update

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "editor.wordWrap": "on"
+}

Physics_Thesis_Template/bib-refs.bib

@@ -1,3 +1,33 @@
+@misc{pyqt5,
+  title={PyQt5},
+  url={https://www.riverbankcomputing.com/static/Docs/PyQt5/introduction.html},
+  author={{Riverbank Computing Limited}},
+  urldate = {2025-03-25}
+} 
+
+@misc{sqlite,
+  title={SQLite},
+  url={https://www.sqlite.org/},
+  author={{SQLite Development Team}},
+  urldate = {2025-03-26}
+} 
+
+@article{kepler_archive_manual,
+      author = {{Thompson}, Susan E. and {Fraquelli}, Dorothy and {Van Cleve}, Jeffrey E. and {Caldwell}, Douglas A.},
+      title = "{Kepler Archive Manual}",
+      publisher = {Ames Research Center},
+      year = 2016,
+      month = may
+}
+
+@article{tess_science_data_products,
+      author = {{Twicken}, Joseph D. and {Caldwell}, Douglas A. and {Jenkins}, Jon M. and {Tenenbaum}, Peter and {Smith}, Jeffrey C. and {Wohler}, Bill and {Rose}, Mark and {Ting}, Eric B. and {Vanderspek}, Roland and {Morgan}, Ed and {Rudat}, Alexander and {Fausnaugh}, Michael and {Fleming}, Scott and {Quintana}, Elisa},
+      title = "{TESS Science Data Products Description Document}",
+      publisher = {Ames Research Center},
+      year = 2020,
+      month = sep
+}
+
 @ARTICLE{simbad,
        author = {{Wenger}, M. and {Ochsenbein}, F. and {Egret}, D. and {Dubois}, P. and {Bonnarel}, F. and {Borde}, S. and {Genova}, F. and {Jasniewicz}, G. and {Lalo{\"e}}, S. and {Lesteven}, S. and {Monier}, R.},
         title = "{The SIMBAD astronomical database. The CDS reference database for astronomical objects}",

Physics_Thesis_Template/content/acknowledgement.tex

@@ -8,26 +8,36 @@
 
 % Acknowledge infrastructure and people that supported you in your thesis. This can also cover family, friends, etc.
 
-I gratefully acknowledge my supervisor xxx for guiding me ... the technical team xxx, yyy, for the continuous support...
+I gratefully acknowledge my supervisors \thesisFirstSupervisor and \thesisSecondSupervisor for guiding me through the process.
 
-I thank my family and friends...
+I thank my family and friends for supporting me.
 
 This thesis made use of the experimental setups, laboratory and technical infrastructure, general resources and observational facilities of the Institute of Physics of the University of Graz. This thesis also made use of infrastructure, which was supported by NAWI Graz. 
 
 
 % you may also list missions, telescopes, data bases or code packages you have used. Copy here the predefined sentence you are requested on the project webpage to cite. Also make sure that you cite the requested papers, as mentioned in the text below. 
 %
-\par
-\textit{Software:} \texttt{Python} \citep{10.5555/1593511}, 
-\texttt{numpy} \citep{numpy,Harris_2020},  
-\texttt{matplotlib} \citep{4160265},  
-\texttt{scipy} \citep{2020SciPy-NMeth}, 
-\texttt{pandas} \citep{reback2020pandas, mckinney-proc-scipy-2010}.
-This research made use of \texttt{astropy} \citep{astropy:2013, astropy:2018}., a community-developed core Python package for Astronomy. 
+%\par
+%\textit{Software:} \texttt{Python} \citep{10.5555/1593511}, 
+%\texttt{numpy} \citep{numpy,Harris_2020},  
+%\texttt{matplotlib} \citep{4160265},  
+%\texttt{scipy} \citep{2020SciPy-NMeth}, 
+%\texttt{pandas} \citep{reback2020pandas, mckinney-proc-scipy-2010}.
+%This research made use of \texttt{astropy} \citep{astropy:2013, astropy:2018}., a community-developed core Python package for Astronomy. 
+This research made use of pandas \citep{reback2020pandas, mckinney-proc-scipy-2010}.
+This research made use of Astropy, a community-developed core Python package for Astronomy \citep{astropy:2013, astropy:2018}.
+This research made use of SciPy \citep{2020SciPy-NMeth}.
+This research made use of matplotlib, a Python library for publication quality graphics \citep{4160265}.
+This research made use of NumPy \citep{numpy,Harris_2020}.
+This research made use of Astroquery \citep{astroquery}.
+
+This research has made use of the SIMBAD database, operated at CDS, Strasbourg, France. 
+
+This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is provided by the NASA Science Mission Directorate. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–26555.
+
+This paper includes data collected with the TESS mission, obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the TESS mission is provided by the NASA Explorer Program. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–26555.
 
