Merge branch 'master' of whale.am28.uni-tuebingen.de:scientificComputing
This commit is contained in:
commit
abad56902b
5
.gitignore
vendored
5
.gitignore
vendored
@ -3,14 +3,19 @@
|
||||
*.lol
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||||
*.loe
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||||
*.idx
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||||
*.ilg
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||||
*.ind
|
||||
*.log
|
||||
*.loi
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||||
*.loiboxf
|
||||
*.aux
|
||||
*.nav
|
||||
*.out
|
||||
*.snm
|
||||
*.toc
|
||||
*.mat
|
||||
*.pdf
|
||||
*.eps
|
||||
.#*
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||||
#*#
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||||
*.~
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||||
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||||
@ -19,12 +19,15 @@
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||||
\section{TODO}
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||||
\begin{itemize}
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||||
\item Beispiele schlechter plots sollten mehr Bezug zu den Typen von
|
||||
plots haben, die wir machen!
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||||
plots haben, die wir machen! Check WS1617 presentations for examples.
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||||
\item subplot
|
||||
\item Uebersicht zu wichtigen plot Befehlen (plot, scatter, bar, step, ...)
|
||||
\item Funktionenplotten (siehe auch Design patterns) und untersampleter Sinus
|
||||
\item Verschiedene Stile fuer Achsenbeschriftung (gross/kleinschreibungen, Kalmmertyp fuer Einheiten), stay with one style!
|
||||
\item Stay with a coherent style (font type/style/size, colors schemes, line styles/thickness, point styles)
|
||||
\item Verschiedene Stile fuer Achsenbeschriftung (gross/kleinschreibungen, Klammertyp fuer Einheiten), stay with one style!
|
||||
\item Stay with a coherent style (font type/style/size, colors schemes, line styles/thickness, point styles), same line style in all plots for the same quantity. How to do consistent line styles in matlab (python: dictionary for kwargs)?
|
||||
\item Different plots for journal papers and presentations!
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||||
\item Color universal design for color blind people:
|
||||
\url{http://jfly.iam.u-tokyo.ac.jp/color/}
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||||
\end{itemize}
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||||
|
||||
\end{document}
|
||||
|
||||
@ -20,6 +20,11 @@
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||||
\begin{itemize}
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||||
\item Add spikeraster function
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||||
\item Multitrial firing rates
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||||
\item Choice of bin width for PSTH, kernel width, also in relation sto
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||||
stimulus time scale
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||||
\item Kernle firing rate: discuss different kernel shapes, in
|
||||
particular causal kernels (gamma, exponential), relation to synaptic
|
||||
potentials
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||||
\end{itemize}
|
||||
|
||||
\end{document}
|
||||
|
||||
@ -1,95 +0,0 @@
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||||
% GNUPLOT: LaTeX picture with Postscript
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||||
\begingroup
|
||||
\makeatletter
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||||
\providecommand\color[2][]{%
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||||
\GenericError{(gnuplot) \space\space\space\@spaces}{%
|
||||
Package color not loaded in conjunction with
|
||||
terminal option `colourtext'%
|
||||
}{See the gnuplot documentation for explanation.%
|
||||
}{Either use 'blacktext' in gnuplot or load the package
|
||||
color.sty in LaTeX.}%
|
||||
\renewcommand\color[2][]{}%
|
||||
}%
|
||||
\providecommand\includegraphics[2][]{%
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||||
\GenericError{(gnuplot) \space\space\space\@spaces}{%
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||||
Package graphicx or graphics not loaded%
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||||
}{See the gnuplot documentation for explanation.%
|
||||
}{The gnuplot epslatex terminal needs graphicx.sty or graphics.sty.}%
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||||
\renewcommand\includegraphics[2][]{}%
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||||
}%
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||||
\providecommand\rotatebox[2]{#2}%
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||||
\@ifundefined{ifGPcolor}{%
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||||
\newif\ifGPcolor
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||||
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||||
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||||
\newif\ifGPblacktext
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||||
\GPblacktexttrue
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||||
}{}%
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||||
% define a \g@addto@macro without @ in the name:
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||||
\let\gplgaddtomacro\g@addto@macro
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||||
% define empty templates for all commands taking text:
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||||
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||||
\gdef\gplfronttext{}%
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||||
\makeatother
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||||
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||||
% no textcolor at all
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||||
\def\colorrgb#1{}%
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||||
\def\colorgray#1{}%
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||||
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||||
% gray or color?
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||||
\ifGPcolor
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||||
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||||
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||||
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\expandafter\def\csname LT3\endcsname{\color[rgb]{1,0,1}}%
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\expandafter\def\csname LT4\endcsname{\color[rgb]{0,1,1}}%
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\expandafter\def\csname LT5\endcsname{\color[rgb]{1,1,0}}%
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\expandafter\def\csname LT6\endcsname{\color[rgb]{0,0,0}}%
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\expandafter\def\csname LT7\endcsname{\color[rgb]{1,0.3,0}}%
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\expandafter\def\csname LT8\endcsname{\color[rgb]{0.5,0.5,0.5}}%
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\else
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||||
% gray
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||||
\def\colorrgb#1{\color{black}}%
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||||
\def\colorgray#1{\color[gray]{#1}}%
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||||
\expandafter\def\csname LTw\endcsname{\color{white}}%
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\expandafter\def\csname LTb\endcsname{\color{black}}%
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\expandafter\def\csname LTa\endcsname{\color{black}}%
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\expandafter\def\csname LT0\endcsname{\color{black}}%
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\expandafter\def\csname LT1\endcsname{\color{black}}%
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\expandafter\def\csname LT2\endcsname{\color{black}}%
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\expandafter\def\csname LT3\endcsname{\color{black}}%
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\expandafter\def\csname LT4\endcsname{\color{black}}%
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\expandafter\def\csname LT5\endcsname{\color{black}}%
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\expandafter\def\csname LT6\endcsname{\color{black}}%
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\expandafter\def\csname LT7\endcsname{\color{black}}%
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\expandafter\def\csname LT8\endcsname{\color{black}}%
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\fi
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\fi
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\setlength{\unitlength}{0.0500bp}%
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\begin{picture}(6462.00,1700.00)%
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\gplgaddtomacro\gplbacktext{%
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\csname LTb\endcsname%
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\put(6329,421){\makebox(0,0){\strut{}Time}}%
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\put(910,270){\makebox(0,0){\strut{}$t_{1}$}}%
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\put(1412,270){\makebox(0,0){\strut{}$t_{2}$}}%
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\put(2123,270){\makebox(0,0){\strut{}$t_{3}$}}%
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\put(2413,270){\makebox(0,0){\strut{}$t_{4}$}}%
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\put(2717,270){\makebox(0,0){\strut{}$t_{5}$}}%
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\put(3167,270){\makebox(0,0){\strut{}$t_{6}$}}%
