diff --git a/chapter.mk b/chapter.mk
index f642e2e..44553f5 100644
--- a/chapter.mk
+++ b/chapter.mk
@@ -1,5 +1,5 @@
# plots:
-plots : pythonplots gnuplots
+plots : pythonplots
# python plots:
PYFILES=$(wildcard *.py)
@@ -16,21 +16,6 @@ $(PYPDFFILES) : %.pdf: %.py ../../plotstyle.py
cleanpythonplots :
rm -f $(PYPDFFILES)
-
-# gnuplot plots:
-GPTFILES=$(wildcard *.gpt)
-GPTTEXFILES=$(GPTFILES:.gpt=.tex)
-
-gnuplots : $(GPTTEXFILES)
-
-$(GPTTEXFILES) : %.tex: %.gpt whitestyles.gp
- gnuplot whitestyles.gp $<
- epstopdf $*.eps
-
-cleangnuplots :
- rm -f $(GPTTEXFILES)
-
-
# script:
chapter : $(BASENAME)-chapter.pdf
@@ -52,7 +37,7 @@ cleantex:
rm -f $(BASENAME).aux $(BASENAME).log *.idx
rm -f $(BASENAME)-chapter.aux $(BASENAME)-chapter.log $(BASENAME)-chapter.out $(BASENAME)-chapter.idx $(BASENAME)-chapter-solutions.tex $(BASENAME)-solutions.tex
-cleanplots: cleanpythonplots cleangnuplots
+cleanplots: cleanpythonplots
cleanchapter : cleanplots cleantex
diff --git a/header.tex b/header.tex
index 464bb56..2f2360d 100644
--- a/header.tex
+++ b/header.tex
@@ -68,10 +68,6 @@
\pagecolor{white}
%%%%% figures %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% gnuplot figures:
-\newcommand{\texinputpath}{}
-\newcommand{\texpicture}[1]{{\sffamily\footnotesize\input{\texinputpath#1.tex}}}
-\newcommand{\figlabel}[1]{\textsf{\textbf{\large \uppercase{#1}}}}
% maximum number of floats:
\setcounter{topnumber}{1}
diff --git a/pointprocesses/lecture/pointprocesses-slides.tex b/pointprocesses/lecture/pointprocesses-slides.tex
index ff49cb2..75a084c 100644
--- a/pointprocesses/lecture/pointprocesses-slides.tex
+++ b/pointprocesses/lecture/pointprocesses-slides.tex
@@ -49,7 +49,6 @@
%%%% graphics %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{graphicx}
-\newcommand{\texpicture}[1]{{\sffamily\small\input{#1.tex}}}
%%%%% listings %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{listings}
@@ -95,7 +94,7 @@
\begin{frame}
\frametitle{Point process}
\vspace{-3ex}
- \texpicture{pointprocessscetchA}
+ \includegraphics{pointprocesssketch}
A point process is a stochastic (or random) process that generates a sequence of events
at times $\{t_i\}$, $t_i \in \reZ$.
@@ -113,7 +112,7 @@
\begin{frame}
\frametitle{Point process}
- \texpicture{pointprocessscetchB}
+ \includegraphics{pointprocesssketch}
\end{frame}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/pointprocesses/lecture/pointprocesses.tex b/pointprocesses/lecture/pointprocesses.tex
index da03d13..f2286e2 100644
--- a/pointprocesses/lecture/pointprocesses.tex
+++ b/pointprocesses/lecture/pointprocesses.tex
@@ -57,8 +57,8 @@ process]{Punktprozess}{point processes}.
\end{ibox}
\begin{figure}[tb]
- \texpicture{pointprocessscetch}
- \titlecaption{\label{pointprocessscetchfig} Statistics of point
+ \includegraphics{pointprocesssketch}
+ \titlecaption{\label{pointprocesssketchfig} Statistics of point
processes.}{A point process is a sequence of instances in time
$t_i$ that can be also characterized by inter-event intervals
$T_i=t_{i+1}-t_i$ and event counts $n_i$.}
@@ -78,7 +78,7 @@ event from two different point processes are shown in
\figref{rasterexamplesfig}. In addition to the event times, point
processes can be described using the intervals $T_i=t_{i+1}-t_i$
between successive events or the number of observed events within a
-certain time window $n_i$ (\figref{pointprocessscetchfig}).
