lisp/ob-octave.el

   1 ;;; ob-octave.el --- org-babel functions for octave and matlab evaluation
   2
   3 ;; Copyright (C) 2010-2014 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          (gfx-file (ignore-errors (org-babel-graphical-output-file params)))
  86          (result (org-babel-octave-evaluate
  87                   session
  88                   (if gfx-file
  89                       (mapconcat 'identity
  90                                  (list
  91                                   "set (0, \"defaultfigurevisible\", \"off\");"
  92                                   full-body
  93                                   (format "print -dpng %s" gfx-file))
  94                                  "\n")
  95                     full-body)
  96                   result-type matlabp)))
  97     (if gfx-file
  98         nil
  99       (org-babel-reassemble-table
 100        result
 101        (org-babel-pick-name
 102         (cdr (assoc :colname-names params)) (cdr (assoc :colnames params)))
 103        (org-babel-pick-name
 104         (cdr (assoc :rowname-names params)) (cdr (assoc :rownames params)))))))
 105
 106 (defun org-babel-prep-session:matlab (session params)
 107   "Prepare SESSION according to PARAMS."
 108   (org-babel-prep-session:octave session params 'matlab))
 109
 110 (defun org-babel-variable-assignments:octave (params)
 111   "Return list of octave statements assigning the block's variables."
 112   (mapcar
 113    (lambda (pair)
 114      (format "%s=%s;"
 115              (car pair)
 116              (org-babel-octave-var-to-octave (cdr pair))))
 117    (mapcar #'cdr (org-babel-get-header params :var))))
 118
 119 (defalias 'org-babel-variable-assignments:matlab
 120   'org-babel-variable-assignments:octave)
 121
 122 (defun org-babel-octave-var-to-octave (var)
 123   "Convert an emacs-lisp value into an octave variable.
 124 Converts an emacs-lisp variable into a string of octave code
 125 specifying a variable of the same value."
 126   (if (listp var)
 127       (concat "[" (mapconcat #'org-babel-octave-var-to-octave var
 128                              (if (listp (car var)) "; " ",")) "]")
 129     (cond
 130      ((stringp var)
 131       (format "\'%s\'" var))
 132      (t
 133       (format "%s" var)))))
 134
 135 (defun org-babel-prep-session:octave (session params &optional matlabp)
 136   "Prepare SESSION according to the header arguments specified in PARAMS."
 137   (let* ((session (org-babel-octave-initiate-session session params matlabp))
 138          (var-lines (org-babel-variable-assignments:octave params)))
 139     (org-babel-comint-in-buffer session
 140       (mapc (lambda (var)
 141               (end-of-line 1) (insert var) (comint-send-input nil t)
 142               (org-babel-comint-wait-for-output session)) var-lines))
 143     session))
 144
 145 (defun org-babel-matlab-initiate-session (&optional session params)
 146   "Create a matlab inferior process buffer.
 147 If there is not a current inferior-process-buffer in SESSION then
 148 create.  Return the initialized session."
 149   (org-babel-octave-initiate-session session params 'matlab))
 150
 151 (defun org-babel-octave-initiate-session (&optional session params matlabp)
 152   "Create an octave inferior process buffer.
 153 If there is not a current inferior-process-buffer in SESSION then
 154 create.  Return the initialized session."
 155   (if matlabp (require 'matlab) (or (require 'octave-inf nil 'noerror)
 156                                     (require 'octave)))
 157   (unless (string= session "none")
 158     (let ((session (or session
 159                        (if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
 160       (if (org-babel-comint-buffer-livep session) session
 161         (save-window-excursion
 162           (if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
 163             (run-octave))
 164           (rename-buffer (if (bufferp session) (buffer-name session)
 165                            (if (stringp session) session (buffer-name))))
 166           (current-buffer))))))
 167
 168 (defun org-babel-octave-evaluate
 169   (session body result-type &optional matlabp)
 170   "Pass BODY to the octave process in SESSION.
 171 If RESULT-TYPE equals 'output then return the outputs of the
 172 statements in BODY, if RESULT-TYPE equals 'value then return the
 173 value of the last statement in BODY, as elisp."
 174   (if session
 175       (org-babel-octave-evaluate-session session body result-type matlabp)
 176     (org-babel-octave-evaluate-external-process body result-type matlabp)))
 177
 178 (defun org-babel-octave-evaluate-external-process (body result-type matlabp)
 179   "Evaluate BODY in an external octave process."
