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Store views in the models and store child views in the views
Store views in the models and store child views in the views

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rmagic.py
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# -*- coding: utf-8 -*-
"""
======
Rmagic
======
Magic command interface for interactive work with R via rpy2
.. note::
The ``rpy2`` package needs to be installed separately. It
can be obtained using ``easy_install`` or ``pip``.
You will also need a working copy of R.
Usage
=====
To enable the magics below, execute ``%load_ext rmagic``.
``%R``
{R_DOC}
``%Rpush``
{RPUSH_DOC}
``%Rpull``
{RPULL_DOC}
``%Rget``
{RGET_DOC}
"""
from __future__ import print_function
#-----------------------------------------------------------------------------
# Copyright (C) 2012 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distributed as part of this software.
#-----------------------------------------------------------------------------
import sys
import tempfile
from glob import glob
from shutil import rmtree
# numpy and rpy2 imports
import numpy as np
import rpy2.rinterface as ri
import rpy2.robjects as ro
try:
from rpy2.robjects import pandas2ri
pandas2ri.activate()
except ImportError:
pandas2ri = None
from rpy2.robjects import numpy2ri
numpy2ri.activate()
# IPython imports
from IPython.core.displaypub import publish_display_data
from IPython.core.magic import (Magics, magics_class, line_magic,
line_cell_magic, needs_local_scope)
from IPython.testing.skipdoctest import skip_doctest
from IPython.core.magic_arguments import (
argument, magic_arguments, parse_argstring
)
from IPython.external.simplegeneric import generic
from IPython.utils.py3compat import (str_to_unicode, unicode_to_str, PY3,
unicode_type)
from IPython.utils.text import dedent
class RInterpreterError(ri.RRuntimeError):
"""An error when running R code in a %%R magic cell."""
def __init__(self, line, err, stdout):
self.line = line
self.err = err.rstrip()
self.stdout = stdout.rstrip()
def __unicode__(self):
s = 'Failed to parse and evaluate line %r.\nR error message: %r' % \
(self.line, self.err)
if self.stdout and (self.stdout != self.err):
s += '\nR stdout:\n' + self.stdout
return s
if PY3:
__str__ = __unicode__
else:
def __str__(self):
return unicode_to_str(unicode(self), 'utf-8')
def Rconverter(Robj, dataframe=False):
"""
Convert an object in R's namespace to one suitable
for ipython's namespace.
For a data.frame, it tries to return a structured array.
It first checks for colnames, then names.
If all are NULL, it returns np.asarray(Robj), else
it tries to construct a recarray
Parameters
----------
Robj: an R object returned from rpy2
"""
is_data_frame = ro.r('is.data.frame')
colnames = ro.r('colnames')
rownames = ro.r('rownames') # with pandas, these could be used for the index
names = ro.r('names')
if dataframe:
as_data_frame = ro.r('as.data.frame')
cols = colnames(Robj)
_names = names(Robj)
if cols != ri.NULL:
Robj = as_data_frame(Robj)
names = tuple(np.array(cols))
elif _names != ri.NULL:
names = tuple(np.array(_names))
else: # failed to find names
return np.asarray(Robj)
Robj = np.rec.fromarrays(Robj, names = names)
return np.asarray(Robj)
@generic
def pyconverter(pyobj):
"""Convert Python objects to R objects. Add types using the decorator:
@pyconverter.when_type
"""
return pyobj
# The default conversion for lists seems to make them a nested list. That has
# some advantages, but is rarely convenient, so for interactive use, we convert
# lists to a numpy array, which becomes an R vector.
@pyconverter.when_type(list)
def pyconverter_list(pyobj):
return np.asarray(pyobj)
if pandas2ri is None:
# pandas2ri was new in rpy2 2.3.3, so for now we'll fallback to pandas'
# conversion function.
try:
from pandas import DataFrame
from pandas.rpy.common import convert_to_r_dataframe
@pyconverter.when_type(DataFrame)
def pyconverter_dataframe(pyobj):
return convert_to_r_dataframe(pyobj, strings_as_factors=True)
except ImportError:
pass
@magics_class
class RMagics(Magics):
"""A set of magics useful for interactive work with R via rpy2.
"""
def __init__(self, shell, Rconverter=Rconverter,
pyconverter=pyconverter,
cache_display_data=False):
"""
Parameters
----------
shell : IPython shell
Rconverter : callable
To be called on values taken from R before putting them in the
IPython namespace.
pyconverter : callable
To be called on values in ipython namespace before
assigning to variables in rpy2.
cache_display_data : bool
If True, the published results of the final call to R are
cached in the variable 'display_cache'.