+certain time window $n_i$ (\figref{pointprocesssketchfig}).
\begin{exercise}{rasterplot.m}{}
Implement a function \varcode{rasterplot()} that displays the times of
diff --git a/pointprocesses/lecture/pointprocesses_de.tex b/pointprocesses/lecture/pointprocesses_de.tex
index 4b0850f..60c0f80 100644
--- a/pointprocesses/lecture/pointprocesses_de.tex
+++ b/pointprocesses/lecture/pointprocesses_de.tex
@@ -56,7 +56,7 @@ erzeugt. Zum Beispiel:
\end{ibox}
\begin{figure}[t]
- \texpicture{pointprocessscetch}
+ \includegraphics{pointprocesssketch}
\titlecaption{\label{pointprocessscetchfig} Statistik von
Punktprozessen.}{Ein Punktprozess ist eine Abfolge von
Zeitpunkten $t_i$ die auch durch die Intervalle $T_i=t_{i+1}-t_i$
diff --git a/pointprocesses/lecture/pointprocessscetch.gpt b/pointprocesses/lecture/pointprocessscetch.gpt
deleted file mode 100644
index d045938..0000000
--- a/pointprocesses/lecture/pointprocessscetch.gpt
+++ /dev/null
@@ -1,205 +0,0 @@
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diff --git a/pointprocesses/lecture/pointprocessscetchA.eps b/pointprocesses/lecture/pointprocessscetchA.eps
deleted file mode 100644
index 910c42e..0000000
--- a/pointprocesses/lecture/pointprocessscetchA.eps
+++ /dev/null
@@ -1,546 +0,0 @@
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diff --git a/pointprocesses/lecture/pointprocessscetchB.gpt b/pointprocesses/lecture/pointprocessscetchB.gpt
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index e1cda52..0000000
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-
-9.77964 9
-10.7899 9
-e
-0.724649 0
-1.67586 1
-3.02389 2
-3.57466 3
-4.15121 4
-5.00412 5
-6.64549 6
-7.81657 7
-9.77964 8
-e
-0.724649 0
-1.67586 1
-3.02389 2
-3.57466 3
-4.15121 4
-5.00412 5
-6.64549 6
-7.81657 7
-9.77964 8
-e
-0.724649 1
-1.67586 2
-3.02389 3
-3.57466 4
-4.15121 5
-5.00412 6
-6.64549 7
-7.81657 8
-9.77964 9
-e
-
-unset multiplot
diff --git a/pointprocesses/lecture/pointprocessscetchB.pdf b/pointprocesses/lecture/pointprocessscetchB.pdf
deleted file mode 100644
index c466f9a..0000000
Binary files a/pointprocesses/lecture/pointprocessscetchB.pdf and /dev/null differ
diff --git a/pointprocesses/lecture/pointprocesssketch.py b/pointprocesses/lecture/pointprocesssketch.py
new file mode 100644
index 0000000..fad7f5c
--- /dev/null
+++ b/pointprocesses/lecture/pointprocesssketch.py
@@ -0,0 +1,69 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
+from plotstyle import *
+
+
+spikes = [0.724649, 1.67586, 3.02389, 3.57466, 4.15121, 5.00412, 6.64549, 7.81657, 9.77964]
+
+
+def plot_spikes(ax, spikes):
+ ax.show_spines('')
+ ax.text(-0.06, 1.1, r'Event times $\{t_i\}$', transform=ax.transAxes)
+ ax.annotate('', xy=(0.0, 0.5), xytext=(11.0, 0.5), zorder=-10,
+ arrowprops=dict(arrowstyle='<-'))
+ ax.text(10.5, -0.2, 'Time')
+ for i, t in enumerate(spikes):
+ ax.plot([t, t], [0.0, 1.0], **lsA)
+ ax.text(t, -0.6, '$t_{%d}$' % i, ha='center')
