summaryrefslogtreecommitdiff
path: root/lisp/org/ob-octave.el
blob: 8cc66b6f9c84331d688c9501408bc131266d40e0 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
;;; ob-octave.el --- org-babel functions for octave and matlab evaluation

;; Copyright (C) 2010-2014 Free Software Foundation, Inc.

;; Author: Dan Davison
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org

;; This file is part of GNU Emacs.

;; GNU Emacs is free software: you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation, either version 3 of the License, or
;; (at your option) any later version.

;; GNU Emacs is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.

;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>.

;;; Commentary:

;;; Requirements:

;; octave
;; octave-mode.el and octave-inf.el come with GNU emacs

;;; Code:
(require 'ob)
(eval-when-compile (require 'cl))

(declare-function matlab-shell "ext:matlab-mode")
(declare-function matlab-shell-run-region "ext:matlab-mode")

(defvar org-babel-default-header-args:matlab '())
(defvar org-babel-default-header-args:octave '())

(defvar org-babel-matlab-shell-command "matlab -nosplash"
  "Shell command to run matlab as an external process.")
(defvar org-babel-octave-shell-command "octave -q"
  "Shell command to run octave as an external process.")

(defvar org-babel-matlab-with-emacs-link nil
  "If non-nil use matlab-shell-run-region for session evaluation.
  This will use EmacsLink if (matlab-with-emacs-link) evaluates
  to a non-nil value.")

(defvar org-babel-matlab-emacs-link-wrapper-method
  "%s
if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
else, save -ascii %s ans
end
delete('%s')
")
(defvar org-babel-octave-wrapper-method
  "%s
if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
else, dlmwrite('%s', ans, '\\t')
end")

(defvar org-babel-octave-eoe-indicator "\'org_babel_eoe\'")

(defvar org-babel-octave-eoe-output "ans = org_babel_eoe")

(defun org-babel-execute:matlab (body params)
  "Execute a block of matlab code with Babel."
  (org-babel-execute:octave body params 'matlab))

(defun org-babel-execute:octave (body params &optional matlabp)
  "Execute a block of octave code with Babel."
  (let* ((session
	  (funcall (intern (format "org-babel-%s-initiate-session"
				   (if matlabp "matlab" "octave")))
		   (cdr (assoc :session params)) params))
         (vars (mapcar #'cdr (org-babel-get-header params :var)))
         (result-params (cdr (assoc :result-params params)))
         (result-type (cdr (assoc :result-type params)))
	 (out-file (cdr (assoc :file params)))
	 (full-body
	  (org-babel-expand-body:generic
	   body params (org-babel-variable-assignments:octave params)))
	 (result (org-babel-octave-evaluate
		  session
		  (if (org-babel-octave-graphical-output-file params)
		      (mapconcat 'identity
				 (list
				  "set (0, \"defaultfigurevisible\", \"off\");"
				  full-body
				  (format "print -dpng %s" (org-babel-octave-graphical-output-file params)))
				 "\n")
		    full-body)
		  result-type matlabp)))
    (if (org-babel-octave-graphical-output-file params)
	nil
      (org-babel-reassemble-table
       result
       (org-babel-pick-name
	(cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
       (org-babel-pick-name
	(cdr (assoc :rowname-names params)) (cdr (assoc :rownames params)))))))

(defun org-babel-prep-session:matlab (session params)
  "Prepare SESSION according to PARAMS."
  (org-babel-prep-session:octave session params 'matlab))

(defun org-babel-variable-assignments:octave (params)
  "Return list of octave statements assigning the block's variables."
  (mapcar
   (lambda (pair)
     (format "%s=%s;"
	     (car pair)
	     (org-babel-octave-var-to-octave (cdr pair))))
   (mapcar #'cdr (org-babel-get-header params :var))))

(defalias 'org-babel-variable-assignments:matlab
  'org-babel-variable-assignments:octave)

(defun org-babel-octave-var-to-octave (var)
  "Convert an emacs-lisp value into an octave variable.
Converts an emacs-lisp variable into a string of octave code
specifying a variable of the same value."
  (if (listp var)
      (concat "[" (mapconcat #'org-babel-octave-var-to-octave var
			     (if (listp (car var)) "; " ",")) "]")
    (cond
     ((stringp var)
      (format "\'%s\'" var))
     (t
      (format "%s" var)))))

(defun org-babel-prep-session:octave (session params &optional matlabp)
  "Prepare SESSION according to the header arguments specified in PARAMS."
  (let* ((session (org-babel-octave-initiate-session session params matlabp))
	 (var-lines (org-babel-variable-assignments:octave params)))
    (org-babel-comint-in-buffer session
      (mapc (lambda (var)
              (end-of-line 1) (insert var) (comint-send-input nil t)
              (org-babel-comint-wait-for-output session)) var-lines))
    session))

(defun org-babel-matlab-initiate-session (&optional session params)
  "Create a matlab inferior process buffer.
If there is not a current inferior-process-buffer in SESSION then
create.  Return the initialized session."
  (org-babel-octave-initiate-session session params 'matlab))

