From b7007223bd7c99b9d92911c66411b2143a791ce4 Mon Sep 17 00:00:00 2001 From: John Ciolfi Date: Mon, 10 Apr 2023 16:05:31 -0400 Subject: [PATCH] matlab and org mode example --- examples/matlab-and-org-mode/.gitignore | 1 + .../css/styles-from-org.css | 3331 +++++++++++++++++ examples/matlab-and-org-mode/css/styles.css | 33 + .../matlab-and-org-mode.html | 440 +++ .../matlab-and-org-mode.org | 169 + examples/matlab-and-org-mode/sinewave.png | Bin 0 -> 16705 bytes 6 files changed, 3974 insertions(+) create mode 100644 examples/matlab-and-org-mode/.gitignore create mode 100644 examples/matlab-and-org-mode/css/styles-from-org.css create mode 100644 examples/matlab-and-org-mode/css/styles.css create mode 100644 examples/matlab-and-org-mode/matlab-and-org-mode.html create mode 100644 examples/matlab-and-org-mode/matlab-and-org-mode.org create mode 100644 examples/matlab-and-org-mode/sinewave.png diff --git a/examples/matlab-and-org-mode/.gitignore b/examples/matlab-and-org-mode/.gitignore new file mode 100644 index 0000000..397b4a7 --- /dev/null +++ b/examples/matlab-and-org-mode/.gitignore @@ -0,0 +1 @@ +*.log diff --git a/examples/matlab-and-org-mode/css/styles-from-org.css b/examples/matlab-and-org-mode/css/styles-from-org.css new file mode 100644 index 0000000..c09b134 --- /dev/null +++ b/examples/matlab-and-org-mode/css/styles-from-org.css @@ -0,0 +1,3331 @@ + diff --git a/examples/matlab-and-org-mode/css/styles.css b/examples/matlab-and-org-mode/css/styles.css new file mode 100644 index 0000000..746c730 --- /dev/null +++ b/examples/matlab-and-org-mode/css/styles.css @@ -0,0 +1,33 @@ +/* + * Used by ../*.org via + * #+HTML_HEAD_EXTRA: + */ + +body { + font-size: 11pt; + text-align: left; + line-height:1.2em; +} + +h1 {font-size: 14pt;} + +.title { + padding-bottom: 7px; + margin-bottom: 20px; + border-bottom: 1px solid #222; +} + +h2 { + font-size: 12pt; + padding-bottom: 4px; + margin-top: 5px; + margin-bottom: 5px; + border-bottom: 1px solid #DDD; +} + +h3 {font-size: 11pt; color: #0000ff;} +h4 {font-size: 9pt; color: #a34d32;} + +a {text-decoration: none; color: #537d7b} +a:visited {text-decoration: none; color: #98855b} +a:hover {text-decoration: underline; color: #a34d32} diff --git a/examples/matlab-and-org-mode/matlab-and-org-mode.html b/examples/matlab-and-org-mode/matlab-and-org-mode.html new file mode 100644 index 0000000..808d35b --- /dev/null +++ b/examples/matlab-and-org-mode/matlab-and-org-mode.html @@ -0,0 +1,440 @@ + + + + + + + +‎ + + + + + + + + +
+ +
+

1 Overview

+
+

+Org-mode and matlab-mode provide a very efficient and effective system for creating scientific +documents which contain MATLAB code and/or Simulink models along with the results of these. The +results of running MATLAB code or simulating Simulink models is placed into the org-mode file by +org-mode using org babel. Org babel is org-mode's ability to execute source code within org-mode +files and optionally insert the results back in to the org-mode file. You define source code in code +blocks, e.g. +

+ +
+#+begin_src LANGUAGE <OPTIONS>
+  <CODE>
+#+end_src
+
+
+
+ +
+

2 Example

+
+

+With org-mode you can embed semantically colored code such as MATLAB within your document and +semantically edit it using "Org -> Editing -> Edit Source Example" menu or C-c '. For example, +here's a MATLAB enumeration class: +

+ +
+
classdef WeekDays
+   enumeration
+       Monday, Tuesday, Wednesday, Thursday, Friday
+   end
+end
+
+
+ +

+You can use org-mode babel to evaluate MATLAB code blocks. For example, if you type C-c C-c in the +code block, org-mode will evaluate the code in the *MATLAB* session and insert the value of ans +just below the code block. +

+ +
+
a=1+3+5+7;
+ans=a
+
+
+ +
+16
+
+ + +

+You can also use org-mode babel evaluate MATLAB code blocks to plot and insert figures back in +to this file. For example: +

