From 9c0bdba5e6304f18808cba78880e0a7ed5099fd3 Mon Sep 17 00:00:00 2001 From: Jan Benda Date: Sun, 10 Jan 2021 20:54:23 +0100 Subject: [PATCH] no more gnuplot! --- chapter.mk | 19 +- header.tex | 4 - .../lecture/pointprocesses-slides.tex | 5 +- pointprocesses/lecture/pointprocesses.tex | 6 +- pointprocesses/lecture/pointprocesses_de.tex | 2 +- pointprocesses/lecture/pointprocessscetch.gpt | 205 ---- .../lecture/pointprocessscetchA.eps | 546 ----------- .../lecture/pointprocessscetchA.gpt | 62 -- .../lecture/pointprocessscetchA.pdf | 84 -- .../lecture/pointprocessscetchB.eps | 891 ------------------ .../lecture/pointprocessscetchB.gpt | 204 ---- .../lecture/pointprocessscetchB.pdf | Bin 4877 -> 0 bytes pointprocesses/lecture/pointprocesssketch.py | 69 ++ pointprocesses/lecture/whitestyles.gp | 67 -- scientificcomputing-script.tex | 1 - 15 files changed, 77 insertions(+), 2088 deletions(-) delete mode 100644 pointprocesses/lecture/pointprocessscetch.gpt delete mode 100644 pointprocesses/lecture/pointprocessscetchA.eps delete mode 100644 pointprocesses/lecture/pointprocessscetchA.gpt delete mode 100644 pointprocesses/lecture/pointprocessscetchA.pdf delete mode 100644 pointprocesses/lecture/pointprocessscetchB.eps delete mode 100644 pointprocesses/lecture/pointprocessscetchB.gpt delete mode 100644 pointprocesses/lecture/pointprocessscetchB.pdf create mode 100644 pointprocesses/lecture/pointprocesssketch.py delete mode 100644 pointprocesses/lecture/whitestyles.gp 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 @@ -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 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 @@ -%!PS-Adobe-2.0 EPSF-2.0 -%%Title: pointprocessscetchA.tex -%%Creator: gnuplot 5.2 patchlevel 8 -%%CreationDate: Mon Dec 21 20:05:25 2020 -%%DocumentFonts: -%%BoundingBox: 50 50 373 135 -%%EndComments -%%BeginProlog -/gnudict 256 dict def -gnudict begin -% -% The following true/false flags may be edited by hand if desired. -% The unit line width and grayscale image gamma correction may also be changed. -% -/Color true def -/Blacktext true def -/Solid false def -/Dashlength 1 def -/Landscape false def -/Level1 false def -/Level3 false def -/Rounded true def -/ClipToBoundingBox false def -/SuppressPDFMark false def -/TransparentPatterns false def -/gnulinewidth 5.000 def -/userlinewidth gnulinewidth def -/Gamma 1.0 def -/BackgroundColor {-1.000 -1.000 -1.000} def -% -/vshift -73 def -/dl1 { - 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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}% }