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

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

;; Copyright (C) 2010-2011  Free Software Foundation, Inc.

;; Author: Dan Davison
;; Keywords: literate programming, reproducible research
;; Homepage: http://orgmode.org
;; Version: 7.4

;; 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 full-body result-type matlabp)))
    (or out-file
        (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)) "; " ",")) "]")
    (format "%s" (or var "nil"))))

(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))

(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
73b0cd50	3	;; Copyright (C) 2010-2011 Free Software Foundation, Inc.
86fbb8ca CD	4
	5	;; Author: Dan Davison
	6	;; Keywords: literate programming, reproducible research
	7	;; Homepage: http://orgmode.org
acedf35c	8	;; Version: 7.4
86fbb8ca CD	9
	10	;; This file is part of GNU Emacs.
	11
	12	;; GNU Emacs is free software: you can redistribute it and/or modify
	13	;; it under the terms of the GNU General Public License as published by
	14	;; the Free Software Foundation, either version 3 of the License, or
	15	;; (at your option) any later version.
	16
	17	;; GNU Emacs is distributed in the hope that it will be useful,
	18	;; but WITHOUT ANY WARRANTY; without even the implied warranty of
	19	;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	20	;; GNU General Public License for more details.
	21
	22	;; You should have received a copy of the GNU General Public License
	23	;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
	24
	25	;;; Commentary:
	26
	27	;;; Requirements:
	28
	29	;; octave
	30	;; octave-mode.el and octave-inf.el come with GNU emacs
	31
	32	;;; Code:
	33	(require 'ob)
	34	(require 'ob-ref)
	35	(require 'ob-comint)
	36	(require 'ob-eval)
	37	(eval-when-compile (require 'cl))
	38
	39	(declare-function matlab-shell "ext:matlab-mode")
	40	(declare-function matlab-shell-run-region "ext:matlab-mode")
	41
	42	(defvar org-babel-default-header-args:matlab '())
	43	(defvar org-babel-default-header-args:octave '())
	44
	45	(defvar org-babel-matlab-shell-command "matlab -nosplash"
	46	"Shell command to run matlab as an external process.")
	47	(defvar org-babel-octave-shell-command "octave -q"
	48	"Shell command to run octave as an external process.")
	49
86fbb8ca CD	50	(defvar org-babel-matlab-with-emacs-link nil
	51	"If non-nil use matlab-shell-run-region for session evaluation.
	52	This will use EmacsLink if (matlab-with-emacs-link) evaluates
	53	to a non-nil value.")
	54
	55	(defvar org-babel-matlab-emacs-link-wrapper-method
	56	"%s
	57	if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
	58	else, save -ascii %s ans
	59	end
	60	delete('%s')
	61	")
	62	(defvar org-babel-octave-wrapper-method
	63	"%s
	64	if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
afe98dfa	65	else, dlmwrite('%s', ans, '\\t')
86fbb8ca CD	66	end")
	67
	68	(defvar org-babel-octave-eoe-indicator "\'org_babel_eoe\'")
	69
	70	(defvar org-babel-octave-eoe-output "ans = org_babel_eoe")
	71
	72	(defun org-babel-execute:matlab (body params)
	73	"Execute a block of matlab code with Babel."
86fbb8ca	74	(org-babel-execute:octave body params 'matlab))
afe98dfa	75
86fbb8ca CD	76	(defun org-babel-execute:octave (body params &optional matlabp)
86fbb8ca CD	77	"Execute a block of octave code with Babel."
afe98dfa	78	(let* ((session
86fbb8ca CD	79	(funcall (intern (format "org-babel-%s-initiate-session"
86fbb8ca CD	80	(if matlabp "matlab" "octave")))
afe98dfa CD	81	(cdr (assoc :session params)) params))
	82	(vars (mapcar #'cdr (org-babel-get-header params :var)))
	83	(result-params (cdr (assoc :result-params params)))
	84	(result-type (cdr (assoc :result-type params)))
