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This commit is contained in:
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96997a8299
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20
spike_trains/lecture/Makefile
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spike_trains/lecture/Makefile
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TEXFILES=$(wildcard *.tex)
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TEXFILES=psth_sta.tex
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PDFFILES=$(TEXFILES:.tex=.pdf)
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pdf : $(PDFFILES)
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$(PDFFILES) : %.pdf : %.tex
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pdflatex -interaction=scrollmode $< | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex -interaction=scrollmode $< || true
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clean :
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rm -f *~ $(TEXFILES:.tex=.aux) $(TEXFILES:.tex=.log) $(TEXFILES:.tex=.out) $(TEXFILES:.tex=.nav) $(TEXFILES:.tex=.snm) $(TEXFILES:.tex=.toc) $(TEXFILES:.tex=.vrb)
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cleanall : clean
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rm -f $(PDFFILES)
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watch :
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while true; do ! make -q pdf && make pdf; sleep 0.5; done
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spike_trains/lecture/beamercolorthemetuebingen.sty
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spike_trains/lecture/beamercolorthemetuebingen.sty
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% Copyright 2007 by Till Tantau
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%
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% This file may be distributed and/or modified
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%
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% 1. under the LaTeX Project Public License and/or
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% 2. under the GNU Public License.
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%
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% See the file doc/licenses/LICENSE for more details.
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\usepackage{color}
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\definecolor{karminrot}{RGB}{165,30,55}
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\definecolor{gold}{RGB}{180,160,105}
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\definecolor{anthrazit}{RGB}{50 ,65 ,75 }
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\mode<presentation>
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\setbeamercolor*{normal text}{fg=anthrazit,bg=white}
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\setbeamercolor*{alerted text}{fg=anthrazit}
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\setbeamercolor*{example text}{fg=anthrazit}
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\setbeamercolor*{structure}{fg=gold,bg=karminrot}
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\providecommand*{\beamer@bftext@only}{%
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\relax
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\ifmmode
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\expandafter\beamer@bftext@warning
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\else
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\expandafter\bfseries
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\fi
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}
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\providecommand*{\beamer@bftext@warning}{%
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\ClassWarning{beamer}
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{Cannot use bold for alerted text in math mode}%
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}
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\setbeamerfont{alerted text}{series=\beamer@bftext@only}
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\setbeamercolor{palette primary}{fg=karminrot,bg=white}
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\setbeamercolor{palette secondary}{fg=gold,bg=white}
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\setbeamercolor{palette tertiary}{fg=anthrazit,bg=white}
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\setbeamercolor{palette quaternary}{fg=black,bg=white}
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\setbeamercolor{sidebar}{bg=karminrot!100}
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\setbeamercolor{palette sidebar primary}{fg=karminrot}
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\setbeamercolor{palette sidebar secondary}{fg=karminrot}
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\setbeamercolor{palette sidebar tertiary}{fg=karminrot}
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\setbeamercolor{palette sidebar quaternary}{fg=karminrot}
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\setbeamercolor{item projected}{fg=black,bg=black!20}
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\setbeamercolor*{block body}{}
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\setbeamercolor*{block body alerted}{}
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\setbeamercolor*{block body example}{}
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\setbeamercolor*{block title}{parent=structure}
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\setbeamercolor*{block title alerted}{parent=alerted text}
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\setbeamercolor*{block title example}{parent=example text}
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\setbeamercolor*{titlelike}{parent=structure}
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\mode
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<all>
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BIN
spike_trains/lecture/images/psth_comparison.pdf
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BIN
spike_trains/lecture/images/psth_comparison.pdf
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36
spike_trains/lecture/psth_sta.tex
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spike_trains/lecture/psth_sta.tex
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\chapter{Spiketrainanalyse}
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Die zeitliche Abfolge von Aktionspotentialen, die ein Neuron generiert
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enth\"alt die Information \"uber den Stimulus, die das Neuron
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codiert. Aus der Analyse dieser Aktionspotentialfolgen oder,
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kompakter, Spiketrains k\"onnen wir herausfinden welche Aspekte des
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Stimulus codiert wird und somit nachfolgenden Verarbeitungsschritten
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zur Verf\"ugung steht.
