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"""
Collection of utilities to manipulate structured arrays.
Most of these functions were initially implemented by John Hunter for
matplotlib. They have been rewritten and extended for convenience.
"""
from __future__ import division, absolute_import, print_function
import sys
import itertools
import numpy as np
import numpy.ma as ma
from numpy import ndarray, recarray
from numpy.ma import MaskedArray
from numpy.ma.mrecords import MaskedRecords
from numpy.lib._iotools import _is_string_like
from numpy.compat import basestring
if sys.version_info[0] < 3:
from future_builtins import zip
_check_fill_value = np.ma.core._check_fill_value
__all__ = [
'append_fields', 'drop_fields', 'find_duplicates',
'get_fieldstructure', 'join_by', 'merge_arrays',
'rec_append_fields', 'rec_drop_fields', 'rec_join',
'recursive_fill_fields', 'rename_fields', 'stack_arrays',
]
def recursive_fill_fields(input, output):
"""
Fills fields from output with fields from input,
with support for nested structures.
Parameters
----------
input : ndarray
Input array.
output : ndarray
Output array.
Notes
-----
* `output` should be at least the same size as `input`
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> a = np.array([(1, 10.), (2, 20.)], dtype=[('A', int), ('B', float)])
>>> b = np.zeros((3,), dtype=a.dtype)
>>> rfn.recursive_fill_fields(a, b)
array([(1, 10.0), (2, 20.0), (0, 0.0)],
dtype=[('A', '<i4'), ('B', '<f8')])
"""
newdtype = output.dtype
for field in newdtype.names:
try:
current = input[field]
except ValueError:
continue
if current.dtype.names:
recursive_fill_fields(current, output[field])
else:
output[field][:len(current)] = current
return output
def get_names(adtype):
"""
Returns the field names of the input datatype as a tuple.
Parameters
----------
adtype : dtype
Input datatype
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> rfn.get_names(np.empty((1,), dtype=int)) is None
True
>>> rfn.get_names(np.empty((1,), dtype=[('A',int), ('B', float)]))
('A', 'B')
>>> adtype = np.dtype([('a', int), ('b', [('ba', int), ('bb', int)])])
>>> rfn.get_names(adtype)
('a', ('b', ('ba', 'bb')))
"""
listnames = []
names = adtype.names
for name in names:
current = adtype[name]
if current.names:
listnames.append((name, tuple(get_names(current))))
else:
listnames.append(name)
return tuple(listnames) or None
def get_names_flat(adtype):
"""
Returns the field names of the input datatype as a tuple. Nested structure
are flattend beforehand.
Parameters
----------
adtype : dtype
Input datatype
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> rfn.get_names_flat(np.empty((1,), dtype=int)) is None
True
>>> rfn.get_names_flat(np.empty((1,), dtype=[('A',int), ('B', float)]))
('A', 'B')
>>> adtype = np.dtype([('a', int), ('b', [('ba', int), ('bb', int)])])
>>> rfn.get_names_flat(adtype)
('a', 'b', 'ba', 'bb')
"""
listnames = []
names = adtype.names
for name in names:
listnames.append(name)
current = adtype[name]
if current.names:
listnames.extend(get_names_flat(current))
return tuple(listnames) or None
def flatten_descr(ndtype):
"""
Flatten a structured data-type description.
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> ndtype = np.dtype([('a', '<i4'), ('b', [('ba', '<f8'), ('bb', '<i4')])])
>>> rfn.flatten_descr(ndtype)
(('a', dtype('int32')), ('ba', dtype('float64')), ('bb', dtype('int32')))
"""
names = ndtype.names
if names is None:
return ndtype.descr
else:
descr = []
for field in names:
(typ, _) = ndtype.fields[field]
if typ.names:
descr.extend(flatten_descr(typ))
else:
descr.append((field, typ))
return tuple(descr)
def zip_descr(seqarrays, flatten=False):
"""
Combine the dtype description of a series of arrays.
Parameters
----------
seqarrays : sequence of arrays
Sequence of arrays
flatten : {boolean}, optional
Whether to collapse nested descriptions.
