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|
;;; 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
|