 % acknowledge FUNDING that you have received as financial support  
 
 %acknowledge sources of funding like a travel grant or a Erasmus fellowship, e.g.:
 I gratefully acknowledge the Austrian Science Fund (FWF): P30949-N36 (PI: xxx) for supporting this project. 
-This work was supported with funding of the Dr. Heinrich-Jörg Foundation at the Faculty of Natural Sciences at the Karl-Franzens University of Graz.
-The authors acknowledge the support from ERASMUS+ grant number 2017-1-CZ01-KA203-035562.

Physics_Thesis_Template/content/chapter-data.tex

@@ -5,21 +5,13 @@
 
 This chapter will explain how the used data was gathered, as well as the criteria for which data was used for the final results. Lastly, I will describe the algorithms used.
 
-\section{Source}
-
-The data used in this thesis was gathered with the help of the astroquery (\cite{astroquery}) python package. For this purpose, as well as displaying the downloaded data, a GUI application was created with the python package PyQt5 (\cite{pyqt5}). The GUI window for downloads can be seen in \ref{fig:download_new_star_data_gui}. 
-
-\begin{figure}[pt!]
-  \includegraphics[width=\linewidth]{gui/download_star_data_gui.png}
-  \caption{GUI window for downloading new fit files with astroquery. }
-  \label{fig:download_new_star_data_gui}
-\end{figure}
-
 \section{Data selection}
+\label{sec:data:data_selection}
 
 
 
 \section{Data reduction}
+\label{sec:data:data_reduction}
 
 
 \begin{table}[tp!]

