def __call__(self, *args, **kwargs):
new_args = [conversion.py2ri(a) for a in args]
new_kwargs = {}
for k, v in kwargs.iteritems():
new_kwargs[k] = conversion.py2ri(v)
res = super(RFunction, self).__call__(*new_args, **new_kwargs)
res = conversion.ri2py(res)
return res
def numpy2ri(o):
if isinstance(o, numpy.ndarray):
if not o.dtype.isnative:
raise(ValueError("Cannot pass numpy arrays with non-native byte orders at the moment."))
# The possible kind codes are listed at
# http://numpy.scipy.org/array_interface.shtml
kinds = {
# "t" -> not really supported by numpy
"b": rinterface.LGLSXP,
"i": rinterface.INTSXP,
# "u" -> special-cased below
"f": rinterface.REALSXP,
"c": rinterface.CPLXSXP,
# "O" -> special-cased below
"S": rinterface.STRSXP,
"U": rinterface.STRSXP,
# "V" -> special-cased below
}
# Most types map onto R arrays:
if o.dtype.kind in kinds:
# "F" means "use column-major order"
vec = rinterface.SexpVector(o.ravel("F"), kinds[o.dtype.kind])
dim = rinterface.SexpVector(o.shape, rinterface.INTSXP)
res = ro.r.array(vec, dim=dim)
# R does not support unsigned types:
elif o.dtype.kind == "u":
raise(ValueError("Cannot convert numpy array of unsigned values -- R does not have unsigned integers."))
# Array-of-PyObject is treated like a Python list:
elif o.dtype.kind == "O":
res = conversion.py2ri(list(o))
# Record arrays map onto R data frames:
elif o.dtype.kind == "V":
if o.dtype.names is None:
raise(ValueError("Nothing can be done for this numpy array type %s at the moment." % (o.dtype,)))
df_args = []
for field_name in o.dtype.names:
df_args.append((field_name,
conversion.py2ri(o[field_name])))
res = ro.baseenv["data.frame"].rcall(tuple(df_args), ro.globalenv)
# It should be impossible to get here:
else:
raise(ValueError("Unknown numpy array type."))
else:
res = ro.default_py2ri(o)
return res
def default_py2ri(o):
""" Convert arbitrary Python object to :class:`rpy2.rinterface.Sexp` to objects,
creating an R object with the content of the Python object in the process
(wichi means data copying).
:param o: object
:rtype: :class:`rpy2.rinterface.Sexp` (and subclasses)
"""
if isinstance(o, RObject):
res = rinterface.Sexp(o)
if isinstance(o, rinterface.Sexp):
res = o
elif isinstance(o, array.array):
if o.typecode in ('h', 'H', 'i', 'I'):
res = rinterface.SexpVector(o, rinterface.INTSXP)
elif o.typecode in ('f', 'd'):
res = rinterface.SexpVector(o, rinterface.REALSXP)
else:
raise(ValueError("Nothing can be done for this array type at the moment."))
elif isinstance(o, bool):
res = rinterface.SexpVector([o, ], rinterface.LGLSXP)
elif isinstance(o, int) or isinstance(o, long):
res = rinterface.SexpVector([o, ], rinterface.INTSXP)
elif isinstance(o, float):
res = rinterface.SexpVector([o, ], rinterface.REALSXP)
elif isinstance(o, str):
res = rinterface.SexpVector([o, ], rinterface.STRSXP)
elif isinstance(o, unicode):
res = rinterface.SexpVector([o, ], rinterface.STRSXP)
elif isinstance(o, list):
res = r.list(*[conversion.ri2py(conversion.py2ri(x)) for x in o])
elif isinstance(o, complex):
res = rinterface.SexpVector([o, ], rinterface.CPLXSXP)
else:
raise(ValueError("Nothing can be done for the type %s at the moment." %(type(o))))
return res
def __setitem__(self, i, value):
value = conversion.py2ri(value)
res = super(RVector, self).__setitem__(i, value)
def __init__(self, o):
if not isinstance(o, rinterface.SexpVector):
o = conversion.py2ri(o)
super(RVector, self).__init__(o)
self.r = RVectorDelegator(self)
