move plotting stuff to own folder

plotting/lecture/Makefile

@@ -0,0 +1,70 @@
+BASENAME=plotting
+
+PYFILES=$(wildcard *.py)
+PYPDFFILES=$(PYFILES:.py=.pdf)
+
+GPTFILES=$(wildcard *.gpt)
+GPTTEXFILES=$(GPTFILES:.gpt=.tex)
+
+
+all: pdf slides thumbs
+
+# script:
+pdf : $(BASENAME)-chapter.pdf
+$(BASENAME)-chapter.pdf : $(BASENAME)-chapter.tex $(BASENAME).tex $(GPTTEXFILES) $(PYPDFFILES)
+	pdflatex -interaction=scrollmode $< | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex -interaction=scrollmode $< || true
+
+
+# slides:
+slides: $(BASENAME)-slides.pdf
+$(BASENAME)-slides.pdf : $(BASENAME)-slides.tex $(GPTTEXFILES) $(PYPDFFILES)
+	pdflatex -interaction=scrollmode $< | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex -interaction=scrollmode $< || true
+
+# thumbnails:
+thumbs: $(BASENAME)-handout.pdf
+$(BASENAME)-handout.pdf: $(BASENAME)-slides.tex $(GPTTEXFILES)
+	sed -e 's/setboolean{presentation}{true}/setboolean{presentation}{false}/; s/usepackage{crop}/usepackage[frame]{crop}/' $< > thumbsfoils.tex
+	pdflatex thumbsfoils | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex thumbsfoils || true
+	pdfnup --nup 2x4 --no-landscape --paper a4paper --trim "-1cm -1cm -1cm -1cm" --outfile $@ thumbsfoils.pdf # 1-19
+	rm thumbsfoils.*
+
+watchpdf :
+	while true; do ! make -q pdf && make pdf; sleep 0.5; done
+
+watchslides :
+	while true; do ! make -q slides && make slides; sleep 0.5; done
+
+# python plots:
+$(PYPDFFILES) : %.pdf: %.py
+	python $<
+
+# gnuplot plots:
+$(GPTTEXFILES) : %.tex: %.gpt whitestyles.gp
+	gnuplot whitestyles.gp $<
+	epstopdf $*.eps
+
+
+clean :
+	rm -f *~ 
+	rm -f $(BASENAME).aux $(BASENAME).log
+	rm -f $(BASENAME)-chapter.aux $(BASENAME)-chapter.log $(BASENAME)-chapter.out
+	rm -f $(BASENAME)-slides.aux $(BASENAME)-slides.log $(BASENAME)-slides.out $(BASENAME)-slides.toc $(BASENAME)-slides.nav $(BASENAME)-slides.snm $(BASENAME)-slides.vrb
+	rm -f $(PYPDFFILES) $(GPTTEXFILES)
+
+cleanall : clean
+	rm -f $(BASENAME)-chapter.pdf $(BASENAME)-slides.pdf $(BASENAME)-handout.pdf
+
+
+help : 
+	@echo -e \
+	"make pdf:        make the pdf file of the script.\n"\
+	"make slides:     make the pdf file of the slides.\n"\
+	"make thumbs:     make color thumbnails of the talk.\n"\
+	"make watchpdf:   make the pdf file of the script\n"\
+        "                 whenever the tex file is modified.\n"\
+	"make watchpdf:   make the pdf file of the slides\n"\
+        "                 whenever the tex file is modified.\n"\
+	"make clean:      remove all intermediate files,\n"\
+        "                 just leave the source files and the final .pdf files.\n"\
+	"make cleanup:    remove all intermediate files as well as\n"\
+        "                 the final .pdf files.\n"\

