lisp/ob-octave.el

   1 ;;; ob-octave.el --- org-babel functions for octave and matlab evaluation
   2
   3 ;; Copyright (C) 2010-2013 Free Software Foundation, Inc.
   4
   5 ;; Author: Dan Davison
   6 ;; Keywords: literate programming, reproducible research
   7 ;; Homepage: http://orgmode.org
   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 (eval-when-compile (require 'cl))
  34
  35 (declare-function matlab-shell "ext:matlab-mode")
  36 (declare-function matlab-shell-run-region "ext:matlab-mode")
  37
  38 (defvar org-babel-default-header-args:matlab '())
  39 (defvar org-babel-default-header-args:octave '())
  40
  41 (defvar org-babel-matlab-shell-command "matlab -nosplash"
  42   "Shell command to run matlab as an external process.")
  43 (defvar org-babel-octave-shell-command "octave -q"
  44   "Shell command to run octave as an external process.")
  45
  46 (defvar org-babel-matlab-with-emacs-link nil
  47   "If non-nil use matlab-shell-run-region for session evaluation.
  48   This will use EmacsLink if (matlab-with-emacs-link) evaluates
  49   to a non-nil value.")
  50
  51 (defvar org-babel-matlab-emacs-link-wrapper-method
  52   "%s
  53 if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
  54 else, save -ascii %s ans
  55 end
  56 delete('%s')
  57 ")
  58 (defvar org-babel-octave-wrapper-method
  59   "%s
  60 if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
  61 else, dlmwrite('%s', ans, '\\t')
  62 end")
  63
  64 (defvar org-babel-octave-eoe-indicator "\'org_babel_eoe\'")
  65
  66 (defvar org-babel-octave-eoe-output "ans = org_babel_eoe")
  67
  68 (defun org-babel-execute:matlab (body params)
  69   "Execute a block of matlab code with Babel."
  70   (org-babel-execute:octave body params 'matlab))
  71
  72 (defun org-babel-execute:octave (body params &optional matlabp)
  73   "Execute a block of octave code with Babel."
  74   (let* ((session
  75           (funcall (intern (format "org-babel-%s-initiate-session"
  76                                    (if matlabp "matlab" "octave")))
  77                    (cdr (assoc :session params)) params))
  78          (vars (mapcar #'cdr (org-babel-get-header params :var)))
  79          (result-params (cdr (assoc :result-params params)))
  80          (result-type (cdr (assoc :result-type params)))
  81          (out-file (cdr (assoc :file params)))
  82          (full-body
  83           (org-babel-expand-body:generic
  84            body params (org-babel-variable-assignments:octave params)))
  85          (result (org-babel-octave-evaluate
  86                   session
  87                   (if (org-babel-octave-graphical-output-file params)
  88                       (mapconcat 'identity
  89                                  (list
  90                                   "set (0, \"defaultfigurevisible\", \"off\");"
  91                                   full-body
  92                                   (format "print -dpng %s" (org-babel-octave-graphical-output-file params)))
  93                                  "\n")
  94                     full-body)
  95                   result-type matlabp)))
  96     (if (org-babel-octave-graphical-output-file params)
  97         nil
  98       (org-babel-reassemble-table
  99        result
 100        (org-babel-pick-name
 101         (cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
 102        (org-babel-pick-name
 103         (cdr (assoc :rowname-names params)) (cdr (assoc :rownames params)))))))
 104
 105 (defun org-babel-prep-session:matlab (session params)
 106   "Prepare SESSION according to PARAMS."
 107   (org-babel-prep-session:octave session params 'matlab))
 108
 109 (defun org-babel-variable-assignments:octave (params)
 110   "Return list of octave statements assigning the block's variables."
 111   (mapcar
 112    (lambda (pair)
 113      (format "%s=%s;"
 114              (car pair)
 115              (org-babel-octave-var-to-octave (cdr pair))))
 116    (mapcar #'cdr (org-babel-get-header params :var))))
 117
 118 (defalias 'org-babel-variable-assignments:matlab
 119   'org-babel-variable-assignments:octave)
 120
 121 (defun org-babel-octave-var-to-octave (var)
 122   "Convert an emacs-lisp value into an octave variable.
 123 Converts an emacs-lisp variable into a string of octave code
 124 specifying a variable of the same value."
 125   (if (listp var)
 126       (concat "[" (mapconcat #'org-babel-octave-var-to-octave var
 127                              (if (listp (car var)) "; " ",")) "]")
 128     (cond
 129      ((stringp var)
 130       (format "\'%s\'" var))
 131      (t
 132       (format "%s" var)))))
 133
 134 (defun org-babel-prep-session:octave (session params &optional matlabp)
 135   "Prepare SESSION according to the header arguments specified in PARAMS."
 136   (let* ((session (org-babel-octave-initiate-session session params matlabp))
 137          (var-lines (org-babel-variable-assignments:octave params)))
 138     (org-babel-comint-in-buffer session
 139       (mapc (lambda (var)
 140               (end-of-line 1) (insert var) (comint-send-input nil t)
 141               (org-babel-comint-wait-for-output session)) var-lines))
 142     session))
 143
 144 (defun org-babel-matlab-initiate-session (&optional session params)
 145   "Create a matlab inferior process buffer.
 146 If there is not a current inferior-process-buffer in SESSION then
 147 create.  Return the initialized session."
 148   (org-babel-octave-initiate-session session params 'matlab))
 149
 150 (defun org-babel-octave-initiate-session (&optional session params matlabp)
 151   "Create an octave inferior process buffer.
