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1 | # -*- coding: utf-8 -*- |
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1 | # -*- coding: utf-8 -*- | |
2 | """ |
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2 | """ | |
3 | ====== |
|
3 | ====== | |
4 | Rmagic |
|
4 | Rmagic | |
5 | ====== |
|
5 | ====== | |
6 |
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6 | |||
7 | Magic command interface for interactive work with R via rpy2 |
|
7 | Magic command interface for interactive work with R via rpy2 | |
8 |
|
8 | |||
9 | Usage |
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9 | Usage | |
10 | ===== |
|
10 | ===== | |
11 |
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11 | |||
12 | ``%R`` |
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12 | ``%R`` | |
13 |
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13 | |||
14 | {R_DOC} |
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14 | {R_DOC} | |
15 |
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15 | |||
16 | ``%Rpush`` |
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16 | ``%Rpush`` | |
17 |
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17 | |||
18 | {RPUSH_DOC} |
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18 | {RPUSH_DOC} | |
19 |
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19 | |||
20 | ``%Rpull`` |
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20 | ``%Rpull`` | |
21 |
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21 | |||
22 | {RPULL_DOC} |
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22 | {RPULL_DOC} | |
23 |
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23 | |||
24 | """ |
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24 | """ | |
25 |
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25 | |||
26 | #----------------------------------------------------------------------------- |
|
26 | #----------------------------------------------------------------------------- | |
27 | # Copyright (C) 2012 The IPython Development Team |
|
27 | # Copyright (C) 2012 The IPython Development Team | |
28 | # |
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28 | # | |
29 | # Distributed under the terms of the BSD License. The full license is in |
|
29 | # Distributed under the terms of the BSD License. The full license is in | |
30 | # the file COPYING, distributed as part of this software. |
|
30 | # the file COPYING, distributed as part of this software. | |
31 | #----------------------------------------------------------------------------- |
|
31 | #----------------------------------------------------------------------------- | |
32 |
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32 | |||
33 | import sys |
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33 | import sys | |
34 | import tempfile |
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34 | import tempfile | |
35 | from glob import glob |
|
35 | from glob import glob | |
36 | from shutil import rmtree |
|
36 | from shutil import rmtree | |
37 | from getopt import getopt |
|
37 | from getopt import getopt | |
38 |
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38 | |||
39 | # numpy and rpy2 imports |
|
39 | # numpy and rpy2 imports | |
40 |
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40 | |||
41 | import numpy as np |
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41 | import numpy as np | |
42 |
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42 | |||
43 | import rpy2.rinterface as ri |
|
43 | import rpy2.rinterface as ri | |
44 | import rpy2.robjects as ro |
|
44 | import rpy2.robjects as ro | |
45 | from rpy2.robjects.numpy2ri import numpy2ri |
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45 | from rpy2.robjects.numpy2ri import numpy2ri | |
46 | ro.conversion.py2ri = numpy2ri |
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46 | ro.conversion.py2ri = numpy2ri | |
47 |
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47 | |||
48 | # IPython imports |
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48 | # IPython imports | |
49 |
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49 | |||
50 | from IPython.core.displaypub import publish_display_data |
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50 | from IPython.core.displaypub import publish_display_data | |
51 | from IPython.core.magic import (Magics, magics_class, cell_magic, line_magic, |