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\put(4033,270){\makebox(0,0){\strut{}$t_{7}$}}%
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\put(4650,270){\makebox(0,0){\strut{}$t_{8}$}}%
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\put(5685,270){\makebox(0,0){\strut{}$t_{9}$}}%
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}%
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\gplgaddtomacro\gplfronttext{%
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}%
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\gplbacktext
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\put(0,0){\includegraphics{pointprocessscetchA}}%
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\gplfronttext
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||||
\end{picture}%
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\endgroup
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||||
@ -1,130 +0,0 @@
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% GNUPLOT: LaTeX picture with Postscript
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||||
\begingroup
|
||||
\makeatletter
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||||
\providecommand\color[2][]{%
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||||
\GenericError{(gnuplot) \space\space\space\@spaces}{%
|
||||
Package color not loaded in conjunction with
|
||||
terminal option `colourtext'%
|
||||
}{See the gnuplot documentation for explanation.%
|
||||
}{Either use 'blacktext' in gnuplot or load the package
|
||||
color.sty in LaTeX.}%
|
||||
\renewcommand\color[2][]{}%
|
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}%
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||||
\providecommand\includegraphics[2][]{%
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\GenericError{(gnuplot) \space\space\space\@spaces}{%
|
||||
Package graphicx or graphics not loaded%
|
||||
}{See the gnuplot documentation for explanation.%
|
||||
}{The gnuplot epslatex terminal needs graphicx.sty or graphics.sty.}%
|
||||
\renewcommand\includegraphics[2][]{}%
|
||||
}%
|
||||
\providecommand\rotatebox[2]{#2}%
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||||
\@ifundefined{ifGPcolor}{%
|
||||
\newif\ifGPcolor
|
||||
\GPcolortrue
|
||||
}{}%
|
||||
\@ifundefined{ifGPblacktext}{%
|
||||
\newif\ifGPblacktext
|
||||
\GPblacktexttrue
|
||||
}{}%
|
||||
% define a \g@addto@macro without @ in the name:
|
||||
\let\gplgaddtomacro\g@addto@macro
|
||||
% define empty templates for all commands taking text:
|
||||
\gdef\gplbacktext{}%
|
||||
\gdef\gplfronttext{}%
|
||||
\makeatother
|
||||
\ifGPblacktext
|
||||
% no textcolor at all
|
||||
\def\colorrgb#1{}%
|
||||
\def\colorgray#1{}%
|
||||
\else
|
||||
% gray or color?
|
||||
\ifGPcolor
|
||||
\def\colorrgb#1{\color[rgb]{#1}}%
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||||
\def\colorgray#1{\color[gray]{#1}}%
|
||||
\expandafter\def\csname LTw\endcsname{\color{white}}%
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||||
\expandafter\def\csname LTb\endcsname{\color{black}}%
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||||
\expandafter\def\csname LTa\endcsname{\color{black}}%
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||||
\expandafter\def\csname LT0\endcsname{\color[rgb]{1,0,0}}%
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||||
\expandafter\def\csname LT1\endcsname{\color[rgb]{0,1,0}}%
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\expandafter\def\csname LT2\endcsname{\color[rgb]{0,0,1}}%
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\expandafter\def\csname LT3\endcsname{\color[rgb]{1,0,1}}%
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\expandafter\def\csname LT4\endcsname{\color[rgb]{0,1,1}}%
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\expandafter\def\csname LT5\endcsname{\color[rgb]{1,1,0}}%
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||||
\expandafter\def\csname LT6\endcsname{\color[rgb]{0,0,0}}%
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\expandafter\def\csname LT7\endcsname{\color[rgb]{1,0.3,0}}%
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\expandafter\def\csname LT8\endcsname{\color[rgb]{0.5,0.5,0.5}}%
|
||||
\else
|
||||
% gray
|
||||
\def\colorrgb#1{\color{black}}%
|
||||
\def\colorgray#1{\color[gray]{#1}}%
|
||||
\expandafter\def\csname LTw\endcsname{\color{white}}%
|
||||
\expandafter\def\csname LTb\endcsname{\color{black}}%
|
||||
\expandafter\def\csname LTa\endcsname{\color{black}}%
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||||
\expandafter\def\csname LT0\endcsname{\color{black}}%
|
||||
\expandafter\def\csname LT1\endcsname{\color{black}}%
|
||||
\expandafter\def\csname LT2\endcsname{\color{black}}%
|
||||
\expandafter\def\csname LT3\endcsname{\color{black}}%
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||||
\expandafter\def\csname LT4\endcsname{\color{black}}%
|
||||
\expandafter\def\csname LT5\endcsname{\color{black}}%
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||||
\expandafter\def\csname LT6\endcsname{\color{black}}%
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||||
\expandafter\def\csname LT7\endcsname{\color{black}}%
|
||||
\expandafter\def\csname LT8\endcsname{\color{black}}%
|
||||
\fi
|
||||
\fi
|
||||
\setlength{\unitlength}{0.0500bp}%
|
||||
\begin{picture}(6462.00,3740.00)%
|
||||
\gplgaddtomacro\gplbacktext{%
|
||||
\csname LTb\endcsname%
|
||||
\put(122,3587){\makebox(0,0)[l]{\strut{}\normalsize Event times $\{t_i\}$}}%
|
||||
\put(6329,2947){\makebox(0,0){\strut{}Time}}%
|
||||
\put(910,2865){\makebox(0,0){\strut{}$t_{1}$}}%
|
||||
\put(1412,2865){\makebox(0,0){\strut{}$t_{2}$}}%
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||||
\put(2123,2865){\makebox(0,0){\strut{}$t_{3}$}}%
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||||
\put(2413,2865){\makebox(0,0){\strut{}$t_{4}$}}%
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||||
\put(2717,2865){\makebox(0,0){\strut{}$t_{5}$}}%
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||||
\put(3167,2865){\makebox(0,0){\strut{}$t_{6}$}}%
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||||
\put(4033,2865){\makebox(0,0){\strut{}$t_{7}$}}%
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\put(4650,2865){\makebox(0,0){\strut{}$t_{8}$}}%
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\put(5685,2865){\makebox(0,0){\strut{}$t_{9}$}}%
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}%
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\gplgaddtomacro\gplfronttext{%
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}%
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\gplgaddtomacro\gplbacktext{%
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\csname LTb\endcsname%
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||||
\put(122,2465){\makebox(0,0)[l]{\strut{}\normalsize Intervals $\{T_i\}, \; T_i = t_{i+1} - t_i$}}%
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||||
\put(6329,1825){\makebox(0,0){\strut{}Time}}%
|
||||
\put(1161,1770){\makebox(0,0){\strut{}$T_{1}$}}%
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||||
\put(1767,1770){\makebox(0,0){\strut{}$T_{2}$}}%
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||||
\put(2268,1770){\makebox(0,0){\strut{}$T_{3}$}}%
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||||
\put(2565,1770){\makebox(0,0){\strut{}$T_{4}$}}%
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\put(2942,1770){\makebox(0,0){\strut{}$T_{5}$}}%
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\put(3600,1770){\makebox(0,0){\strut{}$T_{6}$}}%
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||||
\put(4341,1770){\makebox(0,0){\strut{}$T_{7}$}}%
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||||
\put(5168,1770){\makebox(0,0){\strut{}$T_{8}$}}%
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||||
}%
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||||
\gplgaddtomacro\gplfronttext{%
|
||||
}%
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||||
\gplgaddtomacro\gplbacktext{%
|
||||
\colorrgb{0.00,0.00,0.00}%
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||||
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||||
\colorrgb{0.00,0.00,0.00}%
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||||
\put(333,460){\makebox(0,0)[r]{\strut{}$2$}}%
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||||
\colorrgb{0.00,0.00,0.00}%
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||||
\put(333,652){\makebox(0,0)[r]{\strut{}$4$}}%
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||||
\colorrgb{0.00,0.00,0.00}%
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||||
\put(333,844){\makebox(0,0)[r]{\strut{}$6$}}%
|
||||
\colorrgb{0.00,0.00,0.00}%
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\put(333,1036){\makebox(0,0)[r]{\strut{}$8$}}%
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\colorrgb{0.00,0.00,0.00}%
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\put(333,1228){\makebox(0,0)[r]{\strut{}$10$}}%
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||||
\csname LTb\endcsname%
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||||
\put(122,1487){\makebox(0,0)[l]{\strut{}\normalsize Event counts $\{ n_i \}$}}%
|
||||
\put(6329,57){\makebox(0,0){\strut{}Time}}%
|
||||
}%
|
||||
\gplgaddtomacro\gplfronttext{%
|
||||
}%
|
||||
\gplbacktext
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||||
\put(0,0){\includegraphics{pointprocessscetchB}}%
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||||
\gplfronttext
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||||
\end{picture}%
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||||
\endgroup
|
||||
@ -28,7 +28,11 @@
|
||||
\item Random-walk behutsam mit einer Schleife, dann zwei Schleifen. Plus Bildchen.