+ +
+
t=[0:.1:2*pi];
+y=sin(t);
+plot(t,y);
+
+
+ + +
+

sinewave.png +

+
+
+
+
+

3 HTML Export

+
+

+You need the htmlize package to get coloring in HTML. +

+ +

+We set the "#+html_head_extra" properties above to configure CSS. We used M-x +org-html-htmlize-generate-css to create ./css/styles-from-org.css and added our customizations in +./css/styles.css. +

+
+
+ +
+

4 Setup

+
+

+The following is known to work with Emacs 27 which includes org-mode 9.3. It is also know to work +with Emacs 27 and org-mode 9.6.1. +

+ +

+To use matlab-mode with org-mode, you need to configure org-mode for matlab-mode. See README.org to +install matlab-mode. +

+ +

+We configure matlab-mode to use buffer name *MATLAB* and we alter org-mode to use this buffer by +adding the following to your ~/.emacs. +

+ +
+
;;-----------------------------------------------------------------------------------------;;
+;; org babel for matlab - make all matlab code blocks execute in the same *MATLAB* session ;;
+;;-----------------------------------------------------------------------------------------;;
+
+;; A better approach to setting org-babel-load-languages is to customize it:
+;;   M-x customize-variable RET org-babel-load-languages RET
+;; However, we are doing this here to illustrate how matlab interacts with org
+(setq org-babel-load-languages '((emacs-lisp . t)
+                                 (matlab . t)))
+
+(setq org-babel-default-header-args:matlab '((:session . "*MATLAB*")))
+
+(defun matlab-org-session-advice (orig-fun &rest args)
+  "Advice for org to reuse the *MATLAB* buffer"
+  ;; ob-octave.el leverages both org-babel-matlab-emacs-link-wrapper-method and
+  ;; org-babel-octave-wrapper-method when interacting with the *MATLAB* buffer.
+  ;; Here we fix a couple items such as adding cd default-directory:
+  (setq org-babel-matlab-emacs-link-wrapper-method
+        (concat "\
+    cd('" default-directory "');
+    %s
+    if ~exist('ans','var') ans=''; end
+    if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
+    else, save -ascii %s ans
+    end
+    delete('%s')
+    "))
+  (setq org-babel-octave-wrapper-method
+        (concat "\
+    cd('" default-directory "');
+    %s
+    if ~exist('ans','var') ans=''; end
+    if ischar(ans) || isstring(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid);
+    else, dlmwrite('%s', ans, '\\t')
+    end"))
+  (apply orig-fun args))
+
+(defun matlab-org-fixup-print (orig-fun session body result-type &optional matlabp)
+  "Fixup figure print to make it work with MATLAB"
+  ;; org 9.3 correctly does:     print -dpng figure.png
+  ;; org 9.6.1 incorrectly does: print -dpng "figure.png"
+  ;; and thus 9.6.1 creates on disk a file name containing quotes which is incorrect, so this
+  ;; advice fixes that.
+  (setq body (replace-regexp-in-string "^\\(print -dpng \\)\"\\([^\"]+\\)\"" "\\1\\2"  body t))
+  (funcall orig-fun session body result-type matlabp))
+
+(defun org-export-dispatch-no-babel-advice (orig-fun &rest args)
+  "Instruct babel to not evaluate code blocks (and hence no
+prompt) during export, e.g. conversion of org to say html."
+  (let* ((org-babel-default-header-args
+          (cons '(:eval . "never-export") org-babel-default-header-args))
+         (result (apply orig-fun args)))
+    result))
+
+(eval-after-load 'ox
+  '(progn
+     ;; Make C-c C-e `org-export-dispatch' work without prompting to evaluate code blocks
+     (advice-add 'org-export-dispatch :around #'org-export-dispatch-no-babel-advice)))
+
+;; org babel for matlab - make all matlab code blocks execute in the same *MATLAB* session
+(eval-after-load "org"
+  '(progn
+     (advice-add 'org-babel-octave-evaluate-external-process :around #'matlab-org-session-advice)
+     (advice-add 'org-babel-octave-evaluate-session :around #'matlab-org-session-advice)
+     (advice-add 'org-babel-octave-evaluate :around #'matlab-org-fixup-print)))
+
+
+ +

+To try this using "stock" emacs, place the above in org-matlab-setup.el and use: +

+ +
+emacs -q -L /path/to/matlab-mode -l /path/to/matlab-load.el -l org-matlab-setup.el
+
+
+
+
+
+

