From d7da728e2bb172a45e08cce2173751bf1e8b51d1 Mon Sep 17 00:00:00 2001
From: Yoann Guilhem <yoann.guilhem@esrf.fr>
Date: Wed, 24 Jul 2013 19:29:33 +0200
Subject: [PATCH] Update documentation and README file with the new
installation procedure.
Signed-off-by: Yoann Guilhem <yoann.guilhem@esrf.fr>
---
DCT_Documentation/DCTDoc.cls | 25 +++++++----
DCT_Documentation/functions/gtSetup.tex | 4 +-
.../user_manual/General_introduction.tex | 45 ++++++++++++++-----
README.txt | 6 ++-
4 files changed, 55 insertions(+), 25 deletions(-)
diff --git a/DCT_Documentation/DCTDoc.cls b/DCT_Documentation/DCTDoc.cls
index 2387f536..bab7b389 100644
--- a/DCT_Documentation/DCTDoc.cls
+++ b/DCT_Documentation/DCTDoc.cls
@@ -1,6 +1,6 @@
\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 %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
diff --git a/DCT_Documentation/functions/gtSetup.tex b/DCT_Documentation/functions/gtSetup.tex
index 5227d9e6..1a2a0b72 100644
--- a/DCT_Documentation/functions/gtSetup.tex
+++ b/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
diff --git a/DCT_Documentation/user_manual/General_introduction.tex b/DCT_Documentation/user_manual/General_introduction.tex
index 4a67567d..c1533ec6 100644
--- a/DCT_Documentation/user_manual/General_introduction.tex
+++ b/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}
diff --git a/README.txt b/README.txt
index fe652e3b..9a10cb4f 100644
--- a/README.txt
+++ b/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
--
GitLab