"""
super(RMagics, self).__init__(shell)
self.cache_display_data = cache_display_data
self.r = ro.R()
self.Rstdout_cache = []
self.pyconverter = pyconverter
self.Rconverter = Rconverter
def eval(self, line):
'''
Parse and evaluate a line of R code with rpy2.
Returns the output to R's stdout() connection,
the value generated by evaluating the code, and a
boolean indicating whether the return value would be
visible if the line of code were evaluated in an R REPL.
R Code evaluation and visibility determination are
done via an R call of the form withVisible({<code>})
'''
old_writeconsole = ri.get_writeconsole()
ri.set_writeconsole(self.write_console)
try:
res = ro.r("withVisible({%s})" % line)
value = res[0] #value (R object)
visible = ro.conversion.ri2py(res[1])[0] #visible (boolean)
except (ri.RRuntimeError, ValueError) as exception:
warning_or_other_msg = self.flush() # otherwise next return seems to have copy of error
raise RInterpreterError(line, str_to_unicode(str(exception)), warning_or_other_msg)
text_output = self.flush()
ri.set_writeconsole(old_writeconsole)
return text_output, value, visible
def write_console(self, output):
'''
A hook to capture R's stdout in a cache.
'''
self.Rstdout_cache.append(output)
def flush(self):
'''
Flush R's stdout cache to a string, returning the string.
'''
value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache])
self.Rstdout_cache = []
return value
@skip_doctest
@needs_local_scope
@line_magic
def Rpush(self, line, local_ns=None):
'''
A line-level magic for R that pushes
variables from python to rpy2. The line should be made up
of whitespace separated variable names in the IPython
namespace::
In [7]: import numpy as np
In [8]: X = np.array([4.5,6.3,7.9])
In [9]: X.mean()
Out[9]: 6.2333333333333343
In [10]: %Rpush X
In [11]: %R mean(X)
Out[11]: array([ 6.23333333])
'''
if local_ns is None:
local_ns = {}
inputs = line.split(' ')
for input in inputs:
try:
val = local_ns[input]
except KeyError:
try:
val = self.shell.user_ns[input]
except KeyError:
# reraise the KeyError as a NameError so that it looks like
# the standard python behavior when you use an unnamed
# variable
raise NameError("name '%s' is not defined" % input)
self.r.assign(input, self.pyconverter(val))
@skip_doctest
@magic_arguments()
@argument(
'-d', '--as_dataframe', action='store_true',
default=False,
help='Convert objects to data.frames before returning to ipython.'
)
@argument(
'outputs',
nargs='*',
)
@line_magic
def Rpull(self, line):
'''
A line-level magic for R that pulls
variables from python to rpy2::
In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4)
In [19]: %Rpull x y z
In [20]: x
Out[20]: array([ 3. , 4. , 6.7])
In [21]: y
Out[21]: array([ 4., 6., 7.])
In [22]: z
Out[22]:
array(['a', '3', '4'],
dtype='|S1')
If --as_dataframe, then each object is returned as a structured array
after first passed through "as.data.frame" in R before
being calling self.Rconverter.
This is useful when a structured array is desired as output, or
when the object in R has mixed data types.
See the %%R docstring for more examples.
Notes
-----
Beware that R names can have '.' so this is not fool proof.
To avoid this, don't name your R objects with '.'s...
'''
args = parse_argstring(self.Rpull, line)
outputs = args.outputs
for output in outputs:
self.shell.push({output:self.Rconverter(self.r(output),dataframe=args.as_dataframe)})
@skip_doctest
@magic_arguments()
@argument(
'-d', '--as_dataframe', action='store_true',
default=False,
help='Convert objects to data.frames before returning to ipython.'
)
@argument(
'output',
nargs=1,
type=str,
)
@line_magic
def Rget(self, line):
'''
Return an object from rpy2, possibly as a structured array (if possible).
Similar to Rpull except only one argument is accepted and the value is
returned rather than pushed to self.shell.user_ns::
In [3]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]
In [4]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype)
In [5]: %R -i datapy
In [6]: %Rget datapy
Out[6]:
array([['1', '2', '3', '4'],
['2', '3', '2', '5'],
['a', 'b', 'c', 'e']],
dtype='|S1')
In [7]: %Rget -d datapy
Out[7]:
array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')],
dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')])
'''
args = parse_argstring(self.Rget, line)
output = args.output
return self.Rconverter(self.r(output[0]),dataframe=args.as_dataframe)
@skip_doctest
@magic_arguments()
@argument(
'-i', '--input', action='append',
help='Names of input variable from shell.user_ns to be assigned to R variables of the same names after calling self.pyconverter. Multiple names can be passed separated only by commas with no whitespace.'