|
51 | from IPython.core.magic import (Magics, magics_class, cell_magic, line_magic, | |
52 | line_cell_magic) |
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52 | line_cell_magic) | |
53 | from IPython.testing.skipdoctest import skip_doctest |
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53 | from IPython.testing.skipdoctest import skip_doctest | |
54 | from IPython.core.magic_arguments import ( |
|
54 | from IPython.core.magic_arguments import ( | |
55 | argument, magic_arguments, parse_argstring |
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55 | argument, magic_arguments, parse_argstring | |
56 | ) |
|
56 | ) | |
57 | from IPython.utils.py3compat import str_to_unicode |
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57 | from IPython.utils.py3compat import str_to_unicode | |
58 |
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58 | |||
59 | class RMagicError(ValueError): |
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59 | class RMagicError(ValueError): | |
60 | pass |
|
60 | pass | |
61 |
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61 | |||
62 | @magics_class |
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62 | @magics_class | |
63 | class RMagics(Magics): |
|
63 | class RMagics(Magics): | |
|
64 | """A set of magics useful for interactive work with R via rpy2. | |||
|
65 | """ | |||
64 |
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66 | |||
65 | def __init__(self, shell, Rconverter=np.asarray, |
|
67 | def __init__(self, shell, Rconverter=np.asarray, | |
66 | pyconverter=np.asarray, |
|
68 | pyconverter=np.asarray, | |
67 | cache_display_data=False): |
|
69 | cache_display_data=False): | |
|
70 | """ | |||
|
71 | Parameters | |||
|
72 | ---------- | |||
|
73 | ||||
|
74 | shell : IPython shell | |||
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75 | ||||
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76 | Rconverter : callable | |||
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77 | To be called on return values from R before returning | |||
|
78 | to ipython. | |||
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79 | ||||
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80 | pyconverter : callable | |||
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81 | To be called on values in ipython namespace before | |||
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82 | assigning to variables in rpy2. | |||
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83 | ||||
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84 | cache_display_data : bool | |||
|
85 | If True, the published results of the final call to R are | |||
|
86 | cached in the variable 'display_cache'. | |||
|
87 | ||||
|
88 | """ | |||
68 | super(RMagics, self).__init__(shell) |
|
89 | super(RMagics, self).__init__(shell) | |
69 | self.cache_display_data = cache_display_data |
|
90 | self.cache_display_data = cache_display_data | |
70 |
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91 | |||
71 | self.r = ro.R() |
|
92 | self.r = ro.R() | |
72 | self.Rstdout_cache = [] |
|
93 | self.Rstdout_cache = [] | |
73 | self.Rconverter = Rconverter |
|
94 | self.Rconverter = Rconverter | |
74 | self.pyconverter = pyconverter |
|
95 | self.pyconverter = pyconverter | |
75 |
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96 | |||
76 | def eval(self, line): |
|
97 | def eval(self, line): | |
77 | ''' |
|
98 | ''' | |
78 | Parse and evaluate a line with rpy2. |
|
99 | Parse and evaluate a line with rpy2. | |
79 | Returns the output to R's stdout() connection |
|
100 | Returns the output to R's stdout() connection | |
80 | and the value of eval(parse(line)). |
|
101 | and the value of eval(parse(line)). | |
81 | ''' |
|
102 | ''' | |
82 | old_writeconsole = ri.get_writeconsole() |
|
103 | old_writeconsole = ri.get_writeconsole() | |
83 | ri.set_writeconsole(self.write_console) |
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104 | ri.set_writeconsole(self.write_console) | |
84 | try: |
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105 | try: | |
85 | value = ri.baseenv['eval'](ri.parse(line)) |
|
106 | value = ri.baseenv['eval'](ri.parse(line)) | |
86 | except (ri.RRuntimeError, ValueError) as msg: |
|
107 | except (ri.RRuntimeError, ValueError) as msg: | |
87 | raise RMagicError('error parsing and evaluating "%s": %s\n' % |
|
