From dec76e93d475b85e4de9bcea2badf7e0acc88de2 Mon Sep 17 00:00:00 2001
From: "Jeroen F.J. Laros" <jlaros@fixedpoint.nl>
Date: Sat, 28 Nov 2015 21:43:07 +0100
Subject: [PATCH] Cleaning up.

---
 beamerthemelumc.sty | 246 +++++++++++---------------------------------
 presentation.tex    |  43 ++++----
 2 files changed, 80 insertions(+), 209 deletions(-)

diff --git a/beamerthemelumc.sty b/beamerthemelumc.sty
index be627e0..117e01d 100644
--- a/beamerthemelumc.sty
+++ b/beamerthemelumc.sty
@@ -11,41 +11,24 @@
 
 \mode<presentation>
 
-\newlength{\LUMCCell}
-\setlength{\LUMCCell}{1.17cm}
-
-% For the header.
-\usepackage{tikz}
-\usetikzlibrary{patterns}
-
-% For the footer.
-\usepackage{tabularx}
+\usepackage{bibentry}
+\usepackage{caption}
+\usepackage{cleveref}
 \usepackage{colortbl}
-
-% Always nice to have.
-\usepackage{multirow}
-\usepackage{multicol}
+\usepackage{eurosym}
+\usepackage{gastex}
 \usepackage{ifthen}
+\usepackage{listings}
+\usepackage{multicol}
+\usepackage{multirow}
+\usepackage{pgfpages}
+\usepackage{tabularx}
+\usepackage{tikz}
 \usepackage{url}
 
-% Some defaults for using a bibliography.
-\usepackage{bibentry}
-\setbeamertemplate{bibliography item}[triangle]
-\bibliographystyle{plain}
-
-%% Select a nicer font.
-%\usepackage{newcent}
-%\renewcommand{\sfdefault}{pnc}
-\usepackage{eurosym}
 
-% Package for making graphs and automata.
-\usepackage{gastex}
-% Spaces around `=' break functionality.
-%\gasset{linecolor=white, linewidth=0.5, AHLength=3}
-\gasset{linewidth=0.5, AHLength=3}
-
-% Custom colours (use the gimp colour picker and divide by 255).
-\definecolor{LUMCBlue}{rgb}{0, 0.11372, 0.38039}
+\newlength{\LUMCCell}
+\setlength{\LUMCCell}{1.17cm}
 
 % Custom colours.
 % https://www.lumc.nl/over-het-lumc/leveranciers/huisstijl/kleuren/
@@ -56,23 +39,25 @@
 \definecolor{LUMCRood}{HTML}{E3004F}
 \definecolor{LUMCBruin}{HTML}{C0965C}
 
-\definecolor{ULBlue}{rgb}{0.06274, 0.07843, 0.38823}
+% TikZ settings.
+\usetikzlibrary{patterns}
+
+% Some defaults for using a bibliography.
+\setbeamertemplate{bibliography item}[triangle]
+\bibliographystyle{plain}
+
+% GasTeX settings.
+\gasset{linewidth=0.5, AHLength=3}
 
 % Disable the navigation bar.
 \usenavigationsymbolstemplate{}
 
-% Set default colours.
-%\alt<handout>{}{
-%  \setbeamercolor{structure}{fg=white}
-%  \setbeamercolor{normal text}{fg=white}
-%  \setbeamercolor{frametitle}{fg=white}
-%}
-
 % Change the bullets in the itemize environment.
 \setbeamertemplate{itemize items}[circle]
 \setbeamercolor{itemize item}{fg=black}
 \newcommand{\fakeitem}{\,\ \ \ $\bullet$\ \,}
 
+% Captions also in black.
 \setbeamercolor{caption name}{fg=black}
 
 % Macros for bold text.
@@ -83,35 +68,18 @@
 \newcommand{\permfoot}[1]{\onslide<1->\bs{#1}}
 
 % Macro for highlighting.
-%\alt<handout>{
-  \newcommand{\hlColour}{\color{LUMCRood}}
-  \newcommand{\defaultColour}{\color{black}}
-%}{
-%  \newcommand{\hlColour}{\color{yellow}}
-%  \newcommand{\defaultColour}{\color{white}}
-%}
-\newcommand{\hl}[1]{\hlColour#1\defaultColour}
+\newcommand{\hl}[1]{\color{LUMCRood}#1\color{black}}
 