 152 If there is not a current inferior-process-buffer in SESSION then
 153 create.  Return the initialized session."
 154   (if matlabp (require 'matlab) (or (require 'octave-inf nil 'noerror)
 155                                     (require 'octave)))
 156   (unless (string= session "none")
 157     (let ((session (or session
 158                        (if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
 159       (if (org-babel-comint-buffer-livep session) session
 160         (save-window-excursion
 161           (if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
 162             (run-octave))
 163           (rename-buffer (if (bufferp session) (buffer-name session)
 164                            (if (stringp session) session (buffer-name))))
 165           (current-buffer))))))
 166
 167 (defun org-babel-octave-evaluate
 168   (session body result-type &optional matlabp)
 169   "Pass BODY to the octave process in SESSION.
 170 If RESULT-TYPE equals 'output then return the outputs of the
 171 statements in BODY, if RESULT-TYPE equals 'value then return the
 172 value of the last statement in BODY, as elisp."
 173   (if session
 174       (org-babel-octave-evaluate-session session body result-type matlabp)
 175     (org-babel-octave-evaluate-external-process body result-type matlabp)))
 176
 177 (defun org-babel-octave-evaluate-external-process (body result-type matlabp)
 178   "Evaluate BODY in an external octave process."
 179   (let ((cmd (if matlabp
 180                  org-babel-matlab-shell-command
 181                org-babel-octave-shell-command)))
 182     (case result-type
 183       (output (org-babel-eval cmd body))
 184       (value (let ((tmp-file (org-babel-temp-file "octave-")))
 185                (org-babel-eval
 186                 cmd
 187                 (format org-babel-octave-wrapper-method body
 188                         (org-babel-process-file-name tmp-file 'noquote)
 189                         (org-babel-process-file-name tmp-file 'noquote)))
 190                (org-babel-octave-import-elisp-from-file tmp-file))))))
 191
 192 (defun org-babel-octave-evaluate-session
 193   (session body result-type &optional matlabp)
 194   "Evaluate BODY in SESSION."
 195   (let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
 196          (wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
 197          (full-body
 198           (case result-type
 199             (output
 200              (mapconcat
 201               #'org-babel-chomp
 202               (list body org-babel-octave-eoe-indicator) "\n"))
 203             (value
 204              (if (and matlabp org-babel-matlab-with-emacs-link)
 205                  (concat
 206                   (format org-babel-matlab-emacs-link-wrapper-method
 207                           body
 208                           (org-babel-process-file-name tmp-file 'noquote)
 209                           (org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
 210                (mapconcat
 211                 #'org-babel-chomp
 212                 (list (format org-babel-octave-wrapper-method
 213                               body
 214                               (org-babel-process-file-name tmp-file 'noquote)
 215                               (org-babel-process-file-name tmp-file 'noquote))
 216                       org-babel-octave-eoe-indicator) "\n")))))
 217          (raw (if (and matlabp org-babel-matlab-with-emacs-link)
 218                   (save-window-excursion
 219                     (with-temp-buffer
 220                       (insert full-body)
 221                       (write-region "" 'ignored wait-file nil nil nil 'excl)
 222                       (matlab-shell-run-region (point-min) (point-max))
 223                       (message "Waiting for Matlab Emacs Link")
 224                       (while (file-exists-p wait-file) (sit-for 0.01))
 225                       "")) ;; matlab-shell-run-region doesn't seem to
 226                 ;; make *matlab* buffer contents easily
 227                 ;; available, so :results output currently
 228                 ;; won't work
 229                 (org-babel-comint-with-output
 230                     (session
 231                      (if matlabp
 232                          org-babel-octave-eoe-indicator
 233                        org-babel-octave-eoe-output)
 234                      t full-body)
 235                   (insert full-body) (comint-send-input nil t)))) results)
 236     (case result-type
 237       (value
 238        (org-babel-octave-import-elisp-from-file tmp-file))
 239       (output
 240        (progn
 241          (setq results
 242                (if matlabp
 243                    (cdr (reverse (delq "" (mapcar
 244                                            #'org-babel-octave-read-string
 245                                            (mapcar #'org-babel-trim raw)))))
 246                  (cdr (member org-babel-octave-eoe-output
 247                               (reverse (mapcar
 248                                         #'org-babel-octave-read-string
 249                                         (mapcar #'org-babel-trim raw)))))))
 250          (mapconcat #'identity (reverse results) "\n"))))))
 251
 252 (defun org-babel-octave-import-elisp-from-file (file-name)
 253   "Import data from FILE-NAME.
 254 This removes initial blank and comment lines and then calls
 255 `org-babel-import-elisp-from-file'."
 256   (let ((temp-file (org-babel-temp-file "octave-matlab-")) beg end)
 257     (with-temp-file temp-file
 258       (insert-file-contents file-name)
 259       (re-search-forward "^[ \t]*[^# \t]" nil t)
 260       (if (< (setq beg (point-min))
 261              (setq end (point-at-bol)))
 262           (delete-region beg end)))
 263     (org-babel-import-elisp-from-file temp-file '(16))))
 264
 265 (defun org-babel-octave-read-string (string)
 266   "Strip \\\"s from around octave string."
 267   (if (string-match "^\"\\([^\000]+\\)\"$" string)
 268       (match-string 1 string)
 269     string))
 270
 271 (defun org-babel-octave-graphical-output-file (params)
 272   "Name of file to which maxima should send graphical output."
 273   (and (member "graphics" (cdr (assq :result-params params)))
 274        (cdr (assq :file params))))
 275
 276 (provide 'ob-octave)
 277
 278
 279
 280 ;;; ob-octave.el ends here