plotting/lecture/beamercolorthemetuebingen.sty

@@ -0,0 +1,61 @@
+% Copyright 2007 by Till Tantau
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Public License.
+%
+% See the file doc/licenses/LICENSE for more details.
+
+\usepackage{color} 
+\definecolor{karminrot}{RGB}{165,30,55}
+\definecolor{gold}{RGB}{180,160,105}
+\definecolor{anthrazit}{RGB}{50 ,65 ,75 }
+
+\mode<presentation>
+
+\setbeamercolor*{normal text}{fg=anthrazit,bg=white}
+\setbeamercolor*{alerted text}{fg=anthrazit}
+\setbeamercolor*{example text}{fg=anthrazit}
+\setbeamercolor*{structure}{fg=gold,bg=karminrot}
+
+\providecommand*{\beamer@bftext@only}{%
+  \relax
+  \ifmmode
+    \expandafter\beamer@bftext@warning
+  \else
+    \expandafter\bfseries
+  \fi
+}
+\providecommand*{\beamer@bftext@warning}{%
+  \ClassWarning{beamer}
+    {Cannot use bold for alerted text in math mode}%
+}
+
+\setbeamerfont{alerted text}{series=\beamer@bftext@only}
+
+\setbeamercolor{palette primary}{fg=karminrot,bg=white}
+\setbeamercolor{palette secondary}{fg=gold,bg=white}
+\setbeamercolor{palette tertiary}{fg=anthrazit,bg=white}
+\setbeamercolor{palette quaternary}{fg=black,bg=white}
+
+\setbeamercolor{sidebar}{bg=karminrot!100}
+
+\setbeamercolor{palette sidebar primary}{fg=karminrot}
+\setbeamercolor{palette sidebar secondary}{fg=karminrot}
+\setbeamercolor{palette sidebar tertiary}{fg=karminrot}
+\setbeamercolor{palette sidebar quaternary}{fg=karminrot}
+
+\setbeamercolor{item projected}{fg=black,bg=black!20}
+
+\setbeamercolor*{block body}{}
+\setbeamercolor*{block body alerted}{}
+\setbeamercolor*{block body example}{}
+\setbeamercolor*{block title}{parent=structure}
+\setbeamercolor*{block title alerted}{parent=alerted text}
+\setbeamercolor*{block title example}{parent=example text}
+
+\setbeamercolor*{titlelike}{parent=structure}
+
+\mode
+<all>

plotting/lecture/plotting-chapter.tex

@@ -0,0 +1,17 @@
+\documentclass[12pt]{report}
+
+\input{../../header}
+
+\lstset{inputpath=../code}
+
+\graphicspath{{images/}}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{document} 
+
+\include{psth_sta}
+
+\end{document}
+