 % Enable numbering of figures and tables.
 \setbeamertemplate{caption}[numbered]
 
 % Put a frame title on the slide.
 \renewcommand{\frametitle}[1]{
-  {\it{\textbf{#1}}}
+  {\textbf{#1}}
   \bigskip
 
 }
 
-%% A filled frame, use this to make use of the \vfill command.
-%\newenvironment{fframe}{
-%  \begin{frame}
-%    \vspace{.15cm}
-%    \vbox to 1.15\textheight \bgroup
-%}{
-%    \egroup
-%  \end{frame}
-%}
-
 % A filled fragile frame.
 \newenvironment{pframe}{
   \begin{frame}[fragile, environment=pframe]
@@ -126,10 +94,6 @@
 % Settings for displaying code.
 %
 
-% This is for code listing in a presentation and to use references in captions.
-\usepackage{listings}
-\usepackage{cleveref}
-
 % Prevent an overlay to increase the listing counter.
 \resetcounteronoverlays{lstlisting}
 
@@ -148,7 +112,6 @@
 }
 
 % Change the font of the captions of listings.
-\usepackage{caption}
 \captionsetup[lstlisting]{font={footnotesize}}
 
 % Define an empty language to use only for typesetting.
@@ -161,9 +124,6 @@
 % Settings for handouts.
 %
 
-% Side by side pages.
-\usepackage{pgfpages}
-
 % Use items for displaying notes, remove the bullets and indentation.
 \def\beamer@setupnote{
   \gdef\beamer@notesactions{
@@ -189,7 +149,7 @@
 % Style of the notes page.
 \defbeamertemplate{note page}{plainitemnotes}{
   \vspace{21pt}
-  {\normalsize {\bf \color{LUMCBlue}Notes}}
+  {\normalsize {\bf Notes}}
   \vspace{29pt}
   {\normalsize
     \insertnote
@@ -202,16 +162,23 @@
   \setbeamertemplate{note page}[plainitemnotes]
 }{}
 
-%
-% Settings for the title page.
-%
+\pgfdeclarepatternformonly{custom north east lines}{
+  \pgfqpoint{-1pt}{-1pt}}{\pgfqpoint{4pt}{4pt}}{\pgfqpoint{1.4pt}{1.4pt}}{
+  \pgfsetlinewidth{0.6pt}
+  \pgfpathmoveto{\pgfqpoint{0pt}{0pt}}
+  \pgfpathlineto{\pgfqpoint{3.1pt}{3.1pt}}
+  \pgfusepath{stroke}
+}
 
-\providecommand{\makeTitleSlide}{
+% Title slide.
+\providecommand{\makeTitleSlide}[1]{
   {
     \hoffset=-1cm
     \voffset=-2mm
     \begin{frame}[plain]
-      \vspace{0.25cm}
+      \alt<handout>{}{
+        \vspace{0.25cm}
+      }
       \begin{tikzpicture}[scale=1.6]
         \node[right] at (0.4,4.5)
           {\includegraphics[height=0.8cm]{logos/lumc_logo_white}};
@@ -224,13 +191,13 @@
         \node[LUMCDonkerblauw, right] at (1.05,2.45)
           {\normalsize \bf \mySubTitle};
 
-        \node[anchor=north] at (6.5,2.60)
-          {\includegraphics[height=4cm]{\titlePicture}};
+        \node[anchor=north] at (6.5,2.60) {#1};
 
         \node[right] at (0.9,0.7) {
           \begin{tabular}{l}
             \insertauthor \\
             \myGroup \\
+            \myDepartment \\
             \myCenter
           \end{tabular}
         };
@@ -248,6 +215,7 @@
   \setcounter{framenumber}{0}
 }
 
+% Acknowledgement slide.
 \providecommand{\makeAcknowledgementsSlide}[1]{
   {
     \hoffset=-1cm
@@ -263,7 +231,11 @@
 
         \fill[LUMCKobaltblauw, opacity=0.5] (0,1.75) rectangle +(1,1);
 
-        \node[anchor=north west] at (0.9,2.75) {#1};
+        \node[anchor=north west] at (0.9,2.75) {
+          \begin{minipage}[t]{\textwidth}
+            #1
+          \end{minipage}
+        };
 
         \node[right] at (0.45,-0.3)
           {\includegraphics[height=0.8cm]{logos/ul_logo_white}};
@@ -277,129 +249,31 @@
   }
 }
 
