no more gnuplot!

This commit is contained in:
Jan Benda 2021-01-10 20:54:23 +01:00
parent ea8add517c
commit 9c0bdba5e6
15 changed files with 77 additions and 2088 deletions

View File

@ -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

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@ -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}

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@ -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}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

View File

@ -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

View File

@ -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 $T_i=t_{i+1}-t_i$

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@ -1,205 +0,0 @@
set term epslatex size 11.4cm, 6.4cm
set out 'pointprocessscetch.tex'
set border 0
set lmarg 4
set rmarg 1
set tmarg 1
set bmarg 1
set xrange [0:11]
unset xtics
set yrange [-0.7:1.8]
unset ytics
set label 1 at graph -0.07, graph 1.1
set multiplot
set origin 0, 0.7
set size 1, 0.3
set label 1 '\normalsize Event times $\{t_i\}$'
set arrow 1 from 0, 0.5 to 11, 0.5 head filled
set label 2 'Time' at 11, -0.3 center
set label 3 "$t_{1}$" at 0.724649, -0.6 center
set label 4 "$t_{2}$" at 1.67586, -0.6 center
set label 5 "$t_{3}$" at 3.02389, -0.6 center
set label 6 "$t_{4}$" at 3.57466, -0.6 center
set label 7 "$t_{5}$" at 4.15121, -0.6 center
set label 8 "$t_{6}$" at 5.00412, -0.6 center
set label 9 "$t_{7}$" at 6.64549, -0.6 center
set label 10 "$t_{8}$" at 7.81657, -0.6 center
set label 11 "$t_{9}$" at 9.77964, -0.6 center
plot '-' w l lt 1 lc rgb 'black' lw 10
0.724649 0
0.724649 1
1.67586 0
1.67586 1
3.02389 0
3.02389 1
3.57466 0
3.57466 1
4.15121 0
4.15121 1
5.00412 0
5.00412 1
6.64549 0
6.64549 1
7.81657 0
7.81657 1
9.77964 0
9.77964 1
e
unset label 3
unset label 4
unset label 5
unset label 6
unset label 7
unset label 8
unset label 9
unset label 10
unset label 11
set origin 0, 0.4
set label 1 '\normalsize Intervals $\{T_i\}, \; T_i = t_{i+1} - t_i$'
set label 3 "$T_{1}$" at 1.20025, -0.5 center
set arrow 3 from 0.724649, 0.2 to 1.67586, 0.2 heads
set label 4 "$T_{2}$" at 2.34987, -0.5 center
set arrow 4 from 1.67586, 0.2 to 3.02389, 0.2 heads
set label 5 "$T_{3}$" at 3.29927, -0.5 center
set arrow 5 from 3.02389, 0.2 to 3.57466, 0.2 heads
set label 6 "$T_{4}$" at 3.86293, -0.5 center
set arrow 6 from 3.57466, 0.2 to 4.15121, 0.2 heads
set label 7 "$T_{5}$" at 4.57767, -0.5 center
set arrow 7 from 4.15121, 0.2 to 5.00412, 0.2 heads
set label 8 "$T_{6}$" at 5.82481, -0.5 center
set arrow 8 from 5.00412, 0.2 to 6.64549, 0.2 heads
set label 9 "$T_{7}$" at 7.23103, -0.5 center
set arrow 9 from 6.64549, 0.2 to 7.81657, 0.2 heads
set label 10 "$T_{8}$" at 8.79811, -0.5 center
set arrow 10 from 7.81657, 0.2 to 9.77964, 0.2 heads
plot '-' w l lt 1 lc rgb 'black' lw 10
0.724649 0
0.724649 1
1.67586 0
1.67586 1
3.02389 0
3.02389 1
3.57466 0
3.57466 1
4.15121 0
4.15121 1
5.00412 0
5.00412 1
6.64549 0
6.64549 1
7.81657 0
7.81657 1
9.77964 0
9.77964 1
e
unset label 3
unset label 4
unset label 5
unset label 6
unset label 7
unset label 8
unset label 9
unset label 10
unset arrow 3
unset arrow 4
unset arrow 5
unset arrow 6
unset arrow 7
unset arrow 8
unset arrow 9
unset arrow 10
set origin 0, 0
set size 1, 0.4
set border 2
set yrange [-0.5:10.5]
set ytics 2 nomirror out
set arrow 1 from 0, 0.0 to 11, 0.0 head filled
set label 2 'Time' at 11, -2.2 center
set label 1 '\normalsize Event counts $\{ n_i \}$' at graph -0.07, graph 1.2
plot '-' w l lt 1 lc rgb 'black' lw 3, \
'-' w p lt 1 lc rgb 'black' pt 7 ps 1.5 lw 2, \
'-' w p lt 1 lc rgb 'white' pt 7 ps 1.0 lw 2, \
'-' w p lt 1 lc rgb 'black' pt 7 ps 1.5 lw 2
0 0
0.724649 0
0.724649 1
1.67586 1
1.67586 2
3.02389 2
3.02389 3
3.57466 3
3.57466 4
4.15121 4
4.15121 5
5.00412 5
5.00412 6
6.64549 6
6.64549 7
7.81657 7
7.81657 8
9.77964 8
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

