💅🏼 Formatting changes for final layout

- different textwidth - adjust table layouts
fionaEyoung · Jan 12, 2024 · 15f7185 · 15f7185
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diff --git a/src/Atlas/Atlas.tex b/src/Atlas/Atlas.tex
@@ -281,20 +281,20 @@ \section{Streamline tractography and filtering}\label{sec:atlasmethods}
   \label{tab:filt}
   \small
   \begin{tabularx}{\textwidth}{llllll X}\toprule
-   &  & Original & Filtered & Difference & Reduction & Reasons for discarding \\
+      &      & Original & Filtered & Reduction & Reasons for discarding \\
    \midrule
-  CST & left & 148833 & 145300 & 3533 & 2.37\% & \multirow{3}{=}{Contamination from: AF / SLF, SFOF, CC, CrP} \\
-   & right & 144759 & 139019 & 5740 & 3.97\% &  \\
-   & total & 293592 & 284319 & 9273 & 3.16\% &  \\ \addlinespace
-  AF & left & 61922 & 49778 & 12144 & 19.61\% & \multirow{3}{=}{Contamination from:  EC, CST, CC Overextension into: Motor, anterior temporal, and superior frontal cortex} \\
-   & right & 61834 & 43027 & 18807 & 30.42\% &  \\
-   & total & 123756 & 92805 & 30951 & 25.01\% &  \\ \addlinespace
-  OR & left & 123842 & 99984 & 23858 & 19.26\% & \multirow{3}{=}{Contamination from: Tapetum of CC, SLF} \\
-   & right & 122534 & 109265 & 13269 & 10.83\% &  \\
-   & total & 246376 & 209249 & 37127 & 15.07\% & \\ \addlinespace
-  IFOF & left & 80000 & 44224 & 35776 & 44.72\% & \multirow{3}{=}{Contamination from: Tapetum of CC, VOF, superior frontal cortex} \\
-   & right & 80000 & 31753 & 48247 & 60.31\% &  \\
-   & total & 160000 & 75977 & 84023 & 52.51 \% & \\ \toprule
+  CST & left & 148833 & 145300 & 2.37\% & \multirow{3}{0.45\textwidth}{Contamination from: AF, SLF, SFOF, CC, CrP} \\
+   & right & 144759 & 139019 & 3.97\% &  \\
+   & total & 293592 & 284319 & 3.16\% &  \\ \addlinespace
+  AF & left & 61922 & 49778 & 19.61\% & \multirow{3}{0.45\textwidth}{Contamination from:  EC, CST, CC Overextension into: Motor, anterior temporal, and superior frontal cortex} \\
+   & right & 61834 & 43027 & 30.42\% &  \\
+   & total & 123756 & 92805 & 25.01\% &  \\ \addlinespace
+  OR & left & 123842 & 99984 & 19.26\% & \multirow{3}{0.45\textwidth}{Contamination from: Tapetum of CC, SLF} \\
+   & right & 122534 & 109265 & 10.83\% &  \\
+   & total & 246376 & 209249 & 15.07\% & \\ \addlinespace
+  IFOF & left & 80000 & 44224 & 44.72\% & \multirow{3}{0.45\textwidth}{Contamination from: Tapetum of CC, VOF, superior frontal cortex} \\
+   & right & 80000 & 31753 & 60.31\% &  \\
+   & total & 160000 & 75977 & 52.51 \% & \\ \toprule
  \end{tabularx}
 \end{table*}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