-%% The header of the title page.
-%\providecommand{\titletemplate}{
-%  \setbeamertemplate{headline}{
-%    \colorbox{LUMCBlue}{
-%      \begin{tabularx}{0.98\textwidth}{X}
-%        \vspace{-0.3cm} % Space above the logo.
-%        \hfill
-%        \includegraphics[scale=0.25, angle=270]{logos/lumc_logo}
-%        \hfill \phantom{.}
-%        \vspace{0.1cm} % Space above the logo.
-%      \end{tabularx}
-%    }
-%  }
-%}
-%
-%% The footer of the title page.
-%\setbeamertemplate{footline}{
-%  \colorbox{ULBlue}{
-%    \begin{tabularx}{0.98\textwidth}{X}
-%      \vspace{0.05cm}    % Space above the logo.
-%      \hfill
-%      \includegraphics[scale=0.25]{logos/ul_logo}
-%      \hfill \phantom{.}
-%      \vspace{0.1cm}    % Space below the logo.
-%    \end{tabularx}
-%  }
-%}
-
-%
-% Settings for the body.
-%
-
-\pgfdeclarepatternformonly{custom north east lines}{
-  \pgfqpoint{-1pt}{-1pt}}{\pgfqpoint{4pt}{4pt}}{\pgfqpoint{1.4pt}{1.4pt}}{
-  \pgfsetlinewidth{0.6pt}
-  \pgfpathmoveto{\pgfqpoint{0pt}{0pt}}
-  \pgfpathlineto{\pgfqpoint{3.1pt}{3.1pt}}
-  \pgfusepath{stroke}
-}
-
 % The header of the body.
 \setbeamertemplate{headline}{
   \begin{tikzpicture}
     \fill[LUMCDonkerblauw]
       (0,0) -- (10.03,0) -- +(\LUMCCell,\LUMCCell) -- (0,\LUMCCell) -- (0,0);
-    \fill[pattern=custom north east lines, pattern color=LUMCKobaltblauw, opacity=0.25]
+    \fill[pattern=custom north east lines, pattern color=LUMCKobaltblauw,
+      opacity=0.25]
       (0,0) -- (10.45,0) -- +(\LUMCCell,\LUMCCell) -- (0,\LUMCCell) -- (0,0);
     \node [white, right] at (1,0.3)
       {\color{white} \normalsize \bf \insertsection};
   \end{tikzpicture}
 }
 
-% Switch to the normal layout.
-\providecommand{\bodytemplate}{}
-%  % The title page.
-%  {
-%    \titletemplate
-%    \begin{frame}
-%      \begin{minipage}[b][6cm][c]{0.98\textwidth}
-%        \begin{center}
-%          \vspace{1.5cm}
-%
-%          \color{black} {\Large {\bf \inserttitle}}
-%
-%          \vfill
-%          {\bf 
-%            {\scriptsize
-%              \color{LUMCBlue} 
-%              \insertauthor
-%              \smallskip
-%
-%              \myGroup
-%              \smallskip
-%
-%              \myDepartment
-%
-%              \vspace{-0.05cm}
-%              \myCenter
-%            }
-%          }
-%        \end{center}
-%      \end{minipage}
-%    \end{frame}
-%  }
-%
-%  % Set the background colour.
-%  %\alt<handout>{}{\beamersetaveragebackground{LUMCBlue}}
-%
-%  % Reset the frame counter.
-%  \setcounter{framenumber}{0}
-%
-  % The footer of the body.
-  \setbeamertemplate{footline}{
-    \color{white}
-    \renewcommand{\arraystretch}{1.65}
-    \begin{tabularx}{\textwidth}{p{\LUMCCell}Xp{\LUMCCell}p{\LUMCCell}}
-      \centering
-      \cellcolor{LUMCDonkerblauw} \insertframenumber/\inserttotalframenumber &
-      \cellcolor{LUMCKobaltblauw} \myConference &
-      \cellcolor{LUMCAquablauw} &
-      \cellcolor{LUMCGrijsblauw} \myDate
-    \end{tabularx}
-  }
-%}
-
-\providecommand{\lastpagetemplate}{}
-%  % The header of the body.
-%  \setbeamertemplate{headline}{
-%    \colorbox{white}{\color{LUMCBlue}
-%      \begin{tabularx}{0.98\textwidth}{llXX}
-%        \includegraphics[scale=0.25]{logos/lumc_logo_small} & 
-%        \hspace{0.8cm}    % Space between the logo and the title of the section.
-%        {\normalsize {\bf \insertsection}} & 
-%        \hfill
-%        \lastCenterLogo
-%        \hfill \phantom{.} &
-%        \hfill
-%        \lastRightLogo
-%        \hfill \phantom{.}
-%      \end{tabularx}
-%    }
-%  }
-%}
+% The footer of the body.
+\setbeamertemplate{footline}{
+  \color{white}
+  \renewcommand{\arraystretch}{1.65}
+  \begin{tabularx}{\textwidth}{p{\LUMCCell}Xp{\LUMCCell}p{\LUMCCell}}
+    \centering
+    \cellcolor{LUMCDonkerblauw} \insertframenumber/\inserttotalframenumber &
+    \cellcolor{LUMCKobaltblauw} \myConference &
+    \cellcolor{LUMCAquablauw} &
+    \cellcolor{LUMCGrijsblauw} \myDate
+  \end{tabularx}
+}
 
