From 7f5c905c8d9c40c716b2f935fa42fe61e02418b3 Mon Sep 17 00:00:00 2001
From: Lionel GUEZ <guez@lmd.ens.fr>
Date: Tue, 9 Mar 2021 16:22:54 +0100
Subject: [PATCH] Add documentation for `Convert_Matlab`

---
 .../Documentation_texfol/.gitignore           |   9 +
 .../Graphiques/.gitignore                     |   2 +
 .../Graphiques/GNUmakefile                    |  10 ++
 .../Documentation_texfol/Graphiques/SHPC.odg  | Bin 0 -> 14452 bytes
 .../Graphiques/convert_Matlab.odg             | Bin 0 -> 19033 bytes
 .../Documentation_texfol/documentation.tex    | 155 ++++++++++++++++++
 6 files changed, 176 insertions(+)
 create mode 100644 Convert_Matlab/Documentation_texfol/.gitignore
 create mode 100644 Convert_Matlab/Documentation_texfol/Graphiques/.gitignore
 create mode 100644 Convert_Matlab/Documentation_texfol/Graphiques/GNUmakefile
 create mode 100644 Convert_Matlab/Documentation_texfol/Graphiques/SHPC.odg
 create mode 100644 Convert_Matlab/Documentation_texfol/Graphiques/convert_Matlab.odg
 create mode 100644 Convert_Matlab/Documentation_texfol/documentation.tex

diff --git a/Convert_Matlab/Documentation_texfol/.gitignore b/Convert_Matlab/Documentation_texfol/.gitignore
new file mode 100644
index 00000000..db719652
--- /dev/null
+++ b/Convert_Matlab/Documentation_texfol/.gitignore
@@ -0,0 +1,9 @@
+/*.aux
+/*.log
+/*.out
+/*.pdf
+/*.synctex*
+/*.toc
+/*.lof
+/*.lot
+/auto/
diff --git a/Convert_Matlab/Documentation_texfol/Graphiques/.gitignore b/Convert_Matlab/Documentation_texfol/Graphiques/.gitignore
new file mode 100644
index 00000000..ec1fa5dd
--- /dev/null
+++ b/Convert_Matlab/Documentation_texfol/Graphiques/.gitignore
@@ -0,0 +1,2 @@
+SHPC.pdf
+convert_Matlab.pdf
diff --git a/Convert_Matlab/Documentation_texfol/Graphiques/GNUmakefile b/Convert_Matlab/Documentation_texfol/Graphiques/GNUmakefile
new file mode 100644
index 00000000..2a8f0df5
--- /dev/null
+++ b/Convert_Matlab/Documentation_texfol/Graphiques/GNUmakefile
@@ -0,0 +1,10 @@
+sources = convert_Matlab
+objects := $(addsuffix .pdf, ${sources})
+
+%.pdf: %.odg
+	unoconv --doctype=graphics $<
+
+all: ${objects}
+
+clean:
+	rm -f ${objects}
diff --git a/Convert_Matlab/Documentation_texfol/Graphiques/SHPC.odg b/Convert_Matlab/Documentation_texfol/Graphiques/SHPC.odg
new file mode 100644
index 0000000000000000000000000000000000000000..9cc0fe42e05db614949c69e1439ccb43a29baa9c
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diff --git a/Convert_Matlab/Documentation_texfol/documentation.tex b/Convert_Matlab/Documentation_texfol/documentation.tex
new file mode 100644
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+\documentclass[a4paper,french]{article}
+
+\usepackage[utf8]{inputenc}
+
+\usepackage[T1]{fontenc}
+\usepackage{lmodern}
+
+\usepackage{babel}
+\usepackage{graphicx}
+\usepackage[super]{nth}
+
+\usepackage{hyperref}
+
+\hypersetup{pdftitle={Documentation convert Matlab}, pdfauthor={Lionel
+    Guez}, hypertexnames=false}
+
+                                %---------------
+
+\graphicspath{{Graphiques/}}
+
+\title{Documentation for scripts converting Matlab data}
+\author{Lionel GUEZ}
+
+                                %---------------
+
+\begin{document}
+
+\maketitle
+
+Pour utiliser le script \verb+overlap.m+, placer le script
+lui-même et tous les fichiers d'entrée nécessaires dans le répertoire
+courant, où je dois avoir l'autorisation d'écriture. Créer
+éventuellement des liens symboliques. Puis :
+\begin{verbatim}
+matlab -nojvm -r overlap
+\end{verbatim}
+
+Sur le domaine Eurec4A entier (toutes les dates, soit 117 dates), au
+total pour les deux orientations. \verb+inst_eddies_v6.py+ prend
+environ 11 mn et produit 3 MiB, pour 2951 tourbillons
+instantanés. \verb+overlap.m+ prend 0 mn. \verb+overlap_v6.py+ prend 0
+mn et produit 48 KiB, pour 2793 arêtes. \verb+survival.m+ prend 0 mn.
+\verb+survival.py+ prend 0 mn et produit 64 KiB pour 2863 n\oe{}uds et
+169 trajectoires.
+
+Sur le domaine \verb+PhD_Lax+, le script \verb+overlap_HDF5.py+ prend
+2 h 21 mn au total pour les deux graphes. Le script
+\verb+overlap_v6.py+ prend 3 mn, auxquelles il faut ajouter 12 mn de
+conversion au format v6 (total pour les fichiers nécessaires aux deux
+graphes).
