;;; ob-octave.el --- org-babel functions for octave and matlab evaluation ;; Copyright (C) 2010-2013 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 . ;;; Commentary: ;;; Requirements: ;; octave ;; octave-mode.el and octave-inf.el come with GNU emacs ;;; Code: (require 'ob) (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