108 | raise RMagicError('error parsing and evaluating "%s": %s\n' % | |
88 | (line, str_to_unicode(msg, 'utf-8'))) |
|
109 | (line, str_to_unicode(msg, 'utf-8'))) | |
89 | text_output = self.flush() |
|
110 | text_output = self.flush() | |
90 | ri.set_writeconsole(old_writeconsole) |
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111 | ri.set_writeconsole(old_writeconsole) | |
91 | return text_output, value |
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112 | return text_output, value | |
92 |
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113 | |||
93 | def write_console(self, output): |
|
114 | def write_console(self, output): | |
94 | ''' |
|
115 | ''' | |
95 | A hook to capture R's stdout in a cache. |
|
116 | A hook to capture R's stdout in a cache. | |
96 | ''' |
|
117 | ''' | |
97 | self.Rstdout_cache.append(output) |
|
118 | self.Rstdout_cache.append(output) | |
98 |
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119 | |||
99 | def flush(self): |
|
120 | def flush(self): | |
100 | ''' |
|
121 | ''' | |
101 | Flush R's stdout cache to a string, returning the string. |
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122 | Flush R's stdout cache to a string, returning the string. | |
102 | ''' |
|
123 | ''' | |
103 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) |
|
124 | value = ''.join([str_to_unicode(s, 'utf-8') for s in self.Rstdout_cache]) | |
104 | self.Rstdout_cache = [] |
|
125 | self.Rstdout_cache = [] | |
105 | return value |
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126 | return value | |
106 |
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127 | |||
107 | @skip_doctest |
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128 | @skip_doctest | |
108 | @line_magic |
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129 | @line_magic | |
109 | def Rpush(self, line): |
|
130 | def Rpush(self, line): | |
110 | ''' |
|
131 | ''' | |
111 | A line-level magic for R that pushes |
|
132 | A line-level magic for R that pushes | |
112 | variables from python to rpy2. The line should be made up |
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133 | variables from python to rpy2. The line should be made up | |
113 | of whitespace separated variable names in the IPython |
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134 | of whitespace separated variable names in the IPython | |
114 | namespace:: |
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135 | namespace:: | |
115 |
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136 | |||
116 | In [7]: import numpy as np |
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137 | In [7]: import numpy as np | |
117 |
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138 | |||
118 | In [8]: X = np.array([4.5,6.3,7.9]) |
|
139 | In [8]: X = np.array([4.5,6.3,7.9]) | |
119 |
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140 | |||
120 | In [9]: X.mean() |
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141 | In [9]: X.mean() | |
121 | Out[9]: 6.2333333333333343 |
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142 | Out[9]: 6.2333333333333343 | |
122 |
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143 | |||
123 | In [10]: %Rpush X |
|
144 | In [10]: %Rpush X | |
124 |
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145 | |||
125 | In [11]: %R mean(X) |
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146 | In [11]: %R mean(X) | |
126 | Out[11]: array([ 6.23333333]) |
|
147 | Out[11]: array([ 6.23333333]) | |
127 |
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148 | |||
128 | ''' |
|
149 | ''' | |
129 |
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150 | |||
130 | inputs = line.split(' ') |
|
151 | inputs = line.split(' ') | |
131 | for input in inputs: |
|
152 | for input in inputs: | |
132 | self.r.assign(input, self.pyconverter(self.shell.user_ns[input])) |
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153 | self.r.assign(input, self.pyconverter(self.shell.user_ns[input])) | |
133 |
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154 | |||
134 | @skip_doctest |
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155 | @skip_doctest | |
135 | @line_magic |
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156 | @line_magic | |
136 | def Rpull(self, line): |
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157 | def Rpull(self, line): | |
137 | ''' |
|
