Matthias Pospiech

Erstellung von Bachelor und Masterarbeiten mit LaTeX

pospiech — Fri, 09 Dec 2011 07:22:29 +0000

Im Rahmen meiner Lehrverpflichtungen an der Leibniz Universität Hannover habe ich die folgende Vorlesung zur Erstellung von Bachelor und Masterarbeiten mit LaTeX gehalten

Note: There is a file embedded within this post, please visit this post to download the file.
Note: There is a file embedded within this post, please visit this post to download the file.

Die Verlesung richtetete sich an Studenten mit Vorkenntnissen in LaTeX, da die Inhalte hier die speziellen Probleme beim Schreiben von Abschlussarbeiten sein sollten. Effektiv habe ich aber auch grundlegende Kenntnisse wiederholt. Die folgenden Kenntnisse wurde in der Vorlesungsankündigung vorausgesetzt:

Syntax von Klassen, Befehlen, Umgebungen und Sonderzeichen
Grundlegende Pakete für die Präambel (babel, inputenc, graphicx, amsmath, . . .).
Textsatz (Kapitel, Abschnitte, Listen, Paragraphen)
Mathematik: einzeilige Formeln
Einbinden von Bildern
einfache Tabellen

Dementsprechend waren die teilnehmenden Studenten mehrheitlich am Ende ihres Bachelor oder Anfang des Masterstudiums. Die meisten kamen aus meiner Fakultät (Mathematik/Physik), aber es waren auch Informatiker und Lehramtstudenten dabei.

Voraussetzung für den Kurs war eine vollständige Installation von Miktex 2.9 oder TeX Live 2011, sowie der Editor TexStudio. Der Editor selber stellte für keinen der Studenten ein Problem dar. Allerdings ist es empfehlenswert die voreingestellten Optionen anzupassen. Problematisch waren hingegen die Distributionen. Fast alle Studenten hatten nur die Minimalversion von Miktex installiert, die nicht annähernd ausreicht. Und die Installation von TeXLive unter Linux, spezieller Ubunutu ist eine Katastrophe. Die Version der Distribution ist von 2009 und damit für den Kurs nicht verwendbar, da ich siunitx und biblatex verwende. Eine manuelle Installation von der 2011er Version nach der Originalanleitung funktioniert nicht. Man muss auf spezielle Ubunutu Anleitungen zurückgreifen. Effektiv hatte die mehrheit der Studenten zu Beginn der Vorlesung ein nicht verwendbares LaTeX System.

Die Vorlesung umfasste 6 Vorlesungstermine mit jeweils 2-3 Zeitstunden. Die Inhalte waren:

Installation, Vorkenntnisse, Begriffe, Editor (TexStudio)
Kapitel, Überschriften, Paragraphen
Strukturierung des Inhaltes
Verweise
Seitenlayout
Aufteilung komplexer Dokumente
Schriften
Silbentrennung
Literaturverzeichnis (mit biblatex und biber)
Literatur erstellen und verwalten (JabRef)
Mathematik und Einheiten (siunitx)
Abbildungen und Beschriftungen
Tabellen
Fragen und Antworten
sonstiges (tikz/pgf, pgfplots)

Einführung in Bibliographien mit LaTeX, biblatex und biber.

pospiech — Sun, 16 Oct 2011 11:24:25 +0000

Im Rahmen eines Arbeitsgruppenseminars der AG Morgner wurde der folgende Vortrag zur Einführung in Bibliographien mit LaTeX gehalten. Zielpublikum waren Masterstudenten und Doktoranden, die zuvor schon mit Bibtex gearbeitet hatten.

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Note: There is a file embedded within this post, please visit this post to download the file.

pcolor plots with publication ready formating

pospiech — Wed, 01 Jun 2011 06:34:01 +0000

Matlab has many possibilities to create plots even fancy ones. However its defaults are very seldom suitable to use the plots directly for a publication. The following minimal code demonstrates how to generate a pcolor plot for 2D data with x- and y-axis. The data was calculated using the function shown here.

pcolor(xAxis, yAxis, Data2D); 
shading flat; % do not interpolate pixels
colorbar % add colorbar
 
xlabel('x / µm');
ylabel('y / µm');

This however is not optimal. Font and fontsizes are not optimal, the color depth should be higher and tics are not shown anymore. Furthermore the colorbar should have an label as well.