)
@argument(
'-o', '--output', action='append',
help='Names of variables to be pushed from rpy2 to shell.user_ns after executing cell body and applying self.Rconverter. Multiple names can be passed separated only by commas with no whitespace.'
)
@argument(
'-w', '--width', type=int,
help='Width of png plotting device sent as an argument to *png* in R.'
)
@argument(
'-h', '--height', type=int,
help='Height of png plotting device sent as an argument to *png* in R.'
)
@argument(
'-d', '--dataframe', action='append',
help='Convert these objects to data.frames and return as structured arrays.'
)
@argument(
'-u', '--units', type=unicode_type, choices=["px", "in", "cm", "mm"],
help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].'
)
@argument(
'-r', '--res', type=int,
help='Resolution of png plotting device sent as an argument to *png* in R. Defaults to 72 if *units* is one of ["in", "cm", "mm"].'
)
@argument(
'-p', '--pointsize', type=int,
help='Pointsize of png plotting device sent as an argument to *png* in R.'
)
@argument(
'-b', '--bg',
help='Background of png plotting device sent as an argument to *png* in R.'
)
@argument(
'-n', '--noreturn',
help='Force the magic to not return anything.',
action='store_true',
default=False
)
@argument(
'code',
nargs='*',
)
@needs_local_scope
@line_cell_magic
def R(self, line, cell=None, local_ns=None):
'''
Execute code in R, and pull some of the results back into the Python namespace.
In line mode, this will evaluate an expression and convert the returned value to a Python object.
The return value is determined by rpy2's behaviour of returning the result of evaluating the
final line.
Multiple R lines can be executed by joining them with semicolons::
In [9]: %R X=c(1,4,5,7); sd(X); mean(X)
Out[9]: array([ 4.25])
In cell mode, this will run a block of R code. The resulting value
is printed if it would printed be when evaluating the same code
within a standard R REPL.
Nothing is returned to python by default in cell mode::
In [10]: %%R
....: Y = c(2,4,3,9)
....: summary(lm(Y~X))
Call:
lm(formula = Y ~ X)
Residuals:
1 2 3 4
0.88 -0.24 -2.28 1.64
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 0.0800 2.3000 0.035 0.975
X 1.0400 0.4822 2.157 0.164
Residual standard error: 2.088 on 2 degrees of freedom
Multiple R-squared: 0.6993,Adjusted R-squared: 0.549
F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638
In the notebook, plots are published as the output of the cell::
%R plot(X, Y)
will create a scatter plot of X bs Y.
If cell is not None and line has some R code, it is prepended to
the R code in cell.
Objects can be passed back and forth between rpy2 and python via the -i -o flags in line::
In [14]: Z = np.array([1,4,5,10])
In [15]: %R -i Z mean(Z)
Out[15]: array([ 5.])
In [16]: %R -o W W=Z*mean(Z)
Out[16]: array([ 5., 20., 25., 50.])
In [17]: W
Out[17]: array([ 5., 20., 25., 50.])
The return value is determined by these rules:
* If the cell is not None, the magic returns None.
* If the cell evaluates as False, the resulting value is returned
unless the final line prints something to the console, in
which case None is returned.
* If the final line results in a NULL value when evaluated
by rpy2, then None is returned.
* No attempt is made to convert the final value to a structured array.
Use the --dataframe flag or %Rget to push / return a structured array.
* If the -n flag is present, there is no return value.
* A trailing ';' will also result in no return value as the last
value in the line is an empty string.
The --dataframe argument will attempt to return structured arrays.
This is useful for dataframes with
mixed data types. Note also that for a data.frame,
if it is returned as an ndarray, it is transposed::
In [18]: dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')]
In [19]: datapy = np.array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5, 'e')], dtype=dtype)
In [20]: %%R -o datar
datar = datapy
....:
In [21]: datar
Out[21]:
array([['1', '2', '3', '4'],
['2', '3', '2', '5'],
['a', 'b', 'c', 'e']],
dtype='|S1')
In [22]: %%R -d datar
datar = datapy
....:
In [23]: datar
Out[23]:
array([(1, 2.9, 'a'), (2, 3.5, 'b'), (3, 2.1, 'c'), (4, 5.0, 'e')],
dtype=[('x', '<i4'), ('y', '<f8'), ('z', '|S1')])
The --dataframe argument first tries colnames, then names.