|
||||
\item Random-Walk with drift is model for decision making! See resoures/GoldShadlen2007 paper, Figure 2. Das wird auch in Systems Neurosciene \texttt{9 - Kognitive Kontrolle II.pdf} behandelt.
|
||||
\item Doppelte for-Schleife
|
||||
\item File output and input (load, save, fprintf, scanf) (extra chapter?)
|
||||
\item File handling: (extra chapter?)
|
||||
\begin{itemize}
|
||||
\item output and input (load, save, fprintf, scanf)
|
||||
\item dir() function
|
||||
\end{itemize}
|
||||
\item help() und doc()
|
||||
\item A box about sampling of contiunous data.
|
||||
\item A box about foo and bar?
|
||||
|
||||
@ -1,9 +1,15 @@
|
||||
all:
|
||||
for d in `ls -d project_*/`; do \
|
||||
echo "Processing $$d" ; \
|
||||
a=$$(echo $$d*.tex) ; \
|
||||
rm $${a%.tex}.zip ; \
|
||||
cd $$d; $(MAKE) zip ; cd .. ; \
|
||||
all: projects evalutation
|
||||
|
||||
evaluation: evaluation.pdf
|
||||
evaluation.pdf: evaluation.tex
|
||||
pdflatex $<
|
||||
|
||||
projects:
|
||||
for d in `ls -d project_*`; do \
|
||||
if test "x$$d" != "xproject_template"; then \
|
||||
echo "Processing $$d" ; \
|
||||
cd $$d; $(MAKE) zip ; cd .. ; \
|
||||
fi \
|
||||
done
|
||||
|
||||
mv project_*/*zip .
|
||||
@ -11,8 +17,10 @@ all:
|
||||
clean:
|
||||
for d in `ls -d project_*/`; do \
|
||||
echo "Cleaning up $$d" ; \
|
||||
cd $$d; $(MAKE) clean ; cd .. ; \
|
||||
$(MAKE) -C $$d clean ; \
|
||||
done
|
||||
|
||||
rm -f *~
|
||||
rm -f evaluation.aux evaluation.log
|
||||
rm -f *.zip
|
||||
rm -rf auto
|
||||
|
||||
@ -1,44 +0,0 @@
|
||||
\fbox{\parbox{0.985\linewidth}{ \small
|
||||
|
||||
{\bf Evaluation criteria:}
|
||||
|
||||
Each project has three elements that are graded: (i) the code,
|
||||
(ii) the slides/figures, and (iii) the presentation.
|
||||
|
||||
\vspace{1ex}
|
||||
|
||||
The {\bf code} and the {\bf presentation} should be uploaded to
|
||||
ILIAS at latest on Thursday, February 9th, 12:59h. We will
|
||||
store all presentations on one computer to allow fast
|
||||
transitions between talks. The presentations start on Thursday,
|
||||
February 9th at 1:00h c.t.. Please hand in your presentation as
|
||||
a pdf file. Bundle everything (the pdf, the code, and the data)
|
||||
into a {\em single} zip-file.
|
||||
|
||||
\vspace{1ex}
|
||||
|
||||
The {\bf code} should be executable without any further
|
||||
adjustments from our side. A single \texttt{main.m} script should
|
||||
coordinate the analysis by calling functions and sub-scripts and
|
||||
should produce the {\em same} figures that you use in your
|
||||
slides. The code should be properly commented and comprehensible
|
||||
by a third person (use proper and consistent variable and
|
||||
function names).
|
||||
|
||||
\vspace{1ex}
|
||||
|
||||
\textbf{Please write your name and matriculation number as a
|
||||
comment at the top of the \texttt{main.m} script.}
|
||||
|
||||
\vspace{1ex}
|
||||
|
||||
The {\bf presentation} should be {\em at most} 10min long and be
|
||||
held in English. In the presentation you should (i) briefly
|
||||
describe the problem, (ii) present figures introducing, showing,
|
||||
and discussing your results, and (iii) explain how you solved
|
||||
the problem algorithmically (don't show your entire code). All
|
||||
data-related figures you show in the presentation should be
|
||||
produced by your program. It is always a good idea to illustrate
|
||||
the problem with basic plots of the raw-data. Make sure the axis
|
||||
labels are large enough!