"""
newdtype = []
if flatten:
for a in seqarrays:
newdtype.extend(flatten_descr(a.dtype))
else:
for a in seqarrays:
current = a.dtype
names = current.names or ()
if len(names) > 1:
newdtype.append(('', current.descr))
else:
newdtype.extend(current.descr)
return np.dtype(newdtype).descr
def get_fieldstructure(adtype, lastname=None, parents=None,):
"""
Returns a dictionary with fields indexing lists of their parent fields.
This function is used to simplify access to fields nested in other fields.
Parameters
----------
adtype : np.dtype
Input datatype
lastname : optional
Last processed field name (used internally during recursion).
parents : dictionary
Dictionary of parent fields (used interbally during recursion).
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> ndtype = np.dtype([('A', int),
... ('B', [('BA', int),
... ('BB', [('BBA', int), ('BBB', int)])])])
>>> rfn.get_fieldstructure(ndtype)
... # XXX: possible regression, order of BBA and BBB is swapped
{'A': [], 'B': [], 'BA': ['B'], 'BB': ['B'], 'BBA': ['B', 'BB'], 'BBB': ['B', 'BB']}
"""
if parents is None:
parents = {}
names = adtype.names
for name in names:
current = adtype[name]
if current.names:
if lastname:
parents[name] = [lastname, ]
else:
parents[name] = []
parents.update(get_fieldstructure(current, name, parents))
else:
lastparent = [_ for _ in (parents.get(lastname, []) or [])]
if lastparent:
lastparent.append(lastname)
elif lastname:
lastparent = [lastname, ]
parents[name] = lastparent or []
return parents or None
def _izip_fields_flat(iterable):
"""
Returns an iterator of concatenated fields from a sequence of arrays,
collapsing any nested structure.
"""
for element in iterable:
if isinstance(element, np.void):
for f in _izip_fields_flat(tuple(element)):
yield f
else:
yield element
def _izip_fields(iterable):
"""
Returns an iterator of concatenated fields from a sequence of arrays.
"""
for element in iterable:
if (hasattr(element, '__iter__') and
not isinstance(element, basestring)):
for f in _izip_fields(element):
yield f
elif isinstance(element, np.void) and len(tuple(element)) == 1:
for f in _izip_fields(element):
yield f
else:
yield element
def izip_records(seqarrays, fill_value=None, flatten=True):
"""
Returns an iterator of concatenated items from a sequence of arrays.
Parameters
----------
seqarrays : sequence of arrays
Sequence of arrays.
fill_value : {None, integer}
Value used to pad shorter iterables.
flatten : {True, False},
Whether to
"""
# Should we flatten the items, or just use a nested approach
if flatten:
zipfunc = _izip_fields_flat
else:
zipfunc = _izip_fields
if sys.version_info[0] >= 3:
zip_longest = itertools.zip_longest
else:
zip_longest = itertools.izip_longest
for tup in zip_longest(*seqarrays, fillvalue=fill_value):
yield tuple(zipfunc(tup))
def _fix_output(output, usemask=True, asrecarray=False):
"""
Private function: return a recarray, a ndarray, a MaskedArray
or a MaskedRecords depending on the input parameters
"""
if not isinstance(output, MaskedArray):
usemask = False
if usemask:
if asrecarray:
output = output.view(MaskedRecords)
else:
output = ma.filled(output)
if asrecarray:
output = output.view(recarray)
return output
def _fix_defaults(output, defaults=None):
"""
Update the fill_value and masked data of `output`
from the default given in a dictionary defaults.
"""
names = output.dtype.names
(data, mask, fill_value) = (output.data, output.mask, output.fill_value)
for (k, v) in (defaults or {}).items():
if k in names:
fill_value[k] = v
data[k][mask[k]] = v
return output
def merge_arrays(seqarrays, fill_value=-1, flatten=False,
usemask=False, asrecarray=False):
"""
Merge arrays field by field.
