lisp/ob-octave.el

   1 ;;; ob-octave.el --- Babel Functions for Octave and Matlab -*- lexical-binding: t; -*-
   2
   3 ;; Copyright (C) 2010-2017 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
  34 (declare-function matlab-shell "ext:matlab-mode")
  35 (declare-function matlab-shell-run-region "ext:matlab-mode")
  36 (declare-function org-trim "org" (s &optional keep-lead))
  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 (assq :session params)) params))
  78          (result-type (cdr (assq :result-type params)))
  79          (full-body
  80           (org-babel-expand-body:generic
  81            body params (org-babel-variable-assignments:octave params)))
  82          (gfx-file (ignore-errors (org-babel-graphical-output-file params)))
  83          (result (org-babel-octave-evaluate
  84                   session
  85                   (if gfx-file
  86                       (mapconcat 'identity
  87                                  (list
  88                                   "set (0, \"defaultfigurevisible\", \"off\");"
  89                                   full-body
  90                                   (format "print -dpng %s" gfx-file))
  91                                  "\n")
  92                     full-body)
  93                   result-type matlabp)))
  94     (if gfx-file
  95         nil
  96       (org-babel-reassemble-table
  97        result
  98        (org-babel-pick-name
  99         (cdr (assq :colname-names params)) (cdr (assq :colnames params)))
 100        (org-babel-pick-name
 101         (cdr (assq :rowname-names params)) (cdr (assq :rownames params)))))))
 102
 103 (defun org-babel-prep-session:matlab (session params)
 104   "Prepare SESSION according to PARAMS."
 105   (org-babel-prep-session:octave session params 'matlab))
 106
 107 (defun org-babel-variable-assignments:octave (params)
 108   "Return list of octave statements assigning the block's variables."
 109   (mapcar
 110    (lambda (pair)
 111      (format "%s=%s;"
 112              (car pair)
 113              (org-babel-octave-var-to-octave (cdr pair))))
 114    (org-babel--get-vars params)))
 115
 116 (defalias 'org-babel-variable-assignments:matlab
 117   'org-babel-variable-assignments:octave)
 118
 119 (defun org-babel-octave-var-to-octave (var)
 120   "Convert an emacs-lisp value into an octave variable.
 121 Converts an emacs-lisp variable into a string of octave code
 122 specifying a variable of the same value."
 123   (if (listp var)
 124       (concat "[" (mapconcat #'org-babel-octave-var-to-octave var
 125                              (if (listp (car var)) "; " ",")) "]")
 126     (cond
 127      ((stringp var)
 128       (format "'%s'" var))
 129      (t
 130       (format "%s" var)))))
 131
 132 (defun org-babel-prep-session:octave (session params &optional matlabp)
 133   "Prepare SESSION according to the header arguments specified in PARAMS."
 134   (let* ((session (org-babel-octave-initiate-session session params matlabp))
 135          (var-lines (org-babel-variable-assignments:octave params)))
 136     (org-babel-comint-in-buffer session
 137       (mapc (lambda (var)
 138               (end-of-line 1) (insert var) (comint-send-input nil t)
 139               (org-babel-comint-wait-for-output session)) var-lines))
 140     session))
 141
 142 (defun org-babel-matlab-initiate-session (&optional session params)
 143   "Create a matlab inferior process buffer.
 144 If there is not a current inferior-process-buffer in SESSION then
 145 create.  Return the initialized session."
 146   (org-babel-octave-initiate-session session params 'matlab))
 147
 148 (defun org-babel-octave-initiate-session (&optional session _params matlabp)
 149   "Create an octave inferior process buffer.
 150 If there is not a current inferior-process-buffer in SESSION then
 151 create.  Return the initialized session."
 152   (if matlabp (require 'matlab) (or (require 'octave-inf nil 'noerror)
 153                                     (require 'octave)))
 154   (unless (string= session "none")
 155     (let ((session (or session
 156                        (if matlabp "*Inferior Matlab*" "*Inferior Octave*"))))
 157       (if (org-babel-comint-buffer-livep session) session
 158         (save-window-excursion
 159           (if matlabp (unless org-babel-matlab-with-emacs-link (matlab-shell))
 160             (run-octave))
 161           (rename-buffer (if (bufferp session) (buffer-name session)
 162                            (if (stringp session) session (buffer-name))))
 163           (current-buffer))))))
 164
 165 (defun org-babel-octave-evaluate
 166   (session body result-type &optional matlabp)
 167   "Pass BODY to the octave process in SESSION.