The following code demonstrates a general approach how to solve all these problems and achieve directly a plot output which can be used directly for publications. The followin picture shows the resulting image:

First the environment is set up (not necessary if you just want to plot) and variables for plotting are defined.

% clear command window, figures and all variables
clc; clf; clear all; 
 
%% Common variables
FontSize = 12;
FontName = 'MyriadPro-Regular'; % or choose any other font
 
doExportPlot = true;
languageEnglish = false;

Next, the data for plotting is created. Here a previous shown example is used

%% Calculation
% calculate in single line (fastest method)
xMat = (xAxis' * ones([1 yPoints]))';
yMat = yAxis' * ones([1 xPoints]);
Data2D = Ripple(xMat, yMat);
 
Data2D = Data2D - min(min(Data2D)); % normalize to 0-1
Data2D = Data2D / max(max(Data2D));

Then the plot window is opened and configured. Here a fixed size in cm is used. The z-buffer is used because opengl has rounding errors and should therefore be avoided if not necessary. Furthermore the position of the plot within the window is configured.

%% start plot
 
% figure dimensions in cm. I choose 1.5 or 2 times 
% the target size typically. If figure is display in
% document much smaller increase the fontsize.
 
figure_width = 14;  
figure_height = 10;
 
% --- setup plot windows
figuresVisible = 'on'; % 'off' for non displayed plots (will still be exported)
hfig = figure(1); clf;
    set(hfig,'Visible', figuresVisible)
 
    set(hfig, 'units', 'centimeters', 'pos', [5 5 figure_width figure_height])   
    set(hfig, 'PaperPositionMode', 'auto');    
    set(hfig, 'Renderer','Zbuffer'); 
    set(hfig, 'Color', [1 1 1]); % Sets figure background
    set(gca, 'Color', [1 1 1]); % Sets axes background
 
% --- dimensions and position of plot 
hsp = subplot(1,1,1, 'Parent', hfig);
set(hsp,'Position',[0.15 0.17 0.75 0.80]);

The actual plot is still a few lines:

%% plot
colorDepth = 1000;
colormap(jet(colorDepth));
pcolor(xAxis, yAxis, Data2D);

Now the plot needs to be configured. First the pcolor must not have black lines between each data point (the plot would be black). This is achieved by setting the shading. In case of flat not interpolation is done. This might look nicer, but in case of scientific data is close to cheating. The axis properties are important, because matlab does not care itself about scaling. This means that the x- and y-axis might be square although the axis values have a factor of 1:10. The image ratio is set to the axis ratio by the property ‘image’. Additionally several properties for the figure can be set. Most important are the TickLength and the LineWidth.

%%  setup axis plot properties
% shading interp; % interpolate pixels
shading flat; % do not interpolate pixels
axis on;      % display axis
axis tight;   % no white borders
axis image;   % real x,y scaling
 
set(gca, ...
    'CLim' , [0 1], ...
    'Box'         , 'on'      , ...
    'TickDir'     , 'in'      , ...
    'TickLength'  , [.015 .015] , ...
    'XMinorTick'  , 'off'      , ...
    'YMinorTick'  , 'off'     , ...
    'XGrid'       , 'off'     , ...
    'YGrid'       , 'off'     , ...
    'XColor'      , [.0 .0 .0], ...
    'YColor'      , [.0 .0 .0], ...
    'LineWidth'   , 0.6        );

optionally the axis ticks can be configured

%% axis ticks
set(gca,'XTick',-15:5:15)
set(gca,'YTick',-10:5:10)

Next the axis labels are set up. Here I define them in both german end english. That has the advantage, that I can create the figure easily in both languages. The labels are all set with saving of handles, to be able to configure them later.

%% label texts
TITLE = '';
if (languageEnglish)
    xLabelText = 'x / µm';  
    yLabelText = 'y / µm';
    zLabelText = 'normalized intensity';
else
    xLabelText = 'x / µm';
    yLabelText = 'y / µm';
    zLabelText = 'normierte Intensität';
end
 
% save handles to set up label properties
hTitle = title(TITLE);
hXLabel = xlabel(xLabelText);
hYLabel = ylabel(yLabelText);

The colorbar is still missing. Here a label and ticks are defined, and the TickLength and LineWidth is configured.