Parameters
----------
seqarrays : sequence of ndarrays
Sequence of arrays
fill_value : {float}, optional
Filling value used to pad missing data on the shorter arrays.
flatten : {False, True}, optional
Whether to collapse nested fields.
usemask : {False, True}, optional
Whether to return a masked array or not.
asrecarray : {False, True}, optional
Whether to return a recarray (MaskedRecords) or not.
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> rfn.merge_arrays((np.array([1, 2]), np.array([10., 20., 30.])))
masked_array(data = [(1, 10.0) (2, 20.0) (--, 30.0)],
mask = [(False, False) (False, False) (True, False)],
fill_value = (999999, 1e+20),
dtype = [('f0', '<i4'), ('f1', '<f8')])
>>> rfn.merge_arrays((np.array([1, 2]), np.array([10., 20., 30.])),
... usemask=False)
array([(1, 10.0), (2, 20.0), (-1, 30.0)],
dtype=[('f0', '<i4'), ('f1', '<f8')])
>>> rfn.merge_arrays((np.array([1, 2]).view([('a', int)]),
... np.array([10., 20., 30.])),
... usemask=False, asrecarray=True)
rec.array([(1, 10.0), (2, 20.0), (-1, 30.0)],
dtype=[('a', '<i4'), ('f1', '<f8')])
Notes
-----
* Without a mask, the missing value will be filled with something,
* depending on what its corresponding type:
-1 for integers
-1.0 for floating point numbers
'-' for characters
'-1' for strings
True for boolean values
* XXX: I just obtained these values empirically
"""
# Only one item in the input sequence ?
if (len(seqarrays) == 1):
seqarrays = np.asanyarray(seqarrays[0])
# Do we have a single ndarray as input ?
if isinstance(seqarrays, (ndarray, np.void)):
seqdtype = seqarrays.dtype
if (not flatten) or \
(zip_descr((seqarrays,), flatten=True) == seqdtype.descr):
# Minimal processing needed: just make sure everythng's a-ok
seqarrays = seqarrays.ravel()
# Make sure we have named fields
if not seqdtype.names:
seqdtype = [('', seqdtype)]
# Find what type of array we must return
if usemask:
if asrecarray:
seqtype = MaskedRecords
else:
seqtype = MaskedArray
elif asrecarray:
seqtype = recarray
else:
seqtype = ndarray
return seqarrays.view(dtype=seqdtype, type=seqtype)
else:
seqarrays = (seqarrays,)
else:
# Make sure we have arrays in the input sequence
seqarrays = [np.asanyarray(_m) for _m in seqarrays]
# Find the sizes of the inputs and their maximum
sizes = tuple(a.size for a in seqarrays)
maxlength = max(sizes)
# Get the dtype of the output (flattening if needed)
newdtype = zip_descr(seqarrays, flatten=flatten)
# Initialize the sequences for data and mask
seqdata = []
seqmask = []
# If we expect some kind of MaskedArray, make a special loop.
if usemask:
for (a, n) in zip(seqarrays, sizes):
nbmissing = (maxlength - n)
# Get the data and mask
data = a.ravel().__array__()
mask = ma.getmaskarray(a).ravel()
# Get the filling value (if needed)
if nbmissing:
fval = _check_fill_value(fill_value, a.dtype)
if isinstance(fval, (ndarray, np.void)):
if len(fval.dtype) == 1:
fval = fval.item()[0]
fmsk = True
else:
fval = np.array(fval, dtype=a.dtype, ndmin=1)
fmsk = np.ones((1,), dtype=mask.dtype)
else:
fval = None
fmsk = True
# Store an iterator padding the input to the expected length
seqdata.append(itertools.chain(data, [fval] * nbmissing))
seqmask.append(itertools.chain(mask, [fmsk] * nbmissing))
# Create an iterator for the data
data = tuple(izip_records(seqdata, flatten=flatten))
output = ma.array(np.fromiter(data, dtype=newdtype, count=maxlength),
mask=list(izip_records(seqmask, flatten=flatten)))
if asrecarray:
output = output.view(MaskedRecords)
else:
