[bpt/emacs.git] / lisp / org / ob-octave.el

;;; ob-octave.el --- org-babel functions for octave and matlab evaluation

;; Copyright (C) 2010-2012  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)
(require 'ob-ref)
(require 'ob-comint)
(require 'ob-eval)
(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) (require 'octave-inf))
  (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
Commit	Line	Data
86fbb8ca CD	1	;;; ob-octave.el --- org-babel functions for octave and matlab evaluation
86fbb8ca CD	2
b9db31c7	3	;; Copyright (C) 2010-2012 Free Software Foundation, Inc.
86fbb8ca CD	4
	5	;; Author: Dan Davison
	6	;; Keywords: literate programming, reproducible research
	7	;; Homepage: http://orgmode.org
86fbb8ca CD	8
	9	;; This file is part of GNU Emacs.
	10
	11	;; GNU Emacs is free software: you can redistribute it and/or modify
	12	;; it under the terms of the GNU General Public License as published by
	13	;; the Free Software Foundation, either version 3 of the License, or
	14	;; (at your option) any later version.
	15
	16	;; GNU Emacs is distributed in the hope that it will be useful,
	17	;; but WITHOUT ANY WARRANTY; without even the implied warranty of
	18	;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	19	;; GNU General Public License for more details.
	20
	21	;; You should have received a copy of the GNU General Public License
	22	;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
	23
	24	;;; Commentary:
	25
	26	;;; Requirements:
	27
	28	;; octave
	29	;; octave-mode.el and octave-inf.el come with GNU emacs
	30
	31	;;; Code:
	32	(require 'ob)
	33	(require 'ob-ref)
	34	(require 'ob-comint)
	35	(require 'ob-eval)
	36	(eval-when-compile (require 'cl))
	37
	38	(declare-function matlab-shell "ext:matlab-mode")
	39	(declare-function matlab-shell-run-region "ext:matlab-mode")
	40
	41	(defvar org-babel-default-header-args:matlab '())
	42	(defvar org-babel-default-header-args:octave '())
	43
	44	(defvar org-babel-matlab-shell-command "matlab -nosplash"
	45	"Shell command to run matlab as an external process.")
	46	(defvar org-babel-octave-shell-command "octave -q"
	47	"Shell command to run octave as an external process.")
	48
86fbb8ca CD	49	(defvar org-babel-matlab-with-emacs-link nil
	50	"If non-nil use matlab-shell-run-region for session evaluation.
	51	This will use EmacsLink if (matlab-with-emacs-link) evaluates
	52	to a non-nil value.")
	53
	54	(defvar org-babel-matlab-emacs-link-wrapper-method
8223b1d2	55	"%s
86fbb8ca CD	56	if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
	57	else, save -ascii %s ans
	58	end
	59	delete('%s')
	60	")
	61	(defvar org-babel-octave-wrapper-method
	62	"%s
	63	if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
afe98dfa	64	else, dlmwrite('%s', ans, '\\t')
86fbb8ca CD	65	end")
	66
	67	(defvar org-babel-octave-eoe-indicator "\'org_babel_eoe\'")
	68
	69	(defvar org-babel-octave-eoe-output "ans = org_babel_eoe")
	70
	71	(defun org-babel-execute:matlab (body params)
	72	"Execute a block of matlab code with Babel."
86fbb8ca	73	(org-babel-execute:octave body params 'matlab))
afe98dfa	74
86fbb8ca CD	75	(defun org-babel-execute:octave (body params &optional matlabp)
86fbb8ca CD	76	"Execute a block of octave code with Babel."
afe98dfa	77	(let* ((session
86fbb8ca CD	78	(funcall (intern (format "org-babel-%s-initiate-session"
86fbb8ca CD	79	(if matlabp "matlab" "octave")))
afe98dfa CD	80	(cdr (assoc :session params)) params))
	81	(vars (mapcar #'cdr (org-babel-get-header params :var)))
	82	(result-params (cdr (assoc :result-params params)))
	83	(result-type (cdr (assoc :result-type params)))
86fbb8ca	84	(out-file (cdr (assoc :file params)))
afe98dfa CD	85	(full-body
	86	(org-babel-expand-body:generic
	87	body params (org-babel-variable-assignments:octave params)))
86fbb8ca	88	(result (org-babel-octave-evaluate
e66ba1df BG	89	session
	90	(if (org-babel-octave-graphical-output-file params)
	91	(mapconcat 'identity
	92	(list
	93	"set (0, \"defaultfigurevisible\", \"off\");"
	94	full-body
	95	(format "print -dpng %s" (org-babel-octave-graphical-output-file params)))
	96	"\n")
	97	full-body)
	98	result-type matlabp)))
	99	(if (org-babel-octave-graphical-output-file params)
	100	nil
	101	(org-babel-reassemble-table
	102	result
	103	(org-babel-pick-name
	104	(cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
	105	(org-babel-pick-name
	106	(cdr (assoc :rowname-names params)) (cdr (assoc :rownames params)))))))
86fbb8ca CD	107
	108	(defun org-babel-prep-session:matlab (session params)
	109	"Prepare SESSION according to PARAMS."