%% colorbar
caxis([0 1]);
hcb = colorbar('location','EastOutside');
hcLabel = ylabel(hcb,zLabelText);
set(hcb,'YTickLabel',0:0.2:1, 'Ytick', 0:0.2:1)
set(hcb,'YTickMode','manual')
set(hcb, ...
  'Box'         , 'on'     , ...
  'TickDir'     , 'in'     , ...
  'TickLength'  , [.015 .015] , ...
  'LineWidth'   , 0.6);

Last all handles need to be configured. Basically that means setting up the fonts for all.

%% set properties for all handles
set([gca, hcb, hTitle, hXLabel, hYLabel, hcLabel], ...
    'FontSize'   , FontSize    , ...
    'FontName'   , FontName);

And finally some bugs need to be fixed. fixLabels changes the decimal point character to ‘,’ (see below) and the last line brings the tics to the top again, which are overwritten by matlab.

%% last 'bug' fixes
 
% change decimal point to ',' for german text
if (~languageEnglish)
     fixLabels(gca);
     fixLabels(hcb);
end
% bring axis on top again (fix matlab bug)
set(gca,'Layer', 'top');

fixLabels (not optimal, be nevertheless working):

function fixLabels( axis )
 
xlabels = get(axis, 'XTickLabel');
for k=1:size(xlabels,1)
    xlabels(k,:) = strrep(xlabels(k,:), '.', ',');
end
set(axis, 'XTickLabel', xlabels);
 
ylabels = get(axis, 'YTickLabel');
for k=1:size(ylabels,1)
    ylabels(k,:) = strrep(ylabels(k,:), '.', ',');
end
set(axis, 'YTickLabel', ylabels);
 
set(axis, 'XTickMode', 'manual');
set(axis, 'YTickMode', 'manual');
 
end

In the end we might want to export the plot. Here the printing is done to a png file with a resolution of 400 dpi. Since matlab is not filling the plot window and large white borders might surround the actual plot, the png file is cropped using the crop function by Andrew Bliss.

%% export
drawnow
 
SaveDir = '';
SaveName = 'pcolor-example';
 
if (doExportPlot)
    IMAGENAME = [SaveDir SaveName]; 
    print(hfig, ['-r' num2str(400)], [IMAGENAME '.png' ], ['-d' 'png']);    
    crop([IMAGENAME '.png']);
    display('finished plot export')
end
 
% close(hfig);

Download the complete file: Note: There is a file embedded within this post, please visit this post to download the file.

fast calculation of functions with two variables

pospiech — Tue, 31 May 2011 21:05:40 +0000

If you come from the programming world of C/C++ or java or any other traditional programming languages you might fall into the trap of using for loops for the calculation of functions. This works as expected but it is much slower than what matlab can do. The following example demonstrates this principle (which you should not use if you can)

Data2D = zeros([xPoints yPoints]);
for xi = 1:xPoints
    x = xAxis(xi);
    for yi = 1:yPoints        
        y = yAxis(yi);
        Data2D(xi,yi) = Ripple(x, y);
    end
end

On my computer it takes 10.3 seconds for 1.000.000 datapoints.

If the function depends on a single variable one should use a vector and for two variables one should use matrices instead. The following example demonstrates how to calculate a functions with two variables in a single step:

xMat = (xAxis' * ones([1 yPoints]))';
yMat = yAxis' * ones([1 xPoints]);
Data2D = Ripple(xMat, yMat);

On my computer it takes 0.12 seconds for 1.000.000 datapoints, which is approx 90 times faster.