# Same as before, without the mask we don't need...
for (a, n) in zip(seqarrays, sizes):
nbmissing = (maxlength - n)
data = a.ravel().__array__()
if nbmissing:
fval = _check_fill_value(fill_value, a.dtype)
if isinstance(fval, (ndarray, np.void)):
if len(fval.dtype) == 1:
fval = fval.item()[0]
else:
fval = np.array(fval, dtype=a.dtype, ndmin=1)
else:
fval = None
seqdata.append(itertools.chain(data, [fval] * nbmissing))
output = np.fromiter(tuple(izip_records(seqdata, flatten=flatten)),
dtype=newdtype, count=maxlength)
if asrecarray:
output = output.view(recarray)
# And we're done...
return output
def drop_fields(base, drop_names, usemask=True, asrecarray=False):
"""
Return a new array with fields in `drop_names` dropped.
Nested fields are supported.
Parameters
----------
base : array
Input array
drop_names : string or sequence
String or sequence of strings corresponding to the names of the
fields to drop.
usemask : {False, True}, optional
Whether to return a masked array or not.
asrecarray : string or sequence, optional
Whether to return a recarray or a mrecarray (`asrecarray=True`) or
a plain ndarray or masked array with flexible dtype. The default
is False.
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> a = np.array([(1, (2, 3.0)), (4, (5, 6.0))],
... dtype=[('a', int), ('b', [('ba', float), ('bb', int)])])
>>> rfn.drop_fields(a, 'a')
array([((2.0, 3),), ((5.0, 6),)],
dtype=[('b', [('ba', '<f8'), ('bb', '<i4')])])
>>> rfn.drop_fields(a, 'ba')
array([(1, (3,)), (4, (6,))],
dtype=[('a', '<i4'), ('b', [('bb', '<i4')])])
>>> rfn.drop_fields(a, ['ba', 'bb'])
array([(1,), (4,)],
dtype=[('a', '<i4')])
"""
if _is_string_like(drop_names):
drop_names = [drop_names]
else:
drop_names = set(drop_names)
def _drop_descr(ndtype, drop_names):
names = ndtype.names
newdtype = []
for name in names:
current = ndtype[name]
if name in drop_names:
continue
if current.names:
descr = _drop_descr(current, drop_names)
if descr:
newdtype.append((name, descr))
else:
newdtype.append((name, current))
return newdtype
newdtype = _drop_descr(base.dtype, drop_names)
if not newdtype:
return None
output = np.empty(base.shape, dtype=newdtype)
output = recursive_fill_fields(base, output)
return _fix_output(output, usemask=usemask, asrecarray=asrecarray)
def _keep_fields(base, keep_names, usemask=True, asrecarray=False):
"""
Return a new array keeping only the fields in `keep_names`,
and preserving the order of those fields.
Parameters
----------
base : array
Input array
keep_names : string or sequence
String or sequence of strings corresponding to the names of the
fields to keep. Order of the names will be preserved.
usemask : {False, True}, optional
Whether to return a masked array or not.
asrecarray : string or sequence, optional
Whether to return a recarray or a mrecarray (`asrecarray=True`) or
a plain ndarray or masked array with flexible dtype. The default
is False.
"""
newdtype = [(n, base.dtype[n]) for n in keep_names]
output = np.empty(base.shape, dtype=newdtype)
output = recursive_fill_fields(base, output)
return _fix_output(output, usemask=usemask, asrecarray=asrecarray)
def rec_drop_fields(base, drop_names):
"""
Returns a new numpy.recarray with fields in `drop_names` dropped.
"""
return drop_fields(base, drop_names, usemask=False, asrecarray=True)
def rename_fields(base, namemapper):
"""
Rename the fields from a flexible-datatype ndarray or recarray.
Nested fields are supported.
Parameters
----------
base : ndarray
Input array whose fields must be modified.
namemapper : dictionary
Dictionary mapping old field names to their new version.