|
||||
}}
|
||||
44
projects/evaluation.tex
Normal file
44
projects/evaluation.tex
Normal file
@ -0,0 +1,44 @@
|
||||
\documentclass[12pt,a4paper]{article}
|
||||
|
||||
\usepackage[ngerman]{babel}
|
||||
\usepackage{pslatex}
|
||||
|
||||
%%%%% page style %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage[left=10mm,right=10mm,top=10mm,bottom=10mm,headsep=0ex,headheight=0ex,footskip=0ex]{geometry}
|
||||
\pagestyle{empty}
|
||||
|
||||
\newcounter{studentnum}
|
||||
\newcommand{\num}{\rule{0pt}{5.8ex}{\stepcounter{studentnum}\small \arabic{studentnum}}}
|
||||
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\begin{document}
|
||||
|
||||
\sffamily
|
||||
\section*{Scientific computing WS16/17}
|
||||
|
||||
\begin{tabular}{|p{0.15\textwidth}|p{0.07\textwidth}|p{0.07\textwidth}|p{0.07\textwidth}|p{0.07\textwidth}|p{0.07\textwidth}|p{0.07\textwidth}|p{0.07\textwidth}|p{0.07\textwidth}|p{0.07\textwidth}|}
|
||||
\hline
|
||||
Name & \multicolumn{5}{l|}{Code} & \multicolumn{3}{l|}{Functions} & Figures \\
|
||||
& runs & docu & variable function script names & style & extras & NOT \newline used as scripts & docu & sep. \newline algo./ plot & saved \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\num & & & & & & & & & \\ \hline
|
||||
\end{tabular}
|
||||
|
||||
\end{document}
|
||||
56
projects/header.tex
Normal file
56
projects/header.tex
Normal file
@ -0,0 +1,56 @@
|
||||
\usepackage{pslatex}
|
||||
\usepackage[mediumspace,mediumqspace,squaren]{SIunits} % \ohm, \micro
|
||||
\usepackage{xcolor}
|
||||
\usepackage{graphicx}
|
||||
\usepackage[breaklinks=true,bookmarks=true,bookmarksopen=true,pdfpagemode=UseNone,pdfstartview=FitH,colorlinks=true,citecolor=blue]{hyperref}
|
||||
|
||||
%%%%% layout %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage[left=20mm,right=20mm,top=25mm,bottom=25mm]{geometry}
|
||||
\pagestyle{headandfoot}
|
||||
\header{{\bfseries\large Scientific Computing}}{{\bfseries\large Project: \ptitle}}{{\bfseries\large Januar 24th, 2017}}
|
||||
\runningfooter{}{\thepage}{}
|
||||
|
||||
\setlength{\baselineskip}{15pt}
|
||||
\setlength{\parindent}{0.0cm}
|
||||
\setlength{\parskip}{0.3cm}
|
||||
\renewcommand{\baselinestretch}{1.15}
|
||||
|
||||
%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{listings}
|
||||
\lstset{
|
||||
language=Matlab,
|
||||
basicstyle=\ttfamily\footnotesize,
|
||||
numbers=left,
|
||||
numberstyle=\tiny,
|
||||
title=\lstname,
|
||||
showstringspaces=false,
|
||||
commentstyle=\itshape\color{darkgray},
|
||||
breaklines=true,
|
||||
breakautoindent=true,
|
||||
columns=flexible,
|
||||
frame=single,
|
||||
xleftmargin=1em,
|
||||
xrightmargin=1em,
|
||||
aboveskip=10pt
|
||||
}
|
||||
|
||||
%%%%% math stuff: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{amsmath}
|
||||
\usepackage{amssymb}
|
||||
\usepackage{bm}
|
||||
\usepackage{dsfont}
|
||||
\newcommand{\naZ}{\mathds{N}}
|
||||
\newcommand{\gaZ}{\mathds{Z}}
|
||||
\newcommand{\raZ}{\mathds{Q}}
|
||||
\newcommand{\reZ}{\mathds{R}}
|
||||
\newcommand{\reZp}{\mathds{R^+}}
|
||||
\newcommand{\reZpN}{\mathds{R^+_0}}
|
||||
\newcommand{\koZ}{\mathds{C}}
|
||||
|
||||
%%%%% page breaks %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\newcommand{\continue}{\vfill\hspace*{\fill}$\rightarrow$\newpage}
|
||||
|
||||
%%%%% new commands %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\newcommand{\qt}[1]{\textbf{#1}\\}
|
||||
\newcommand{\code}[1]{\texttt{#1}}
|
||||
|
||||
59
projects/instructions.tex
Normal file
59
projects/instructions.tex
Normal file
@ -0,0 +1,59 @@
|
||||
\setlength{\fboxsep}{2ex}
|
||||
\fbox{\parbox{1\linewidth}{\small
|
||||
|
||||
{\bf Evaluation criteria:}
|
||||
|
||||
Each project has three elements that are graded: (i) the code,
|
||||
(ii) the slides/figures, and (iii) the presentation.
|
||||
|
||||
\vspace{1ex}
|
||||
{\bf Dates:}
|
||||
|
||||
The {\bf code} and the {\bf presentation} should be uploaded to
|
||||
ILIAS at latest on Thursday, February 9th, 12:59h. We will
|
||||
store all presentations on one computer to allow fast
|
||||
transitions between talks. The presentations start on Thursday,
|
||||
February 9th at 1:00h c.t..
|
||||
|
||||
\vspace{1ex}
|
||||
{\bf Files:}
|
||||
|
||||
Please hand in your presentation as a pdf file. Bundle
|
||||
everything (the pdf, the code, and the data) into a {\em single}
|
||||
zip-file.
|
||||
|
||||
\vspace{1ex}
|
||||
{\bf Code:}
|
||||
|
||||
The {\bf code} should be executable without any further
|
||||
adjustments from our side. A single \texttt{main.m} script
|
||||
should coordinate the analysis by calling functions and
|
||||
sub-scripts and should produce the {\em same} figures
|
||||
(\texttt{saveas()}-function, pdf or png format) that you use in
|
||||
your slides. The code should be properly commented and
|
||||
comprehensible by a third person (use proper and consistent
|
||||
variable and function names).
|
||||
% Hint: make the zip file you want to upload, unpack it
|
||||
% somewhere else and check if your main script is running.
|
||||
|
||||
\vspace{1ex}
|
||||
|
||||
\emph{Please write your name and matriculation number as a
|
||||
comment at the top of the \texttt{main.m} script.}
|
||||
|
||||
|
||||
\vspace{1ex}
|
||||
{\bf Presentation:}
|
||||
|
||||
The {\bf presentation} should be {\em at most} 10min long and be
|
||||
held in English. In the presentation you should (i) briefly
|
||||
describe the problem, (ii) present figures introducing, showing,
|
||||
and discussing your results, and (iii) explain how you solved
|
||||
the problem algorithmically (don't show your entire code). All
|
||||
data-related figures you show in the presentation should be
|
||||
produced by your program --- no editing or labeling by
|
||||
PowerPoint or other software. It is always a good idea to
|
||||
illustrate the problem with basic plots of the raw-data. Make
|
||||
sure the axis labels are large enough!