This is the complete code that was used

% clear command window, figures and all variables
clc; clf; clear all; 
 
%% Definition of calculation constants
 
% calculation of axis
xMax = 15;
xPoints = 1000;
xAxis = linspace(-xMax, xMax, xPoints);
 
yMax = 12;
yPoints = 1000;
yAxis = linspace(-yMax, yMax, yPoints);
 
%% function, here inline since it is rather simple
Ripple = @(x,y) ( (cos(sqrt(x.*x+y.*y) + cos(sqrt(((x+.913*2*pi).*(x+.913*2*pi))+y.*y)) + cos(sqrt(((x-.913*2*pi).*(x-.913*2*pi))+(y.*y))))*4) );
 
%% Calculation
% calculate in single line (fastest method)
xMat = (xAxis' * ones([1 yPoints]))';
yMat = yAxis' * ones([1 xPoints]);
tic;
Data2D = Ripple(xMat, yMat);
display(['calculated ' num2str(xPoints*yPoints) ' datapoints in ' num2str(toc) ' seconds']);
 
Data2D = Data2D / max(max(Data2D)); % normalize

plotting a filled curve

pospiech — Tue, 31 May 2011 20:23:44 +0000

A search on how to fill the area under a curve reveals that such questions are quite often asked. Here is the solution in a function file that I created for simplifying filled curve plots using matlabs fill function.

function handle = filledcurve(x, y, zero, colorspec)
 
if (nargin < 3)
    zero = 0;
end
 
if (nargin < 4)
    colorspec = 'b';
end
 
 
xtemp = [x(1) ; x(:) ; x(end)] ;
ytemp = [zero ; y(:) ; zero ] ;
 
% plot
handle = fill(xtemp,ytemp,colorspec);

fast reading of structured text data with matlab

pospiech — Tue, 31 May 2011 20:18:08 +0000

In the following I present a solution to read data from a textfile which has the number of x-values (columns) in the first line, the number of y-values (rows) in the second line and in all following lines the matrix with size x times y.

The principle reading of the data is achieved by the following code

% open file
display(['reading ' FILENAME]);
fid = fopen(FILENAME, 'r');
fseek(fid, 0, 'bof');
 
% read single line: number of x-values
tline = fgetl(fid);
valueLine = strrep(tline, '#', '');
valueLine = strrep(valueLine, ' ', '');
x = str2double(valueLine);
 
% read single line: number of y-values
tline = fgetl(fid);
valueLine = strrep(tline, '#', '');
valueLine = strrep(valueLine, ' ', '');
y = str2double(valueLine);
 
% read full matrix with size x * y
DATACELL = textscan(fid,'%f',[x,y]);
DATA = DATACELL{1};
 
% convert data to correct matrix format
DATA = reshape(DATA, y, x);
 
% close file
fclose(fid);

This can however be slow, especially for matrices with text-file size of several hundred MB. Since disk space is usually not a limit an time much more expensive than disk space I save the data again in matlabs binary format. If I have to read the file a second time I can read the matlab file instead which is 10-100 times faster. Additionally If the data of the file is requested a second time this can be skipped if the data is kept persistent in the function reading the data. In total this is achieved with the following code:

function [r_Data, r_xsize, r_ysize] = ReadSimulationData(FILENAME)
 
persistent lastImageName;
persistent DATA;
persistent xsize;
persistent ysize;
 
% if this file is equal to last file reuse data
if (not(isempty(lastImageName)) && (strcmp(lastImageName,FILENAME)))
    display(['using ' FILENAME]);
else
    % check if converted matlab file exists
    MatlabDataName = strrep(FILENAME, '.txt', '.mat');
    if (exist(MatlabDataName, 'file'))
        display(['loading ' MatlabDataName]);
        load(MatlabDataName, '-mat', 'DATA', 'xsize', 'ysize');
    else                
        %% read data from file
 
        % open file
        display(['reading ' FILENAME]);
        fid = fopen(FILENAME, 'r');
        fseek(fid, 0, 'bof');
 
        % read single line: number of x-values
        tline = fgetl(fid);
        valueLine = strrep(tline, '#', '');
        valueLine = strrep(valueLine, ' ', '');
        x = str2double(valueLine);
 
        % read single line: number of y-values
        tline = fgetl(fid);
        valueLine = strrep(tline, '#', '');
        valueLine = strrep(valueLine, ' ', '');
        y = str2double(valueLine);
 
        % read full matrix with size x * y
        DATACELL = textscan(fid,'%f',[x,y]);
        DATA = DATACELL{1};
 
