move plotting stuff to own folder

plotting/lecture/Makefile

@@ -0,0 +1,70 @@
+BASENAME=plotting
+
+PYFILES=$(wildcard *.py)
+PYPDFFILES=$(PYFILES:.py=.pdf)
+
+GPTFILES=$(wildcard *.gpt)
+GPTTEXFILES=$(GPTFILES:.gpt=.tex)
+
+
+all: pdf slides thumbs
+
+# script:
+pdf : $(BASENAME)-chapter.pdf
+$(BASENAME)-chapter.pdf : $(BASENAME)-chapter.tex $(BASENAME).tex $(GPTTEXFILES) $(PYPDFFILES)
+	pdflatex -interaction=scrollmode $< | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex -interaction=scrollmode $< || true
+
+
+# slides:
+slides: $(BASENAME)-slides.pdf
+$(BASENAME)-slides.pdf : $(BASENAME)-slides.tex $(GPTTEXFILES) $(PYPDFFILES)
+	pdflatex -interaction=scrollmode $< | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex -interaction=scrollmode $< || true
+
+# thumbnails:
+thumbs: $(BASENAME)-handout.pdf
+$(BASENAME)-handout.pdf: $(BASENAME)-slides.tex $(GPTTEXFILES)
+	sed -e 's/setboolean{presentation}{true}/setboolean{presentation}{false}/; s/usepackage{crop}/usepackage[frame]{crop}/' $< > thumbsfoils.tex
+	pdflatex thumbsfoils | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex thumbsfoils || true
+	pdfnup --nup 2x4 --no-landscape --paper a4paper --trim "-1cm -1cm -1cm -1cm" --outfile $@ thumbsfoils.pdf # 1-19
+	rm thumbsfoils.*
+
+watchpdf :
+	while true; do ! make -q pdf && make pdf; sleep 0.5; done
+
+watchslides :
+	while true; do ! make -q slides && make slides; sleep 0.5; done
+
+# python plots:
+$(PYPDFFILES) : %.pdf: %.py
+	python $<
+
+# gnuplot plots:
+$(GPTTEXFILES) : %.tex: %.gpt whitestyles.gp
+	gnuplot whitestyles.gp $<
+	epstopdf $*.eps
+
+
+clean :
+	rm -f *~ 
+	rm -f $(BASENAME).aux $(BASENAME).log
+	rm -f $(BASENAME)-chapter.aux $(BASENAME)-chapter.log $(BASENAME)-chapter.out
+	rm -f $(BASENAME)-slides.aux $(BASENAME)-slides.log $(BASENAME)-slides.out $(BASENAME)-slides.toc $(BASENAME)-slides.nav $(BASENAME)-slides.snm $(BASENAME)-slides.vrb
+	rm -f $(PYPDFFILES) $(GPTTEXFILES)
+
+cleanall : clean
+	rm -f $(BASENAME)-chapter.pdf $(BASENAME)-slides.pdf $(BASENAME)-handout.pdf
+
+
+help : 
+	@echo -e \
+	"make pdf:        make the pdf file of the script.\n"\
+	"make slides:     make the pdf file of the slides.\n"\
+	"make thumbs:     make color thumbnails of the talk.\n"\
+	"make watchpdf:   make the pdf file of the script\n"\
+        "                 whenever the tex file is modified.\n"\
+	"make watchpdf:   make the pdf file of the slides\n"\
+        "                 whenever the tex file is modified.\n"\
+	"make clean:      remove all intermediate files,\n"\
+        "                 just leave the source files and the final .pdf files.\n"\
+	"make cleanup:    remove all intermediate files as well as\n"\
+        "                 the final .pdf files.\n"\