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> a = np.array([(1, (2, [3.0, 30.])), (4, (5, [6.0, 60.]))],
... dtype=[('a', int),('b', [('ba', float), ('bb', (float, 2))])])
>>> rfn.rename_fields(a, {'a':'A', 'bb':'BB'})
array([(1, (2.0, [3.0, 30.0])), (4, (5.0, [6.0, 60.0]))],
dtype=[('A', '<i4'), ('b', [('ba', '<f8'), ('BB', '<f8', 2)])])
"""
def _recursive_rename_fields(ndtype, namemapper):
newdtype = []
for name in ndtype.names:
newname = namemapper.get(name, name)
current = ndtype[name]
if current.names:
newdtype.append(
(newname, _recursive_rename_fields(current, namemapper))
)
else:
newdtype.append((newname, current))
return newdtype
newdtype = _recursive_rename_fields(base.dtype, namemapper)
return base.view(newdtype)
def append_fields(base, names, data, dtypes=None,
fill_value=-1, usemask=True, asrecarray=False):
"""
Add new fields to an existing array.
The names of the fields are given with the `names` arguments,
the corresponding values with the `data` arguments.
If a single field is appended, `names`, `data` and `dtypes` do not have
to be lists but just values.
Parameters
----------
base : array
Input array to extend.
names : string, sequence
String or sequence of strings corresponding to the names
of the new fields.
data : array or sequence of arrays
Array or sequence of arrays storing the fields to add to the base.
dtypes : sequence of datatypes, optional
Datatype or sequence of datatypes.
If None, the datatypes are estimated from the `data`.
fill_value : {float}, optional
Filling value used to pad missing data on the shorter arrays.
usemask : {False, True}, optional
Whether to return a masked array or not.
asrecarray : {False, True}, optional
Whether to return a recarray (MaskedRecords) or not.
"""
# Check the names
if isinstance(names, (tuple, list)):
if len(names) != len(data):
msg = "The number of arrays does not match the number of names"
raise ValueError(msg)
elif isinstance(names, basestring):
names = [names, ]
data = [data, ]
#
if dtypes is None:
data = [np.array(a, copy=False, subok=True) for a in data]
data = [a.view([(name, a.dtype)]) for (name, a) in zip(names, data)]
else:
if not isinstance(dtypes, (tuple, list)):
dtypes = [dtypes, ]
if len(data) != len(dtypes):
if len(dtypes) == 1:
dtypes = dtypes * len(data)
else:
msg = "The dtypes argument must be None, a dtype, or a list."
raise ValueError(msg)
data = [np.array(a, copy=False, subok=True, dtype=d).view([(n, d)])
for (a, n, d) in zip(data, names, dtypes)]
#
base = merge_arrays(base, usemask=usemask, fill_value=fill_value)
if len(data) > 1:
data = merge_arrays(data, flatten=True, usemask=usemask,
fill_value=fill_value)
else:
data = data.pop()
#
output = ma.masked_all(max(len(base), len(data)),
dtype=base.dtype.descr + data.dtype.descr)
output = recursive_fill_fields(base, output)
output = recursive_fill_fields(data, output)
#
return _fix_output(output, usemask=usemask, asrecarray=asrecarray)
def rec_append_fields(base, names, data, dtypes=None):
"""
Add new fields to an existing array.
The names of the fields are given with the `names` arguments,
the corresponding values with the `data` arguments.
If a single field is appended, `names`, `data` and `dtypes` do not have
to be lists but just values.
Parameters
----------
base : array
Input array to extend.
names : string, sequence
String or sequence of strings corresponding to the names
of the new fields.
data : array or sequence of arrays
Array or sequence of arrays storing the fields to add to the base.
dtypes : sequence of datatypes, optional
Datatype or sequence of datatypes.
If None, the datatypes are estimated from the `data`.