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Im elektrophysiologischen Experiment werden h\"aufig nur die
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Zeitpunkte registriert an denen Aktionspotentiale, Spikes,
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auftraten. Die Neuronale Aktivit\"at wird mitunter als Punktprozess
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aufgefasst. Erstaunlicherweise lassen sich die Spiketrains mancher
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kortikaler Neurone sehr gut durch ratenmodulierte Poissonprozesse
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modellieren.
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Die Analyse von Spiketrains beinhaltet demnach einige der Methoden,
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die auch f\"r die Beschreibung von Punktprozessen angewandt
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werden. Dar\"uber hinaus wird versucht die Beziehung zwischen der
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zeitabh\"aengigen neuronalen Antwort und dem zugrundeliegenden
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Stimulus zu analysieren.
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\section{Darstellung der zeitabh\"angigen Feuerrate}
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Eine klassische Darstellung zeitabh\"angiger neuronaler Aktivit\"at
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ist das sog. Peri Stimulus Zeithistogramm (peri stimulus time
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histogram, PSTH). Es wird der zeitliche Verlauf der Feuerrate $r(t)$
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dargestellt. Die Einheit der Feuerrate ist Hertz, das heisst, die
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Anzahl Aktionspotentiale pro Sekunde. Dabei gibt es verschiedene
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Methoden diese zu bestimmen. Jede dieser Methoden hat ihre Vor- und
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Nachteile. Abbildung \ref{psthfig} zeigt drei dieser Methoden.
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\begin{figure}
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\includegraphics[width=0.75\columnwidth]{images/psth_comparison}
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\caption{}\label{psthfig}
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\end{figure}
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226
spike_trains/lecture/spike_trains-chapter.tex
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spike_trains/lecture/spike_trains-chapter.tex
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\documentclass[12pt]{report}
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%%%%% title %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\title{\tr{Introduction to Scientific Computing}{Einf\"uhrung in die wissenschaftliche Datenverarbeitung}}
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\author{Jan Benda\\Abteilung Neuroethologie\\[2ex]\includegraphics[width=0.3\textwidth]{UT_WBMW_Rot_RGB}}
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\date{WS 15/16}
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%%%% language %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% \newcommand{\tr}[2]{#1} % en
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% \usepackage[english]{babel}
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\newcommand{\tr}[2]{#2} % de
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\usepackage[german]{babel}
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%%%%% packages %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage{pslatex} % nice font for pdf file
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\usepackage[breaklinks=true,bookmarks=true,bookmarksopen=true,pdfpagemode=UseNone,pdfstartview=FitH,colorlinks=true,citecolor=blue]{hyperref}
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%%%% layout %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage[left=25mm,right=25mm,top=20mm,bottom=30mm]{geometry}
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\setcounter{tocdepth}{1}
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%%%%% section style %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage[sf,bf,it,big,clearempty]{titlesec}
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\setcounter{secnumdepth}{1}
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%%%%% units %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage[mediumspace,mediumqspace,Gray]{SIunits} % \ohm, \micro
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%%%%% figures %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage{graphicx}
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\usepackage{xcolor}
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\pagecolor{white}
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\newcommand{\ruler}{\par\noindent\setlength{\unitlength}{1mm}\begin{picture}(0,6)%
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\put(0,4){\line(1,0){170}}%
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\multiput(0,2)(10,0){18}{\line(0,1){4}}%
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\multiput(0,3)(1,0){170}{\line(0,1){2}}%
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\put(0,0){\makebox(0,0){{\tiny 0}}}%
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\put(10,0){\makebox(0,0){{\tiny 1}}}%
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\put(20,0){\makebox(0,0){{\tiny 2}}}%
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\put(30,0){\makebox(0,0){{\tiny 3}}}%
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\put(40,0){\makebox(0,0){{\tiny 4}}}%
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\put(50,0){\makebox(0,0){{\tiny 5}}}%
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\put(60,0){\makebox(0,0){{\tiny 6}}}%
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\put(70,0){\makebox(0,0){{\tiny 7}}}%
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\put(80,0){\makebox(0,0){{\tiny 8}}}%
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\put(90,0){\makebox(0,0){{\tiny 9}}}%
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\put(100,0){\makebox(0,0){{\tiny 10}}}%
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\put(110,0){\makebox(0,0){{\tiny 11}}}%
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\put(120,0){\makebox(0,0){{\tiny 12}}}%