Author: John Ciolfi

+

Created: 2023-04-10 Mon 15:58

+

Validate

+
+ + diff --git a/examples/matlab-and-org-mode/matlab-and-org-mode.org b/examples/matlab-and-org-mode/matlab-and-org-mode.org new file mode 100644 index 0000000..d45fa65 --- /dev/null +++ b/examples/matlab-and-org-mode/matlab-and-org-mode.org @@ -0,0 +1,169 @@ +# // File: matlab-emacs-src/examples/matlab-and-org-mode/matlab-and-org-mode.org +# // Abstract: +# // Use this as a template for creating org-files with MATLAB and other language code blocks + +#+startup: showall +#+startup: inlineimages // C-c C-x C-v to toggle, C-c C-x C-M-v to redisplay +#+startup: latexpreview // C-c C-x C-l to toggle + +#+html_head_extra: +#+html_head_extra: +#+options: ^:{} +#+options: toc:nil +#+latex_header: \usepackage[margin=0.5in]{geometry} +#+latex_header: \usepackage{parskip} +#+latex_header: \usepackage{tocloft} +#+latex_header: \advance\cftsecnumwidth 0.5em\relax +#+latex_header: \advance\cftsubsecindent 0.5em\relax +#+latex_header: \advance\cftsubsecnumwidth 0.5em\relax + +* Overview + +[[https://orgmode.org/][Org-mode]] and [[https://sourceforge.net/projects/matlab-emacs/][matlab-mode]] provide an efficient and effective system for creating scientific documents +which contain MATLAB code and/or Simulink models along with the results of these. The results of +running MATLAB code or simulating Simulink models is placed into the org-mode file by org-mode using +org babel. [[https://orgmode.org/worg/org-contrib/babel/][Org babel]] is org-mode's ability to execute source code within org-mode files and +optionally insert the results back in to the org-mode file. You define source code in code blocks, +e.g. + + : #+begin_src LANGUAGE + : + : #+end_src + +* Example + +With org-mode you can embed semantically colored code such as MATLAB within your document and +semantically edit it using "Org -> Editing -> Edit Source Example" menu or =C-c '=. For example, +here's a MATLAB [[https://www.mathworks.com/help/matlab/enumeration-classes.html][enumeration class]]: + +#+begin_src matlab + classdef WeekDays + enumeration + Monday, Tuesday, Wednesday, Thursday, Friday + end + end +#+end_src + +You can use org-mode babel to evaluate MATLAB code blocks. For example, if you type =C-c C-c= in the +following code block, org-mode will evaluate the code in the =*MATLAB*= session and insert the value +of =ans= just below the code block. + +#+begin_src matlab :exports both :results verbatim + a=1+3+5+7; + ans=a +#+end_src + +#+RESULTS: +: 16 + +You can also use org-mode babel evaluate MATLAB code blocks to plot and insert figures back in to +this file. For example: + +#+begin_src matlab :file sinewave.png :exports both :results file graphics + t=[0:.1:2*pi]; + y=sin(t); + plot(t,y); +#+end_src + +#+RESULTS: +[[file:sinewave.png]] +* Export to HTML, PDF, etc. + +You need the htmlize package to get coloring. + +For HTML export we set the "#+html_head_extra" properties above to configure CSS. We used ~M-x +org-html-htmlize-generate-css~ to create ./css/styles-from-org.css and added our customizations in +./css/styles.css. + +For PDF export we configured several "#+latex_header" properties above. + +After this setup, you can use the "Org -> Export/Publish" or ~C-c C-e~ to export to HTML, PDF, etc. + +See the example *.html in this directory. + +* Setup + +The following is known to work with Emacs 27 which includes org-mode 9.3. It is also know to work +with Emacs 27 and org-mode 9.6.1. + +To use matlab-mode with org-mode, you need to configure org-mode for matlab-mode. See [[file:../../README.org][README.org]] to +install matlab-mode. + +We configure matlab-mode to use buffer name =*MATLAB*= and we alter org-mode to use this buffer by +adding the following to your =~/.emacs=. + +#+begin_src emacs-lisp + ;;-----------------------------------------------------------------------------------------;; + ;; org babel for matlab - make all matlab code blocks execute in the same *MATLAB* session ;; + ;;-----------------------------------------------------------------------------------------;; + + ;; A