Physics_Thesis_Template/content/chapter-gui.tex

@@ -0,0 +1,59 @@
+\chapter{GUI}
+\label{sec:gui}
+
+The data used in this thesis was gathered with the help of the astroquery (\cite{astroquery}) python package. For this purpose, as well as displaying the downloaded data, a GUI application was created with the python package PyQt5 (\cite{pyqt5}). The GUI window for downloads can be seen in figure \ref{fig:download_new_star_data_gui}.\\
+The first step is to enter the identifier of the star(s). In case of multiple, they have to be seperated by a semicolon. Then the missions from which the data should be fetched can be selected. The supported missions are TESS and Kepler/K2. For Kepler and K2 short and/or long cadence can be selected. The differeces are described in section \ref{sec:intro:space_missions}. After the selection has been made, the fetch button needs to be pressed. The program will then request metadata matching the star identifier(s) and selected missions from the MAST archive. The found mission data is then displayed in the preview field. It can then be downloaded by pressing the "Ok" button. The program the proceeds to download the according fits-files. The filename and TESS sector or Kepler/K2 target table ID is appended to the previously fetched metadata and handed back to the main GUI.\\
+There a request to Simbad is made to fetch additional metadata. First the alternative identifiers are fetched from Simbad, which also has a MAIN\_ID attribute. This is to make sure we only have one entry in the local database per star and no duplicates. Afterwards additional data is fetched from Simbad (\cite{simbad}) like spectral type, radial velocity and distance. After the data is gathered, the main identifier, the alternative identifiers, spectral type, rotational velocity and distance (and their respective units) as well as the file path, source (TESS, Kepler or K2), and sector/target table id are saved into a local database using SQLite3 (\cite{sqlite}).
+
+\begin{figure}[pt!]
+  \includegraphics[width=\linewidth]{gui/download_star_data_gui.png}
+  \caption{GUI window for downloading new fit files with astroquery designed using the Qt5 designer shipped with PyQt5 (\cite{pyqt5}). The star identifier field supports one or more (separated by a semicolon) identifiers. There are checkboxes to select TESS, Kepler (long and/or short cadence) and K2 (long and/or short cadence) data. The preview field shows metadata (Identifier, TESS quarter or Kepler/K2 target table ID) to check the data which was found and which can be downloaded. The "Ok" button then proceeds to download the data and hands information back to the main GUI.}
+  \label{fig:download_new_star_data_gui}
+\end{figure}
+
+Afterwards the list of stars seen in figure \ref{fig:full_gui_normal_selection} will be refreshed. It shows the via Simbad determined main identifier alphabetically sorted. When one of the stars in the list is selected, the program will show the additional saved informations. This includes all known IDs (in the Alt. IDs list), the spectral type, its rotational velocity and its distance. Additionally a fit type for the folded lightcurves which are described in section \ref{sec:data:data_reduction}. The default for this is "sine". The list to the right of the information section shows the available fit files. The formating for the list entries is "TESS - <sequence>" and "Kepler/K2 - <target table id>". The combine button allows to show multiple fit files at once if multiple are selected. Select one or combining multiple fit files, enables the plot options.\\
+The main plot options allow the user to change the type of flux thats plotted. This is either "SAP\_FLUX" (simple aperture photometry) or "PDCSAP\_FLUX" (presearch data conditioning simple aperture photometry) (\cite{lightkurve}). The PDCSAP\_FLUX has parts of its data removed depending on the quality flags (e.g. indicating systematic errors like an attitude tweak or a cosmic ray (\cite{tess_science_data_products}, \cite{kepler_archive_manual})) as well as corrected long-term brightness changes (\cite{lightkurve}). An example of a PDCSAP\_FLUX is shown in figure \ref{fig:full_gui_normal_selection}.\\
+The lightkurve python package also supports normalizing (to unscaled, percent, parts per thousands (ppt) or parts per million (ppm)) which can be seen in figure \ref{fig:full_gui_normal_selection_normalize_options}. Flattened lightcurves (see figure \ref{fig:full_gui_normal_selection_flattened} as an example for $BD-08\ 995$) is used to identify flares. The "remove outliers", "remove nans/infs" and "bin" features are exposed in the GUI, but are not actively used in this thesis.\\
+The checkboxes to flatten the lightcurve (figure \ref{fig:full_gui_normal_selection_flattened}), fold the lighhtcurve (figure \ref{fig:full_gui_normal_selection_folded}) and showing the periodogram (figures \ref{fig:full_gui_normal_selection_periodogram_lombscargle} and \ref{fig:full_gui_normal_selection_periodogram_boxleastsquares}) are exclusive of each other. Only one can be used at a time.
+
+\begin{figure}[pt!]
+  \includegraphics[width=\linewidth]{gui/full_gui_normal_selection.png}
+  \caption{Main GUI window. This window was designed with the Qt5 designer shipped with PyQz5 (\cite{pyqt5}). It shows a list of all available stars with their main identifier (taken from SIMBAD (\cite{simbad})) sorted alphabetically. The "Star infos" box contains additional information on the star gathered from SIMBAD. There is a list of alternative IDs, the spectral type, the roational velocity, and the distance. It also shows the prefered fit type for folding lightcurves. On the right of the information box is a list of all available lightcurves, with an option to combine multiple to plot at once. To the right of the list of available lightcurves are multiple different plot options, which utilize the different capabilities of the lightkurve python package (\cite{lightkurve}). The values for "Period" and "Epoch Time" are automatically calculated and used as default for the selected lightcurve. In this image the TESS Sector 32 lightcurve of $BD-08\ 995$ is shown. The red crosses show the peaks of the found flares, while the red overall over the lightcurve indicates the duration of the flare.}
+  \label{fig:full_gui_normal_selection}
+\end{figure}
+
+\begin{figure}[pt!]
+  \includegraphics[width=\linewidth]{gui/full_gui_normal_selection_show_quality.png}
+  \caption{Main GUI window. Same as in figure \ref{fig:full_gui_normal_selection}, with the difference that the data quality flag is also shown.}
+  \label{fig:full_gui_normal_selection_show_quality}
+\end{figure}
+
+\begin{figure}[pt!]
+  \includegraphics[width=\linewidth]{gui/full_gui_normal_selection_normalize_options.png}
+  \caption{Main GUI window. Same as in figure \ref{fig:full_gui_normal_selection}, with the difference that the lightcurve was normalized. It also shows all possible normalize options the lightkurve python package (\cite{lightkurve}) supports.}
+  \label{fig:full_gui_normal_selection_normalize_options}
+\end{figure}
+
+\begin{figure}[pt!]
+  \includegraphics[width=\linewidth]{gui/full_gui_normal_selection_flattened.png}
+  \caption{Main GUI window. Showing the same lightcurve as figure \ref{fig:full_gui_normal_selection}, with the difference that it is now flattened. The green line shows a fit of the flare. This is described in chapter \ref{sec:data:data_reduction}.}
+  \label{fig:full_gui_normal_selection_flattened}
+\end{figure}
+
+\begin{figure}[pt!]
+  \includegraphics[width=\linewidth]{gui/full_gui_normal_selection_folded.png}
+  \caption{Main GUI window. Showing the same lightcurve as figure \ref{fig:full_gui_normal_selection}, with the difference that it is now folded with an period of ~2.697 days. Additionally vertical lines are shown which indicate the region around the minima and maxima of the folded lightcurve respectively.}
+  \label{fig:full_gui_normal_selection_folded}
+\end{figure}
+
+\begin{figure}[pt!]
+  \includegraphics[width=\linewidth]{gui/full_gui_normal_selection_periodogram_lombscargle.png}
+  \caption{Main GUI window. Showing the periodogram of the lightcurve in figure \ref{fig:full_gui_normal_selection} using the lombscargle algorithm. Furthermore it shows the four highest peaks (which are atleast 100 datapoints separated). The method is explained in chapter \ref{sec:data:data_reduction}.}
+  \label{fig:full_gui_normal_selection_periodogram_lombscargle}
+\end{figure}
+
+\begin{figure}[pt!]
+  \includegraphics[width=\linewidth]{gui/full_gui_normal_selection_periodogram_boxleastsquares.png}
+  \caption{Main GUI window. Showing the periodogram of the lightcurve in figure \ref{fig:full_gui_normal_selection} using the box least square algorithm. Similarly to figure \ref{fig:full_gui_normal_selection_periodogram_lombscargle} the four highest peaks are marked with a red "x".}
+  \label{fig:full_gui_normal_selection_periodogram_boxleastsquares}
+\end{figure}

