Update documentation and README file with the new installation procedure.

Signed-off-by: Yoann Guilhem <yoann.guilhem@esrf.fr>

DCT_Documentation/DCTDoc.cls

 \NeedsTeXFormat{LaTeX2e}
  
-\ProvidesClass{DCTDoc}[2012/08/30 v1.0 DCT documentation class]
+\ProvidesClass{DCTDoc}[2013/06/27 v1.0 DCT documentation class]
 
 % Passes and class options to the underlying article class
 \DeclareOption*{\PassOptionsToClass{\CurrentOption}{scrreprt}}
@@ -11,13 +11,21 @@
            pagesize,
            headsepline,
            nofootsepline,
-           onelinecaption,
-           tablecaptionabove,
-           liststotoc,
-           idxtotoc,
-           bibtotoc,
-           tocindent,
-           nochapterprefix,
+           %onelinecaption,
+           %tablecaptionabove,
+           %liststotoc,
+           %idxtotoc,
+           %bibtotoc,
+           %tocindent,
+           %nochapterprefix,
+           version=first,
+           captions=oneline,
+           captions=tableheading,
+           listof=totoc,
+           index=totoc,
+           bibliography=totoc,
+           toc=graduated,
+           chapterprefix=false,
            appendixprefix]{scrreprt}[2009/07/24]
 
 % \@ifclasslater{scrreprt}{2009/07/24}{
@@ -99,7 +107,6 @@
 \RequirePackage{caption}     % Latest caption package
 %\RequirePackage{subcaption}  % Too recent for teTeX-3.0
 
-
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %                   (2) SETTINGS                       %
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

DCT_Documentation/functions/gtSetup.tex

@@ -2,9 +2,9 @@
 \label{sec:gtSetup}
 
 \subsection{Description}
-{\it Setup} is the first step in the data reconstruction process. 
+\textit{Setup} is the first step in the data reconstruction process. 
 Before starting with the actual analysis you need
-crystallographic information such as crystal system, spacegroup, 
+crystallographic information such as crystal system, space group, 
 unit cell dimensions and unit cell angles.
 These information can be provided by a \acs{CIF} file created by \href{http://accelrys.com/products/materials-studio/}{Materials Studio}. 
 Except for that, a list of possible reflections generated by

DCT_Documentation/user_manual/General_introduction.tex

@@ -4,12 +4,13 @@
 This document is designed for assisting DCT users who are not involved in the DCT code developing. 
 It shows you how to set up data processing and guides you through the different steps.
 
-\section*{Setting up Environment}
+\section{Setting up Environment}
+
 First, you need an user account. We assume here, you are user \verb+ma0001+. 
 In the present version, the DCT code is only usable on the \ac{NICE} computer cluster at \ac{ESRF}. 
 So you need to access the network. This is possible with \ac{NX} or ssh. 
 The \ac{NX} client is a program which let you connect to the \ac{ESRF} network. 
-It is recommended to use this tool. In case of a network interupt, it is possible to resume the session without problems. 
+It is recommended to use this tool. In case of a network interrupt, it is possible to resume the session without problems. 
 In that case just restart the client. Download the client from 
 \href{http://www.nomachine.com/download.php}{NoMachineDownload} and configure it according to 
 \href{http://www.esrf.eu/Infrastructure/Computing/Networks/InternetAndTheFirewall/NX\_SOFTWARE/index\_html}{NXconfig}.
@@ -20,29 +21,49 @@ ssh -X -p 5022 -l ma0001 firewall.esrf.fr
 \end{shCode}
 Once you are connected to the network, open a terminal window and type:
 \begin{shCode}
-tet:~ % ssh -X rnice
+ma0001@tet:~ $ ssh -X rnice6
 \end{shCode}
 This will connect you to the rnice cluster. The rnice machines are not very powerful, therefore it is recommended to use
 the OAR cluster. To do this, type:
 \begin{shCode}
-rnice:~ % oarsub -I -l "walltime=12:00:00" -p "mem>6000"
+ma0001@rnice6-0101:~ $ oarsub -I -l "walltime=12:00:00" -p "mem_total_mb>6000"
 \end{shCode}
 This will give you an interactive shell (I), for 12 hours, with at least 6GB system memory. Throughout the reconstruction we
 will submit jobs to that cluster. More information about OAR can be found here: \href{http://wikiserv.esrf.fr/software/index.php/Main\_Page}{Software Wiki}.
 