|
||||
|
||||
}}
|
||||
25
projects/project.mk
Normal file
25
projects/project.mk
Normal file
@ -0,0 +1,25 @@
|
||||
BASENAME=$(subst project_,,$(notdir $(CURDIR)))
|
||||
|
||||
latex:
|
||||
pdflatex $(BASENAME).tex
|
||||
pdflatex $(BASENAME).tex
|
||||
|
||||
|
||||
pdf: $(BASENAME).pdf
|
||||
|
||||
$(BASENAME).pdf : $(BASENAME).tex ../header.tex ../instructions.tex
|
||||
pdflatex -interaction=scrollmode $< | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex -interaction=scrollmode $< || true
|
||||
|
||||
|
||||
watch :
|
||||
while true; do ! make -q pdf && make pdf; sleep 0.5; done
|
||||
|
||||
clean:
|
||||
rm -f *~ code/*~ solution/*~ data/*~
|
||||
rm -rf *.log *.aux *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
rm -f *.zip
|
||||
|
||||
zip: latex
|
||||
rm -f zip $(BASENAME).zip
|
||||
zip $(BASENAME).zip *.pdf *.m data/* $(ZIPFILES)
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat data/*.mat
|
||||
include ../project.mk
|
||||
|
||||
@ -1,32 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{WS 2016/17}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Adaptation time-constant}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Grewe}{phone: 29 74588}%
|
||||
{email: jan.grewe@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\section*{Estimating the adaptation time-constant.}
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf data/*.mat
|
||||
include ../project.mk
|
||||
|
||||
@ -1,32 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{WS 2016/17}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{EOD waveform}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Grewe}{phone: 29 74588}%
|
||||
{email: jan.grewe@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf data/*.mat
|
||||
include ../project.mk
|
||||
|
||||
@ -1,32 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{WS 2016/17}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Eye tracker}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Grewe}{phone: 29 74588}%
|
||||
{email: jan.grewe@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\section*{Analysis of eye trajectories.}
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat *.m
|
||||
include ../project.mk
|
||||
|
||||
@ -1,52 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2014
|
||||
-- 11/05/2014}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Benda}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
|
||||
%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{listings}
|
||||
\lstset{
|
||||
basicstyle=\ttfamily,
|
||||
numbers=left,
|
||||
showstringspaces=false,
|
||||
language=Matlab,
|
||||
breaklines=true,
|
||||
breakautoindent=true,
|
||||
columns=flexible,
|
||||
frame=single,
|
||||
% captionpos=t,
|
||||
xleftmargin=2em,
|
||||
xrightmargin=1em,
|
||||
% aboveskip=11pt,
|
||||
%title=\lstname,
|
||||
% title={\protect\filename@parse{\lstname}\protect\filename@base.\protect\filename@ext}
|
||||
}
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Stimulus discrimination}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Benda}{phone: 29 74573}%
|
||||
{email: jan.benda@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
|
||||
35
projects/project_fano_slope/lifboltzmannspikes.m
Normal file
35
projects/project_fano_slope/lifboltzmannspikes.m
Normal file
@ -0,0 +1,35 @@
|
||||
function spikes = lifboltzmannspikes(trials, input, tmax, gain)
|
||||
% Generate spike times of a leaky integrate-and-fire neuron.
|
||||
% trials: the number of trials to be generated.
|
||||
% input: the stimulus intensity.
|
||||
% tmax: the duration of a trial.
|
||||
% gain: gain of the neuron, i.e. the slope factor of the boltzmann input.
|
||||
|
||||
tau = 0.01;
|
||||
D = 1e-2;
|
||||
imax = 25;
|
||||
ithresh = 10;
|
||||
slope = gain;
|
||||
vreset = 0.0;
|
||||
vthresh = 10.0;
|
||||
dt = 1e-4;
|
||||
|
||||
n = ceil(tmax/dt);
|
||||
inb = imax./(1.0+exp(-slope.*(input - ithresh)));
|
||||
spikes = cell(trials, 1);
|
||||
for k=1:trials
|
||||
times = [];
|
||||
j = 1;
|
||||
v = vreset + (vthresh - vreset) * rand();
|
||||
noise = sqrt(2.0*D)*randn(n, 1)/sqrt(dt);
|
||||
for i=1:n
|
||||
v = v + (- v + noise(i) + inb)*dt/tau;
|
||||
if v >= vthresh
|
||||
v = vreset;
|
||||
times(j) = i*dt;
|
||||
j = j + 1;
|
||||
end
|
||||
end
|
||||
spikes{k} = times;
|
||||
end
|
||||
end
|
||||
@ -76,7 +76,8 @@ plot(false2s, true1s);
|
||||
T = 0.1;
|
||||
gains = 0.01:0.01:1.0;
|
||||
cmax = 100;
|
||||
ds = zeros(length(gains), 1);
|
||||
dstt = zeros(length(gains), 1);
|
||||
dsff = zeros(length(gains), 1);
|
||||
for k = 1:length(gains)
|
||||
gain = gains(k);
|
||||
spikes1 = lifboltzmannspikes(trials, I1, tmax, gain);
|
||||
@ -84,9 +85,11 @@ for k = 1:length(gains)
|
||||
[c1, b1] = counthist(spikes1, 0.0, tmax, T, cmax);
|
||||
[c2, b2] = counthist(spikes2, 0.0, tmax, T, cmax);
|
||||
[d, thresholds, true1s, false1s, true2s, false2s, pratio] = discriminability(spikes1, spikes2, tmax, T, cmax);
|
||||
ds(k) = d;
|
||||
dstt(k) = d;
|
||||
dsff(k) = min(false1s + false2s);
|
||||
end
|
||||
figure()
|
||||
plot(gains, ds)
|
||||
|
||||
|
||||
plot(gains, dstt);
|
||||
hold on;
|
||||
plot(gains, dsff);
|
||||
hold off;
|
||||
|
||||
@ -20,7 +20,7 @@ function spikes = lifboltzmannspikes(trials, input, tmax, gain)
|
||||
for k=1:trials
|
||||
times = [];
|
||||
j = 1;
|
||||
v = vreset;
|
||||
v = vreset + (vthresh - vreset) * rand();
|
||||
noise = sqrt(2.0*D)*randn(n, 1)/sqrt(dt);
|
||||
for i=1:n
|
||||
v = v + (- v + noise(i) + inb)*dt/tau;
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat
|
||||
include ../project.mk
|
||||
|
||||
@ -1,37 +1,16 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014
|
||||
-- 11/06/2014}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Fabian Sinz}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Fano factor test}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Benda}{phone: 29 74573}%
|
||||
{email: jan.benda@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\begin{questions}
|
||||
\question The Fano factor $F=\frac{\sigma^2}{\mu}$ relates the
|
||||
variance of a spike count $\sigma^2$ to the mean spike count
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat *.m
|
||||
include ../project.mk
|
||||
|
||||
@ -1,52 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2014
|
||||
-- 11/05/2014}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Benda}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
|
||||
%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{listings}
|
||||
\lstset{
|
||||
basicstyle=\ttfamily,
|
||||
numbers=left,
|
||||
showstringspaces=false,
|
||||
language=Matlab,
|
||||
breaklines=true,
|
||||
breakautoindent=true,
|
||||
columns=flexible,
|
||||
frame=single,
|
||||
% captionpos=t,
|
||||
xleftmargin=2em,
|
||||
xrightmargin=1em,
|
||||
% aboveskip=11pt,
|
||||
%title=\lstname,
|
||||
% title={\protect\filename@parse{\lstname}\protect\filename@base.\protect\filename@ext}
|
||||
}
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Stimulus discrimination}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Benda}{phone: 29 74573}%
|
||||
{email: jan.benda@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
|
||||
@ -19,7 +19,7 @@ function spikes = lifspikes(trials, input, tmax)
|
||||
for k=1:trials
|
||||
times = [];
|
||||
j = 1;
|
||||
v = vreset + (vthresh-vreset)*rand(1);
|
||||
v = vreset + (vthresh-vreset)*rand();
|
||||
noise = sqrt(2.0*D)*randn(n, 1)/sqrt(dt);
|
||||
for i=1:length(noise)
|
||||
v = v + (- v + noise(i) + input)*dt/tau;
|
||||
|
||||
@ -19,7 +19,7 @@ function spikes = lifspikes(trials, input, tmax)
|
||||
for k=1:trials
|
||||
times = [];
|
||||
j = 1;
|
||||
v = vreset + (vthresh-vreset)*rand(1);
|
||||
v = vreset + (vthresh-vreset)*rand();
|
||||
noise = sqrt(2.0*D)*randn(n, 1)/sqrt(dt);
|
||||
for i=1:length(noise)
|
||||
v = v + (- v + noise(i) + input)*dt/tau;
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf data/*.mat
|
||||
include ../project.mk
|
||||
|
||||
BIN
projects/project_input_resistance/data/resistance_CMS_1.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_CMS_1.mat
Normal file
Binary file not shown.