See Also
--------
append_fields
Returns
-------
appended_array : np.recarray
"""
return append_fields(base, names, data=data, dtypes=dtypes,
asrecarray=True, usemask=False)
def stack_arrays(arrays, defaults=None, usemask=True, asrecarray=False,
autoconvert=False):
"""
Superposes arrays fields by fields
Parameters
----------
arrays : array or sequence
Sequence of input arrays.
defaults : dictionary, optional
Dictionary mapping field names to the corresponding default values.
usemask : {True, False}, optional
Whether to return a MaskedArray (or MaskedRecords is
`asrecarray==True`) or a ndarray.
asrecarray : {False, True}, optional
Whether to return a recarray (or MaskedRecords if `usemask==True`)
or just a flexible-type ndarray.
autoconvert : {False, True}, optional
Whether automatically cast the type of the field to the maximum.
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> x = np.array([1, 2,])
>>> rfn.stack_arrays(x) is x
True
>>> z = np.array([('A', 1), ('B', 2)], dtype=[('A', '|S3'), ('B', float)])
>>> zz = np.array([('a', 10., 100.), ('b', 20., 200.), ('c', 30., 300.)],
... dtype=[('A', '|S3'), ('B', float), ('C', float)])
>>> test = rfn.stack_arrays((z,zz))
>>> test
masked_array(data = [('A', 1.0, --) ('B', 2.0, --) ('a', 10.0, 100.0) ('b', 20.0, 200.0)
('c', 30.0, 300.0)],
mask = [(False, False, True) (False, False, True) (False, False, False)
(False, False, False) (False, False, False)],
fill_value = ('N/A', 1e+20, 1e+20),
dtype = [('A', '|S3'), ('B', '<f8'), ('C', '<f8')])
"""
if isinstance(arrays, ndarray):
return arrays
elif len(arrays) == 1:
return arrays[0]
seqarrays = [np.asanyarray(a).ravel() for a in arrays]
nrecords = [len(a) for a in seqarrays]
ndtype = [a.dtype for a in seqarrays]
fldnames = [d.names for d in ndtype]
#
dtype_l = ndtype[0]
newdescr = dtype_l.descr
names = [_[0] for _ in newdescr]
for dtype_n in ndtype[1:]:
for descr in dtype_n.descr:
name = descr[0] or ''
if name not in names:
newdescr.append(descr)
names.append(name)
else:
nameidx = names.index(name)
current_descr = newdescr[nameidx]
if autoconvert:
if np.dtype(descr[1]) > np.dtype(current_descr[-1]):
current_descr = list(current_descr)
current_descr[-1] = descr[1]
newdescr[nameidx] = tuple(current_descr)
elif descr[1] != current_descr[-1]:
raise TypeError("Incompatible type '%s' <> '%s'" %
(dict(newdescr)[name], descr[1]))
# Only one field: use concatenate
if len(newdescr) == 1:
output = ma.concatenate(seqarrays)
else:
#
output = ma.masked_all((np.sum(nrecords),), newdescr)
offset = np.cumsum(np.r_[0, nrecords])
seen = []
for (a, n, i, j) in zip(seqarrays, fldnames, offset[:-1], offset[1:]):
names = a.dtype.names
if names is None:
output['f%i' % len(seen)][i:j] = a
else:
for name in n:
output[name][i:j] = a[name]
if name not in seen:
seen.append(name)
#
return _fix_output(_fix_defaults(output, defaults),
usemask=usemask, asrecarray=asrecarray)
def find_duplicates(a, key=None, ignoremask=True, return_index=False):
"""
Find the duplicates in a structured array along a given key
Parameters
----------
a : array-like
Input array
key : {string, None}, optional
Name of the fields along which to check the duplicates.
If None, the search is performed by records
ignoremask : {True, False}, optional
Whether masked data should be discarded or considered as duplicates.
return_index : {False, True}, optional
Whether to return the indices of the duplicated values.
