Manual: improve layout here and there

doc/usermanual/chapters/tools.tex

-\section{Additional Tools \& Resources}
-\label{sec:additional_tools_resources}
+\chapter{Additional Tools \& Resources}
+\label{ch:additional_tools_resources}
 
 The following section briefly describes tools provided with the Corryvreckan framework.
 

doc/usermanual/config.tex

@@ -73,7 +73,7 @@
 \newcommand{\project}{@CMAKE_PROJECT_NAME@}
 
 % Create addreferences command (overwritten for HTML in config)
-\newcommand{\addreferencesline}{\addcontentsline{toc}{section}{References}}
+\newcommand{\addreferencesline}{\addcontentsline{toc}{chapter}{References}}
 
 % Command to add the license (overwritten for HTML in config)
 \newcommand{\addlicense}{

doc/usermanual/references.bib

@@ -54,3 +54,9 @@
   Journal                  = {PoS},
   Slaccitation             = {%%CITATION = POSCI,ICHEP2010,002;%%}
 }
+@misc{timepix3-talk,
+  author = "X. Llopart",
+  title = "The Timepix3 chip",
+  note = {{EP-ESE seminar}},
+  URL = {https://indico.cern.ch/event/267425},
+}

src/modules/Alignment/README.md

@@ -30,6 +30,7 @@ For the detector specified by the `detectorToAlign` parameter, this method moves
 
 ### Plots produced
 For each detector the following plots are produced when using `alignmentMethod = 0`:
+
 * Translational shift along X-axis vs. iteration number
 * Translational shift along Y-axis vs. iteration number
 * Translational shift along Z-axis vs. iteration number
@@ -38,6 +39,7 @@ For each detector the following plots are produced when using `alignmentMethod =
 * Rotational shift around Z-axis vs. iteration number
 
 For the `detectorToAlign` the following plots are produced when using `alignmentMethod = 1`:
+
 * Residual in X (calculated in local coordinates)
 * Residual in Y
 * Profile plot of residual in X vs. X position

src/modules/BasicTracking/README.md

@@ -25,6 +25,7 @@ Clusters from the first plane in Z (named the seed plane) are related to cluster
 * Track angle with respect to Y-axis histogram
 
 For each detector the following plots are produced:
+
 * Residual in X
 * Residual in Y
 * Residual in X for clusters with a width in X of 1

src/modules/Clicpix2Correlator/README.md

@@ -11,6 +11,7 @@ This module makes plots of the correlations in X and Y for angles between 0 and
 
 ### Plots produced
 For each angle between 0 and 2pi in steps of 0.6 radians the following plots are produced:
+
 * Correlation (track difference) in X
 * Correlation (track difference) in Y
 

src/modules/ClicpixAnalysis/README.md

@@ -13,6 +13,7 @@ This module associates CLICpix2 DUT clusters to tracks using a spatial cut (devi
 
 ### Plots produced
 For the DUT the following plots are produced:
+
 * 2D hitmap
 * Column hits histogram
 * Row hits histogram
@@ -37,7 +38,7 @@ For the DUT the following plots are produced:
 * Global residuals in X vs row width
 * Global residuals in Y vs column width
 * Global residuals in Y vs row width
-*
+
 * Track intercept in rows
 * Track intercept in columns
 * Absolute residual map histogram

src/modules/DataDump/README.md

@@ -9,9 +9,6 @@ This module reads in raw data files with extension `-1.dat`, and outputs the pix
 * `DeviceToDumpData`: The name of the device data is to be read from.
 * `inputDirectory`: Path to the directory above the data directory named `DeviceToDumpData`.
 