(defun org-babel-octave-initiate-session (&optional session params matlabp)
  "Create an octave inferior process buffer.
If there is not a current inferior-process-buffer in SESSION then
create.  Return the initialized session."
  (if matlabp (require 'matlab) (or (require 'octave-inf nil 'noerror)
				    (require 'octave)))
  (unless (string= session "none")
    (let ((session (or session
		       (if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
      (if (org-babel-comint-buffer-livep session) session
	(save-window-excursion
	  (if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
	    (run-octave))
	  (rename-buffer (if (bufferp session) (buffer-name session)
			   (if (stringp session) session (buffer-name))))
	  (current-buffer))))))

(defun org-babel-octave-evaluate
  (session body result-type &optional matlabp)
  "Pass BODY to the octave process in SESSION.
If RESULT-TYPE equals 'output then return the outputs of the
statements in BODY, if RESULT-TYPE equals 'value then return the
value of the last statement in BODY, as elisp."
  (if session
      (org-babel-octave-evaluate-session session body result-type matlabp)
    (org-babel-octave-evaluate-external-process body result-type matlabp)))

(defun org-babel-octave-evaluate-external-process (body result-type matlabp)
  "Evaluate BODY in an external octave process."
  (let ((cmd (if matlabp
		 org-babel-matlab-shell-command
	       org-babel-octave-shell-command)))
    (case result-type
      (output (org-babel-eval cmd body))
      (value (let ((tmp-file (org-babel-temp-file "octave-")))
	       (org-babel-eval
		cmd
		(format org-babel-octave-wrapper-method body
			(org-babel-process-file-name tmp-file 'noquote)
			(org-babel-process-file-name tmp-file 'noquote)))
	       (org-babel-octave-import-elisp-from-file tmp-file))))))

(defun org-babel-octave-evaluate-session
  (session body result-type &optional matlabp)
  "Evaluate BODY in SESSION."
  (let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
	 (wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
	 (full-body
	  (case result-type
	    (output
	     (mapconcat
	      #'org-babel-chomp
	      (list body org-babel-octave-eoe-indicator) "\n"))
	    (value
	     (if (and matlabp org-babel-matlab-with-emacs-link)
		 (concat
		  (format org-babel-matlab-emacs-link-wrapper-method
			  body
			  (org-babel-process-file-name tmp-file 'noquote)
			  (org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
	       (mapconcat
		#'org-babel-chomp
		(list (format org-babel-octave-wrapper-method
			      body
			      (org-babel-process-file-name tmp-file 'noquote)
			      (org-babel-process-file-name tmp-file 'noquote))
		      org-babel-octave-eoe-indicator) "\n")))))
	 (raw (if (and matlabp org-babel-matlab-with-emacs-link)
		  (save-window-excursion
		    (with-temp-buffer
		      (insert full-body)
		      (write-region "" 'ignored wait-file nil nil nil 'excl)
		      (matlab-shell-run-region (point-min) (point-max))
		      (message "Waiting for Matlab Emacs Link")
		      (while (file-exists-p wait-file) (sit-for 0.01))
		      "")) ;; matlab-shell-run-region doesn't seem to
		;; make *matlab* buffer contents easily
		;; available, so :results output currently
		;; won't work
		(org-babel-comint-with-output
		    (session
		     (if matlabp
			 org-babel-octave-eoe-indicator
		       org-babel-octave-eoe-output)
		     t full-body)
		  (insert full-body) (comint-send-input nil t)))) results)
    (case result-type
      (value
       (org-babel-octave-import-elisp-from-file tmp-file))
      (output
       (progn
	 (setq results
	       (if matlabp
		   (cdr (reverse (delq "" (mapcar
					   #'org-babel-octave-read-string
					   (mapcar #'org-babel-trim raw)))))
		 (cdr (member org-babel-octave-eoe-output
			      (reverse (mapcar
					#'org-babel-octave-read-string
					(mapcar #'org-babel-trim raw)))))))
	 (mapconcat #'identity (reverse results) "\n"))))))

(defun org-babel-octave-import-elisp-from-file (file-name)
  "Import data from FILE-NAME.
This removes initial blank and comment lines and then calls
`org-babel-import-elisp-from-file'."
  (let ((temp-file (org-babel-temp-file "octave-matlab-")) beg end)
    (with-temp-file temp-file
      (insert-file-contents file-name)
      (re-search-forward "^[ \t]*[^# \t]" nil t)
      (if (< (setq beg (point-min))
	     (setq end (point-at-bol)))
	  (delete-region beg end)))
    (org-babel-import-elisp-from-file temp-file '(16))))

(defun org-babel-octave-read-string (string)
  "Strip \\\"s from around octave string."
  (if (string-match "^\"\\([^\000]+\\)\"$" string)
      (match-string 1 string)
    string))

(defun org-babel-octave-graphical-output-file (params)
  "Name of file to which maxima should send graphical output."
  (and (member "graphics" (cdr (assq :result-params params)))
       (cdr (assq :file params))))

(provide 'ob-octave)



;;; ob-octave.el ends here