Examples
--------
>>> from numpy.lib import recfunctions as rfn
>>> ndtype = [('a', int)]
>>> a = np.ma.array([1, 1, 1, 2, 2, 3, 3],
... mask=[0, 0, 1, 0, 0, 0, 1]).view(ndtype)
>>> rfn.find_duplicates(a, ignoremask=True, return_index=True)
... # XXX: judging by the output, the ignoremask flag has no effect
"""
a = np.asanyarray(a).ravel()
# Get a dictionary of fields
fields = get_fieldstructure(a.dtype)
# Get the sorting data (by selecting the corresponding field)
base = a
if key:
for f in fields[key]:
base = base[f]
base = base[key]
# Get the sorting indices and the sorted data
sortidx = base.argsort()
sortedbase = base[sortidx]
sorteddata = sortedbase.filled()
# Compare the sorting data
flag = (sorteddata[:-1] == sorteddata[1:])
# If masked data must be ignored, set the flag to false where needed
if ignoremask:
sortedmask = sortedbase.recordmask
flag[sortedmask[1:]] = False
flag = np.concatenate(([False], flag))
# We need to take the point on the left as well (else we're missing it)
flag[:-1] = flag[:-1] + flag[1:]
duplicates = a[sortidx][flag]
if return_index:
return (duplicates, sortidx[flag])
else:
return duplicates
def join_by(key, r1, r2, jointype='inner', r1postfix='1', r2postfix='2',
defaults=None, usemask=True, asrecarray=False):
"""
Join arrays `r1` and `r2` on key `key`.
The key should be either a string or a sequence of string corresponding
to the fields used to join the array. An exception is raised if the
`key` field cannot be found in the two input arrays. Neither `r1` nor
`r2` should have any duplicates along `key`: the presence of duplicates
will make the output quite unreliable. Note that duplicates are not
looked for by the algorithm.
Parameters
----------
key : {string, sequence}
A string or a sequence of strings corresponding to the fields used
for comparison.
r1, r2 : arrays
Structured arrays.
jointype : {'inner', 'outer', 'leftouter'}, optional
If 'inner', returns the elements common to both r1 and r2.
If 'outer', returns the common elements as well as the elements of
r1 not in r2 and the elements of not in r2.
If 'leftouter', returns the common elements and the elements of r1
not in r2.
r1postfix : string, optional
String appended to the names of the fields of r1 that are present
in r2 but absent of the key.
r2postfix : string, optional
String appended to the names of the fields of r2 that are present
in r1 but absent of the key.
defaults : {dictionary}, optional
Dictionary mapping field names to the corresponding default values.
usemask : {True, False}, optional
Whether to return a MaskedArray (or MaskedRecords is
`asrecarray==True`) or a ndarray.
asrecarray : {False, True}, optional
Whether to return a recarray (or MaskedRecords if `usemask==True`)
or just a flexible-type ndarray.
Notes
-----
* The output is sorted along the key.
* A temporary array is formed by dropping the fields not in the key for
the two arrays and concatenating the result. This array is then
sorted, and the common entries selected. The output is constructed by
filling the fields with the selected entries. Matching is not
preserved if there are some duplicates...
"""
# Check jointype
if jointype not in ('inner', 'outer', 'leftouter'):
raise ValueError(
"The 'jointype' argument should be in 'inner', "
"'outer' or 'leftouter' (got '%s' instead)" % jointype
)
# If we have a single key, put it in a tuple
if isinstance(key, basestring):
key = (key,)
# Check the keys
if len(set(key)) != len(key):
dup = next(x for n,x in enumerate(key) if x in key[n+1:])
raise ValueError("duplicate join key %r" % dup)
for name in key:
if name not in r1.dtype.names:
raise ValueError('r1 does not have key field %r' % name)
if name not in r2.dtype.names:
raise ValueError('r2 does not have key field %r' % name)
# Make sure we work with ravelled arrays
r1 = r1.ravel()
r2 = r2.ravel()