        % check if read length is equal
        % to expected length.
        % if not resize x accordingly
        % (typically not necessary)
        lengthdiff = length(DATA) - x*y;
        if (lengthdiff ~= 0)
            x = x + lengthdiff/y;
        end
        % convert data to correct matrix format
        DATA = reshape(DATA, y, x);
 
        % close file
        fclose(fid);
 
        % save last read filename
        lastImageName = FILENAME;        
 
        xsize = x;
        ysize = y;
        display(['saving ' MatlabDataName]);
 
        % save data in binary format
        % this speeds up reading of big matrices
        % enormously
        save(MatlabDataName, 'DATA', 'xsize', 'ysize', '-mat');        
    end
end
 
% copy read, or old persistent data to
% return data values
r_Data = DATA;
r_xsize = xsize;
r_ysize = ysize;
 
return;

LaTeX-Vorlage für Protokolle

pospiech — Sun, 15 May 2011 21:08:45 +0000

Neue LaTeX-Vorlage zur Erstellung von Labor-Protokollen:

Note: There is a file embedded within this post, please visit this post to download the file.

Die Vorlage beruht auf Koma Script (scrartcl) und ist für pdflatex ausgelegt (kein LuaTeX oder XeteX). Unter anderem werden diese Pakete verwendet: inputenc, grffile, fontenc, textcomp, lmodern, babel, xcolor, graphicx, epstopdf, caption, amsmath, siunitx, booktabs, tabularx, setspace, scrpage2, microtype. Anpassungen im Layout wurden mit koma script Optionen sowie den Einstellungsmöglichkeiten der Pakete caption und scrpage2 vorgenommen.

LaTeX Einführung

pospiech — Sun, 15 May 2011 16:44:24 +0000

Im Rahmen eines Workshops der jDPG Hannover wurde der folgende Vortrag zur Einführung in LaTeX gehalten:

Note: There is a file embedded within this post, please visit this post to download the file.
Note: There is a file embedded within this post, please visit this post to download the file.
Note: There is a file embedded within this post, please visit this post to download the file.

Das Publikum bestand aus Physik-Studenten des 2ten Semesters. Der Vortrag und die dazu abgehaltenen Übungen umfassten 4 Stunden. Dieser Zeitraum reichte aus, um grundlegende Konzepte zu erklären, allerdings nicht um alle benötigten Inhalte zum Schreiben einer Abschlussarbeit zu behandeln. Insbesondere Labels/Referenzen, Zitate und Literaturverzeichnisse sowie die Strukturierung in verschiedene Dokumente mit \input bzw \include war in diesem Zeitrahmen nicht mehr möglich. Das Ziele war allerdings auch zunächst die Studenten zu befähigen 3-5 seitige Praktikumsberichte anzufertigen, wofür diese Inhalte nicht benötigt werden.

Voraussetzung für den Kurs war eine vollständige Installation von Miktex 2.9 oder TeX Live 2010, sowie der Editor TexMakerX. Im vorangegangenen Jahr war TeXnicCenter als Editor verwendet worden, was aber dazu geführt hatte, dass viele Studenten primär Probleme mit dem Editor hatte. Derartige Probleme konnten diesmal nicht beobachtet werden. Interessanterweise war der Tabellenassistent von besonderem Interesse.

In den Übungen hatten die Studenten, soweit ich das mitbekommen habe, die folgenden Probleme:

Der Unterschied in den Optionen zwischen article und scrartcl war verwirrend. Da ich nicht auf die Analyse von Fehlermeldungen im Vortrag eingegangen bin, hatten die Studenten auch nicht auf die Warnungen geachtet (‘unused option’).
Da \text, \mathrm und \si (siunitx) im Mathematikmodus aufrechte Schriften erzeugen wurde der Unterschied zwischen den Befehlen nicht klar.