BIN
projects/project_input_resistance/data/resistance_CMS_2.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_CMS_2.mat
Normal file
Binary file not shown.
BIN
projects/project_input_resistance/data/resistance_CMS_3.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_CMS_3.mat
Normal file
Binary file not shown.
BIN
projects/project_input_resistance/data/resistance_CMS_4.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_CMS_4.mat
Normal file
Binary file not shown.
BIN
projects/project_input_resistance/data/resistance_CMS_5.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_CMS_5.mat
Normal file
Binary file not shown.
BIN
projects/project_input_resistance/data/resistance_MS_1.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_MS_1.mat
Normal file
Binary file not shown.
BIN
projects/project_input_resistance/data/resistance_MS_2.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_MS_2.mat
Normal file
Binary file not shown.
BIN
projects/project_input_resistance/data/resistance_MS_3.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_MS_3.mat
Normal file
Binary file not shown.
BIN
projects/project_input_resistance/data/resistance_MS_4.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_MS_4.mat
Normal file
Binary file not shown.
BIN
projects/project_input_resistance/data/resistance_MS_5.mat
Normal file
BIN
projects/project_input_resistance/data/resistance_MS_5.mat
Normal file
Binary file not shown.
@ -1,32 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{WS 2016/17}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Cellular properties}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Grewe}{phone: 29 74588}%
|
||||
{email: jan.grewe@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\section*{Estimating cellular properties of different cell types.}
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat *.m
|
||||
include ../project.mk
|
||||
|
||||
@ -1,55 +1,16 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014
|
||||
-- 11/06/2014}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Benda}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
|
||||
%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{listings}
|
||||
\lstset{
|
||||
basicstyle=\ttfamily,
|
||||
numbers=left,
|
||||
showstringspaces=false,
|
||||
language=Matlab,
|
||||
breaklines=true,
|
||||
breakautoindent=true,
|
||||
columns=flexible,
|
||||
frame=single,
|
||||
% captionpos=t,
|
||||
xleftmargin=2em,
|
||||
xrightmargin=1em,
|
||||
% aboveskip=11pt,
|
||||
%title=\lstname,
|
||||
% title={\protect\filename@parse{\lstname}\protect\filename@base.\protect\filename@ext}
|
||||
}
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Interspike-intervall correlations}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Benda}{phone: 29 74573}%
|
||||
{email: jan.benda@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\begin{questions}
|
||||
\question You are recording the activity of a neuron in response to
|
||||
constant stimuli of intensity $I$ (think of that, for example,
|
||||
|
||||
@ -32,7 +32,7 @@ function spikes = lifadaptspikes( trials, input, tmaxdt, D, tauadapt, adaptincr
|
||||
for k=1:trials
|
||||
times = [];
|
||||
j = 1;
|
||||
v = vreset;
|
||||
v = vreset + (vthresh-vreset)*rand();
|
||||
a = 0.0;
|
||||
noise = sqrt(2.0*D)*randn( length( input ), 1 )/sqrt(dt);
|
||||
for i=1:length( noise )
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat *.m
|
||||
include ../project.mk
|
||||
|
||||
@ -1,52 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2014
|
||||
-- 11/05/2014}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Benda}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
|
||||
%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{listings}
|
||||
\lstset{
|
||||
basicstyle=\ttfamily,
|
||||
numbers=left,
|
||||
showstringspaces=false,
|
||||
language=Matlab,
|
||||
breaklines=true,
|
||||
breakautoindent=true,
|
||||
columns=flexible,
|
||||
frame=single,
|
||||
% captionpos=t,
|
||||
xleftmargin=2em,
|
||||
xrightmargin=1em,
|
||||
% aboveskip=11pt,
|
||||
%title=\lstname,
|
||||
% title={\protect\filename@parse{\lstname}\protect\filename@base.\protect\filename@ext}
|
||||
}
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{ISI distributions}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Benda}{phone: 29 74573}%
|
||||
{email: jan.benda@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
|
||||
@ -28,7 +28,7 @@ function spikes = lifouspikes( trials, input, tmaxdt, D, outau )
|
||||
times = [];
|
||||
j = 1;
|
||||
n = 0.0;
|
||||
v = vreset;
|
||||
v = vreset + (vthresh-vreset)*rand();
|
||||
noise = sqrt(2.0*D)*randn( length( input ), 1 )/sqrt(dt);
|
||||
for i=1:length( noise )