plotting/lecture/plotting-slides.tex

@@ -0,0 +1,358 @@
+\documentclass{beamer}
+\usepackage{xcolor}
+\usepackage{listings}
+\usepackage{pgf}
+%\usepackage{pgf,pgfarrows,pgfnodes,pgfautomata,pgfheaps,pgfshade} 
+%\usepackage{multimedia}
+
+\usepackage[english]{babel}
+\usepackage{movie15}
+\usepackage[latin1]{inputenc}
+\usepackage{times}
+\usepackage{amsmath}
+\usepackage{bm} 
+\usepackage[T1]{fontenc}
+\usepackage[scaled=.90]{helvet}
+\usepackage{scalefnt}
+\usepackage{tikz}
+\usepackage{ textcomp }
+\usepackage{soul}
+\usepackage{hyperref}
+\definecolor{lightblue}{rgb}{.7,.7,1.}
+\definecolor{mygreen}{rgb}{0,1.,0}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\mode<presentation>
+{
+  \usetheme{Singapore}
+  \setbeamercovered{opaque}
+  \usecolortheme{tuebingen}
+  \setbeamertemplate{navigation symbols}{}
+  \usefonttheme{default}
+  \useoutertheme{infolines}
+  % \useoutertheme{miniframes}
+}
+
+\AtBeginSection[]
+{
+  \begin{frame}<beamer>
+    \begin{center}
+      \Huge \insertsectionhead
+    \end{center}
+    % \frametitle{\insertsectionhead}
+    % \tableofcontents[currentsection,hideothersubsections]
+  \end{frame}
+}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
+
+\setbeamertemplate{blocks}[rounded][shadow=true]
+
+\title[]{Scientific Computing -- Grundlagen der Programmierung }
+\author[]{Jan Grewe\\Abteilung f\"ur Neuroethologie\\
+  Universit\"at T\"ubingen}
+
+\institute[Wissenschaftliche Datenverarbeitung]{}
+ \date{12.10.2015 - 06.11.2015}
+ %\logo{\pgfuseimage{../../resources/UT_BM_Rot_RGB.pdf}}
+
+\subject{Einf\"uhrung in die wissenschaftliche Datenverarbeitung}
+\vspace{1em}
+\titlegraphic{
+  \includegraphics[width=0.5\linewidth]{../../resources/UT_WBMW_Rot_RGB}
+}
+%%%%%%%%%% configuration for code
+\lstset{
+ basicstyle=\ttfamily,
+ numbers=left,
+ showstringspaces=false,
+ language=Matlab,
+ commentstyle=\itshape\color{darkgray},
+ keywordstyle=\color{blue},
+ stringstyle=\color{green},
+ backgroundcolor=\color{blue!10},
+ breaklines=true,
+ breakautoindent=true,
+ columns=flexible,
+ frame=single,
+ captionpos=b,
+ xleftmargin=1em,
+ xrightmargin=1em,
+ aboveskip=10pt
+ }
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\newcommand{\mycite}[1]{
+\begin{flushright}
+\tiny \color{black!80} #1
+\end{flushright}
+}
+
+\newcommand{\code}[1]{\texttt{#1}}
+
+\input{../../latex/environments.tex}
+\makeatother
+ 
+\begin{document} 
+
+\begin{frame}[plain]
+  \frametitle{}
+  \vspace{-1cm}
+  \titlepage % erzeugt Titelseite
+\end{frame}
+
+\begin{frame}
+  \frametitle{Grundlagen der Programmierung}
+  \frametitle{Inhalt}
+  \begin{enumerate}
+  \item Graphische Darstellung von Daten
+  \end{enumerate}
+\end{frame}
+
+
+\begin{frame}[plain]
+  \huge{1. Graphische Darstellung von Daten}\pause
+  \begin{figure}
+    \includegraphics[width=0.9\columnwidth]{images/convincing}
+  \end{figure}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Graphische Darstellung von Daten}
+  \framesubtitle{Was soll ein Datenplot erreichen?}
+
+  \begin{itemize}
+  \item Ist eine m\"oglichst neutrale Darstellung der Daten.
+  \item Soll dem Leser die Daten greifbar machen und die Aussagen der
+    Analyse darstellen.
+  \item Erlaubt dem Leser die gezeigten Effekte selbst zu beguachten
+    und zu validieren.
+  \item Muss vollst\"andig annotiert sein.
+  \item Folgt dem Prinzip der \textbf{ink minimization}. (Das
+    Verh\"altnis aus Tinte, die f\"ur die Darstellung der Daten
+    gebraucht wird und der Menge Tinte, die f\"ur die Graphik
+    ben\"otigt wird sollte m\"oglichst gro{\ss} sein )
+  \end{itemize}
+\end{frame}
+
+\begin{frame}
+  \frametitle{Graphische Darstellung von Daten}
+  \framesubtitle{Was sollte vermieden werden?}