Konzeptionell würde ich beim nächsten Mal, sofern mehr Zeit zur Verfügung steht

den grundlegenden Umgang mit einem Texteditor mit Tastaturkommandos üben lassen,
den Unterschied zwischen Distribution und Editor stärker hervorheben (wie auch immer),
das Verstehen von Fehlermeldungen und das Erstellen eines Minimalbeispiels behandeln
sowie das Auffinden und gezielte Lesen von Dokumentationen einüben.

plotting tutorials

pospiech — Thu, 16 Dec 2010 07:37:46 +0000

Here are some tutorials about plotting in matlab:

tutorials on many other topics can be found at http://www.advancedmcode.org/.

batch script for automatic backup using winrar

pospiech — Sun, 24 Oct 2010 14:01:15 +0000

For a regular full backup of all my important data I am using a bash script on Linux. This is now an example to achieve the same under Windows 7 using batch scripting and winrar as the compressor. Zip files can not be used since this is limited in total number of files which I typically overcome.

@ECHO OFF
cls
::-------------------------------------------------------------------------------------
SET PACKER="c:\Program Files\WinRAR\RAR.exe"

:: %APPDATA% = "C:\Users\Matthias\AppData\Roaming"
:: %USERNAME% = "Matthias"
:: %HOMEPATH% = "Users\Matthias"
:: %HOMEDRIVE% = "C:\"
SET DIRUSER="%HOMEDRIVE%%HOMEPATH%"
SET DIRUSERDOC="%DIRUSER%\Documents"
::SET SAVEDIR="c:\temp\%DATE%\"
SET SAVEDIR="Y:\%DATE%"
call:funcCreateDir %SAVEDIR%

 
::--------------------------------------------------------
:: --- MAIN ----------------------------------------------
::--------------------------------------------------------

::Backup home:AppData:Thunderbird
	SET TARGET="%SAVEDIR%\Win7.AppData.Thunderbird.rar"
	SET FILES="%APPDATA%\Thunderbird\*"
	::call:funcBackup %TARGET% %FILES%

::Backup home:User (without AppData, Documents and other real data)
	SET TARGET="%SAVEDIR%\Win7.User.Matthias.rar"
	SET FILES="%DIRUSER%\*"
	SET EXLUCDE="-x%DIRUSER%\AppData -x%DIRUSER%\Downloads -x%DIRUSER%\Pictures -x%DIRUSER%\Documents -x%DIRUSER%\Music -x%DIRUSER%\Videos " 
	::call:funcBackup %TARGET% %FILES% %EXLUCDE%

::Backup home:User:Documents
	SET TARGET="%SAVEDIR%\Win7.User.Matthias.Documents.rar"
	SET FILES="%DIRUSER%\Documents"		
	SET EXLUCDE="-x%DIRUSER%\Documents\SVN" 
	call:funcBackup %TARGET% %FILES% %EXLUCDE%
	
::Backup system:Fonts	
	SET TARGET="%SAVEDIR%\Win7.Fonts.rar"
	SET FILES="%WINDIR%\Fonts\*"
	::call:funcBackup %TARGET% %FILES%
	
::Backup latex:texmf
	SET TARGET="%SAVEDIR%\Win7.localtexmf.rar"
	SET FILES="c:\localtexmf\*"
	::call:funcBackup %TARGET% %FILES%

::Backup home:AppData (without Thunderbird)
	SET TARGET="%SAVEDIR%\Win7.AppData.rar"
	SET FILES="%DIRUSER%\AppData\*"
	SET EXLUCDE="-x%APPDATA%\Thunderbird"
	::call:funcBackup %TARGET% %FILES% %EXLUCDE%
 
echo.&pause&goto:eof

::--------------------------------------------------------
::-- Function section starts below here
::--------------------------------------------------------
 
:funcBackup
	SET TARGET=%~1
	SET FILES=%~2
	SET EXCLUDE=%~3
	echo."%PACKER% a -r %EXCLUDE% %TARGET% %FILES%"
	call %PACKER% a -r %EXCLUDE% %TARGET% %FILES%
goto:eof
 
:funcCreateDir
	echo "creating %~1"
	IF NOT EXIST "%~1" md "%~1"
goto:eof

Matthias Pospiech

Erstellung von Bachelor und Masterarbeiten mit LaTeX

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Einführung in Bibliographien mit LaTeX, biblatex und biber.

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pcolor plots with publication ready formating

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fast calculation of functions with two variables

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plotting a filled curve

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fast reading of structured text data with matlab

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LaTeX-Vorlage für Protokolle

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plotting tutorials

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batch script for automatic backup using winrar

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