|
||||
n = n + ( - n + noise(i))*dt/outau;
|
||||
|
||||
@ -28,7 +28,7 @@ function spikes = pifouspikes( trials, input, tmaxdt, D, outau )
|
||||
times = [];
|
||||
j = 1;
|
||||
n = 0.0;
|
||||
v = vreset;
|
||||
v = vreset + (vthresh-vreset)*rand();
|
||||
noise = sqrt(2.0*D)*randn( length( input ), 1 )/sqrt(dt);
|
||||
for i=1:length( noise )
|
||||
n = n + ( - n + noise(i))*dt/outau;
|
||||
|
||||
11
projects/project_isipdffit/solution/invgauss.m
Normal file
11
projects/project_isipdffit/solution/invgauss.m
Normal file
@ -0,0 +1,11 @@
|
||||
function p = invgauss(x, mu, D)
|
||||
if abs(x) < 1e-8
|
||||
p = zeros(size(x))
|
||||
else
|
||||
if x < 0
|
||||
x = -x;
|
||||
end
|
||||
p = exp(-(x-mu).^2./4.0./D./x./mu./mu)./sqrt(4.*pi.*D.*x.^3.0);
|
||||
end
|
||||
p(p<1e-16) = 1e-16;
|
||||
end
|
||||
72
projects/project_isipdffit/solution/isipdffit.m
Normal file
72
projects/project_isipdffit/solution/isipdffit.m
Normal file
@ -0,0 +1,72 @@
|
||||
%% check Pig implementation:
|
||||
mu = 0.01;
|
||||
D = 1.0;
|
||||
dx=0.0001;
|
||||
x = dx:dx:10.0;
|
||||
|
||||
for D = [0.1 1 10 100]
|
||||
for mu = [0.01 0.03 0.1 .03]
|
||||
%pig = exp(-(x-mu).^2/4.0/D./x./mu/mu)./sqrt(4*pi*D*x.^3.0);
|
||||
pig = invgauss(x,mu,D);
|
||||
P = sum(pig)*dx;
|
||||
mig = sum(x.*pig)*dx;
|
||||
qig = sum(x.*x.*pig)*dx;
|
||||
vig = qig - mig*mig;
|
||||
dig = 0.5*vig/mig^3;
|
||||
fprintf('Integral=%.3f\n', P);
|
||||
fprintf('Average=%.3f = %.3f\n', mig, mu);
|
||||
%fprintf('Variance=%.3f\n', vig);
|
||||
fprintf('Diffusion=%.3f = %.3f\n\n', dig, D);
|
||||
|
||||
plot(x, pig)
|
||||
hold on
|
||||
plot([mu mu], [0 max(pig)], 'k')
|
||||
hold off
|
||||
xmax = 3.0*mu;
|
||||
if xmax < 0.1
|
||||
xmax = 0.1;
|
||||
end
|
||||
xlim([0 xmax])
|
||||
text(0.6, 0.8, sprintf('D=%.3g', D), 'units', 'normalized')
|
||||
pause( 1.0 )
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
%% fit to data:
|
||||
trials = 1;
|
||||
tmax = 100.0;
|
||||
input = 10.0; % the input I
|
||||
Dnoise = 1.0; % noise strength
|
||||
outau = 0.1; % correlation time of the noise in seconds
|
||||
%for input = [9.5 10.1 11.7 15.9]
|
||||
% spikes = lifouspikes(trials, input, tmax, Dnoise, outau);
|
||||
for input = [1.0 2.0 5.0 10.0]
|
||||
spikes = pifouspikes(trials, input, tmax, Dnoise, outau);
|
||||
isis = diff(spikes{1});
|
||||
mu = mean(isis);
|
||||
fprintf('mean firing rate = %.0f Hz\n', 1.0/mu)
|
||||
v = var(isis);
|
||||
D = 0.5*v/mu^3;
|
||||
[h,b] = hist(isis, 0:0.001:1);
|
||||
h = h/sum(h)/(b(2)-b(1));
|
||||
bar(b, h);
|
||||
hold on;
|
||||
dx=0.0001;
|
||||
x = dx:dx:max(isis);
|
||||
pig = exp(-(x-mu).^2/4.0/D./x./mu/mu)./sqrt(4*pi*D*x.^3.0);
|
||||
plot(x, pig, 'r', 'linewidth', 2);
|
||||
% mle fit:
|
||||
phat = mle(isis, 'pdf', @invgauss, 'start', [0.1 0.1] );
|
||||
mu = phat(1);
|
||||
D = phat(2);
|
||||
pig = exp(-(x-mu).^2/4.0/D./x./mu/mu)./sqrt(4*pi*D*x.^3.0);
|
||||
plot(x, pig, 'c', 'linewidth', 2);
|
||||
xlim([0 4.0*mu])
|
||||
hold off;
|
||||
pause( 4.0 )
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat *.m
|
||||
include ../project.mk
|
||||
|
||||
@ -1,53 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014
|
||||
-- 11/06/2014}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{listings}
|
||||
\lstset{
|
||||
basicstyle=\ttfamily,
|
||||
numbers=left,
|
||||
showstringspaces=false,
|
||||
language=Matlab,
|
||||
breaklines=true,
|
||||
breakautoindent=true,
|
||||
columns=flexible,
|
||||
frame=single,
|
||||
% captionpos=t,
|
||||
xleftmargin=2em,
|
||||
xrightmargin=1em,
|
||||
% aboveskip=11pt,
|
||||
%title=\lstname,
|
||||
% title={\protect\filename@parse{\lstname}\protect\filename@base.\protect\filename@ext}
|
||||
}
|
||||
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Integrate-and-fire neuron}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Benda}{phone: 29 74573}%
|
||||
{email: jan.benda@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
@ -89,12 +50,15 @@ time = [0.0:dt:tmax]; % t_i
|
||||
and compute $V(t)$ for $t_{max}=50$\,ms. Plot $V(t)$ and compare it to
|
||||
the expected result of $V(t) = \exp(-t/\tau)$.
|
||||
|
||||
Vary the time step $\Delta t$ by factors of 10 and discuss
|
||||
accuracy of numerical solutions. What is a good time step?
|
||||
|
||||
Why is $V=0$ the resting potential of this neuron?
|
||||
|
||||
\part Response of the passive membrane to a step input.
|
||||
|
||||
Set $V_0=0$. Construct a vector for the input $E(t)$ such that
|
||||
$E(t)=0$ for $t<20$\,ms and $t>70$\,ms and $E(t)=10$\,mV for
|
||||
$E(t)=0$ for $t\le 20$\,ms and $t\ge 70$\,ms and $E(t)=10$\,mV for
|
||||
$20$\,ms $<t<70$\,ms. Plot $E(t)$ and the resulting $V(t)$ for
|
||||
$t_{max}=120$\,ms.