158 | ''' | |
138 | A line-level magic for R that pulls |
|
159 | A line-level magic for R that pulls | |
139 | variables from python to rpy2:: |
|
160 | variables from python to rpy2:: | |
140 |
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161 | |||
141 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) |
|
162 | In [18]: _ = %R x = c(3,4,6.7); y = c(4,6,7); z = c('a',3,4) | |
142 |
|
163 | |||
143 | In [19]: %Rpull x y z |
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164 | In [19]: %Rpull x y z | |
144 |
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165 | |||
145 | In [20]: x |
|
166 | In [20]: x | |
146 | Out[20]: array([ 3. , 4. , 6.7]) |
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167 | Out[20]: array([ 3. , 4. , 6.7]) | |
147 |
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168 | |||
148 | In [21]: y |
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169 | In [21]: y | |
149 | Out[21]: array([ 4., 6., 7.]) |
|
170 | Out[21]: array([ 4., 6., 7.]) | |
150 |
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171 | |||
151 | In [22]: z |
|
172 | In [22]: z | |
152 | Out[22]: |
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173 | Out[22]: | |
153 | array(['a', '3', '4'], |
|
174 | array(['a', '3', '4'], | |
154 | dtype='|S1') |
|
175 | dtype='|S1') | |
155 |
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176 | |||
156 |
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177 | |||
157 | Notes |
|
178 | Notes | |
158 | ----- |
|
179 | ----- | |
159 |
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180 | |||
160 | Beware that R names can have '.' so this is not fool proof. |
|
181 | Beware that R names can have '.' so this is not fool proof. | |
161 | To avoid this, don't name your R objects with '.'s... |
|
182 | To avoid this, don't name your R objects with '.'s... | |
162 |
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183 | |||
163 | ''' |
|
184 | ''' | |
164 | outputs = line.split(' ') |
|
185 | outputs = line.split(' ') | |
165 | for output in outputs: |
|
186 | for output in outputs: | |
166 | self.shell.push({output:self.Rconverter(self.r(output))}) |
|
187 | self.shell.push({output:self.Rconverter(self.r(output))}) | |
167 |
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188 | |||
168 |
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189 | |||
169 | @skip_doctest |
|
190 | @skip_doctest | |
170 | @magic_arguments() |
|
191 | @magic_arguments() | |
171 | @argument( |
|
192 | @argument( | |
172 | '-i', '--input', action='append', |
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193 | '-i', '--input', action='append', | |
173 | 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.' |
|
194 | 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.' | |
174 | ) |
|
195 | ) | |
175 | @argument( |
|
196 | @argument( | |
176 | '-o', '--output', action='append', |
|
197 | '-o', '--output', action='append', | |
177 | 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.' |
|
198 | 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.' | |
178 | ) |
|
199 | ) | |
179 | @argument( |
|
200 | @argument( | |
180 | '-w', '--width', type=int, |
|
201 | '-w', '--width', type=int, | |
181 | help='Width of png plotting device sent as an argument to *png* in R.' |
|
202 | help='Width of png plotting device sent as an argument to *png* in R.' | |
182 | ) |
|
203 | ) | |
183 | @argument( |
|
204 | @argument( | |
184 | '-h', '--height', type=int, |
|
205 | '-h', '--height', type=int, | |
185 | help='Height of png plotting device sent as an argument to *png* in R.' |
|
206 | help='Height of png plotting device sent as an argument to *png* in R.' | |
186 | ) |
|
207 | ) | |
187 |
|
208 | |||
188 | @argument( |
|
209 | @argument( | |
189 | '-u', '--units', type=int, |
|
210 | '-u', '--units', type=int, | |
190 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' |
|
211 | help='Units of png plotting device sent as an argument to *png* in R. One of ["px", "in", "cm", "mm"].' | |
191 | ) |
|
212 | ) | |
192 | @argument( |
|
213 | @argument( | |
193 | '-p', '--pointsize', type=int, |
|
214 | '-p', '--pointsize', type=int, | |
194 | help='Pointsize of png plotting device sent as an argument to *png* in R.' |
|
215 | help='Pointsize of png plotting device sent as an argument to *png* in R.' | |
195 | ) |
|
216 | ) | |
196 | @argument( |
|
217 | @argument( | |