86fbb8ca	85	(out-file (cdr (assoc :file params)))
afe98dfa CD	86	(full-body
	87	(org-babel-expand-body:generic
	88	body params (org-babel-variable-assignments:octave params)))
86fbb8ca	89	(result (org-babel-octave-evaluate
afe98dfa	90	session full-body result-type matlabp)))
86fbb8ca CD	91	(or out-file
	92	(org-babel-reassemble-table
	93	result
	94	(org-babel-pick-name
afe98dfa	95	(cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
86fbb8ca	96	(org-babel-pick-name
afe98dfa	97	(cdr (assoc :rowname-names params)) (cdr (assoc :rownames params)))))))
86fbb8ca CD	98
	99	(defun org-babel-prep-session:matlab (session params)
	100	"Prepare SESSION according to PARAMS."
86fbb8ca	101	(org-babel-prep-session:octave session params 'matlab))
afe98dfa CD	102
	103	(defun org-babel-variable-assignments:octave (params)
	104	"Return list of octave statements assigning the block's variables"
	105	(mapcar
	106	(lambda (pair)
	107	(format "%s=%s"
	108	(car pair)
	109	(org-babel-octave-var-to-octave (cdr pair))))
	110	(mapcar #'cdr (org-babel-get-header params :var))))
	111
	112	(defalias 'org-babel-variable-assignments:matlab
	113	'org-babel-variable-assignments:octave)
	114
86fbb8ca CD	115	(defun org-babel-octave-var-to-octave (var)
	116	"Convert an emacs-lisp value into an octave variable.
	117	Converts an emacs-lisp variable into a string of octave code
	118	specifying a variable of the same value."
	119	(if (listp var)
afe98dfa CD	120	(concat "[" (mapconcat #'org-babel-octave-var-to-octave var
	121	(if (listp (car var)) "; " ",")) "]")
	122	(format "%s" (or var "nil"))))
86fbb8ca CD	123
	124	(defun org-babel-prep-session:octave (session params &optional matlabp)
	125	"Prepare SESSION according to the header arguments specified in PARAMS."
	126	(let* ((session (org-babel-octave-initiate-session session params matlabp))
afe98dfa	127	(var-lines (org-babel-variable-assignments:octave params)))
86fbb8ca CD	128	(org-babel-comint-in-buffer session
	129	(mapc (lambda (var)
	130	(end-of-line 1) (insert var) (comint-send-input nil t)
	131	(org-babel-comint-wait-for-output session)) var-lines))
	132	session))
	133
	134	(defun org-babel-matlab-initiate-session (&optional session params)
	135	"Create a matlab inferior process buffer.
	136	If there is not a current inferior-process-buffer in SESSION then
	137	create. Return the initialized session."
86fbb8ca	138	(org-babel-octave-initiate-session session params 'matlab))
afe98dfa	139
86fbb8ca CD	140	(defun org-babel-octave-initiate-session (&optional session params matlabp)
	141	"Create an octave inferior process buffer.
	142	If there is not a current inferior-process-buffer in SESSION then
	143	create. Return the initialized session."
afe98dfa	144	(if matlabp (require 'matlab) (require 'octave-inf))
86fbb8ca CD	145	(unless (string= session "none")
	146	(let ((session (or session
	147	(if matlabp "Inferior Matlab" "Inferior Octave"))))
	148	(if (org-babel-comint-buffer-livep session) session
	149	(save-window-excursion
	150	(if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
	151	(run-octave))
	152	(rename-buffer (if (bufferp session) (buffer-name session)
	153	(if (stringp session) session (buffer-name))))
	154	(current-buffer))))))
	155
	156	(defun org-babel-octave-evaluate
afe98dfa	157	(session body result-type &optional matlabp)
86fbb8ca CD	158	"Pass BODY to the octave process in SESSION.
	159	If RESULT-TYPE equals 'output then return the outputs of the
	160	statements in BODY, if RESULT-TYPE equals 'value then return the
	161	value of the last statement in BODY, as elisp."
	162	(if session
	163	(org-babel-octave-evaluate-session session body result-type matlabp)
	164	(org-babel-octave-evaluate-external-process body result-type matlabp)))
	165