-### Plots produced
-No plots are produced.
-
 ### Usage
 ```toml
 [DataDump]

src/modules/DataOutput/README.md

@@ -6,18 +6,21 @@
 This module writes out data from a Timepix3 DUT for timing analysis. The outputted ROOT TTree contains data in branches. This is intended for analysis of the timing capabilities of Timepix3 devices of different thicknesses.
 
 For each track associated DUT `cluster` object the following information is written out:
+
 * Event ID
 * Size in X
 * Size in Y
 * Number of pixels in the cluster
 
 For each `pixel` object in an associated `cluster` the follwing information is written out:
+
 * X position
 * Y position
 * ToT
 * ToA
 
 For each `track` with associated DUT `clusters` the following information is written out:
+
 * Intercept with the DUT (3D position vector)
 
 ### Parameters

src/modules/Dummy/README.md

@@ -13,6 +13,7 @@ No parameters are used from the configuration file.
 * Histogram of event numbers
 
 For each detector the following plots are produced:
+
 * 2D histogram of pixel hit positions
 
 ### Usage

src/modules/EtaCalculation/README.md

@@ -14,6 +14,7 @@ In order to measure the correct $`\eta`$-distribution, no additional $`\eta`$-co
 
 ### Plots produced
 For each detector the following plots are produced:
+
 * 2D histogram of the calculated $`\eta`$-distribution, for X and Y respectively
 * Profile plot of the calculated $`\eta`$-distribution, for X and Y respectively
 

src/modules/OnlineMonitor/README.md

@@ -14,15 +14,18 @@ Users should be able to exit `OnlineMonitor` and leave the reconstruction still
 
 ### Plots produced
 Overview canvas:
+
 * Cluster ToT of reference plane
 * 2D hitmap of reference plane
 * Residual in X of reference plane
 
 Tracking canvas:
+
 * Track chi^2
 * Track angle in X
 
 For each detector the following plots are produced:
+
 * Hitmap canvas: 2D hitmap
 * Residuals canvas: residual in X histogram
 * Event times canvas: event times histogram

src/modules/Prealignment/README.md

@@ -17,6 +17,7 @@ The required translational shifts in X and Y are calculated for each detector as
 
 ### Plots Created
 For each detector the following plots are produced:
+
 * 1D correlation plot for X
 * 1D correlation plot for Y
 * 2D correlation plot for X in local coordinates (comparing to reference plane)

src/modules/SpatialClustering/README.md

@@ -10,6 +10,7 @@ No parameters are used from the configuration file.
 
 ### Plots produced
 For each detector the following plots are produced:
+
 * Cluster size histogram
 * Cluster width (rows, in X) histogram
 * Cluster width (columns, in Y) histogram

src/modules/SpatialTracking/README.md

@@ -21,6 +21,7 @@ This module performs track finding using only positional information (no timing
 * Track angle in Y histogram
 
 Plots produced per device:
+
 * Residual in X
 * Residual in Y
 

src/modules/TelescopeAnalysis/README.md

@@ -14,6 +14,7 @@ Furthermore, the telescope resolution at the position of the DUT detector is plo
 * Telescope resolution at position of DUT
 
 For each detector participating in tracking, the following plots are produced:
+
 * Biased local track residual, for X and Y;
 * Biased global track residual, for X and Y;
 * Local residuals with track and Monte Carlo particle, for X and Y;

src/modules/TestAlgorithm/README.md

@@ -13,6 +13,7 @@ This module collects `pixel` and `cluster` objects from the clipboard and create
 
 ### Plots produced
 For each device the following plots are produced:
+
 * 2D hitmap
 * 2D event times histogram
 * Correlation in X

src/modules/Timepix1Correlator/README.md

@@ -10,6 +10,7 @@ This module collects `pixel` and `cluster` objects from the clipboard for a Time
 
 ### Plots produced
 For each device the following plots are produced:
+
 * 2D hitmap in local coordinates
 * 2D hitmap in global coordinates
 * Cluster size histogram

src/modules/Timepix1EventLoader/README.md

@@ -8,9 +8,6 @@ This module loads raw data from Timepix1 devices and adds it to the clipboard as
 ### Parameters
 * `inputDirectory`: Path of the directory above the data files.
 
-### Plots produced
-No plots are produced.
-
 ### Usage
 ```toml
 [Timepix1EventLoader]

src/modules/Timepix3Clustering/README.md

@@ -14,6 +14,7 @@ Split clusters can be recovered using a larger search radius for neighbouring pi
 
 ### Plots produced
 For each detector the following plots are produced:
+
 * Cluster size histogram
 * Cluster width (rows, in X) histogram
 * Cluster width (columns, in Y) histogram