+  
+  \begin{itemize}
+  \item Suggestive oder gar fehlleitende Darstellung.
+  \item Ablenkung durch unruhige oder \"uberm\"a{\ss}ige Effekte.
+  \item Comicartige Effekte...
+  \end{itemize}\pause
+  \begin{figure}
+    \includegraphics[width=0.35\columnwidth]{images/one_d_problem_c}
+  \end{figure}\pause
+  ... aus{\ss}er sie werden rein zur Illustration benutzt ohne einen
+  Anspruch auf Richtigkeit zu erheben.
+\end{frame}
+
+\begin{frame}
+  \frametitle{Graphische Darstellung von Daten}
+  \framesubtitle{Suboptimale Beispiele}
+  \only <1> {
+    \begin{figure}
+      \includegraphics[width=0.5\columnwidth]{images/nobelbad}
+    \end{figure}
+    \vspace{0.25cm}
+    Aus Hafting et al., Nature, 2005
+  }
+  \only <2> {
+    \begin{figure}
+      \includegraphics[width=0.7\columnwidth]{images/misleading_pie}
+    \end{figure}
+    \vspace{0.5cm}
+    \url{https://en.wikipedia.org/wiki/Misleading_graph}
+  }
+  \only <3> {
+    \begin{figure}
+      \includegraphics[width=0.7\columnwidth]{images/sample_pie}
+    \end{figure}
+    \vspace{0.5cm}
+    \url{https://en.wikipedia.org/wiki/Misleading_graph}
+  }
+  \only <4> {
+    \begin{figure}
+      \includegraphics[width=0.3\columnwidth]{images/badbarright}
+    \end{figure}
+    \vspace{0.5cm}
+    \url{https://en.wikipedia.org/wiki/Misleading_graph}
+  }
+  \only <5> {
+    \begin{figure}
+      \includegraphics[width=0.3\columnwidth]{images/badbarleft}
+    \end{figure}
+    \vspace{0.5cm}
+    \url{https://en.wikipedia.org/wiki/Misleading_graph}
+  }
+  \only <6> {
+    \begin{figure}
+      \includegraphics[width=0.8\columnwidth]{images/badbarplot}
+    \end{figure}
+    \vspace{0.5cm}
+    \url{https://en.wikipedia.org/wiki/Misleading_graph}
+  }
+  \only <7> {
+    Wahl der Zeichenfl\"ache kann den visuellen Eindruck beeinflu{\ss}en.
+    \begin{columns}
+      \begin{column}{4.cm}
+        \begin{figure}
+          \includegraphics[width=0.7\columnwidth]{images/line_graph1}
+        \end{figure}
+      \end{column}
+
+      \begin{column}{4.cm}
+        \begin{figure}
+          \includegraphics[width=0.7\columnwidth]{images/line_graph1_3}
+        \end{figure}
+      \end{column}
+
+      \begin{column}{4.cm}
+        \begin{figure}
+          \includegraphics[width=0.7\columnwidth]{images/line_graph1_4}
+        \end{figure}
+      \end{column}
+    \end{columns}
+    \vspace{0.5cm}
+    \url{https://en.wikipedia.org/wiki/Misleading_graph}
+  }
+    \only <8> {
+     Vorsicht bei der Skalierung von Symbolen!
+    \begin{columns}
+      \begin{column}{4.cm}
+        \begin{figure}
+          \includegraphics[width=0.7\columnwidth]{images/improperly_scaled_graph}
+        \end{figure}
+      \end{column}
+
+      \begin{column}{4.cm}
+        \begin{figure}
+          \includegraphics[width=0.7\columnwidth]{images/properly_scaled_graph}
+        \end{figure}
+      \end{column}
+
+      \begin{column}{4.cm}
+        \begin{figure}
+          \includegraphics[width=0.7\columnwidth]{images/comparison_properly_improperly_graph}
+        \end{figure}
+      \end{column}
+    \end{columns}
+    \vspace{0.5cm}
+    \url{https://en.wikipedia.org/wiki/Misleading_graph}
+   }
+\end{frame}
+
+\begin{frame}[fragile]
+  \frametitle{Graphische Darstellung von Daten}
+  \framesubtitle{Plotting Interfaces in Matlab}
+  Es gibt zwei Wege Graphen zu bearbeiten:
+  \begin{enumerate}
+  \item Interaktiv \"uber das \textit{graphische User Interface}\pause
+  \item Die Kommandozeile bzw. in Skripten und Funktionen.\pause
+  \end{enumerate}
+  Beides hat seine Berechtigung und seine eigenen Vor- und Nachteile. Welche?
+\end{frame}
+
+
+\begin{frame}
+  \frametitle{Graphische Darstellung von Daten}
