lisp/org/ob-octave.el

   1 ;;; ob-octave.el --- org-babel functions for octave and matlab evaluation
   2
   3 ;; Copyright (C) 2010  Free Software Foundation, Inc.
   4
   5 ;; Author: Dan Davison
   6 ;; Keywords: literate programming, reproducible research
   7 ;; Homepage: http://orgmode.org
   8 ;; Version: 7.01
   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
  50 (defun org-babel-expand-body:matlab (body params &optional processed-params)
  51   "Expand BODY according to PARAMS, return the expanded body."
  52   (org-babel-expand-body:octave body params processed-params))
  53 (defun org-babel-expand-body:octave (body params &optional processed-params)
  54   "Expand BODY according to PARAMS, return the expanded body."
  55   (let ((vars (nth 1 (or processed-params (org-babel-process-params params)))))
  56     (concat
  57      (mapconcat
  58       (lambda (pair)
  59         (format "%s=%s"
  60                 (car pair)
  61                 (org-babel-octave-var-to-octave (cdr pair))))
  62       vars "\n") "\n" body "\n")))
  63
  64 (defvar org-babel-matlab-with-emacs-link nil
  65   "If non-nil use matlab-shell-run-region for session evaluation.
  66   This will use EmacsLink if (matlab-with-emacs-link) evaluates
  67   to a non-nil value.")
  68
  69 (defvar org-babel-matlab-emacs-link-wrapper-method
  70    "%s
  71 if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
  72 else, save -ascii %s ans
  73 end
  74 delete('%s')
  75 ")
  76 (defvar org-babel-octave-wrapper-method
  77   "%s
  78 if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
  79 else, save -ascii %s ans
  80 end")
  81
  82 (defvar org-babel-octave-eoe-indicator "\'org_babel_eoe\'")
  83
  84 (defvar org-babel-octave-eoe-output "ans = org_babel_eoe")
  85
  86 (defun org-babel-execute:matlab (body params)
  87   "Execute a block of matlab code with Babel."
  88   (require 'matlab)
  89   (org-babel-execute:octave body params 'matlab))
  90 (defun org-babel-execute:octave (body params &optional matlabp)
  91   "Execute a block of octave code with Babel."
  92   (let* ((processed-params (org-babel-process-params params))
  93          (session
  94           (funcall (intern (format "org-babel-%s-initiate-session"
  95                                    (if matlabp "matlab" "octave")))
  96                    (nth 0 processed-params) params))
  97          (vars (nth 1 processed-params))
  98          (result-params (nth 2 processed-params))
  99          (result-type (nth 3 processed-params))
 100          (out-file (cdr (assoc :file params)))
 101          (augmented-body
 102           (org-babel-expand-body:octave body params processed-params))
 103          (result (org-babel-octave-evaluate
 104                   session augmented-body result-type matlabp)))
 105     (or out-file
 106         (org-babel-reassemble-table
 107          result
 108          (org-babel-pick-name
 109           (nth 4 processed-params) (cdr (assoc :colnames params)))
 110          (org-babel-pick-name
 111           (nth 5 processed-params) (cdr (assoc :rownames params)))))))
 112
 113 (defun org-babel-prep-session:matlab (session params)
 114   "Prepare SESSION according to PARAMS."
 115   (require 'matlab)
 116   (org-babel-prep-session:octave session params 'matlab))
 117 (defun org-babel-octave-var-to-octave (var)
 118   "Convert an emacs-lisp value into an octave variable.
 119 Converts an emacs-lisp variable into a string of octave code
 120 specifying a variable of the same value."
 121   (if (listp var)
 122       (concat "[" (mapconcat #'org-babel-octave-var-to-octave var ", ") "]")
 123     (format "%S" var)))
 124
 125 (defun org-babel-prep-session:octave (session params &optional matlabp)
 126   "Prepare SESSION according to the header arguments specified in PARAMS."
 127   (let* ((session (org-babel-octave-initiate-session session params matlabp))
 128          (vars (org-babel-ref-variables params))
 129          (var-lines (mapcar
 130                      (lambda (pair)
 131                        (format "%s=%s"
 132                                (car pair)
 133                                (org-babel-octave-var-to-octave (cdr pair))))
 134                      vars)))
 135     (org-babel-comint-in-buffer session
 136       (mapc (lambda (var)
 137               (end-of-line 1) (insert var) (comint-send-input nil t)
 138               (org-babel-comint-wait-for-output session)) var-lines))
 139     session))
 140
 141 (defun org-babel-matlab-initiate-session (&optional session params)
 142   "Create a matlab inferior process buffer.
 143 If there is not a current inferior-process-buffer in SESSION then
 144 create. Return the initialized session."
 145   (require 'matlab)
 146   (org-babel-octave-initiate-session session params 'matlab))
 147 (defun org-babel-octave-initiate-session (&optional session params matlabp)
 148   "Create an octave inferior process buffer.
 149 If there is not a current inferior-process-buffer in SESSION then
 150 create. Return the initialized session."