-The next step now is to get the \ac{DCT} code from the \ac{SVN} repository. To do so, type:
+The next step now is to get the \ac{DCT} code from the git repository located on sourceforge.net. To do so, type:
 \begin{shCode}
-htc0000:~ % export https_proxy=http://proxy.esrf.fr:3128
-htc0000:~ % REPO=https://svn.code.sf.net/p/dct/code
-htc0000:~ % wget ${REPO}/trunk/DCTuser_setup.sh
-htc0000:~ % . DCTuser_setup.sh
+ma0001@hpc2-0101:~ $ export https_proxy=http://proxy.esrf.fr:3128
+ma0001@hpc2-0101:~ $ export http_proxy=http://proxy.esrf.fr:3128
+ma0001@hpc2-0101:~ $ REPO=http://sourceforge.net/projects/dct/files
+ma0001@hpc2-0101:~ $ wget $REPO/dct-install.zip
+ma0001@hpc2-0101:~ $ unzip dct-install.zip -d /tmp
+ma0001@hpc2-0101:/tmp/dct-install $ cd /tmp/dct-install
+ma0001@hpc2-0101:/tmp/dct-install $ python dct_setup.py -b stable_1.0 -d ~/dct_1.0
 \end{shCode}
 This script will download the \ac{DCT} code and will set up some necessary configurations.
 You will be asked which version to download. For users, it is recommended to get the stable version (the current stable version is \verb+stable_1.0+).
-The \ac{DCT} source code will be saved to the folder \file|~/matlabDCT_<version_number>| and will be compiled. The total process takes some time.
-Once done, you are ready to start Matlab2012a:
+The \ac{DCT} source code will be saved to the folder you will specify (here \file|~/dct_1.0|). The total process takes some time.
+Once done, you are ready to start Matlab using \ac{DCT} code by running the \file|dct_laucnh.py| script:
 \begin{shCode}
-htc0000:~ % matlab2012a
+ma0001@hpc2-0101:~ $ python ~/dct_1.0/dct_launch.py
 \end{shCode}
 
+\section{DCT Analysis steps}
+
+The whole process of the DCT analysis is carried out by user functions, which have to be runned in the following order
+\begin{enumerate}
+  \item \mCom|gtSetup|
+  \item \mCom|gtPreProcessing|
+  \item \mCom|gtSetupSegmentation| or \mCom|gtSetupSegmentation_doublethr|
+  \item \mCom|gtCheckSegmentation|
+  \item \mCom|gtPostSegmentation|
+  \item \mCom|gtCheckDiffractionBlobs|
+  \item \mCom|gtMATCHGUI|
+  \item \mCom|gtSetupIndexing|
+  \item \mCom|gtSetupForwardSimulation|
+  \item \mCom|gtSetupReconstruction|
+  \item \mCom|GtGrainsManager|
+\end{enumerate}
+
 \input{functions/OAR} 

README.txt

@@ -6,7 +6,7 @@
 # - g++    (version >= 4.4)  www.gcc.gnu.org
 # - matlab (version >= 2012) www.mathworks.com
 # - astra  (version >= 1.0)  www.code.google.com/p/astra-toolbox
-# - cuda   (version >= 4.0)  http://www.nvidia.com/object/cuda_home_new.html
+# - cuda   (version >= 4.0)  www.nvidia.com/object/cuda_home_new.html
 
  1. Download the DCT install bundle from http://sourceforge.net/projects/dct/
 
@@ -106,4 +106,6 @@ $ python /users/user1/dct_1.0/dct_launch.py
  7. Update regularly the code with "update" command and the configuration with
     "update_conf" command.
 
- 8. Submit bug reports to graintracking@esrf.fr
+ 8. Submit bug reports to https://sourceforge.net/p/dct/tickets
+
+ 9. For more information or support, contact graintracking@esrf.fr