 180   (let ((cmd (if matlabp
 181                  org-babel-matlab-shell-command
 182                org-babel-octave-shell-command)))
 183     (case result-type
 184       (output (org-babel-eval cmd body))
 185       (value (let ((tmp-file (org-babel-temp-file "octave-")))
 186                (org-babel-eval
 187                 cmd
 188                 (format org-babel-octave-wrapper-method body
 189                         (org-babel-process-file-name tmp-file 'noquote)
 190                         (org-babel-process-file-name tmp-file 'noquote)))
 191                (org-babel-octave-import-elisp-from-file tmp-file))))))
 192
 193 (defun org-babel-octave-evaluate-session
 194   (session body result-type &optional matlabp)
 195   "Evaluate BODY in SESSION."
 196   (let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
 197          (wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
 198          (full-body
 199           (case result-type
 200             (output
 201              (mapconcat
 202               #'org-babel-chomp
 203               (list body org-babel-octave-eoe-indicator) "\n"))
 204             (value
 205              (if (and matlabp org-babel-matlab-with-emacs-link)
 206                  (concat
 207                   (format org-babel-matlab-emacs-link-wrapper-method
 208                           body
 209                           (org-babel-process-file-name tmp-file 'noquote)
 210                           (org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
 211                (mapconcat
 212                 #'org-babel-chomp
 213                 (list (format org-babel-octave-wrapper-method
 214                               body
 215                               (org-babel-process-file-name tmp-file 'noquote)
 216                               (org-babel-process-file-name tmp-file 'noquote))
 217                       org-babel-octave-eoe-indicator) "\n")))))
 218          (raw (if (and matlabp org-babel-matlab-with-emacs-link)
 219                   (save-window-excursion
 220                     (with-temp-buffer
 221                       (insert full-body)
 222                       (write-region "" 'ignored wait-file nil nil nil 'excl)
 223                       (matlab-shell-run-region (point-min) (point-max))
 224                       (message "Waiting for Matlab Emacs Link")
 225                       (while (file-exists-p wait-file) (sit-for 0.01))
 226                       "")) ;; matlab-shell-run-region doesn't seem to
 227                 ;; make *matlab* buffer contents easily
 228                 ;; available, so :results output currently
 229                 ;; won't work
 230                 (org-babel-comint-with-output
 231                     (session
 232                      (if matlabp
 233                          org-babel-octave-eoe-indicator
 234                        org-babel-octave-eoe-output)
 235                      t full-body)
 236                   (insert full-body) (comint-send-input nil t)))) results)
 237     (case result-type
 238       (value
 239        (org-babel-octave-import-elisp-from-file tmp-file))
 240       (output
 241        (progn
 242          (setq results
 243                (if matlabp
 244                    (cdr (reverse (delq "" (mapcar
 245                                            #'org-babel-octave-read-string
 246                                            (mapcar #'org-babel-trim raw)))))
 247                  (cdr (member org-babel-octave-eoe-output
 248                               (reverse (mapcar
 249                                         #'org-babel-octave-read-string
 250                                         (mapcar #'org-babel-trim raw)))))))
 251          (mapconcat #'identity (reverse results) "\n"))))))
 252
 253 (defun org-babel-octave-import-elisp-from-file (file-name)
 254   "Import data from FILE-NAME.
 255 This removes initial blank and comment lines and then calls
 256 `org-babel-import-elisp-from-file'."
 257   (let ((temp-file (org-babel-temp-file "octave-matlab-")) beg end)
 258     (with-temp-file temp-file
 259       (insert-file-contents file-name)
 260       (re-search-forward "^[ \t]*[^# \t]" nil t)
 261       (if (< (setq beg (point-min))
 262              (setq end (point-at-bol)))
 263           (delete-region beg end)))
 264     (org-babel-import-elisp-from-file temp-file '(16))))
 265
 266 (defun org-babel-octave-read-string (string)
 267   "Strip \\\"s from around octave string."
 268   (if (string-match "^\"\\([^\000]+\\)\"$" string)
 269       (match-string 1 string)
 270     string))
 271
 272 (provide 'ob-octave)
 273
 274
 275
 276 ;;; ob-octave.el ends here