+ ax.set_xlim(0.0, 11.0)
+ ax.set_ylim(-0.7, 1.2)
+
+
+def plot_isis(ax, spikes):
+ ax.show_spines('')
+ ax.text(-0.06, 1.1, r'Intervals $\{T_i\}, \; T_i = t_{i+1} - t_i$', transform=ax.transAxes)
+ ax.annotate('', xy=(0.0, 0.5), xytext=(11.0, 0.5), zorder=-10,
+ arrowprops=dict(arrowstyle='<-'))
+ ax.text(10.5, -0.2, 'Time')
+ for i in range(len(spikes)):
+ t1 = spikes[i]
+ ax.plot([t1, t1], [0., 1.], **lsA)
+ if i > 0:
+ t0 = spikes[i-1]
+ ax.annotate('', xy=(t0, 0.2), xytext=(t1, 0.2), arrowprops=dict(arrowstyle='<->'))
+ ax.text(0.5*(t0+t1), -0.6, '$T_{%d}$' % i, ha='center')
+ ax.set_xlim(0.0, 11.0)
+ ax.set_ylim(-0.7, 1.2)
+
+
+def plot_counts(ax, spikes):
+ ax.show_spines('l')
+ ax.text(-0.06, 1.1, r'Event counts $\{ n_i \}$', transform=ax.transAxes)
+ ax.annotate('', xy=(0.0, 0.0), xytext=(11.0, 0.0), zorder=-10,
+ arrowprops=dict(arrowstyle='<-'))
+ ax.text(10.5, -2.0, 'Time')
+ c = 0
+ t0 = 0.0
+ for i, t in enumerate(spikes):
+ ax.plot([t0, t], [c, c], zorder=10, clip_on=False, **lsBm)
+ ax.plot([t], [c], zorder=20, clip_on=False, **psBo)
+ c += 1
+ ax.plot([t], [c], zorder=30, clip_on=False, **psB)
+ t0 = t
+ ax.plot([t0, 10.5], [c, c], zorder=10, **lsBm)
+ ax.set_xlim(0.0, 11.0)
+ ax.set_ylim(0, 11)
+ ax.set_yticks(np.arange(0.0, 11.0, 2.0))
+
+
+if __name__ == "__main__":
+ fig = plt.figure(figsize=cm_size(figure_width, 1.7*figure_height))
+ gs = gridspec.GridSpec(3, 1, height_ratios=[2, 2, 4])
+ gs.update(hspace=0.6, **adjust_fs(fig, bottom=1.5, top=1.5, left=3.0, right=1.5))
+ ax1, ax2, ax3 = [fig.add_subplot(gs[i,0]) for i in range(3)]
+ plot_spikes(ax1, spikes)
+ plot_isis(ax2, spikes)
+ plot_counts(ax3, spikes)
+ plt.savefig('pointprocesssketch.pdf')
+ plt.close()
diff --git a/pointprocesses/lecture/whitestyles.gp b/pointprocesses/lecture/whitestyles.gp
deleted file mode 100644
index 1eeb255..0000000
--- a/pointprocesses/lecture/whitestyles.gp
+++ /dev/null
@@ -1,67 +0,0 @@
-set tics scale 0.8
-set tics out
-set format '$%g$'
-unset grid
-unset key
-
-# on white background:
-set style line 1 lt -1 lc rgb "black" lw 2 # border
-set border back ls 1
-set style line 2 lt 1 lc rgb "black" lw 4 pt 7 ps 2 # thick line
-set style line 3 lt 1 lc rgb "black" lw 2 # thin line
-set style line 4 lt 3 lc rgb "black" lw 1 # grid line
-
-set style line 10 lt 1 lc rgb "#00DD00" lw 6 # stimulus thick, AM
-set style line 11 lt 1 lc rgb "#00DD00" lw 3 # stimulus thin, AM
-set style line 15 lt 1 lc rgb "black" lw 15 # stimulus bar
-
-set style line 20 lt 1 lc rgb "yellow" lw 4 # thin spikes cell 1
-set style line 21 lt 1 lc rgb "orange" lw 4 # thin spikes cell 2
-set style line 22 lt 1 lc rgb "yellow" lw 6 # thick spikes cell 1
-set style line 23 lt 1 lc rgb "orange" lw 6 # thick spikes cell 2
-set style line 24 lt 1 lc rgb "blue" lw 22 # big sync spikes
-set style line 25 lt 1 lc rgb "blue" lw 6 # thick sync spikes