86fbb8ca	110	(org-babel-prep-session:octave session params 'matlab))
afe98dfa CD	111
afe98dfa CD	112	(defun org-babel-variable-assignments:octave (params)
8223b1d2	113	"Return list of octave statements assigning the block's variables."
afe98dfa CD	114	(mapcar
afe98dfa CD	115	(lambda (pair)
3ab2c837	116	(format "%s=%s;"
afe98dfa CD	117	(car pair)
	118	(org-babel-octave-var-to-octave (cdr pair))))
	119	(mapcar #'cdr (org-babel-get-header params :var))))
	120
	121	(defalias 'org-babel-variable-assignments:matlab
	122	'org-babel-variable-assignments:octave)
	123
86fbb8ca CD	124	(defun org-babel-octave-var-to-octave (var)
	125	"Convert an emacs-lisp value into an octave variable.
	126	Converts an emacs-lisp variable into a string of octave code
	127	specifying a variable of the same value."
	128	(if (listp var)
afe98dfa CD	129	(concat "[" (mapconcat #'org-babel-octave-var-to-octave var
afe98dfa CD	130	(if (listp (car var)) "; " ",")) "]")
e66ba1df BG	131	(cond
	132	((stringp var)
	133	(format "\'%s\'" var))
	134	(t
	135	(format "%s" var)))))
86fbb8ca CD	136
	137	(defun org-babel-prep-session:octave (session params &optional matlabp)
	138	"Prepare SESSION according to the header arguments specified in PARAMS."
	139	(let* ((session (org-babel-octave-initiate-session session params matlabp))
afe98dfa	140	(var-lines (org-babel-variable-assignments:octave params)))
86fbb8ca CD	141	(org-babel-comint-in-buffer session
	142	(mapc (lambda (var)
	143	(end-of-line 1) (insert var) (comint-send-input nil t)
	144	(org-babel-comint-wait-for-output session)) var-lines))
	145	session))
	146
	147	(defun org-babel-matlab-initiate-session (&optional session params)
	148	"Create a matlab inferior process buffer.
	149	If there is not a current inferior-process-buffer in SESSION then
8223b1d2	150	create. Return the initialized session."
86fbb8ca	151	(org-babel-octave-initiate-session session params 'matlab))
afe98dfa	152
86fbb8ca CD	153	(defun org-babel-octave-initiate-session (&optional session params matlabp)
	154	"Create an octave inferior process buffer.
	155	If there is not a current inferior-process-buffer in SESSION then
8223b1d2	156	create. Return the initialized session."
afe98dfa	157	(if matlabp (require 'matlab) (require 'octave-inf))
86fbb8ca CD	158	(unless (string= session "none")
	159	(let ((session (or session
	160	(if matlabp "Inferior Matlab" "Inferior Octave"))))
	161	(if (org-babel-comint-buffer-livep session) session
	162	(save-window-excursion
	163	(if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
	164	(run-octave))
	165	(rename-buffer (if (bufferp session) (buffer-name session)
	166	(if (stringp session) session (buffer-name))))
	167	(current-buffer))))))
	168
	169	(defun org-babel-octave-evaluate
afe98dfa	170	(session body result-type &optional matlabp)
86fbb8ca CD	171	"Pass BODY to the octave process in SESSION.
	172	If RESULT-TYPE equals 'output then return the outputs of the
	173	statements in BODY, if RESULT-TYPE equals 'value then return the
	174	value of the last statement in BODY, as elisp."
	175	(if session
	176	(org-babel-octave-evaluate-session session body result-type matlabp)
	177	(org-babel-octave-evaluate-external-process body result-type matlabp)))
	178
	179	(defun org-babel-octave-evaluate-external-process (body result-type matlabp)
	180	"Evaluate BODY in an external octave process."
