"""
R objects as Python objects.
The module is structured around the singleton r of class R,
that represents an embedded R.
License: GPLv2+
"""
import array
import contextlib
import os
import types
import typing
import rpy2.rinterface as rinterface
import rpy2.rinterface_lib.embedded
import rpy2.rinterface_lib.openrlib
import rpy2.rlike.container as rlc
from rpy2.robjects.robject import RObjectMixin, RObject
import rpy2.robjects.functions
from rpy2.robjects.environments import (Environment,
local_context)
from rpy2.robjects.methods import methods_env
from rpy2.robjects.methods import RS4
from . import conversion
from . import vectors
from . import language
from rpy2.rinterface import (Sexp,
SexpVector,
SexpClosure,
SexpEnvironment,
SexpS4,
StrSexpVector,
SexpExtPtr)
from rpy2.robjects.functions import Function
from rpy2.robjects.functions import SignatureTranslatedFunction
_globalenv = rinterface.globalenv
_reval = rinterface.baseenv['eval']
BoolVector = vectors.BoolVector
IntVector = vectors.IntVector
FloatVector = vectors.FloatVector
ComplexVector = vectors.ComplexVector
StrVector = vectors.StrVector
FactorVector = vectors.FactorVector
Vector = vectors.Vector
PairlistVector = vectors.PairlistVector
ListVector = vectors.ListVector
DateVector = vectors.DateVector
POSIXct = vectors.POSIXct
POSIXlt = vectors.POSIXlt
Array = vectors.Array
Matrix = vectors.Matrix
DataFrame = vectors.DataFrame
# Missing values.
NA_Real = rinterface.NA_Real
NA_Integer = rinterface.NA_Integer
NA_Logical = rinterface.NA_Logical
NA_Character = rinterface.NA_Character
NA_Complex = rinterface.NA_Complex
NULL = rinterface.NULL
# TODO: Something like this could be part of the rpy2 API.
def _print_deferred_warnings() -> None:
"""Print R warning messages.
rpy2's default pattern add a prefix per warning lines.
This should be revised. In the meantime, we clean it
at least for the R magic.
"""
with rpy2.rinterface_lib.openrlib.rlock:
rinterface.evalr('.Internal(printDeferredWarnings())')
def reval(string, envir=_globalenv):
""" Evaluate a string as R code
- string: a string
- envir: an environment in which the environment should take place
(default: R's global environment)
"""
p = rinterface.parse(string)
res = _reval(p, envir=envir)
return res
default_converter = conversion.Converter('base empty converter')
@default_converter.rpy2py.register(RObject)
def _rpy2py_robject(obj):
return obj
VT = typing.TypeVar('VT')
MT = typing.TypeVar('MT')
AT = typing.TypeVar('AT')
def _vector_matrix_array(
obj, vector_cls: typing.Type[VT],
matrix_cls: typing.Type[MT],
array_cls: typing.Type[AT]) -> typing.Union[
typing.Type[VT], typing.Type[MT], typing.Type[AT]]:
# Should it be promoted to array or matrix ?
try:
dim = obj.do_slot("dim")
if len(dim) == 2:
return matrix_cls
else:
return array_cls
except Exception:
return vector_cls
@default_converter.rpy2py.register(rinterface.IntSexpVector)
def _convert_rpy2py_intvector(obj):
clsmap = (conversion.converter_ctx.get()
.rpy2py_nc_name[rinterface.IntSexpVector])
cls = clsmap.find(obj.rclass)
return cls(obj)
@default_converter.rpy2py.register(rinterface.FloatSexpVector)
def _convert_rpy2py_floatvector(obj):
clsmap = (conversion.converter_ctx.get()
.rpy2py_nc_name[rinterface.FloatSexpVector])
cls = clsmap.find(obj.rclass)
return cls(obj)
@default_converter.rpy2py.register(rinterface.ComplexSexpVector)
def _convert_rpy2py_complexvector(obj):
clsmap = (conversion.converter_ctx.get()
.rpy2py_nc_name[rinterface.ComplexSexpVector])
cls = clsmap.find(obj.rclass)
return cls(obj)
@default_converter.rpy2py.register(rinterface.BoolSexpVector)
def _convert_rpy2py_boolvector(obj):
clsmap = (conversion.converter_ctx.get()
.rpy2py_nc_name[rinterface.BoolSexpVector])
cls = clsmap.find(obj.rclass)
return cls(obj)
@default_converter.rpy2py.register(rinterface.StrSexpVector)
def _convert_rpy2py_strvector(obj):
cls = _vector_matrix_array(obj, vectors.StrVector,
vectors.StrMatrix, vectors.StrArray)
return cls(obj)
@default_converter.rpy2py.register(rinterface.ByteSexpVector)
def _convert_rpy2py_bytevector(obj):
cls = _vector_matrix_array(obj, vectors.ByteVector,
vectors.ByteMatrix, vectors.ByteArray)
return cls(obj)
default_converter.rpy2py.register(rinterface.PairlistSexpVector, PairlistVector)
@default_converter.rpy2py.register(rinterface.LangSexpVector)
def _convert_rpy2py_langvector(obj):
if 'formula' in obj.rclass:
cls = Formula
else:
cls = language.LangVector
return cls(obj)
TYPEORDER = {bool: (0, BoolVector),
int: (1, IntVector),
float: (2, FloatVector),
complex: (3, ComplexVector),
str: (4, StrVector)}
def sequence_to_vector(lst):
curr_typeorder = -1
i = None
for i, elt in enumerate(lst):
cls = type(elt)
if cls in TYPEORDER:
if TYPEORDER[cls][0] > curr_typeorder:
curr_typeorder, curr_type = TYPEORDER[cls]
else:
raise ValueError('The element %i in the list has a type '
'that cannot be handled.' % i)
if i is None:
raise ValueError('The parameter "lst" is an empty sequence. '
'The type of the corresponding R vector cannot '
'be determined.')