197 | '-b', '--bg', |
|
218 | '-b', '--bg', | |
198 | help='Background of png plotting device sent as an argument to *png* in R.' |
|
219 | help='Background of png plotting device sent as an argument to *png* in R.' | |
199 | ) |
|
220 | ) | |
200 | @argument( |
|
221 | @argument( | |
201 | '-n', '--noreturn', |
|
222 | '-n', '--noreturn', | |
202 | help='Force the magic to not return anything.', |
|
223 | help='Force the magic to not return anything.', | |
203 | action='store_true', |
|
224 | action='store_true', | |
204 | default=False |
|
225 | default=False | |
205 | ) |
|
226 | ) | |
206 | @argument( |
|
227 | @argument( | |
207 | 'code', |
|
228 | 'code', | |
208 | nargs='*', |
|
229 | nargs='*', | |
209 | ) |
|
230 | ) | |
210 | @line_cell_magic |
|
231 | @line_cell_magic | |
211 | def R(self, line, cell=None): |
|
232 | def R(self, line, cell=None): | |
212 | ''' |
|
233 | ''' | |
213 | Execute code in R, and pull some of the results back into the Python namespace. |
|
234 | Execute code in R, and pull some of the results back into the Python namespace. | |
214 |
|
235 | |||
215 | In line mode, this will evaluate an expression and convert the returned value to a Python object. |
|
236 | In line mode, this will evaluate an expression and convert the returned value to a Python object. | |
216 | The return value is determined by rpy2's behaviour of returning the result of evaluating the |
|
237 | The return value is determined by rpy2's behaviour of returning the result of evaluating the | |
217 | final line. Multiple R lines can be executed by joining them with semicolons:: |
|
238 | final line. Multiple R lines can be executed by joining them with semicolons:: | |
218 |
|
239 | |||
219 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) |
|
240 | In [9]: %R X=c(1,4,5,7); sd(X); mean(X) | |
220 | Out[9]: array([ 4.25]) |
|
241 | Out[9]: array([ 4.25]) | |
221 |
|
242 | |||
222 | As a cell, this will run a block of R code, without bringing anything back by default:: |
|
243 | As a cell, this will run a block of R code, without bringing anything back by default:: | |
223 |
|
244 | |||
224 | In [10]: %%R |
|
245 | In [10]: %%R | |
225 | ....: Y = c(2,4,3,9) |
|
246 | ....: Y = c(2,4,3,9) | |
226 | ....: print(summary(lm(Y~X))) |
|
247 | ....: print(summary(lm(Y~X))) | |
227 | ....: |
|
248 | ....: | |
228 |
|
249 | |||
229 | Call: |
|
250 | Call: | |
230 | lm(formula = Y ~ X) |
|
251 | lm(formula = Y ~ X) | |
231 |
|
252 | |||
232 | Residuals: |
|
253 | Residuals: | |
233 | 1 2 3 4 |
|
254 | 1 2 3 4 | |
234 | 0.88 -0.24 -2.28 1.64 |
|
255 | 0.88 -0.24 -2.28 1.64 | |
235 |
|
256 | |||
236 | Coefficients: |
|
257 | Coefficients: | |
237 | Estimate Std. Error t value Pr(>|t|) |
|
258 | Estimate Std. Error t value Pr(>|t|) | |
238 | (Intercept) 0.0800 2.3000 0.035 0.975 |
|
259 | (Intercept) 0.0800 2.3000 0.035 0.975 | |
239 | X 1.0400 0.4822 2.157 0.164 |
|
260 | X 1.0400 0.4822 2.157 0.164 | |
240 |
|
261 | |||
241 | Residual standard error: 2.088 on 2 degrees of freedom |
|
262 | Residual standard error: 2.088 on 2 degrees of freedom | |
242 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 |
|
263 | Multiple R-squared: 0.6993,Adjusted R-squared: 0.549 | |
243 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 |
|
264 | F-statistic: 4.651 on 1 and 2 DF, p-value: 0.1638 | |
244 |
|
265 | |||
245 | In the notebook, plots are published as the output of the cell. |
|
266 | In the notebook, plots are published as the output of the cell. | |
246 |
|
267 | |||
247 | %R plot(X, Y) |
|
268 | %R plot(X, Y) | |
248 |
|
269 | |||
249 | will create a scatter plot of X bs Y. |
|
270 | will create a scatter plot of X bs Y. | |
250 |
|
271 | |||
251 | If cell is not None and line has some R code, it is prepended to |
|
272 | If cell is not None and line has some R code, it is prepended to | |
252 | the R code in cell. |
|
273 | the R code in cell. | |
253 |
|
274 | |||
254 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: |
|
275 | Objects can be passed back and forth between rpy2 and python via the -i -o flags in line:: | |
255 |
|
276 | |||
256 | In [14]: Z = np.array([1,4,5,10]) |
|
277 | In [14]: Z = np.array([1,4,5,10]) | |
257 |
|
278 | |||
258 | In [15]: %R -i Z mean(Z) |
|
279 | In [15]: %R -i Z mean(Z) | |
259 | Out[15]: array([ 5.]) |
|
280 | Out[15]: array([ 5.]) | |
260 |
|
281 | |||
261 |
|
282 | |||
262 | In [16]: %R -o W W=Z*mean(Z) |