+
+Sur le domaine global, pour une seule date, \verb+inst_eddies_v6.py+
+prend 25 s (dont environ 21 s de conversion en
+v6). \verb+inst_eddies_HDF5.py+ prend 38 s. Il reste le problème du
+stockage intermédiaire pour les fichiers v6. Le fichier produit par
+\verb+inst_eddies.m+ prend environ le quart de l'espace du fichier de
+départ.
+
+\section{Instantaneous eddies}
+
+The data for instantaneous eddies is stored in shapefiles, in the
+directories \verb+SHPC_(anti|cyclo)+. Cf. figure \ref{fig:convert_Matlab}.
+\begin{figure}[htbp]
+  \centering
+  \includegraphics[width=\textwidth]{convert_Matlab}
+  \caption{Correspondance between input Matlab files and files
+    converted from them. Below the names of Matlab files are indicated
+    the names of the variables which were used inside those files, and
+    the fields used inside those variables.}
+  \label{fig:convert_Matlab}
+\end{figure}
+The directory \verb+SHPC_(anti|cyclo)+ contains a set of four
+shapefiles: center, extremum, \verb+max_speed_contour+ and
+\verb+outermost_contour+. The four shapefiles correspond to four \og
+layers\fg{} of eddies. (\og layers\fg{} is a term that you can often
+find in the documentation of software dealing with geographical data.)
+Each layer corresponds to a given type of geometry. Here we have only
+two types of geometry: points and polygons. The layers center and
+extremum contain points, while the layers \verb+max_speed_contour+ and
+\verb+outermost_contour+ contain polygons. The center layer is for the
+geometric center of the maximum-speed contour, which is called
+centroid in the Matlab files. The extremum layer is for the position
+of the extremum of SSH, which is called center in the Matlab
+files. Each eddy has a record, at the same subscript position, in the
+four layers. Cf. figure \ref{fig:SHPC}.
+\begin{figure}[htbp]
+  \centering
+  \includegraphics[width=\textwidth]{SHPC}
+  \caption{Contents of a shapefile collection: SHPC\_(anti|cyclo).}
+  \label{fig:SHPC}
+\end{figure}
+The shapefile collection in \verb+SHPC_(anti|cyclo)+ contains data for
+all the dates. The dates are stored successively in the layers. From
+the computer point of view, each shapefile is made up of three files,
+ending with suffixes \verb+.shp+, \verb+.dbf+ and \verb+.shx+. The
+\verb+.shp+ file contains the positions, the \verb+.dbf+ file contains
+the metadata, and the \verb+.shx+ file is an index. So the \verb+.shp+
+file is the largest file of the three. But the three files form a
+logical unit and you should never separate them. There is also a file
+\verb+ishape_last.txt+ in the directory \verb+SHPC_(anti|cyclo)+ which
+gives the last subscript in the shapefiles for each date. This file is
+used to access directly any instantaneous eddy at any date. Finally,
+there is a file, \verb+grid_nml.txt+, which gives (in Fortran namelist
+format) the grid of SSH data from which the eddies were detected.
+
+The shapefiles are in binary format, so you need special software to
+read them. There is actually a large number of programs to read
+them. The metadata, in the \verb+.dbf+ file, is a spreadsheet, and you
+can open it with LibreOffice. There are also shell commands that can
+read shapefiles: dbfinfo, shpinfo, dbfdump and shpdump (analogous to
+ncdump for NetCDF files). If you have a Linux Debian-type distribution
+(Ubuntu, LinuxMint etc.), you can install these tools with:
+\begin{verbatim}
+sudo apt-get install shapelib
+\end{verbatim}
+The tools are installed on Ciclad in \verb+/data/guez/bin+. You can
+also access the shapefiles programmatically with a number of computer
+languages. From Python, one of the modules you can use is
+\href{https://fiona.readthedocs.io/en/latest/}{Fiona}. Matlab has the
+shaperead function.
+
+\section{Overlapping}
+
+The data on overlapping instantaneous eddies is in the files
+\verb+edgelist_(anti|cyclo)+. The overlapping of eddies is represented
+by an abstract graph. In the graph, a node is an instantaneous
+eddy. Two nodes of the graph are connected by an edge if the two
+corresponding eddies overlap. The graph is directed, which means that
+the edges have a direction: the direction is chronological.
+
+The file \verb+edgelist_(anti|cyclo)+ stores, for a given orientation
+of eddies, the whole graph as a list of edges. (This is a common graph
+storage format.) Each line stores one edge: the origin node of the
+edge followed by the target node of the edge. One edge is defined by a
+couple of integers: the date index and the eddy index at that
+date. The date index is the number of days since January \nth{1},
+1950. The eddy index is between 1 and the number of eddies at the
+date.
+
+\section{Survival}
+
+We call survival the data that identifies several instantaneous
+eddies as a same evolving physical object. The result of this analysis
+is a dictionary of trajectories, stored in a file
+\verb+traj_(anti|cyclo).json+. The key for each trajectory is the
+identifying number of the trajectory and the value is the
+corresponding list of instantaneous eddies. Here, an instantaneous
+eddy is not identified by the couple date index and eddy
+index. Rather, it is identified by an equivalent identifying number
+that is constructed from the date index and the eddy index. We could
+call this number the \og node index\fg{}, since it identifies a node
+in the abstract graph of overlapping. The relation between node index,
+$n$, date index, $d$
+
+\end{document}
-- 
GitLab