	166	(defun org-babel-octave-evaluate-external-process (body result-type matlabp)
	167	"Evaluate BODY in an external octave process."
	168	(let ((cmd (if matlabp
	169	org-babel-matlab-shell-command
	170	org-babel-octave-shell-command)))
	171	(case result-type
	172	(output (org-babel-eval cmd body))
afe98dfa	173	(value (let ((tmp-file (org-babel-temp-file "octave-")))
86fbb8ca CD	174	(org-babel-eval
86fbb8ca CD	175	cmd
afe98dfa CD	176	(format org-babel-octave-wrapper-method body
	177	(org-babel-process-file-name tmp-file 'noquote)
	178	(org-babel-process-file-name tmp-file 'noquote)))
	179	(org-babel-octave-import-elisp-from-file tmp-file))))))
86fbb8ca CD	180
	181	(defun org-babel-octave-evaluate-session
	182	(session body result-type &optional matlabp)
	183	"Evaluate BODY in SESSION."
afe98dfa CD	184	(let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
afe98dfa CD	185	(wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
86fbb8ca CD	186	(full-body
	187	(case result-type
	188	(output
	189	(mapconcat
	190	#'org-babel-chomp
	191	(list body org-babel-octave-eoe-indicator) "\n"))
	192	(value
	193	(if (and matlabp org-babel-matlab-with-emacs-link)
	194	(concat
	195	(format org-babel-matlab-emacs-link-wrapper-method
afe98dfa CD	196	body
	197	(org-babel-process-file-name tmp-file 'noquote)
	198	(org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
86fbb8ca CD	199	(mapconcat
	200	#'org-babel-chomp
	201	(list (format org-babel-octave-wrapper-method
afe98dfa CD	202	body
	203	(org-babel-process-file-name tmp-file 'noquote)
	204	(org-babel-process-file-name tmp-file 'noquote))
86fbb8ca CD	205	org-babel-octave-eoe-indicator) "\n")))))
	206	(raw (if (and matlabp org-babel-matlab-with-emacs-link)
	207	(save-window-excursion
	208	(with-temp-buffer
	209	(insert full-body)
	210	(write-region "" 'ignored wait-file nil nil nil 'excl)
	211	(matlab-shell-run-region (point-min) (point-max))
	212	(message "Waiting for Matlab Emacs Link")
	213	(while (file-exists-p wait-file) (sit-for 0.01))
	214	"")) ;; matlab-shell-run-region doesn't seem to
	215	;; make matlab buffer contents easily
	216	;; available, so :results output currently
	217	;; won't work
	218	(org-babel-comint-with-output
	219	(session
	220	(if matlabp
	221	org-babel-octave-eoe-indicator
	222	org-babel-octave-eoe-output)
	223	t full-body)
	224	(insert full-body) (comint-send-input nil t)))) results)
	225	(case result-type
	226	(value
afe98dfa	227	(org-babel-octave-import-elisp-from-file tmp-file))
86fbb8ca CD	228	(output
	229	(progn
	230	(setq results
	231	(if matlabp
	232	(cdr (reverse (delq "" (mapcar
	233	#'org-babel-octave-read-string
	234	(mapcar #'org-babel-trim raw)))))
	235	(cdr (member org-babel-octave-eoe-output
	236	(reverse (mapcar
	237	#'org-babel-octave-read-string
	238	(mapcar #'org-babel-trim raw)))))))
	239	(mapconcat #'identity (reverse results) "\n"))))))
	240
	241	(defun org-babel-octave-import-elisp-from-file (file-name)
	242	"Import data from FILE-NAME.
	243	This removes initial blank and comment lines and then calls
	244	`org-babel-import-elisp-from-file'."
afe98dfa	245	(let ((temp-file (org-babel-temp-file "octave-matlab-")) beg end)
86fbb8ca CD	246	(with-temp-file temp-file
	247	(insert-file-contents file-name)
	248	(re-search-forward "^[ \t]*[^# \t]" nil t)
	249	(if (< (setq beg (point-min))
	250	(setq end (point-at-bol)))
	251	(delete-region beg end)))
afe98dfa	252	(org-babel-import-elisp-from-file temp-file '(16))))
86fbb8ca CD	253
	254	(defun org-babel-octave-read-string (string)
	255	"Strip \\\"s from around octave string"
	256	(if (string-match "^\"\\([^\000]+\\)\"$" string)
	257	(match-string 1 string)
	258	string))
	259
	260	(provide 'ob-octave)
	261
86fbb8ca CD	262
86fbb8ca CD	263	;;; ob-octave.el ends here