From 3da71c927485f0fc00a32a7343010230100c7223 Mon Sep 17 00:00:00 2001
From: Dhanya Maliakal <dhanya.maliakal@psi.ch>
Date: Thu, 17 Aug 2017 14:17:10 +0200
Subject: [PATCH] command line docu. more coming up

---
 .../slsDetectorClientDocs/html/settings.html   | 18 ++++++++++++++++++
 manual/slsDetectorClientDocs/latex/doxygen.sty |  4 ++--
 manual/slsDetectorClientDocs/latex/refman.tex  |  2 +-
 .../slsDetectorClientDocs/latex/settings.tex   | 16 +++++++++++++---
 4 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/manual/slsDetectorClientDocs/html/settings.html b/manual/slsDetectorClientDocs/html/settings.html
index e63bd11c8..53898761c 100644
--- a/manual/slsDetectorClientDocs/html/settings.html
+++ b/manual/slsDetectorClientDocs/html/settings.html
@@ -40,6 +40,15 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 
 <h1><a class="anchor" id="settings">Detector settings commands </a></h1><p>Commands to setup the settings of the detector</p>
 <ul>
+<li><a class="el" href="settings.html#settingsdir">Settings, trim &amp; cal Directories</a>: commands to setup settings/trim/cal directories</li>
+<li><a class="el" href="settings.html#settingssett">Settings and Threshold</a>: commands to configure settings and threshold of detector</li>
+<li><a class="el" href="settings.html#settingsdacs">DACs</a>: commands to configure DACs of detector</li>
+<li><a class="el" href="settings.html#settingsadcs">ADCs</a>: commands to readout ADCs of detector</li>
+</ul>
+<h2><a class="anchor" id="settingsdir">
+Settings, trim &amp; cal Directories</a></h2>
+<p>commands to setup settings/trim/cal directories</p>
+<ul>
 <li><b>settingsdir [dir]</b> Sets/gets the directory where the settings files are located (string)</li>
 </ul>
 <ul>
@@ -51,6 +60,9 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 <ul>
 <li><b>trimen [n e0 e1...e(n-1)]</b> Sets/gets the number of energies n at which the detector has default trim file and their values in eV (int)</li>
 </ul>
+<h2><a class="anchor" id="settingssett">
+Settings and Threshold</a></h2>
+<p>commands to configure settings and threshold of detector</p>
 <ul>
 <li><b>settings [s]</b> sets/gets the settings of the detector. Options: <code>standard</code>, <code>fast</code>, <code>highgain</code>, <code>dynamicgain</code>, <code>lowgain</code>, <code>mediumgain</code>, <code>veryhighgain</code>, <code>lownoise</code>, <code>dynamichg0</code>, <code>fixgain1</code>, <code>fixgain2</code>, <code>forceswitchg1</code>, <code>forceswitchg2</code>. <br/>
  In Eiger, only sets in client shared memory. Use <code>threshold</code> or <code>thresholdnotb</code> to pass to detector. Gets from detector.</li>
@@ -73,6 +85,9 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 <ul>
 <li><b>pedestal [i]</b> starts acquisition for i frames, calculates pedestal and writes back to fpga. Used in GOTTHARD only. Only put!</li>
 </ul>
+<h2><a class="anchor" id="settingsdacs">
+DACs</a></h2>
+<p>commands to configure DACs of detector</p>
 <ul>
 <li><b>vthreshold [i] [mv]</b> Sets/gets detector threshold voltage for single photon counters. Normally in DAC units unless <code>mv</code> is specified at the end of the command line (int)</li>
 </ul>
@@ -211,6 +226,9 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
 <ul>
 <li><b>v_limit [i] mv</b> Sets/gets a soft limit for the power supplies and the DACs on the new chiptest board. Must be in mV (int)</li>
 </ul>
+<h2><a class="anchor" id="settingsadcs">
+ADCs</a></h2>
+<p>commands to readout ADCs of detector</p>
 <ul>
 <li><b>temp_adc</b> Gets the ADC temperature (int)</li>
 </ul>
diff --git a/manual/slsDetectorClientDocs/latex/doxygen.sty b/manual/slsDetectorClientDocs/latex/doxygen.sty
index 5e70890f8..b138dbe41 100644
--- a/manual/slsDetectorClientDocs/latex/doxygen.sty
+++ b/manual/slsDetectorClientDocs/latex/doxygen.sty
@@ -24,9 +24,9 @@
   \fancyplain{}{\bfseries\thepage}%
 }
 \rfoot[\fancyplain{}{\bfseries\scriptsize%
-  Generated on Thu Aug 17 13:55:05 2017 by Doxygen }]{}
+  Generated on Thu Aug 17 14:16:02 2017 by Doxygen }]{}
 \lfoot[]{\fancyplain{}{\bfseries\scriptsize%
-  Generated on Thu Aug 17 13:55:05 2017 by Doxygen }}
+  Generated on Thu Aug 17 14:16:02 2017 by Doxygen }}
 \cfoot{}
 