If both are NULL, it returns an ndarray (i.e. unstructured)::
In [1]: %R mydata=c(4,6,8.3); NULL
In [2]: %R -d mydata
In [3]: mydata
Out[3]: array([ 4. , 6. , 8.3])
In [4]: %R names(mydata) = c('a','b','c'); NULL
In [5]: %R -d mydata
In [6]: mydata
Out[6]:
array((4.0, 6.0, 8.3),
dtype=[('a', '<f8'), ('b', '<f8'), ('c', '<f8')])
In [7]: %R -o mydata
In [8]: mydata
Out[8]: array([ 4. , 6. , 8.3])
'''
args = parse_argstring(self.R, line)
# arguments 'code' in line are prepended to
# the cell lines
if cell is None:
code = ''
return_output = True
line_mode = True
else:
code = cell
return_output = False
line_mode = False
code = ' '.join(args.code) + code
# if there is no local namespace then default to an empty dict
if local_ns is None:
local_ns = {}
if args.input:
for input in ','.join(args.input).split(','):
try:
val = local_ns[input]
except KeyError:
try:
val = self.shell.user_ns[input]
except KeyError:
raise NameError("name '%s' is not defined" % input)
self.r.assign(input, self.pyconverter(val))
if getattr(args, 'units') is not None:
if args.units != "px" and getattr(args, 'res') is None:
args.res = 72
args.units = '"%s"' % args.units
png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'res', 'height', 'width', 'bg', 'pointsize']])
png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None])
# execute the R code in a temporary directory
tmpd = tempfile.mkdtemp()
self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args))
text_output = ''
try:
if line_mode:
for line in code.split(';'):
text_result, result, visible = self.eval(line)
text_output += text_result
if text_result:
# the last line printed something to the console so we won't return it
return_output = False
else:
text_result, result, visible = self.eval(code)
text_output += text_result
if visible:
old_writeconsole = ri.get_writeconsole()
ri.set_writeconsole(self.write_console)
ro.r.show(result)
text_output += self.flush()
ri.set_writeconsole(old_writeconsole)
except RInterpreterError as e:
print(e.stdout)
if not e.stdout.endswith(e.err):
print(e.err)
rmtree(tmpd)
return
self.r('dev.off()')
# read out all the saved .png files
images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)]
# now publish the images
# mimicking IPython/zmq/pylab/backend_inline.py
fmt = 'png'
mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' }
mime = mimetypes[fmt]
# publish the printed R objects, if any
display_data = []
if text_output:
display_data.append(('RMagic.R', {'text/plain':text_output}))
# flush text streams before sending figures, helps a little with output
for image in images:
# synchronization in the console (though it's a bandaid, not a real sln)
sys.stdout.flush(); sys.stderr.flush()
display_data.append(('RMagic.R', {mime: image}))
# kill the temporary directory
rmtree(tmpd)
# try to turn every output into a numpy array
# this means that output are assumed to be castable
# as numpy arrays
if args.output:
for output in ','.join(args.output).split(','):
self.shell.push({output:self.Rconverter(self.r(output), dataframe=False)})
if args.dataframe:
for output in ','.join(args.dataframe).split(','):
self.shell.push({output:self.Rconverter(self.r(output), dataframe=True)})
for tag, disp_d in display_data:
publish_display_data(tag, disp_d)
# this will keep a reference to the display_data
# which might be useful to other objects who happen to use
# this method
if self.cache_display_data:
self.display_cache = display_data
# if in line mode and return_output, return the result as an ndarray
if return_output and not args.noreturn:
if result != ri.NULL:
return self.Rconverter(result, dataframe=False)
__doc__ = __doc__.format(
R_DOC = dedent(RMagics.R.__doc__),
RPUSH_DOC = dedent(RMagics.Rpush.__doc__),
RPULL_DOC = dedent(RMagics.Rpull.__doc__),
RGET_DOC = dedent(RMagics.Rget.__doc__)
)
def load_ipython_extension(ip):
"""Load the extension in IPython."""
ip.register_magics(RMagics)
# Initialising rpy2 interferes with readline. Since, at this point, we've
# probably just loaded rpy2, we reset the delimiters. See issue gh-2759.
if ip.has_readline:
ip.readline.set_completer_delims(ip.readline_delims)