 \mode
 <all>
diff --git a/presentation.tex b/presentation.tex
index 02528a8..274c5b4 100644
--- a/presentation.tex
+++ b/presentation.tex
@@ -1,26 +1,13 @@
-\documentclass[slidestop]{beamer} % Add 'handout' for printable slides.
+\documentclass[slidestop]{beamer}
 
+\author{Jeroen F.J. Laros}
 \title{\LaTeX\ Presentation Template}
 \providecommand{\mySubTitle}{Subtitle}
 \providecommand{\myConference}{Work discussion}
 \providecommand{\myDate}{12-nov-2015}
-\author{Jeroen F.J. Laros}
 \providecommand{\myGroup}{Leiden Genome Technology Center}
 \providecommand{\myDepartment}{Department of Human Genetics}
 \providecommand{\myCenter}{Center for Human and Clinical Genetics}
-\providecommand{\titlePicture}{logos/lgtc_logo}
-\providecommand{\lastCenterLogo}{
-  \raisebox{-0.1cm}{
-    %\includegraphics[height=1cm]{logos/lgtc_logo}
-    %\includegraphics[height=0.7cm]{logos/ngi_logo}
-  }
-}
-\providecommand{\lastRightLogo}{
-  %\includegraphics[height=0.7cm]{logos/nbic_logo}
-  %\includegraphics[height=0.8cm]{logos/nwo_logo_en}
-  %\hspace{1.5cm}\includegraphics[height=0.7cm]{logos/gen2phen_logo}
-  %\includegraphics[height=0.7cm]{logos/generade_logo}
-}
 
 \usetheme{lumc}
 
@@ -29,9 +16,8 @@
 % This disables the \pause command, handy in the editing phase.
 %\renewcommand{\pause}{}
 
-% Make the title page.
-%\bodytemplate
-\makeTitleSlide
+% Make the title slide.
+\makeTitleSlide{\includegraphics[height=3.5cm]{logos/lumc_logo_small}}
 
 % First page of the presentation.
 \section{Short introduction}
@@ -54,7 +40,7 @@
   
   Notice the footer is present on all overlays.
   \vfill
-  \permfoot{https://git.lumc.nl/j.f.j.laros/presentation/tree/master}
+  \permfoot{\url{https://git.lumc.nl/j.f.j.laros/presentation/tree/master}}
 \end{pframe}
 
 \section{New section title which is rather long}
@@ -88,11 +74,22 @@
   \end{minipage}
 \end{pframe}
 
+% Make the acknowledgements slide.
 \makeAcknowledgementsSlide{
-  \begin{tabular}{l}
-    Someone\\
-    My mother\\
-    Flying Spaghetti Monster
+  \begin{tabular}{ll}
+    \bf Department one  & \bf Other department\\
+    Colleague one       & Someone\\
+    Colleague two       & Someone else\\
+    Colleague three     & Someone's supervisor\\
+    Supervisor\\
+  \end{tabular}
+  \bigskip
+
+  \begin{tabular}{llll}
+    \includegraphics[height=1cm]{logos/lumc_logo_small} &
+    \includegraphics[height=1cm]{logos/ul_logo_white} &
+    \includegraphics[height=1cm]{logos/lumc_logo_small} &
+    \includegraphics[height=1cm]{logos/ul_logo_white}
   \end{tabular}
 }
 
-- 
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