+  \framesubtitle{Ver\"anderung des Graphen \"uber die Kommandozeile}
+  \begin{itemize}
+  \item Erstellt ein Skript, dass einen Plot erstellt.
+  \item Dieser soll zwei Sinus unterschiedlicher Frequenz darstellen.
+  \end{itemize}
+  Wir werden jetzt die Kommandozeil bzw. das Skript verbessern um den
+  Plot ``sch\"oner'' zu machen.
+\end{frame}
+
+
+\begin{frame}
+  \frametitle{Graphische Darstellung von Daten}
+  \framesubtitle{Ver\"anderung des Graphen \"uber die Kommandozeile}
+  \begin{enumerate}
+  \item Einstellungen der Linienplots:
+    \begin{itemize}
+    \item St\"arke und Farbe.
+    \item Linienstil, Marker.
+    \end{itemize}\pause
+  \item Achsbeschriftung:
+    \begin{itemize}
+    \item \code{xlabel}, \code{ylabel}.
+    \item Schriftart und Gr\"o{\ss}e.
+    \end{itemize}\pause
+  \item Achsenskalierung und Ticks:
+    \begin{itemize}
+    \item Skalierung der Achsen (Minumum und Maxmimum, logarithmisch oder linear).
+    \item Manuelles Setzen der Ticks, ihrer Richtung und Beschriftung.
+    \item Grid or no Grid?
+    \end{itemize}\pause
+  \item Setzen von globalen Parametern:
+    \begin{itemize}
+    \item Einstellung der Papiergr\"o{\ss}e und plzieren der
+      Zeichenfl\"ache.
+    \item Box oder nicht?
+    \item Speichern der Abbildung als pdf.      
+    \end{itemize}
+  \end{enumerate}
+\end{frame}
+
+
+\begin{frame} [fragile]
+ \frametitle{Graphische Darstellung von Daten}
+ \framesubtitle{Ver\"andern von Eigenschaften \"uber die Kommandozeile}
+ \vspace{-0.75em}
+ \scriptsize
+  \begin{lstlisting}
+fig = figure();
+set(gcf, 'PaperUnits', 'centimeters', 'PaperSize', [11.7 9.0]);
+set(gcf, 'PaperPosition',[0.0 0.0 11.7 9.0], 'Color', 'white')
+hold on
+plot(time, neuronal_data, 'color', [ 0.2 0.5 0.7], 'linewidth', 1.)
+plot(spike_times, ones(size(spike_times))*threshold, 'ro', 'markersize', 4)
+line([time(1) time(end)], [threshold threshold], 'linestyle', '--',
+    'linewidth', 0.75, 'color', [0.9 0.9 0.9])
+ylim([0 35])
+xlim([0 2.25])
+box('off')
+xlabel('time [s]', 'fontname', 'MyriadPro-Regular', 'fontsize', 10)
+ylabel('potential [mV]', 'fontname', 'MyriadPro-Regular', 'fontsize', 10)
+title('pyramidal cell', 'fontname', 'MyriadPro-Regular', 'fontsize', 12)
+set(gca, 'TickDir','out', 'linewidth', 1.5, 'fontname', 'MyriadPro-Regular')
+saveas(fig, 'spike_detection.pdf', 'pdf')
+\end{lstlisting}
+\end{frame}
+
+
+\begin{frame} [fragile]
+ \frametitle{Graphische Darstellung von Daten}
+ \framesubtitle{Ver\"andern von Eigenschaften \"uber die Kommandozeile}
+     \begin{figure}
+      \centering
+      \includegraphics[width=0.75\columnwidth]{./images/spike_detection}
+    \end{figure}
+\end{frame}
+
+
+\begin{frame} [fragile]
+ \frametitle{Graphische Darstellung von Daten}
+ \framesubtitle{Welche Art Plot wof\"ur?}
+ \url{http://www.mathworks.de/discovery/gallery.html}
+\end{frame}
+
+
+\begin{frame} [fragile]
+ \frametitle{Graphische Darstellung von Daten}
+ \framesubtitle{Was macht einen guten Abbildung aus?}
+ \begin{enumerate}
+ \item Klarheit.
+ \item Vollstaendige Beschriftung.
+ \item Deutliche Unterscheidbarkeit von Kurven.
+ \item Keine suggestive Darstellung. 
+ \item Ausgewogenheit von Linienst\"arken Schrift- und Plotgr\"o{\ss}e.
+ \item Fehlerbalken, wenn sie angebracht sind.
+ \end{enumerate}
+\end{frame}
+
+\end{document}

plotting/lecture/plotting.tex

@@ -0,0 +1,11 @@
+\chapter{\tr{Data plotting}{Graphische Darstellung von Daten}}
+
+\section{Graphische Darstellung von Daten}
+
+
+
+\begin{figure}
+  \includegraphics[width=0.9\columnwidth]{convincing}
+  \caption{Die Folgen schlecht annotierter
+    Plots. \url{www.xkcd.com}} \label{xkcdplotting}
+\end{figure}