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@ -1,546 +0,0 @@
%!PS-Adobe-2.0 EPSF-2.0
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%
% PostScript Level 1 Pattern Fill routine for rectangles
% Usage: x y w h s a XX PatternFill
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% w,h = width and height of box
% a = angle in degrees between lines and x-axis
% XX = 0/1 for no/yes cross-hatch
%
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clip
currentlinewidth 0.5 mul setlinewidth
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0 0 M PFa 5 get rotate PFs -2 div dup translate
0 1 PFs PFa 4 get div 1 add floor cvi
{PFa 4 get mul 0 M 0 PFs V} for
0 PFa 6 get ne {
0 1 PFs PFa 4 get div 1 add floor cvi
{PFa 4 get mul 0 2 1 roll M PFs 0 V} for
} if
stroke grestore} def
%
/languagelevel where
{pop languagelevel} {1} ifelse
dup 2 lt
{/InterpretLevel1 true def
/InterpretLevel3 false def}
{/InterpretLevel1 Level1 def
2 gt
{/InterpretLevel3 Level3 def}
{/InterpretLevel3 false def}
ifelse }
ifelse
%
% PostScript level 2 pattern fill definitions
%
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bind def
/KeepColor {currentrgbcolor [/Pattern /DeviceRGB] setcolorspace} bind def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke}
>> matrix makepattern
/Pat1 exch def
<< Tile8x8
/PaintProc {0.5 setlinewidth pop 0 0 M 8 8 L 0 8 M 8 0 L stroke
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/Title (pointprocessscetchB.tex)
/Subject (gnuplot plot)
/Creator (gnuplot 5.2 patchlevel 8)
% /Producer (gnuplot)
% /Keywords ()
/CreationDate (Mon Dec 21 20:05:26 2020)
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end
%%EndProlog
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%%Trailer