-set style line 26 lt 1 lc rgb "orange" lw 4 # all spikes
-
-set style line 30 lt 1 lc rgb "dark-red" lw 6 pt 7 ps 2 # firing rate 1 thick
-set style line 31 lt 1 lc rgb "red" lw 6 pt 7 ps 2 # firing rate 2 thick
-set style line 32 lt 1 lc rgb "orange" lw 6 pt 7 ps 2 # firing rate 3 thick
-set style line 33 lt 1 lc rgb "blue" lw 6 pt 7 ps 2 # firing rate 4 thick
-set style line 34 lt 1 lc rgb "gray" lw 6 # firing rate gray thick
-set style line 35 lt 1 lc rgb "dark-red" lw 3 pt 7 ps 0.7 # firing rate 1 thin
-set style line 36 lt 1 lc rgb "red" lw 3 # firing rate 2 thin
-set style line 37 lt 1 lc rgb "orange" lw 3 # firing rate 3 thin
-set style line 38 lt 1 lc rgb "blue" lw 3 # firing rate 4 thin
-set style line 39 lt 1 lc rgb "gray" lw 3 # firing rate gray thin
-
-set style line 40 lt 1 lc rgb "green" lw 6 pt 5 ps 2 # onset f-I curve thick
-set style line 41 lt 1 lc rgb "green" lw 3 pt 5 ps 2 # onset f-I curve thin
-set style line 42 lt 1 lc rgb "red" lw 6 pt 7 ps 2 # steady-state f-I curve thick
-set style line 43 lt 1 lc rgb "red" lw 3 pt 7 ps 2 # steady-state f-I curve thin
-set style line 44 lt 1 lc rgb "blue" lw 6 pt 9 ps 2 # adapted f-I curve thick
-set style line 45 lt 1 lc rgb "blue" lw 3 pt 9 ps 2 # adapted f-I curve thin
-set style line 47 lt 1 lc rgb "cyan" lw 6 # adaptation level thick
-set style line 48 lt 1 lc rgb "cyan" lw 3 # adaptation level thin
-set style line 49 lt 1 lc rgb "yellow" lw 3 pt 7 ps 4 # current adaptation point
-
-set style line 50 lt 1 lc rgb "dark-red" lw 4 # membrane voltage 1
-set style line 51 lt 1 lc rgb "red" lw 4 # membrane voltage 2
-set style line 52 lt 1 lc rgb "orange" lw 4 # membrane voltage 3
-set style line 55 lt 1 lc rgb "orange" lw 4 # nerve potential
-
-set style line 60 lt 1 lc rgb "blue" lw 4 # gating variable
-set style line 61 lt 1 lc rgb "cyan" lw 4 # gating variable average
-
-set style line 70 lt 1 lc rgb "red" lw 4 # ionic current
-set style line 71 lt 1 lc rgb "orange" lw 4 # ionic current average
-
-set style line 80 lt 1 lc rgb "#77FFFF" lw 4 pt 13 ps 2.4# baseline
-set style line 81 lt 1 lc rgb "#FF5533" lw 4 pt 9 ps 2.8 # beat
-set style line 82 lt 1 lc rgb "yellow" lw 4 pt 7 ps 2.4 # chirp
-set style line 83 lt 1 lc rgb "#FF7700" lw 4 pt 11 ps 2.8# beat shuffled
-set style line 84 lt 1 lc rgb "#FFAA00" lw 4 pt 5 ps 2.2 # chirp shuffled
-
-set style line 90 lt 1 lc rgb "#77FFFF" lw 2 # EOD thin
-set style line 91 lt 1 lc rgb "#77FFFF" lw 4 # EOD thick
-
-set term epslatex input color dashed rounded size 11.4cm, 6.6cm
diff --git a/scientificcomputing-script.tex b/scientificcomputing-script.tex
index 8df08d8..27b369c 100644
--- a/scientificcomputing-script.tex
+++ b/scientificcomputing-script.tex
@@ -5,7 +5,6 @@
\newcommand{\includechapter}[1]{%
\graphicspath{{#1/lecture/}{#1/lecture/figures/}{#1/images/}}%
\setcodepath{#1/code}%
- \renewcommand{\texinputpath}{#1/lecture/}%
\include{#1/lecture/#1}%
}