diff --git a/src/Experiments/Data.tex b/src/Experiments/Data.tex
@@ -90,7 +90,7 @@ \subsection{BTCD}
   \caption{Overview of acquisition parameters for the datasets included in quantitative benchmark evaluation. \dag Resampled from original, see text for details.}
   \label{tab:datasets}
   \footnotesize
-  \begin{tabularx}{0.9\linewidth}{l c c c c c c c c} \toprule
+  \begin{tabularx}{\linewidth}{l c c c c c c c c} \toprule
              & \multicolumn{2}{c}{GOSH} & \multicolumn{2}{c}{NHNN} & \multicolumn{2}{c}{BTC\autocite{Aerts2018, Aerts2020a}} & \gls{hcp}\autocite{Sotiropoulos2013, Glasser2013} & \textit{TractoInferno}\autocite{Poulin2022} \\
              & pre-op.   & intra-op.      & pre-op. & intra-op.        & pre-op. & post-op.       & & \\
   \midrule%
@@ -100,12 +100,12 @@ \subsection{BTCD}
              &            & adult (n=1)      &        &                                 &       &                           &            &         \\[1em]
   Diagnosis  & \multicolumn{2}{c}{low-grade astrocytoma (n=3)}  & \multicolumn{2}{c}{oligodendroglioma (n=2)}& \multicolumn{2}{c}{meningioma (n=4)} & healthy & healthy \\
               &           & healthy (n=1)  & \multicolumn{2}{c}{other tumour (n=2)}     & \multicolumn{2}{c}{glioma (n=5)}  &            & \\[1em]
-  $b$-values  & 800 (n=1)   & 1000           & 1000     & 1000                       & \multicolumn{2}{c}{0, 700, 1200, 2800} & 1000       & 1000 (n=68) \\
-  (s~mm$^2$) & 1000, 2200 (n=2) &          &          &                            &            &                           &            & 700 (n=3) \\[1em]
+  $b$-values (s~mm$^2$) & 800 (n=1)   & 1000           & 1000     & 1000                       & \multicolumn{2}{c}{0, 700, 1200, 2800} & 1000       & 1000 (n=68) \\
+   & 1000, 2200 (n=2) &          &          &                            &            &                           &            & 700 (n=3) \\[1em]
   $n$ directions & 15 (n=1)     & 30             & 64 (n=3) & 30 (n=3)                   & \multicolumn{2}{c}{8, 16, 30, 50}      & 60\dag     & 21--128 \\
            & 60, 60 (n=2) &                & 61 (n=1) & 3\x{}12 (n=1)               &            &                           &            & \\[2em]
-  Voxel size & 1.75\x{}1.75\x{}2.5 (n=1) & 2.5 (n=1) & 2.5 & 2.5\x{}2.5\x{}2.7 & \multicolumn{2}{c}{2.5} & 2.5\dag    & 2.3\dag \\
-  (mm)       & 2\x{}2\x{}2.2 (n=2)       & 2.3 (n=3) & & & & & & \\[1em]
+  Voxel size (mm) & 1.75\x{}1.75\x{}2.5 (n=1) & 2.5 (n=1) & 2.5 & 2.5\x{}2.5\x{}2.7 & \multicolumn{2}{c}{2.5} & 2.5\dag    & 2.3\dag \\
+                  & 2\x{}2\x{}2.2 (n=2)       & 2.3 (n=3) & & & & & & \\[1em]
   Scanner & Philips Ingenia 1.5T (n=1)  & Siemens  & Siemens & Siemens & \multicolumn{2}{c}{Siemens} & Siemens 3T & variable\\
           &  Siemens Prisma 3T (n=2)    &  Vida 3T  & Trio 3T  & Espree 1.5T                & \multicolumn{2}{c}{Trio 3T}           & ``Connectome Skyra” & \\
           &                          &                &          &                            &                   &                   &   & \\ \bottomrule

diff --git a/src/Experiments/Validation.tex b/src/Experiments/Validation.tex
@@ -296,14 +296,15 @@ \subsection{Processing times}
 However, since the time taken depends greatly on several factors, including number of streamlines to select and streamline acceptance rate (often low in brains with pathology due to oedema, deformation etc.), a precise time analysis for manual tractography cannot provided here.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\begin{table*}[h!]
+\begin{landscape}
+\begin{table}[ht!]
   \caption{Measured processing times mean and standard deviation for \textit{TractoInferno} dataset. Individual steps shown and total average for the four different pipelines. Note that the tractography pipeline was partially run on a high performance computing cluster, so the reported total time is not representative of a typical setup. Further note that for the present study, tractography \glspl{roi} were drawn once for the whole dataset, whereas for clinical datasets manual \gls{roi} delineation will have to be repeated for each subject. \dag Desktop Mac with 4 GHz Quad-Core Intel Core i7 \ddag High performance computing cluster, one node per subject, 36 Intel(R) Xeon(R) Gold 6240 CPU @ 2.60 GHz cores per node.}
   \label{tab:time}
   \small
-  \begin{tabularx}{\textwidth}{>{\raggedright}X >{\centering}X ^>{\sffamily}c ^>{\sffamily}c ^>{\sffamily}c ^>{\sffamily}c}
+  \begin{tabularx}{\linewidth}{>{\raggedright}X >{\centering}X ^>{\sffamily}c ^>{\sffamily}c ^>{\sffamily}c ^>{\sffamily}c}
     \toprule
     \rowstyle{\rmfamily}
-    Step & Processing time\newline(s, per subject) & Tractfinder & TractSeg & Atlas & Tractography \\
+    Step & Processing time (s, per subject) & Tractfinder & TractSeg & Atlas & Tractography \\
     \midrule
     \dag Brain masking & 3 $\pm$ 2 &\x{}&\x{}&\x{}&\x{}\\
     \dag Affine MNI registration & 20 $\pm$ 4 &\x{}&  &\x{}&  \\
@@ -317,7 +318,8 @@ \subsection{Processing times}
     \rowstyle{\bfseries\rmfamily}
     Total &  & 2:42~min & 4:25~min & \textless2:42~min & \textgreater 27:32~min \\ \bottomrule
   \end{tabularx}
-\end{table*}
+\end{table}
+\end{landscape}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 \section{Two methods, same training data}\label{sec:tractseg}