|
||||
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat
|
||||
include ../project.mk
|
||||
|
||||
@ -1,36 +1,16 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2014
|
||||
-- 11/05/2014}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Benda}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Mutual information}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Benda}{phone: 29 74573}%
|
||||
{email: jan.benda@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\begin{questions}
|
||||
\question A subject was presented two possible objects for a very
|
||||
brief time ($50$\,ms). The task of the subject was to report which of
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat *.m
|
||||
include ../project.mk
|
||||
|
||||
@ -18,7 +18,7 @@ function spikes = lifspikes(trials, input, tmax, D)
|
||||
for k=1:trials
|
||||
times = [];
|
||||
j = 1;
|
||||
v = vreset;
|
||||
v = vreset + (vthresh-vreset)*rand();
|
||||
noise = sqrt(2.0*D)*randn(n, 1)/sqrt(dt);
|
||||
for i=1:n
|
||||
v = v + (- v + noise(i) + input)*dt/tau;
|
||||
|
||||
@ -1,55 +1,17 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{11/02/2014
|
||||
-- 11/05/2014}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Benda}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
|
||||
%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\usepackage{listings}
|
||||
\lstset{
|
||||
basicstyle=\ttfamily,
|
||||
numbers=left,
|
||||
showstringspaces=false,
|
||||
language=Matlab,
|
||||
breaklines=true,
|
||||
breakautoindent=true,
|
||||
columns=flexible,
|
||||
frame=single,
|
||||
% captionpos=t,
|
||||
xleftmargin=2em,
|
||||
xrightmargin=1em,
|
||||
% aboveskip=11pt,
|
||||
%title=\lstname,
|
||||
% title={\protect\filename@parse{\lstname}\protect\filename@base.\protect\filename@ext}
|
||||
}
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Neural tuning and noise}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Benda}{phone: 29 74573}%
|
||||
{email: jan.benda@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\section{REPLACE BY SUBTHRESHOLD RESONANCE PROJECT!}
|
||||
\begin{questions}
|
||||
\question You are recording the activity of a neuron in response to
|
||||
constant stimuli of intensity $I$ (think of that, for example,
|
||||
|
||||
@ -18,7 +18,7 @@ function spikes = lifspikes(trials, input, tmax, D)
|
||||
for k=1:trials
|
||||
times = [];
|
||||
j = 1;
|
||||
v = vreset;
|
||||
v = vreset + (vthresh-vreset)*rand();
|
||||
noise = sqrt(2.0*D)*randn(n, 1)/sqrt(dt);
|
||||
for i=1:n
|
||||
v = v + (- v + noise(i) + input)*dt/tau;
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat
|
||||
include ../project.mk
|
||||
|
||||
@ -1,32 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{WS 2016/17}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Number coding}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Grewe}{phone: 29 74588}%
|
||||
{email: jan.grewe@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat data/*.mat
|
||||
include ../project.mk
|
||||
|
||||
@ -1,32 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{WS 2016/17}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Onset f-I curve}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Grewe}{phone: 29 74588}%
|
||||
{email: jan.grewe@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\section*{Quantifying the responsiveness of a neuron using the F-I curve.}
|
||||
|
||||
3
projects/project_pca_natural_images/Makefile
Normal file
3
projects/project_pca_natural_images/Makefile
Normal file
@ -0,0 +1,3 @@
|
||||
ZIPFILES=
|
||||
|
||||
include ../project.mk
|
||||
|
Before Width: | Height: | Size: 915 KiB After Width: | Height: | Size: 915 KiB |
35
projects/project_pca_natural_img/pca_natural_images.tex → projects/project_pca_natural_images/pca_natural_images.tex
Executable file → Normal file
35
projects/project_pca_natural_img/pca_natural_images.tex → projects/project_pca_natural_images/pca_natural_images.tex
Executable file → Normal file
@ -1,33 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{11/05/2014
|
||||
-- 11/06/2014}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Fabian Sinz}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Image statistics}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Benda}{phone: 29 74573}%
|
||||
{email: jan.benda@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
|
||||
@ -1,11 +0,0 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto *.bbl *.blg
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.jpg
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat data/*.mat
|
||||
include ../project.mk
|
||||
|
||||
BIN
projects/project_photoreceptor/data/R1_6_step_response_0.mat
Normal file
BIN
projects/project_photoreceptor/data/R1_6_step_response_0.mat
Normal file
Binary file not shown.
BIN
projects/project_photoreceptor/data/R1_6_step_response_1.mat
Normal file
BIN
projects/project_photoreceptor/data/R1_6_step_response_1.mat
Normal file
Binary file not shown.
BIN
projects/project_photoreceptor/data/R1_6_step_response_2.mat
Normal file
BIN
projects/project_photoreceptor/data/R1_6_step_response_2.mat
Normal file
Binary file not shown.
BIN
projects/project_photoreceptor/data/R1_6_step_response_3.mat
Normal file
BIN
projects/project_photoreceptor/data/R1_6_step_response_3.mat
Normal file
Binary file not shown.
BIN
projects/project_photoreceptor/data/R1_6_step_response_4.mat
Normal file
BIN
projects/project_photoreceptor/data/R1_6_step_response_4.mat
Normal file
Binary file not shown.
BIN
projects/project_photoreceptor/data/R1_6_step_response_5.mat
Normal file
BIN
projects/project_photoreceptor/data/R1_6_step_response_5.mat
Normal file
Binary file not shown.
BIN
projects/project_photoreceptor/data/R1_6_step_response_6.mat
Normal file
BIN
projects/project_photoreceptor/data/R1_6_step_response_6.mat
Normal file
Binary file not shown.
@ -1,32 +1,14 @@
|
||||
\documentclass[addpoints,11pt]{exam}
|
||||
\usepackage{url}
|
||||
\usepackage{color}
|
||||
\usepackage{hyperref}
|
||||
|
||||
\pagestyle{headandfoot}
|
||||
\runningheadrule
|
||||
\firstpageheadrule
|
||||
\firstpageheader{Scientific Computing}{Project Assignment}{WS 2016/17}
|
||||
%\runningheader{Homework 01}{Page \thepage\ of \numpages}{23. October 2014}
|
||||
\firstpagefooter{}{}{{\bf Supervisor:} Jan Grewe}
|
||||
\runningfooter{}{}{}
|
||||
\pointsinmargin
|
||||
\bracketedpoints
|
||||
|
||||
%\printanswers
|
||||
%\shadedsolutions
|
||||
\documentclass[a4paper,12pt,pdftex]{exam}
|
||||
|
||||
\newcommand{\ptitle}{Photoreceptor activity}
|
||||
\input{../header.tex}
|
||||
\firstpagefooter{Supervisor: Jan Grewe}{phone: 29 74588}%
|
||||
{email: jan.grewe@uni-tuebingen.de}
|
||||
|
||||
\begin{document}
|
||||
%%%%%%%%%%%%%%%%%%%%% Submission instructions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\sffamily
|
||||
% \begin{flushright}
|
||||
% \gradetable[h][questions]
|
||||
% \end{flushright}
|
||||
|
||||
\begin{center}
|
||||
\input{../disclaimer.tex}
|
||||
\end{center}
|
||||
\input{../instructions.tex}
|
||||
|
||||
|
||||
%%%%%%%%%%%%%% Questions %%%%%%%%%%%%%%%%%%%%%%%%%
|
||||
\section*{Analysis of insect photoreceptor data.}
|
||||
|
||||
@ -1,10 +1,3 @@
|
||||
latex:
|
||||
pdflatex *.tex > /dev/null
|
||||
pdflatex *.tex > /dev/null
|
||||
ZIPFILES=
|
||||
|
||||
clean:
|
||||
rm -rf *.log *.aux *.zip *.out auto
|
||||
rm -f `basename *.tex .tex`.pdf
|
||||
|
||||
zip: latex
|
||||
zip `basename *.tex .tex`.zip *.pdf *.dat *.mat *.m
|
||||
include ../project.mk
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user