=length, name=name,
unit=unit, format=format, description=description, meta=meta)
self = ma.MaskedArray.__new__(cls, data=self_data, mask=mask)
# Note: do not set fill_value in the MaskedArray constructor because this does not
# go through the fill_value workarounds (see _fix_fill_value below).
if fill_value is None and hasattr(data, 'fill_value'):
fill_value = data.fill_value
self.fill_value = fill_value
self.parent_table = None
return self
def _fix_fill_value(self, val):
"""Fix a fill value (if needed) to work around a bug with setting the fill
value of a string array in MaskedArray with Python 3.x. See
https://github.com/numpy/numpy/pull/2733. This mimics the check in
numpy.ma.core._check_fill_value() (version < 1.8) which incorrectly sets
fill_value to a default if self.dtype.char is 'U' (which is the case for Python
3). Here we change the string to a byte string so that in Python 3 the
isinstance(val, basestring) part fails.
"""
if (NUMPY_VERSION < version.LooseVersion('1.8.0') and
isinstance(val, six.string_types) and (self.dtype.char not in 'SV')):
val = val.encode()
return val
@property
def fill_value(self):
return self.get_fill_value() # defer to native ma.MaskedArray method
@fill_value.setter
def fill_value(self, val):
"""Set fill value both in the masked column view and in the parent table
if it exists. Setting one or the other alone doesn't work."""
val = self._fix_fill_value(val)
if self.parent_table:
self.parent_table._data[self._name].fill_value = val
# Yet another ma bug workaround: If the value of fill_value for a string array is
# requested but not yet set then it gets created as 'N/A'. From this point onward
# any new fill_values are truncated to 3 characters. Note that this does not
# occur if the masked array is a structured array (as in the previous block that
# deals with the parent table).
#
# >>> x = ma.array(['xxxx'])
# >>> x.fill_value # fill_value now gets represented as an 'S3' array
# 'N/A'
# >>> x.fill_value='yyyy'
# >>> x.fill_value
# 'yyy'
#
# To handle this we are forced to reset a private variable first:
self._fill_value = None
self.set_fill_value(val) # defer to native ma.MaskedArray method
@property
def data(self):
out = self.view(ma.MaskedArray)
# The following is necessary because of a bug in Numpy, which was
# fixed in numpy/numpy#2703. The fix should be included in Numpy 1.8.0.
out.fill_value = self.fill_value
return out
[docs] def filled(self, fill_value=None):
"""Return a copy of self, with masked values filled with a given value.
Parameters
----------
fill_value : scalar; optional
The value to use for invalid entries (`None` by default). If
`None`, the ``fill_value`` attribute of the array is used
instead.
Returns
-------
filled_column : Column
A copy of ``self`` with masked entries replaced by `fill_value`
(be it the function argument or the attribute of ``self``).
"""
if fill_value is None:
fill_value = self.fill_value
fill_value = self._fix_fill_value(fill_value)
data = super(MaskedColumn, self).filled(fill_value)
# Use parent table definition of Column if available
column_cls = self.parent_table.Column if (self.parent_table is not None) else Column
out = column_cls(name=self.name, data=data, unit=self.unit,
format=self.format, description=self.description,
meta=deepcopy(self.meta))
return out
# We do this to make the methods show up in the API docs
name = BaseColumn.name
copy = BaseColumn.copy
more = BaseColumn.more
pprint = BaseColumn.pprint
pformat = BaseColumn.pformat
convert_unit_to = BaseColumn.convert_unit_to