res = curr_type(lst)
return res
@default_converter.py2rpy.register(rinterface._MissingArgType)
def _py2rpy_missingargtype(obj):
return obj
@default_converter.py2rpy.register(bool)
def _py2rpy_bool(obj):
return obj
@default_converter.py2rpy.register(int)
def _py2rpy_int(obj):
return obj
@default_converter.py2rpy.register(float)
def _py2rpy_float(obj):
return obj
@default_converter.py2rpy.register(bytes)
def _py2rpy_bytes(obj):
return obj
@default_converter.py2rpy.register(str)
def _py2rpy_str(obj):
return obj
@default_converter.rpy2py.register(SexpClosure)
def _rpy2py_sexpclosure(obj):
return SignatureTranslatedFunction(obj)
@default_converter.rpy2py.register(SexpEnvironment)
def _rpy2py_sexpenvironment(obj):
return Environment(obj)
@default_converter.rpy2py.register(rinterface.ListSexpVector)
def _rpy2py_listsexp(obj):
clsmap = (conversion.converter_ctx.get()
.rpy2py_nc_name[rinterface.ListSexpVector])
cls = clsmap.find(obj.rclass)
return cls(obj)
@default_converter.rpy2py.register(SexpS4)
def _rpy2py_sexps4(obj):
clsmap = (conversion.converter_ctx.get()
.rpy2py_nc_name[SexpS4])
cls = clsmap.find(methods_env['extends'](obj.rclass))
return cls(obj)
@default_converter.rpy2py.register(SexpExtPtr)
def _rpy2py_sexpextptr(obj):
clsmap = (conversion.converter_ctx.get()
.rpy2py_nc_name[rinterface.SexpExtPtr])
cls = clsmap.find(obj.rclass)
return cls(obj)
@default_converter.rpy2py.register(object)
def _rpy2py_object(obj):
return RObject(obj)
@default_converter.rpy2py.register(type(NULL))
def _rpy2py_null(obj):
return obj
# TODO: delete ?
def default_py2ri(o):
""" Convert an arbitrary Python object to a
:class:`rpy2.rinterface.Sexp` object.
Creates an R object with the content of the Python object,
wich means data copying.
:param o: object
:rtype: :class:`rpy2.rinterface.Sexp` (and subclasses)
"""
pass
@default_converter.py2rpy.register(RObject)
def _py2rpy_robject(obj):
return rinterface.Sexp(obj)
@default_converter.py2rpy.register(Sexp)
def _py2rpy_sexp(obj):
return obj
@default_converter.py2rpy.register(array.array)
def _py2rpy_array(obj):
if obj.typecode in ('h', 'H', 'i', 'I'):
res = IntVector(obj)
elif obj.typecode in ('f', 'd'):
res = FloatVector(obj)
else:
raise(
ValueError('Nothing can be done for this array '
'type at the moment.')