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\put(130,0){\makebox(0,0){{\tiny 13}}}%
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\put(140,0){\makebox(0,0){{\tiny 14}}}%
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\put(150,0){\makebox(0,0){{\tiny 15}}}%
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\put(160,0){\makebox(0,0){{\tiny 16}}}%
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\put(170,0){\makebox(0,0){{\tiny 17}}}%
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\end{picture}\par}
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% figures:
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\setlength{\fboxsep}{0pt}
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\newcommand{\texpicture}[1]{{\sffamily\footnotesize\input{#1.tex}}}
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%\newcommand{\texpicture}[1]{\fbox{\sffamily\footnotesize\input{#1.tex}}}
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%\newcommand{\texpicture}[1]{\setlength{\fboxsep}{2mm}\fbox{#1}}
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%\newcommand{\texpicture}[1]{}
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\newcommand{\figlabel}[1]{\textsf{\textbf{\large \uppercase{#1}}}}
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% maximum number of floats:
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\setcounter{topnumber}{2}
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\setcounter{bottomnumber}{0}
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\setcounter{totalnumber}{2}
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% float placement fractions:
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\renewcommand{\textfraction}{0.2}
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\renewcommand{\topfraction}{0.8}
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\renewcommand{\bottomfraction}{0.0}
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\renewcommand{\floatpagefraction}{0.5}
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% spacing for floats:
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\setlength{\floatsep}{12pt plus 2pt minus 2pt}
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\setlength{\textfloatsep}{20pt plus 4pt minus 2pt}
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\setlength{\intextsep}{12pt plus 2pt minus 2pt}
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% spacing for a floating page:
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\makeatletter
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\setlength{\@fptop}{0pt}
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\setlength{\@fpsep}{8pt plus 2.0fil}
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\setlength{\@fpbot}{0pt plus 1.0fil}
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\makeatother
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% rules for floats:
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\newcommand{\topfigrule}{\vspace*{10pt}{\hrule height0.4pt}\vspace*{-10.4pt}}
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\newcommand{\bottomfigrule}{\vspace*{-10.4pt}{\hrule height0.4pt}\vspace*{10pt}}
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% captions:
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\usepackage[format=plain,singlelinecheck=off,labelfont=bf,font={small,sf}]{caption}
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% put caption on separate float:
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\newcommand{\breakfloat}{\end{figure}\begin{figure}[t]}
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% references to panels of a figure within the caption:
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\newcommand{\figitem}[1]{\textsf{\bfseries\uppercase{#1}}}
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% references to figures:
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\newcommand{\panel}[1]{\textsf{\uppercase{#1}}}
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\newcommand{\fref}[1]{\textup{\ref{#1}}}
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\newcommand{\subfref}[2]{\textup{\ref{#1}}\,\panel{#2}}
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% references to figures in normal text:
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\newcommand{\fig}{Fig.}
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\newcommand{\Fig}{Figure}
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\newcommand{\figs}{Figs.}
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\newcommand{\Figs}{Figures}
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\newcommand{\figref}[1]{\fig~\fref{#1}}
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\newcommand{\Figref}[1]{\Fig~\fref{#1}}
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\newcommand{\figsref}[1]{\figs~\fref{#1}}
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\newcommand{\Figsref}[1]{\Figs~\fref{#1}}
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\newcommand{\subfigref}[2]{\fig~\subfref{#1}{#2}}
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\newcommand{\Subfigref}[2]{\Fig~\subfref{#1}{#2}}
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\newcommand{\subfigsref}[2]{\figs~\subfref{#1}{#2}}
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\newcommand{\Subfigsref}[2]{\Figs~\subfref{#1}{#2}}
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% references to figures within bracketed text:
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\newcommand{\figb}{Fig.}
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\newcommand{\figsb}{Figs.}
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\newcommand{\figrefb}[1]{\figb~\fref{#1}}
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\newcommand{\figsrefb}[1]{\figsb~\fref{#1}}
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\newcommand{\subfigrefb}[2]{\figb~\subfref{#1}{#2}}
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\newcommand{\subfigsrefb}[2]{\figsb~\subfref{#1}{#2}}
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% references to tables:
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\newcommand{\tref}[1]{\textup{\ref{#1}}}
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% references to tables in normal text:
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\newcommand{\tab}{Tab.}