|
283 | In [16]: %R -o W W=Z*mean(Z) | |
263 | Out[16]: array([ 5., 20., 25., 50.]) |
|
284 | Out[16]: array([ 5., 20., 25., 50.]) | |
264 |
|
285 | |||
265 | In [17]: W |
|
286 | In [17]: W | |
266 | Out[17]: array([ 5., 20., 25., 50.]) |
|
287 | Out[17]: array([ 5., 20., 25., 50.]) | |
267 |
|
288 | |||
268 | The return value is determined by these rules: |
|
289 | The return value is determined by these rules: | |
269 |
|
290 | |||
270 | * If the cell is not None, the magic returns None. |
|
291 | * If the cell is not None, the magic returns None. | |
271 |
|
292 | |||
272 | * If the cell evaluates as False, the resulting value is returned |
|
293 | * If the cell evaluates as False, the resulting value is returned | |
273 | unless the final line prints something to the console, in |
|
294 | unless the final line prints something to the console, in | |
274 | which case None is returned. |
|
295 | which case None is returned. | |
275 |
|
296 | |||
276 | * If the final line results in a NULL value when evaluated |
|
297 | * If the final line results in a NULL value when evaluated | |
277 | by rpy2, then None is returned. |
|
298 | by rpy2, then None is returned. | |
278 |
|
299 | |||
279 |
|
300 | |||
280 | ''' |
|
301 | ''' | |
281 |
|
302 | |||
282 | args = parse_argstring(self.R, line) |
|
303 | args = parse_argstring(self.R, line) | |
283 |
|
304 | |||
284 | # arguments 'code' in line are prepended to |
|
305 | # arguments 'code' in line are prepended to | |
285 | # the cell lines |
|
306 | # the cell lines | |
286 | if not cell: |
|
307 | if not cell: | |
287 | code = '' |
|
308 | code = '' | |
288 | return_output = True |
|
309 | return_output = True | |
289 | line_mode = True |
|
310 | line_mode = True | |
290 | else: |
|
311 | else: | |
291 | code = cell |
|
312 | code = cell | |
292 | return_output = False |
|
313 | return_output = False | |
293 | line_mode = False |
|
314 | line_mode = False | |
294 |
|
315 | |||
295 | code = ' '.join(args.code) + code |
|
316 | code = ' '.join(args.code) + code | |
296 |
|
317 | |||
297 | if args.input: |
|
318 | if args.input: | |
298 | for input in ','.join(args.input).split(','): |
|
319 | for input in ','.join(args.input).split(','): | |
299 | self.r.assign(input, self.pyconverter(self.shell.user_ns[input])) |
|
320 | self.r.assign(input, self.pyconverter(self.shell.user_ns[input])) | |
300 |
|
321 | |||
301 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'height', 'width', 'bg', 'pointsize']]) |
|
322 | png_argdict = dict([(n, getattr(args, n)) for n in ['units', 'height', 'width', 'bg', 'pointsize']]) | |
302 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) |
|
323 | png_args = ','.join(['%s=%s' % (o,v) for o, v in png_argdict.items() if v is not None]) | |
303 | # execute the R code in a temporary directory |
|
324 | # execute the R code in a temporary directory | |
304 |
|
325 | |||
305 | tmpd = tempfile.mkdtemp() |
|
326 | tmpd = tempfile.mkdtemp() | |
306 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd, png_args)) |
|
327 | self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd, png_args)) | |
307 |
|
328 | |||
308 | text_output = '' |
|
329 | text_output = '' | |
309 | if line_mode: |
|
330 | if line_mode: | |
310 | for line in code.split(';'): |
|
331 | for line in code.split(';'): | |
311 | text_result, result = self.eval(line) |
|
332 | text_result, result = self.eval(line) | |
312 | text_output += text_result |
|
333 | text_output += text_result | |
313 | if text_result: |
|
334 | if text_result: | |
314 | # the last line printed something to the console so we won't return it |
|
335 | # the last line printed something to the console so we won't return it | |
315 | return_output = False |
|
336 | return_output = False | |
316 | else: |
|
337 | else: | |
317 | text_result, result = self.eval(code) |
|
338 | text_result, result = self.eval(code) | |
318 | text_output += text_result |
|
339 | text_output += text_result | |
319 |
|
340 | |||
320 | self.r('dev.off()') |
|
341 | self.r('dev.off()') | |
321 |
|
342 | |||
322 | # read out all the saved .png files |
|
343 | # read out all the saved .png files | |
323 |
|
344 | |||
324 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] |
|
345 | images = [open(imgfile, 'rb').read() for imgfile in glob("%s/Rplots*png" % tmpd)] | |
325 |
|
346 | |||
326 | # now publish the images |
|
347 | # now publish the images | |