better approach to setting org-babel-load-languages is to customize it: + ;; M-x customize-variable RET org-babel-load-languages RET + ;; However, we are doing this here to illustrate how matlab interacts with org + (setq org-babel-load-languages '((emacs-lisp . t) + (matlab . t))) + + (setq org-babel-default-header-args:matlab '((:session . "*MATLAB*"))) + + (defun matlab-org-session-advice (orig-fun &rest args) + "Advice for org to reuse the *MATLAB* buffer" + ;; ob-octave.el leverages both org-babel-matlab-emacs-link-wrapper-method and + ;; org-babel-octave-wrapper-method when interacting with the *MATLAB* buffer. + ;; Here we fix a couple items such as adding cd default-directory: + (setq org-babel-matlab-emacs-link-wrapper-method + (concat "\ + cd('" default-directory "'); + %s + if ~exist('ans','var') ans=''; end + if ischar(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid); + else, save -ascii %s ans + end + delete('%s') + ")) + (setq org-babel-octave-wrapper-method + (concat "\ + cd('" default-directory "'); + %s + if ~exist('ans','var') ans=''; end + if ischar(ans) || isstring(ans), fid = fopen('%s', 'w'); fprintf(fid, '%%s\\n', ans); fclose(fid); + else, dlmwrite('%s', ans, '\\t') + end")) + (apply orig-fun args)) + + (defun matlab-org-fixup-print (orig-fun session body result-type &optional matlabp) + "Fixup figure print to make it work with MATLAB" + ;; org 9.3 correctly does: print -dpng figure.png + ;; org 9.6.1 incorrectly does: print -dpng "figure.png" + ;; and thus 9.6.1 creates on disk a file name containing quotes which is incorrect, so this + ;; advice fixes that. + (setq body (replace-regexp-in-string "^\\(print -dpng \\)\"\\([^\"]+\\)\"" "\\1\\2" body t)) + (funcall orig-fun session body result-type matlabp)) + + (defun org-export-dispatch-no-babel-advice (orig-fun &rest args) + "Instruct babel to not evaluate code blocks (and hence no + prompt) during export, e.g. conversion of org to say html." + (let* ((org-babel-default-header-args + (cons '(:eval . "never-export") org-babel-default-header-args)) + (result (apply orig-fun args))) + result)) + + (eval-after-load 'ox + '(progn + ;; Make C-c C-e `org-export-dispatch' work without prompting to evaluate code blocks + (advice-add 'org-export-dispatch :around #'org-export-dispatch-no-babel-advice))) + + ;; org babel for matlab - make all matlab code blocks execute in the same *MATLAB* session + (eval-after-load "org" + '(progn + (advice-add 'org-babel-octave-evaluate-external-process :around #'matlab-org-session-advice) + (advice-add 'org-babel-octave-evaluate-session :around #'matlab-org-session-advice) + (advice-add 'org-babel-octave-evaluate :around #'matlab-org-fixup-print))) +#+end_src + +To try this using "stock" emacs, place the above in org-matlab-setup.el and use: + + : emacs -q -L /path/to/matlab-mode -l /path/to/matlab-load.el -l org-matlab-setup.el + +# LocalWords: showall inlineimages latexpreview usepackage parskip tocloft cftsecnumwidth sinewave +# LocalWords: cftsubsecindent cftsubsecnumwidth setq defun isstring fixup matlabp dpng funcall +# LocalWords: progn htmlize diff --git a/examples/matlab-and-org-mode/sinewave.png b/examples/matlab-and-org-mode/sinewave.png new file mode 100644 index 0000000000000000000000000000000000000000..f2ec6c1ae39ba61421cd0f5099e8a59a495ebda9 GIT binary patch literal 16705 zcmd^nXH-Lo5D}0Jk~2tp-@?7Od!KX9z4zA}Z)3`s^&MpIlnrWkLzmDZs*vJ zAPB8CLE|KXP&gw9c^nNnd=uzZJq-WBoFf=rKoC|&^nYXy=^x=PgxXX4m?rfw<#r|k zjv&trZTJfBscGnW%H7`6$LhQta!gfUM^$Y+HN+Y3Wi;5 za6b;cU;VtDm8X-t8&==R)eeym7g0TTUgUuI0ZFWcw4CHYxdSo=?SV=NfMx{j&dBm9@47C~^mNSQCRf(+Ysa6TovUijAcWCK^G&*SS?2~AC>Wg0NV~c> z!IAIyd(r(@q-q&)m+tL;-WP$ry`4Jp4(*<6t%qqMqO9&_-4?iX*-^T4fK%{h;O0v& znNO6 z$Nz7C=oYnY8%b>+3z~YpR8m^1Y5VTl9^+&Rm=HzAfs|cb2hS}}_wHa7-MMq;Ug6x_ z+^;t%;TpA0LGAox>6DDDtVO`Y^M)HDttBilecU$>NJ(XR(aL@P`c=;1{hgE)HU{mZ zN16QN;Ucbbw>+{(8dhZm-614?_m9=rFLrXU`J&lKN-?2$cWFezV^mrfBmxr`1^)hSoj`jjkC>H zE0z*5+>T)sV11`AtDtpwTx=VHoh8KEoON*toT+Aw%vYGL|1h|cw?Kgq84|EomWN~FwhMek 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