)
return res
default_converter.py2rpy.register(int,
lambda x: x)
@default_converter.py2rpy.register(list)
def _py2rpy_list(obj):
cv = conversion.get_conversion()
return vectors.ListVector(
rinterface.ListSexpVector(
[cv.py2rpy(x) for x in obj]
)
)
@default_converter.py2rpy.register(rlc.TaggedList)
def _py2rpy_taggedlist(obj):
cv = conversion.get_conversion()
res = vectors.ListVector(
rinterface.ListSexpVector([cv.py2rpy(x) for x in obj])
)
res.do_slot_assign('names', rinterface.StrSexpVector(obj.tags))
return res
@default_converter.py2rpy.register(complex)
def _py2rpy_complex(obj):
return obj
@default_converter.py2rpy.register(types.FunctionType)
def _function_to_rpy(func):
def wrap(*args):
res = func(*args)
res = conversion.py2ro(res)
return res
rfunc = rinterface.rternalize(wrap)
return conversion.get_conversion().rpy2py(rfunc)
@default_converter.rpy2py.register(object)
def _(obj):
return obj
class ExternalPointer(RObjectMixin, rinterface.SexpExtPtr):
pass
default_converter._rpy2py_nc_map.update(
{
rinterface.SexpExtPtr: conversion.NameClassMap(ExternalPointer),
rinterface.SexpS4: conversion.NameClassMap(RS4),
rinterface.IntSexpVector: conversion.NameClassMap(
lambda obj: _vector_matrix_array(
obj, vectors.IntVector,
vectors.IntMatrix, vectors.IntArray)(obj),
{'factor': FactorVector}),
rinterface.FloatSexpVector: conversion.NameClassMap(
lambda obj: _vector_matrix_array(
obj, vectors.FloatVector,
vectors.FloatMatrix, vectors.FloatArray)(obj),
{'Date': DateVector,
'POSIXct': POSIXct}),
rinterface.BoolSexpVector: conversion.NameClassMap(
lambda obj: _vector_matrix_array(
obj, vectors.BoolVector,
vectors.BoolMatrix, vectors.BoolArray)(obj)
),
rinterface.ByteSexpVector: conversion.NameClassMap(
lambda obj: _vector_matrix_array(
obj, vectors.ByteVector,
vectors.ByteMatrix, vectors.ByteArray)(obj)
),
rinterface.StrSexpVector: conversion.NameClassMap(
lambda obj: _vector_matrix_array(
obj, vectors.StrVector,
vectors.StrMatrix, vectors.StrArray)(obj)
),
rinterface.ComplexSexpVector: conversion.NameClassMap(
lambda obj: _vector_matrix_array(obj, vectors.ComplexVector,
vectors.ComplexMatrix, vectors.ComplexArray)(obj)
),
rinterface.ListSexpVector: conversion.NameClassMap(
ListVector,
{'data.frame': DataFrame}),
rinterface.SexpEnvironment: conversion.NameClassMap(Environment)
}
)
class R(object):
"""
Singleton representing the embedded R running.
"""
_instance = None
# Default for the evaluation
_print_r_warnings: bool = True
_invisible: bool = True
def __new__(cls):
if cls._instance is None:
rinterface.initr_simple()
cls._instance = object.__new__(cls)
return cls._instance
def __getattribute__(self, attr: str) -> object:
try:
return super(R, self).__getattribute__(attr)
except AttributeError as ae:
orig_ae = str(ae)
try:
return self.__getitem__(attr)
except LookupError:
raise AttributeError(orig_ae)
def __getitem__(self, item: str) -> object:
res = _globalenv.find(item)
res = conversion.get_conversion().rpy2py(res)
if hasattr(res, '__rname__'):
res.__rname__ = item
return res
# TODO: check that this is properly working
def __cleanup__(self) -> None:
rinterface.embedded.endr(0)
del(self)
def __str__(self) -> str:
s = [super(R, self).__str__()]
version = self['version']
version_k: typing.Tuple[str, ...] = tuple(version.names) # type: ignore
version_v: typing.Tuple[str, ...] = tuple(
x[0] for x in version # type: ignore
)
for key, val in zip(version_k, version_v):
s.extend('%s: %s' % (key, val))
return os.linesep.join(s)
def __call__(self, string: str,
invisible: typing.Optional[bool] = None,
print_r_warnings: typing.Optional[bool] = None) -> object:
"""Evaluate a string as R code.
:param string: A string with R code
:param invisible: evaluate the R expression handling R's
invisibility flag. When `True` expressions meant to return
an "invisible" result (for example, `x <- 1`) will return
None. The default is `None`, in which case the attribute
_invisible is used.
:param print_r_warning: When `True` the R deferred warnings
are printed using the R callback function. The default is
`None`, in which case the attribute _print_r_warning
is used.
:return: The value returned by R after rpy2 conversion."""
r_expr = rinterface.parse(string)
if invisible is None:
invisible = self._invisible
if invisible:
res, visible = rinterface.evalr_expr_with_visible( # type: ignore
r_expr
)
if not visible[0]: # type: ignore
res = None
else:
res = rinterface.evalr_expr(r_expr)
if print_r_warnings is None:
print_r_warnings = self._print_r_warnings
if print_r_warnings:
_print_deferred_warnings()
return (None if res is None
else conversion.get_conversion().rpy2py(res))
r = R()
rl = language.LangVector.from_string
conversion.set_conversion(default_converter)
globalenv = conversion.converter_ctx.get().rpy2py(_globalenv)
baseenv = conversion.converter_ctx.get().rpy2py(rinterface.baseenv)
emptyenv = conversion.converter_ctx.get().rpy2py(rinterface.emptyenv)