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@ -1,204 +0,0 @@
set out 'pointprocessscetchB.tex'
set border 0
set lmarg 4
set rmarg 1
set tmarg 1
set bmarg 1
set xrange [0:11]
unset xtics
set yrange [-0.7:1.8]
unset ytics
set label 1 at graph -0.07, graph 1.1
set multiplot
set origin 0, 0.7
set size 1, 0.3
set label 1 '\normalsize Event times $\{t_i\}$'
set arrow 1 from 0, 0.5 to 11, 0.5 head filled
set label 2 'Time' at 11, -0.3 center
set label 3 "$t_{1}$" at 0.724649, -0.6 center
set label 4 "$t_{2}$" at 1.67586, -0.6 center
set label 5 "$t_{3}$" at 3.02389, -0.6 center
set label 6 "$t_{4}$" at 3.57466, -0.6 center
set label 7 "$t_{5}$" at 4.15121, -0.6 center
set label 8 "$t_{6}$" at 5.00412, -0.6 center
set label 9 "$t_{7}$" at 6.64549, -0.6 center
set label 10 "$t_{8}$" at 7.81657, -0.6 center
set label 11 "$t_{9}$" at 9.77964, -0.6 center
plot '-' w l lt 1 lc rgb 'black' lw 10
0.724649 0
0.724649 1
1.67586 0
1.67586 1
3.02389 0
3.02389 1
3.57466 0
3.57466 1
4.15121 0
4.15121 1
5.00412 0
5.00412 1
6.64549 0
6.64549 1
7.81657 0
7.81657 1
9.77964 0
9.77964 1
e
unset label 3
unset label 4
unset label 5
unset label 6
unset label 7
unset label 8
unset label 9
unset label 10
unset label 11
set origin 0, 0.4
set label 1 '\normalsize Intervals $\{T_i\}, \; T_i = t_{i+1} - t_i$'
set label 3 "$T_{1}$" at 1.20025, -0.5 center
set arrow 3 from 0.724649, 0.2 to 1.67586, 0.2 heads
set label 4 "$T_{2}$" at 2.34987, -0.5 center
set arrow 4 from 1.67586, 0.2 to 3.02389, 0.2 heads
set label 5 "$T_{3}$" at 3.29927, -0.5 center
set arrow 5 from 3.02389, 0.2 to 3.57466, 0.2 heads
set label 6 "$T_{4}$" at 3.86293, -0.5 center
set arrow 6 from 3.57466, 0.2 to 4.15121, 0.2 heads
set label 7 "$T_{5}$" at 4.57767, -0.5 center
set arrow 7 from 4.15121, 0.2 to 5.00412, 0.2 heads
set label 8 "$T_{6}$" at 5.82481, -0.5 center
set arrow 8 from 5.00412, 0.2 to 6.64549, 0.2 heads
set label 9 "$T_{7}$" at 7.23103, -0.5 center
set arrow 9 from 6.64549, 0.2 to 7.81657, 0.2 heads
set label 10 "$T_{8}$" at 8.79811, -0.5 center
set arrow 10 from 7.81657, 0.2 to 9.77964, 0.2 heads
plot '-' w l lt 1 lc rgb 'black' lw 10
0.724649 0
0.724649 1
1.67586 0
1.67586 1
3.02389 0
3.02389 1
3.57466 0
3.57466 1
4.15121 0
4.15121 1
5.00412 0
5.00412 1
6.64549 0
6.64549 1
7.81657 0
7.81657 1
9.77964 0
9.77964 1
e
unset label 3
unset label 4
unset label 5
unset label 6
unset label 7
unset label 8
unset label 9
unset label 10
unset arrow 3
unset arrow 4
unset arrow 5
unset arrow 6
unset arrow 7
unset arrow 8
unset arrow 9
unset arrow 10
set origin 0, 0
set size 1, 0.4
set border 2
set yrange [-0.5:10.5]
set ytics 2 nomirror out
set arrow 1 from 0, 0.0 to 11, 0.0 head filled
set label 2 'Time' at 11, -2.2 center
set label 1 '\normalsize Event counts $\{ n_i \}$' at graph -0.07, graph 1.2
plot '-' w l lt 1 lc rgb 'black' lw 3, \
'-' w p lt 1 lc rgb 'black' pt 7 ps 1.5 lw 2, \
'-' w p lt 1 lc rgb 'white' pt 7 ps 1.0 lw 2, \
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4.15121 5
5.00412 5
5.00412 6
6.64549 6
6.64549 7
7.81657 7
7.81657 8
9.77964 8
9.77964 9
10.7899 9
e
0.724649 0
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unset multiplot

View File

@ -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()

View File

@ -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

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