 168 If RESULT-TYPE equals `output' then return the outputs of the
 169 statements in BODY, if RESULT-TYPE equals `value' then return the
 170 value of the last statement in BODY, as elisp."
 171   (if session
 172       (org-babel-octave-evaluate-session session body result-type matlabp)
 173     (org-babel-octave-evaluate-external-process body result-type matlabp)))
 174
 175 (defun org-babel-octave-evaluate-external-process (body result-type matlabp)
 176   "Evaluate BODY in an external octave process."
 177   (let ((cmd (if matlabp
 178                  org-babel-matlab-shell-command
 179                org-babel-octave-shell-command)))
 180     (pcase result-type
 181       (`output (org-babel-eval cmd body))
 182       (`value (let ((tmp-file (org-babel-temp-file "octave-")))
 183                (org-babel-eval
 184                 cmd
 185                 (format org-babel-octave-wrapper-method body
 186                         (org-babel-process-file-name tmp-file 'noquote)
 187                         (org-babel-process-file-name tmp-file 'noquote)))
 188                (org-babel-octave-import-elisp-from-file tmp-file))))))
 189
 190 (defun org-babel-octave-evaluate-session
 191     (session body result-type &optional matlabp)
 192   "Evaluate BODY in SESSION."
 193   (let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
 194          (wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
 195          (full-body
 196           (pcase result-type
 197             (`output
 198              (mapconcat
 199               #'org-babel-chomp
 200               (list body org-babel-octave-eoe-indicator) "\n"))
 201             (`value
 202              (if (and matlabp org-babel-matlab-with-emacs-link)
 203                  (concat
 204                   (format org-babel-matlab-emacs-link-wrapper-method
 205                           body
 206                           (org-babel-process-file-name tmp-file 'noquote)
 207                           (org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
 208                (mapconcat
 209                 #'org-babel-chomp
 210                 (list (format org-babel-octave-wrapper-method
 211                               body
 212                               (org-babel-process-file-name tmp-file 'noquote)
 213                               (org-babel-process-file-name tmp-file 'noquote))
 214                       org-babel-octave-eoe-indicator) "\n")))))
 215          (raw (if (and matlabp org-babel-matlab-with-emacs-link)
 216                   (save-window-excursion
 217                     (with-temp-buffer
 218                       (insert full-body)
 219                       (write-region "" 'ignored wait-file nil nil nil 'excl)
 220                       (matlab-shell-run-region (point-min) (point-max))
 221                       (message "Waiting for Matlab Emacs Link")
 222                       (while (file-exists-p wait-file) (sit-for 0.01))
 223                       "")) ;; matlab-shell-run-region doesn't seem to
 224                 ;; make *matlab* buffer contents easily
 225                 ;; available, so :results output currently
 226                 ;; won't work
 227                 (org-babel-comint-with-output
 228                     (session
 229                      (if matlabp
 230                          org-babel-octave-eoe-indicator
 231                        org-babel-octave-eoe-output)
 232                      t full-body)
 233                   (insert full-body) (comint-send-input nil t)))) results)
 234     (pcase result-type
 235       (`value
 236        (org-babel-octave-import-elisp-from-file tmp-file))
 237       (`output
 238        (setq results
 239              (if matlabp
 240                  (cdr (reverse (delq "" (mapcar
 241                                          #'org-babel-strip-quotes
 242                                          (mapcar #'org-trim raw)))))
 243                (cdr (member org-babel-octave-eoe-output
 244                             (reverse (mapcar
 245                                       #'org-babel-strip-quotes
 246                                       (mapcar #'org-trim raw)))))))
 247        (mapconcat #'identity (reverse results) "\n")))))
 248
 249 (defun org-babel-octave-import-elisp-from-file (file-name)
 250   "Import data from FILE-NAME.
 251 This removes initial blank and comment lines and then calls
 252 `org-babel-import-elisp-from-file'."
 253   (let ((temp-file (org-babel-temp-file "octave-matlab-")) beg end)
 254     (with-temp-file temp-file
 255       (insert-file-contents file-name)
 256       (re-search-forward "^[ \t]*[^# \t]" nil t)
 257       (if (< (setq beg (point-min))
 258              (setq end (point-at-bol)))
 259           (delete-region beg end)))
 260     (org-babel-import-elisp-from-file temp-file '(16))))
 261
 262 (provide 'ob-octave)
 263
 264
 265
 266 ;;; ob-octave.el ends here