Submitted Version

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Latex
+*.aux
+*.glo
+*.idx
+*.log
+*.toc
+*.ist
+*.acn
+*.acr
+*.alg
+*.bbl
+*.blg
+*.dvi
+*.glg
+*.gls
+*.ilg
+*.ind
+*.lof
+*.lot
+*.maf
+*.mtc
+*.mtc1
+*.out
+*.synctex.gz 
+*.llt
+*.obj
+
+

Abstract/abstract.tex

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+% ************************** Thesis Abstract *****************************
+% Use `abstract' as an option in the document class to print only the titlepage and the abstract.
+\begin{abstract}
+
+    There has been ubiquitous observations of wave-like motions in the solar atmosphere for decades and the presence of magneto-acoustic waves in magnetic structures in the solar atmosphere is well-documented.
+    In this thesis, we aim to detect and identify magnetohydrodynamic (MHD) sausage waves in the lower solar atmosphere. 
+    In order to achieve this, high-resolution ground-based data is taken from numerous solar telescopes.
+    For this thesis, two sunspots and three magnetic pore were chosen as examples of MHD waveguides in the lower solar atmosphere.
+    Combining the Wavelet Transform and Empirical Mode Decomposition, we determined characteristic periods within the cross-sectional area and intensity time series and several oscillations have been detected within these waveguides.
+    Then, by applying the theory of linear MHD, we identified the mode of these oscillations and concluded that they can be classified as slow sausage MHD waves. 
+    Further, we determined several key properties of these oscillations such as the radial velocity perturbation, magnetic field perturbation and vertical wavenumber using magneto-seismology.
+    The estimated range of the related wavenumbers reveals that these oscillations are trapped within these magnetic structures.
+    Our results suggest that the detected oscillations are standing harmonics, and, this allows us to estimate the expansion factor of the waveguides by employing magneto-seismology.
+    Finally, we analysed Running Penumbral Waves (RPWs).
+    RPWs have always thought to be radial wave propagation that occur within sunspots.
+    Here, RPWs within a magnetic pore are observed for the first time and are interpreted as Upwardly Propagating Waves (UPWs) due to the lack of a penumbra that is required to support RPWs.
+    These UPWs are also observed co-spatially and co-temporally within two elemental lines that sample the Transition Region and low corona.
+    The observed UPWs are travelling at a horizontal velocity of around 17 $\pm$ 0.5 km s$^{-1}$ and a minimum vertical velocity of 42 $\pm$ 21 km s$^{-1}$.
+    The estimated energy of the waves is around 150 W m$^{-2}$, which is on the lower bounds required to heat the quiet-Sun corona.
+
+\end{abstract}

Acknowledgement/acknowledgement.tex

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+% ************************** Thesis Acknowledgements **************************
+\begin{acknowledgements}      
+
+    There are many people and organizations I would like to thank during the four years of my PhD.
+
+    Firstly, the official acknowledgements.
+    To start, the instruments and their support teams who made this research possible.
+    SDO/AIA and SDO/HMI data are used courtesy of NASA/SDO and the AIA and HMI science teams.
+    The Swedish 1-m Solar Telescope is operated on the island of La Palma by the Institute for Solar Physics of Stockholm University in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofsica de Canarias.
+    I want to thank Luc Rouppe van der Voort (Institute of Theoretical Astrophysics, University of Oslo) and J. de la Cruz Rodriguez (University of Uppsala, Sweden) for data reductions with MOMFBD for SST/CRISP.
+    DST/ROSA and DST/IBIS data used in this thesis were obtained with the facilities of the National Solar Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc.
+    The DOT was operated by Utrecht University (The Netherlands) at Observatorio del Roque de los Muchachos of the Instituto de Astrofsica de Canarias (Spain) funded by the Netherlands Organisation for Scientific Research NWO, The Netherlands Graduate School for Astronomy NOVA, and SOZOU.
+    The DOT efforts were part of the European Solar Magnetism Network.
+    The SVST was operated by the Institute for Solar Physics, Stockholm, at the Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias (La Palma, Spain).
+    The computational tools used to analyse the data provided, AstroPy \cite{theastropycollaboration2013}, Ginga, IPython \citep{perez2007}, Matplotlib \cite{hunter2007}, NumPy \citep{jones2001}, SciPy \citep{jones2001}, scikit-image \citep{vanderwalt2014}, SolarSoft \citep{1998SoPh..182..497F}, SunPy \citep{thesunpycommunity2015a} and SymPy \cite{sympydevelopmentteam2014}
+    I want to thank J. Terradas for providing the EMD routines used in the data analysis.
+    Wavelet power spectra were calculated using a modified computing algorithms of wavelet transform original of which was developed and provided by C. Torrence and G. Compo, and is available at URL: \url{http://paos.colorado.edu/research/wavelets/}.
+    The Science and Technology Facilities Council (STFC) funded my studies and my travels around Europe.
+
+    Secondly, the people I have come across during my PhD.
+    I would like to thank Steven Christie for inviting me to give a talk at NASA GSFC.
+    Chris (and Helen by extension), for helping me throughout my PhD.
+    Without his ability to encourage me to carry on and his technique for fine writing and science, I would have been very lost.
+    Thank you for out doing me at every turn.
+    I want to also thank Chris's seven papers for getting Chris his two jobs and keeping him around for Freddie.
+    Tom, for his ability to ignore me whenever I say hello, I have never been so insulted.
+    Freddie, for those gains, the numerous nights out (getting drunk has never been so fun) and his bitching talk at NASA GSFC.
+    Stevie, for his inability to eat nice food which provided many hours of entertainment and his incredible ability to eat an entire loaf of bread in a single sitting. 
+    Stevie's mother for making sure Stevie had clean socks.
+    Stuart, for all that Python support he provided me, without my papers would of been very barren.
+    Sky (and Beth by extension), for letting me annoy them for 4 years (or was it just 3 months?) with my grating personality.
+    It was an honour for me to be a part of your marriage and long it may continue.
+    I want to thank my fountain pen collection for being there through thick and thin.
+    The office has been a fantastic environment, through the magic craze, the ball games, the breaking incidents and the antics of Freddie. 
+    I do apologise for the loudness that I have caused.
+    But I can say without hesitation, that it has been the best four years so far in my life and I have met some truly amazing human beings.
+    Sorry I can't include everyone by name but I want to thank everyone else I have met during my PhD as well.
+
+    I would like to thank my PhD supervisor Robertus Erd\'elyi.
+    Without him giving me the chance to do this PhD, I would be doing some sort of normal job.
+    He believed in me and gave me this opportunity, which I am very grateful for.
+    He has been a fantastic supervisor, encouraging me to push myself and being patient at the times I've been slow or stupid.
+
+    Last but not least, my family.
+    I want to thank my mother and sister supporting me through my time at Sheffield.
+    It as always been a comfort to know that I can go back whenever I needed to.
+    I'll be home soon.
+
+\end{acknowledgements}