 %---------- Internal commands used in this style file ----------------
diff --git a/manual/slsDetectorClientDocs/latex/refman.tex b/manual/slsDetectorClientDocs/latex/refman.tex
index b07c6d8a6..9c75cbda8 100644
--- a/manual/slsDetectorClientDocs/latex/refman.tex
+++ b/manual/slsDetectorClientDocs/latex/refman.tex
@@ -40,7 +40,7 @@
 \vspace*{1cm}
 {\large Generated by Doxygen 1.6.1}\\
 \vspace*{0.5cm}
-{\small Thu Aug 17 13:55:05 2017}\\
+{\small Thu Aug 17 14:16:02 2017}\\
 \end{center}
 \end{titlepage}
 \pagenumbering{roman}
diff --git a/manual/slsDetectorClientDocs/latex/settings.tex b/manual/slsDetectorClientDocs/latex/settings.tex
index 6cbffeda8..5ce2d57cd 100644
--- a/manual/slsDetectorClientDocs/latex/settings.tex
+++ b/manual/slsDetectorClientDocs/latex/settings.tex
@@ -1,4 +1,11 @@
 Commands to setup the settings of the detector
+\begin{DoxyItemize}
+\item \hyperlink{settings_settingsdir}{Settings, trim \& cal Directories}: commands to setup settings/trim/cal directories
+\item \hyperlink{settings_settingssett}{Settings and Threshold}: commands to configure settings and threshold of detector
+\item \hyperlink{settings_settingsdacs}{DACs}: commands to configure DACs of detector
+\item \hyperlink{settings_settingsadcs}{ADCs}: commands to readout ADCs of detector
+\end{DoxyItemize}\hypertarget{settings_settingsdir}{}\subsection{Settings, trim \& cal Directories}\label{settings_settingsdir}
+commands to setup settings/trim/cal directories
 
 
 \begin{DoxyItemize}
@@ -18,7 +25,8 @@ Commands to setup the settings of the detector
 
 \begin{DoxyItemize}
 \item {\bfseries trimen \mbox{[}n e0 e1...e(n-\/1)\mbox{]}} Sets/gets the number of energies n at which the detector has default trim file and their values in eV (int)
-\end{DoxyItemize}
+\end{DoxyItemize}\hypertarget{settings_settingssett}{}\subsection{Settings and Threshold}\label{settings_settingssett}
+commands to configure settings and threshold of detector
 
 
 \begin{DoxyItemize}
@@ -54,7 +62,8 @@ Commands to setup the settings of the detector
 
 \begin{DoxyItemize}
 \item {\bfseries pedestal \mbox{[}i\mbox{]}} starts acquisition for i frames, calculates pedestal and writes back to fpga. Used in GOTTHARD only. Only put!
-\end{DoxyItemize}
+\end{DoxyItemize}\hypertarget{settings_settingsdacs}{}\subsection{DACs}\label{settings_settingsdacs}
+commands to configure DACs of detector
 
 
 \begin{DoxyItemize}
@@ -284,7 +293,8 @@ Commands to setup the settings of the detector
 
 \begin{DoxyItemize}
 \item {\bfseries v\_\-limit \mbox{[}i\mbox{]} mv} Sets/gets a soft limit for the power supplies and the DACs on the new chiptest board. Must be in mV (int)
-\end{DoxyItemize}
+\end{DoxyItemize}\hypertarget{settings_settingsadcs}{}\subsection{ADCs}\label{settings_settingsadcs}
+commands to readout ADCs of detector
 
 
 \begin{DoxyItemize}