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\newcommand{\Tab}{Table}
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\newcommand{\tabs}{Tabs.}
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\newcommand{\Tabs}{Tables}
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\newcommand{\tabref}[1]{\tab~\tref{#1}}
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\newcommand{\Tabref}[1]{\Tab~\tref{#1}}
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\newcommand{\tabsref}[1]{\tabs~\tref{#1}}
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\newcommand{\Tabsref}[1]{\Tabs~\tref{#1}}
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% references to tables within bracketed text:
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\newcommand{\tabb}{Tab.}
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\newcommand{\tabsb}{Tab.}
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\newcommand{\tabrefb}[1]{\tabb~\tref{#1}}
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\newcommand{\tabsrefb}[1]{\tabsb~\tref{#1}}
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%%%%% equation references %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%\newcommand{\eqref}[1]{(\ref{#1})}
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\newcommand{\eqn}{\tr{Eq}{Gl}.}
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\newcommand{\Eqn}{\tr{Eq}{Gl}.}
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\newcommand{\eqns}{\tr{Eqs}{Gln}.}
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\newcommand{\Eqns}{\tr{Eqs}{Gln}.}
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\newcommand{\eqnref}[1]{\eqn~\eqref{#1}}
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\newcommand{\Eqnref}[1]{\Eqn~\eqref{#1}}
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\newcommand{\eqnsref}[1]{\eqns~\eqref{#1}}
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\newcommand{\Eqnsref}[1]{\Eqns~\eqref{#1}}
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%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage{listings}
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\lstset{
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inputpath=../code,
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basicstyle=\ttfamily\footnotesize,
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numbers=left,
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showstringspaces=false,
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language=Matlab,
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commentstyle=\itshape\color{darkgray},
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keywordstyle=\color{blue},
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stringstyle=\color{green},
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backgroundcolor=\color{blue!10},
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breaklines=true,
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breakautoindent=true,
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columns=flexible,
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frame=single,
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caption={\protect\filename@parse{\lstname}\protect\filename@base},
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captionpos=t,
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xleftmargin=1em,
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xrightmargin=1em,
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aboveskip=10pt
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}
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%%%%% math stuff: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage{amsmath}
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\usepackage{bm}
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\usepackage{dsfont}
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\newcommand{\naZ}{\mathds{N}}
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\newcommand{\gaZ}{\mathds{Z}}
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\newcommand{\raZ}{\mathds{Q}}
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\newcommand{\reZ}{\mathds{R}}
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\newcommand{\reZp}{\mathds{R^+}}
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\newcommand{\reZpN}{\mathds{R^+_0}}
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\newcommand{\koZ}{\mathds{C}}
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%%%%% structure: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\usepackage{ifthen}
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\newcommand{\code}[1]{\texttt{#1}}
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\newcommand{\source}[1]{
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\begin{flushright}
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\color{gray}\scriptsize \url{#1}
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\end{flushright}
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}
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\newenvironment{definition}[1][]{\medskip\noindent\textbf{Definition}\ifthenelse{\equal{#1}{}}{}{ #1}:\newline}%
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{\medskip}
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\newcounter{maxexercise}
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\setcounter{maxexercise}{9} % show listings up to exercise maxexercise
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\newcounter{theexercise}
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\setcounter{theexercise}{1}
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\newenvironment{exercise}[1][]{\medskip\noindent\textbf{\tr{Exercise}{\"Ubung}
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\arabic{theexercise}:}\newline \newcommand{\exercisesource}{#1}}%
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{\ifthenelse{\equal{\exercisesource}{}}{}{\ifthenelse{\value{theexercise}>\value{maxexercise}}{}{\medskip\lstinputlisting{\exercisesource}}}\medskip\stepcounter{theexercise}}
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\graphicspath{{figures/}}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{document}
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\include{psth_sta}
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\end{document}
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Reference in New Issue
Block a user