Physics_Thesis_Template/content/chapter-introduction.tex

@@ -3,19 +3,19 @@
 \chapter{Introduction \label{sec:intro}}
 %\cleanchapterquote{Shoot for the moon. Even if you miss, you'll land among the stars.}{Les Brown} %optional, if you want to place something here.
 
-\section{Current knowledge}
+\section{Current knowledge \label{sec:intro:cur_knowledge}}
 
 % motivation for the thesis
 
-\section{Spectral Types}
+\section{Spectral Types \label{sec:intro:spectral_types}}
 
 % Different Spectral Types
 
-\section{Flares and Starspots}
+\section{Flares and Starspots \label{sec:intro:flares_and_spots}}
 
 % Stellar Activity, 
 
-\section{Spacecrafts}
+\section{Space missions \label{sec:intro:space_missions}}
 
 % TESS, Kepler/K2
 

Physics_Thesis_Template/main.tex

@@ -64,6 +64,7 @@
 \newcommand{\nphysa}{Nuclear Physics A}
 \newcommand{\prd}{Physical Review D}
 \newcommand{\aj}{The Astronomical Journal}
+\newcommand{\aaps}{Astronomy and Astrophysics Supplement Series}
 
 \usepackage{xspace}
 \newcommand{\Figure}[1]{Figure\,\ref{#1}\xspace}
@@ -303,6 +304,7 @@
 \pagestyle{maincontentstyle} 	% fancy header and footer
 %Include various chapters that are in the folder content
 \input{content/chapter-introduction}
+\input{content/chapter-gui}
 \input{content/chapter-data}
 \input{content/chapter-results}
 \input{content/chapter-discussion}