diff --git a/src/FrontBack/UCL-Research-Paper-Declaration-Form.tex b/src/FrontBack/UCL-Research-Paper-Declaration-Form.tex
@@ -225,7 +225,7 @@ \section*{UCL Research Paper Declaration Form: referencing the doctoral candidat
 \item \textbf{In which chapter(s) of your thesis can this material be found?}
 % Answer here
 
-Chapters \ref{chap:Neuroimaging}, \ref{chap:atlas}, \ref{chap:reg} (Section \ref{sec:reg1}), \ref{chap:eval}, Appendix
+Chapters \ref{chap:neuroimaging}, \ref{chap:atlas}, \ref{chap:reg} (Section \ref{sec:reg1}), \ref{chap:eval}, Appendix
 \end{enumerate}
 
 \textbf{e-Signatures confirming that the information above is accurate}

diff --git a/src/Main.tex b/src/Main.tex
@@ -46,7 +46,7 @@
 %  you intend to print double-sided. Note that this is
 %  *specifically permitted* by the UCL thesis formatting
 %  guidelines.
-\documentclass[12pt,phd,a4paper,oneside,draft]{ucl_thesis}
+\documentclass[12pt,phd,a4paper,twoside]{ucl_thesis}
 
 % Package configuration:
 \input{setup/MainPackages}
@@ -85,15 +85,10 @@
 %  published in at the end of that chapter.
 % For more information, see: http://stefaanlippens.net/bibentry
 
-\ifdraft{%
-  \setcounter{tocdepth}{5}
-  \tableofcontents%
-  }{%
-  \include{FrontBack/Preamble}
-  \printglossary[type=\acronymtype]
-  \glsaddallunused[main]
-  \printglossary
-}
+\include{FrontBack/Preamble}
+\printglossary[type=\acronymtype]
+% \glsaddallunused[main]
+\printglossary
 
 \epipage{I'll tell you where the real road lies\\
 Between your ears, behind your eyes}{Anais Mitchell, Hermes in \textit{Wait For Me (Reprise)}}

diff --git a/src/graphics/figutils.py b/src/graphics/figutils.py
@@ -17,7 +17,7 @@ def set_box_colours(bp, index=None, **kwargs):
       b.set(**kwargs)
 
 #https://jwalton.info/Embed-Publication-Matplotlib-Latex/
-def set_size(width=452.9679, ratio=None, fraction=1, subplots=(1, 1)):
+def set_size(width=398.33858, ratio=None, fraction=1, subplots=(1, 1)):
     """Set figure dimensions to avoid scaling in LaTeX.
 
     Parameters
@@ -50,7 +50,7 @@ def set_size(width=452.9679, ratio=None, fraction=1, subplots=(1, 1)):
     return (fig_width_in, fig_height_in)
 
 # https://stackoverflow.com/a/44971177
-def set_ax_size(width=452.9679, ratio=None, fraction=1, ax=None, subplots=(1, 1)):
+def set_ax_size(width=398.33858, ratio=None, fraction=1, ax=None, subplots=(1, 1)):
     """ w, h: width, height in inches """
     if ax is None: ax=plt.gca()
     if not isinstance(ax, (np.ndarray)): ax = np.array([ax])

diff --git a/src/graphics/hcp_sbd_box.py b/src/graphics/hcp_sbd_box.py
@@ -42,8 +42,8 @@ def main():
 
   ## All metrics box plots, grouped by tract
   all_metrics_fig, all_metrics_axs = plt.subplots(nrows=1,
-                                                  ncols=ceil(len(include_metrics)/2),
-                                                  figsize=set_size(subplots=(1,ceil(len(include_metrics)/2)), fraction=0.5))
+                                                  ncols=ceil(len(include_metrics)/2), layout="constrained",
+                                                  figsize=set_size(ratio=0.6, subplots=(1,ceil(len(include_metrics)/2)), fraction=0.6))
 
   for metric, ax in zip(include_metrics, [all_metrics_axs]):
 
@@ -93,7 +93,6 @@ def main():
 
   all_metrics_axs.legend(one_of_each, order, ncol=len(order), loc='lower right')
   all_metrics_fig.suptitle("")
-  plt.margins(0,0)
   all_metrics_fig.savefig(path.join(results_dir, 'hcp_box.pdf'),
               transparent=False, dpi=80, bbox_inches='tight', pad_inches=0.01)