327 | # mimicking IPython/zmq/pylab/backend_inline.py |
|
348 | # mimicking IPython/zmq/pylab/backend_inline.py | |
328 | fmt = 'png' |
|
349 | fmt = 'png' | |
329 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } |
|
350 | mimetypes = { 'png' : 'image/png', 'svg' : 'image/svg+xml' } | |
330 | mime = mimetypes[fmt] |
|
351 | mime = mimetypes[fmt] | |
331 |
|
352 | |||
332 | # publish the printed R objects, if any |
|
353 | # publish the printed R objects, if any | |
333 |
|
354 | |||
334 | display_data = [] |
|
355 | display_data = [] | |
335 | if text_output: |
|
356 | if text_output: | |
336 | display_data.append(('RMagic.R', {'text/plain':text_output})) |
|
357 | display_data.append(('RMagic.R', {'text/plain':text_output})) | |
337 |
|
358 | |||
338 | # flush text streams before sending figures, helps a little with output |
|
359 | # flush text streams before sending figures, helps a little with output | |
339 | for image in images: |
|
360 | for image in images: | |
340 | # synchronization in the console (though it's a bandaid, not a real sln) |
|
361 | # synchronization in the console (though it's a bandaid, not a real sln) | |
341 | sys.stdout.flush(); sys.stderr.flush() |
|
362 | sys.stdout.flush(); sys.stderr.flush() | |
342 | display_data.append(('RMagic.R', {mime: image})) |
|
363 | display_data.append(('RMagic.R', {mime: image})) | |
343 |
|
364 | |||
344 | # kill the temporary directory |
|
365 | # kill the temporary directory | |
345 | rmtree(tmpd) |
|
366 | rmtree(tmpd) | |
346 |
|
367 | |||
347 | # try to turn every output into a numpy array |
|
368 | # try to turn every output into a numpy array | |
348 | # this means that output are assumed to be castable |
|
369 | # this means that output are assumed to be castable | |
349 | # as numpy arrays |
|
370 | # as numpy arrays | |
350 |
|
371 | |||
351 | if args.output: |
|
372 | if args.output: | |
352 | for output in ','.join(args.output).split(','): |
|
373 | for output in ','.join(args.output).split(','): | |
353 | # with self.shell, we assign the values to variables in the shell |
|
374 | # with self.shell, we assign the values to variables in the shell | |
354 | self.shell.push({output:self.Rconverter(self.r(output))}) |
|
375 | self.shell.push({output:self.Rconverter(self.r(output))}) | |
355 |
|
376 | |||
356 | for tag, disp_d in display_data: |
|
377 | for tag, disp_d in display_data: | |
357 | publish_display_data(tag, disp_d) |
|
378 | publish_display_data(tag, disp_d) | |
358 |
|
379 | |||
359 | # this will keep a reference to the display_data |
|
380 | # this will keep a reference to the display_data | |
360 | # which might be useful to other objects who happen to use |
|
381 | # which might be useful to other objects who happen to use | |
361 | # this method |
|
382 | # this method | |
362 |
|
383 | |||
363 | if self.cache_display_data: |
|
384 | if self.cache_display_data: | |
364 | self.display_cache = display_data |
|
385 | self.display_cache = display_data | |
365 |
|
386 | |||
366 | # if in line mode and return_output, return the result as an ndarray |
|
387 | # if in line mode and return_output, return the result as an ndarray | |
367 | if return_output and not args.noreturn: |
|
388 | if return_output and not args.noreturn: | |
368 | if result != ri.NULL: |
|
389 | if result != ri.NULL: | |
369 | return self.Rconverter(result) |
|
390 | return self.Rconverter(result) | |
370 |
|
391 | |||
371 | __doc__ = __doc__.format( |
|
392 | __doc__ = __doc__.format( | |
372 | R_DOC = ' '*8 + RMagics.R.__doc__, |
|
393 | R_DOC = ' '*8 + RMagics.R.__doc__, | |
373 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, |
|
394 | RPUSH_DOC = ' '*8 + RMagics.Rpush.__doc__, | |
374 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__ |
|
395 | RPULL_DOC = ' '*8 + RMagics.Rpull.__doc__ | |
375 | ) |
|
396 | ) | |
376 |
|
397 | |||
377 |
|
398 | |||
378 | _loaded = False |
|
399 | _loaded = False | |
379 | def load_ipython_extension(ip): |
|
400 | def load_ipython_extension(ip): | |
380 | """Load the extension in IPython.""" |
|
401 | """Load the extension in IPython.""" | |
381 | global _loaded |
|
402 | global _loaded | |
382 | if not _loaded: |
|
403 | if not _loaded: | |
383 | ip.register_magics(RMagics) |
|
404 | ip.register_magics(RMagics) | |
384 | _loaded = True |
|
405 | _loaded = True |
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