plotting/lecture/beamercolorthemetuebingen.sty

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+% Copyright 2007 by Till Tantau
+%
+% This file may be distributed and/or modified
+%
+% 1. under the LaTeX Project Public License and/or
+% 2. under the GNU Public License.
+%
+% See the file doc/licenses/LICENSE for more details.
+
+\usepackage{color} 
+\definecolor{karminrot}{RGB}{165,30,55}
+\definecolor{gold}{RGB}{180,160,105}
+\definecolor{anthrazit}{RGB}{50 ,65 ,75 }
+
+\mode<presentation>
+
+\setbeamercolor*{normal text}{fg=anthrazit,bg=white}
+\setbeamercolor*{alerted text}{fg=anthrazit}
+\setbeamercolor*{example text}{fg=anthrazit}
+\setbeamercolor*{structure}{fg=gold,bg=karminrot}
+
+\providecommand*{\beamer@bftext@only}{%
+  \relax
+  \ifmmode
+    \expandafter\beamer@bftext@warning
+  \else
+    \expandafter\bfseries
+  \fi
+}
+\providecommand*{\beamer@bftext@warning}{%
+  \ClassWarning{beamer}
+    {Cannot use bold for alerted text in math mode}%
+}
+
+\setbeamerfont{alerted text}{series=\beamer@bftext@only}
+
+\setbeamercolor{palette primary}{fg=karminrot,bg=white}
+\setbeamercolor{palette secondary}{fg=gold,bg=white}
+\setbeamercolor{palette tertiary}{fg=anthrazit,bg=white}
+\setbeamercolor{palette quaternary}{fg=black,bg=white}
+
+\setbeamercolor{sidebar}{bg=karminrot!100}
+
+\setbeamercolor{palette sidebar primary}{fg=karminrot}
+\setbeamercolor{palette sidebar secondary}{fg=karminrot}
+\setbeamercolor{palette sidebar tertiary}{fg=karminrot}
+\setbeamercolor{palette sidebar quaternary}{fg=karminrot}
+
+\setbeamercolor{item projected}{fg=black,bg=black!20}
+
+\setbeamercolor*{block body}{}
+\setbeamercolor*{block body alerted}{}
+\setbeamercolor*{block body example}{}
+\setbeamercolor*{block title}{parent=structure}
+\setbeamercolor*{block title alerted}{parent=alerted text}
+\setbeamercolor*{block title example}{parent=example text}
+
+\setbeamercolor*{titlelike}{parent=structure}
+
+\mode
+<all>

plotting/lecture/plotting-chapter.tex

@@ -0,0 +1,17 @@
+\documentclass[12pt]{report}
+
+\input{../../header}
+
+\lstset{inputpath=../code}
+
+\graphicspath{{images/}}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{document} 
+
+\include{psth_sta}
+
+\end{document}
+

plotting/lecture/plotting.tex

@@ -0,0 +1,11 @@
+\chapter{\tr{Data plotting}{Graphische Darstellung von Daten}}
+
+\section{Graphische Darstellung von Daten}
+
+
+
+\begin{figure}
+  \includegraphics[width=0.9\columnwidth]{convincing}
+  \caption{Die Folgen schlecht annotierter
+    Plots. \url{www.xkcd.com}} \label{xkcdplotting}
+\end{figure}

programming/code/simplerandomwalk.m

@@ -0,0 +1,26 @@
+num_runs = 10;
+max_steps = 1000;
+
+positions = zeros(max_steps, num_runs);
+
+for run = 1:num_runs
+    for step = 2:max_steps
+        x = randn(1);
+        if x < 0
+            positions(step, run) = positions(step-1, run) + 1;
+        elseif x > 0
+            positions(step, run) = positions(step-1, run) - 1;
+        end
+    end
+end
+
+figure()
+hold on
+for run = 1:num_runs
+    plot(1:max_steps, positions(:, run))
+end
+xlabel('Number of steps')
+ylabel('Position')
+box off
+
+

programming/lectures/logicalIndexingTime.py

@@ -0,0 +1,29 @@
+import matplotlib.pyplot as plt
+import numpy as np
+from IPython import embed
+time = np.arange(0.,10., 0.001)
+x = np.random.randn(len(time))
+selection = x[(time > 5.) & (time < 6.)]
+
+fig = plt.figure()
+fig.set_facecolor("white")
+fig.set_size_inches(5.5, 2.5)
+
+ax = fig.add_subplot(111)
+ax.plot(time, x, label="data", lw=.5)
+ax.plot(time[(time > 5.) & (time < 6.)], selection, color='r', lw=0.5, label="selection")
+ax.spines["right"].set_visible(False)
+ax.spines["top"].set_visible(False)
+ax.yaxis.set_ticks_position('left')
+ax.xaxis.set_ticks_position('bottom')
+ax.xaxis.linewidth=1.5
+ax.yaxis.linewidth=1.5
+ax.tick_params(direction="out", width=1.25)
+ax.tick_params(direction="out", width=1.25)
+ax.set_xlabel("time [s]")
+ax.set_ylabel("intensity")
+ax.legend(fontsize=8)
+fig.tight_layout()
+fig.savefig("images/logicalIndexingTime.pdf")
+
+