	181	(let ((cmd (if matlabp
	182	org-babel-matlab-shell-command
	183	org-babel-octave-shell-command)))
	184	(case result-type
	185	(output (org-babel-eval cmd body))
afe98dfa	186	(value (let ((tmp-file (org-babel-temp-file "octave-")))
86fbb8ca CD	187	(org-babel-eval
86fbb8ca CD	188	cmd
afe98dfa CD	189	(format org-babel-octave-wrapper-method body
	190	(org-babel-process-file-name tmp-file 'noquote)
	191	(org-babel-process-file-name tmp-file 'noquote)))
	192	(org-babel-octave-import-elisp-from-file tmp-file))))))
86fbb8ca CD	193
	194	(defun org-babel-octave-evaluate-session
	195	(session body result-type &optional matlabp)
	196	"Evaluate BODY in SESSION."
afe98dfa CD	197	(let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
afe98dfa CD	198	(wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
86fbb8ca CD	199	(full-body
	200	(case result-type
	201	(output
	202	(mapconcat
	203	#'org-babel-chomp
	204	(list body org-babel-octave-eoe-indicator) "\n"))
	205	(value
	206	(if (and matlabp org-babel-matlab-with-emacs-link)
	207	(concat
	208	(format org-babel-matlab-emacs-link-wrapper-method
afe98dfa CD	209	body
	210	(org-babel-process-file-name tmp-file 'noquote)
	211	(org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
86fbb8ca CD	212	(mapconcat
	213	#'org-babel-chomp
	214	(list (format org-babel-octave-wrapper-method
afe98dfa CD	215	body
	216	(org-babel-process-file-name tmp-file 'noquote)
	217	(org-babel-process-file-name tmp-file 'noquote))
86fbb8ca CD	218	org-babel-octave-eoe-indicator) "\n")))))
	219	(raw (if (and matlabp org-babel-matlab-with-emacs-link)
	220	(save-window-excursion
	221	(with-temp-buffer
	222	(insert full-body)
	223	(write-region "" 'ignored wait-file nil nil nil 'excl)
	224	(matlab-shell-run-region (point-min) (point-max))
	225	(message "Waiting for Matlab Emacs Link")
	226	(while (file-exists-p wait-file) (sit-for 0.01))
	227	"")) ;; matlab-shell-run-region doesn't seem to
8223b1d2 BG	228	;; make matlab buffer contents easily
	229	;; available, so :results output currently
	230	;; won't work
86fbb8ca CD	231	(org-babel-comint-with-output
	232	(session
	233	(if matlabp
	234	org-babel-octave-eoe-indicator
	235	org-babel-octave-eoe-output)
	236	t full-body)
	237	(insert full-body) (comint-send-input nil t)))) results)
	238	(case result-type
	239	(value
afe98dfa	240	(org-babel-octave-import-elisp-from-file tmp-file))
86fbb8ca CD	241	(output
	242	(progn
	243	(setq results
	244	(if matlabp
	245	(cdr (reverse (delq "" (mapcar
	246	#'org-babel-octave-read-string
	247	(mapcar #'org-babel-trim raw)))))
	248	(cdr (member org-babel-octave-eoe-output
	249	(reverse (mapcar
	250	#'org-babel-octave-read-string
	251	(mapcar #'org-babel-trim raw)))))))
	252	(mapconcat #'identity (reverse results) "\n"))))))
	253
	254	(defun org-babel-octave-import-elisp-from-file (file-name)
	255	"Import data from FILE-NAME.
	256	This removes initial blank and comment lines and then calls
	257	`org-babel-import-elisp-from-file'."
afe98dfa	258	(let ((temp-file (org-babel-temp-file "octave-matlab-")) beg end)
86fbb8ca CD	259	(with-temp-file temp-file
	260	(insert-file-contents file-name)
	261	(re-search-forward "^[ \t]*[^# \t]" nil t)
	262	(if (< (setq beg (point-min))
	263	(setq end (point-at-bol)))
	264	(delete-region beg end)))
afe98dfa	265	(org-babel-import-elisp-from-file temp-file '(16))))
86fbb8ca CD	266
86fbb8ca CD	267	(defun org-babel-octave-read-string (string)
8223b1d2	268	"Strip \\\"s from around octave string."
86fbb8ca CD	269	(if (string-match "^\"\\([^\000]+\\)\"$" string)
	270	(match-string 1 string)
	271	string))
	272
e66ba1df BG	273	(defun org-babel-octave-graphical-output-file (params)
	274	"Name of file to which maxima should send graphical output."
	275	(and (member "graphics" (cdr (assq :result-params params)))
	276	(cdr (assq :file params))))
	277
86fbb8ca CD	278	(provide 'ob-octave)
86fbb8ca CD	279
5b409b39	280
86fbb8ca CD	281
86fbb8ca CD	282	;;; ob-octave.el ends here