 151   (require 'octave-inf)
 152   (unless (string= session "none")
 153     (let ((session (or session
 154                        (if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
 155       (if (org-babel-comint-buffer-livep session) session
 156         (save-window-excursion
 157           (if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
 158             (run-octave))
 159           (rename-buffer (if (bufferp session) (buffer-name session)
 160                            (if (stringp session) session (buffer-name))))
 161           (current-buffer))))))
 162
 163 (defun org-babel-octave-evaluate
 164   (session body result-type lang &optional matlabp)
 165   "Pass BODY to the octave process in SESSION.
 166 If RESULT-TYPE equals 'output then return the outputs of the
 167 statements in BODY, if RESULT-TYPE equals 'value then return the
 168 value of the last statement in BODY, as elisp."
 169   (if session
 170       (org-babel-octave-evaluate-session session body result-type matlabp)
 171     (org-babel-octave-evaluate-external-process body result-type matlabp)))
 172
 173 (defun org-babel-octave-evaluate-external-process (body result-type matlabp)
 174   "Evaluate BODY in an external octave process."
 175   (let ((cmd (if matlabp
 176                  org-babel-matlab-shell-command
 177                org-babel-octave-shell-command)))
 178     (case result-type
 179       (output (org-babel-eval cmd body))
 180       (value (let ((tmp-file (make-temp-file "org-babel-results-")))
 181                (org-babel-eval
 182                 cmd
 183                 (format org-babel-octave-wrapper-method body tmp-file tmp-file))
 184                (org-babel-eval-read-file tmp-file))))))
 185
 186 (defun org-babel-octave-evaluate-session
 187   (session body result-type &optional matlabp)
 188   "Evaluate BODY in SESSION."
 189   (let* ((tmp-file (make-temp-file "org-babel-results-"))
 190          (wait-file (make-temp-file "org-babel-matlab-emacs-link-wait-signal-"))
 191          (full-body
 192           (case result-type
 193             (output
 194              (mapconcat
 195               #'org-babel-chomp
 196               (list body org-babel-octave-eoe-indicator) "\n"))
 197             (value
 198              (if (and matlabp org-babel-matlab-with-emacs-link)
 199                  (concat
 200                   (format org-babel-matlab-emacs-link-wrapper-method
 201                           body tmp-file tmp-file wait-file) "\n")
 202                (mapconcat
 203                 #'org-babel-chomp
 204                 (list (format org-babel-octave-wrapper-method
 205                               body tmp-file tmp-file)
 206                       org-babel-octave-eoe-indicator) "\n")))))
 207          (raw (if (and matlabp org-babel-matlab-with-emacs-link)
 208                   (save-window-excursion
 209                     (with-temp-buffer
 210                       (insert full-body)
 211                       (write-region "" 'ignored wait-file nil nil nil 'excl)
 212                       (matlab-shell-run-region (point-min) (point-max))
 213                       (message "Waiting for Matlab Emacs Link")
 214                       (while (file-exists-p wait-file) (sit-for 0.01))
 215                       "")) ;; matlab-shell-run-region doesn't seem to
 216                            ;; make *matlab* buffer contents easily
 217                            ;; available, so :results output currently
 218                            ;; won't work
 219                 (org-babel-comint-with-output
 220                     (session
 221                      (if matlabp
 222                          org-babel-octave-eoe-indicator
 223                        org-babel-octave-eoe-output)
 224                      t full-body)
 225                   (insert full-body) (comint-send-input nil t)))) results)
 226     (case result-type
 227       (value
 228        (org-babel-octave-import-elisp-from-file
 229         (org-babel-maybe-remote-file tmp-file)))
 230       (output
 231        (progn
 232          (setq results
 233                (if matlabp
 234                    (cdr (reverse (delq "" (mapcar
 235                                            #'org-babel-octave-read-string
 236                                            (mapcar #'org-babel-trim raw)))))
 237                  (cdr (member org-babel-octave-eoe-output
 238                               (reverse (mapcar
 239                                         #'org-babel-octave-read-string
 240                                         (mapcar #'org-babel-trim raw)))))))
 241          (mapconcat #'identity (reverse results) "\n"))))))
 242
 243 (defun org-babel-octave-import-elisp-from-file (file-name)
 244   "Import data from FILE-NAME.
 245 This removes initial blank and comment lines and then calls
 246 `org-babel-import-elisp-from-file'."
 247   (let ((temp-file (make-temp-file "org-babel-results-")) beg end)
 248     (with-temp-file temp-file
 249       (insert-file-contents file-name)
 250       (re-search-forward "^[ \t]*[^# \t]" nil t)
 251       (if (< (setq beg (point-min))
 252              (setq end (point-at-bol)))
 253           (delete-region beg end)))
 254     (org-babel-import-elisp-from-file temp-file)))
 255
 256 (defun org-babel-octave-read-string (string)
 257   "Strip \\\"s from around octave string"
 258   (if (string-match "^\"\\([^\000]+\\)\"$" string)
 259       (match-string 1 string)
 260     string))
 261
 262 (provide 'ob-octave)
 263
 264 ;; arch-tag: d8e5f68b-ba13-440a-a495-b653e989e704
 265
 266 ;;; ob-octave.el ends here