# Fixme: nb2 below is never used. Commenting out for pyflakes.
# (nb1, nb2) = (len(r1), len(r2))
nb1 = len(r1)
(r1names, r2names) = (r1.dtype.names, r2.dtype.names)
# Check the names for collision
if (set.intersection(set(r1names), set(r2names)).difference(key) and
not (r1postfix or r2postfix)):
msg = "r1 and r2 contain common names, r1postfix and r2postfix "
msg += "can't be empty"
raise ValueError(msg)
# Make temporary arrays of just the keys
# (use order of keys in `r1` for back-compatibility)
key1 = [ n for n in r1names if n in key ]
r1k = _keep_fields(r1, key1)
r2k = _keep_fields(r2, key1)
# Concatenate the two arrays for comparison
aux = ma.concatenate((r1k, r2k))
idx_sort = aux.argsort(order=key)
aux = aux[idx_sort]
#
# Get the common keys
flag_in = ma.concatenate(([False], aux[1:] == aux[:-1]))
flag_in[:-1] = flag_in[1:] + flag_in[:-1]
idx_in = idx_sort[flag_in]
idx_1 = idx_in[(idx_in < nb1)]
idx_2 = idx_in[(idx_in >= nb1)] - nb1
(r1cmn, r2cmn) = (len(idx_1), len(idx_2))
if jointype == 'inner':
(r1spc, r2spc) = (0, 0)
elif jointype == 'outer':
idx_out = idx_sort[~flag_in]
idx_1 = np.concatenate((idx_1, idx_out[(idx_out < nb1)]))
idx_2 = np.concatenate((idx_2, idx_out[(idx_out >= nb1)] - nb1))
(r1spc, r2spc) = (len(idx_1) - r1cmn, len(idx_2) - r2cmn)
elif jointype == 'leftouter':
idx_out = idx_sort[~flag_in]
idx_1 = np.concatenate((idx_1, idx_out[(idx_out < nb1)]))
(r1spc, r2spc) = (len(idx_1) - r1cmn, 0)
# Select the entries from each input
(s1, s2) = (r1[idx_1], r2[idx_2])
#
# Build the new description of the output array .......
# Start with the key fields
ndtype = [list(_) for _ in r1k.dtype.descr]
# Add the other fields
ndtype.extend(list(_) for _ in r1.dtype.descr if _[0] not in key)
# Find the new list of names (it may be different from r1names)
names = list(_[0] for _ in ndtype)
for desc in r2.dtype.descr:
desc = list(desc)
name = desc[0]
# Have we seen the current name already ?
if name in names:
nameidx = ndtype.index(desc)
current = ndtype[nameidx]
# The current field is part of the key: take the largest dtype
if name in key:
current[-1] = max(desc[1], current[-1])
# The current field is not part of the key: add the suffixes
else:
current[0] += r1postfix
desc[0] += r2postfix
ndtype.insert(nameidx + 1, desc)
#... we haven't: just add the description to the current list
else:
names.extend(desc[0])
ndtype.append(desc)
# Revert the elements to tuples
ndtype = [tuple(_) for _ in ndtype]
# Find the largest nb of common fields :
# r1cmn and r2cmn should be equal, but...
cmn = max(r1cmn, r2cmn)
# Construct an empty array
output = ma.masked_all((cmn + r1spc + r2spc,), dtype=ndtype)
names = output.dtype.names
for f in r1names:
selected = s1[f]
if f not in names or (f in r2names and not r2postfix and f not in key):
f += r1postfix
current = output[f]
current[:r1cmn] = selected[:r1cmn]
if jointype in ('outer', 'leftouter'):
current[cmn:cmn + r1spc] = selected[r1cmn:]
for f in r2names:
selected = s2[f]
if f not in names or (f in r1names and not r1postfix and f not in key):
f += r2postfix
current = output[f]
current[:r2cmn] = selected[:r2cmn]
if (jointype == 'outer') and r2spc:
current[-r2spc:] = selected[r2cmn:]
# Sort and finalize the output
output.sort(order=key)
kwargs = dict(usemask=usemask, asrecarray=asrecarray)
return _fix_output(_fix_defaults(output, defaults), **kwargs)
def rec_join(key, r1, r2, jointype='inner', r1postfix='1', r2postfix='2',
defaults=None):
"""
Join arrays `r1` and `r2` on keys.
Alternative to join_by, that always returns a np.recarray.
See Also
--------
join_by : equivalent function
"""
kwargs = dict(jointype=jointype, r1postfix=r1postfix, r2postfix=r2postfix,
defaults=defaults, usemask=False, asrecarray=True)
return join_by(key, r1, r2, **kwargs)
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