From 801d469e064813c6ea70f8baae850a3447b09ab6 Mon Sep 17 00:00:00 2001
From: ageay <ageay>
Date: Mon, 16 Jul 2012 15:25:22 +0000
Subject: [PATCH] Doc #4

---
 doc/doxygen/figures/MEDFileConcepts.fig |  85 ++++++++++
 doc/doxygen/figures/MEDFileConcepts.png | Bin 0 -> 16178 bytes
 doc/doxygen/medcoupling.dox             |   2 +-
 doc/doxygen/medloader.dox               | 208 ++++++++++++++++++------
 4 files changed, 247 insertions(+), 48 deletions(-)
 create mode 100644 doc/doxygen/figures/MEDFileConcepts.fig
 create mode 100644 doc/doxygen/figures/MEDFileConcepts.png

diff --git a/doc/doxygen/figures/MEDFileConcepts.fig b/doc/doxygen/figures/MEDFileConcepts.fig
new file mode 100644
index 000000000..3dbd216fa
--- /dev/null
+++ b/doc/doxygen/figures/MEDFileConcepts.fig
@@ -0,0 +1,85 @@
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diff --git a/doc/doxygen/medcoupling.dox b/doc/doxygen/medcoupling.dox
index 7a4412d22..b8293f96e 100644
--- a/doc/doxygen/medcoupling.dox
+++ b/doc/doxygen/medcoupling.dox
@@ -46,7 +46,7 @@ For beginners in \ref medcoupling "MEDCoupling" world, it is advisable to read t
 A mesh has a the following properties :
 
 - name
-- a dimension (called mesh dimension) and only one (it implies that \b all cells constituting
+- **a dimension (called mesh dimension) and only one** (it implies that \b all cells constituting
 mesh have the same dimension)
 - a space dimension (relative to coordinates)
 - a number of nodes
diff --git a/doc/doxygen/medloader.dox b/doc/doxygen/medloader.dox
index d1bb0fe29..630c7b5f6 100644
--- a/doc/doxygen/medloader.dox
+++ b/doc/doxygen/medloader.dox
@@ -1,45 +1,168 @@
 /*!
 \page medloader MEDLoader
 
+[TOC]
+
 \section MEDLoaderIntro Introduction
 
-%MEDLoader is a package in charge of loading from a file or write to a file
+\ref medloader "MEDLoader" is a package in charge of loading from a file or write to a file
 in MED format a \ref medcoupling data structure. The fact that these
 functionalities are not merged in \ref medcoupling is explained by a
 willingness of reducing as much as possible the dependancies of \ref medcoupling libraries.
 
 As a MED file can combine several \ref medcoupling aspects in one (for exemple meshes in
 MED file on different mesh dimension with families and groups) the API
-of %MEDLoader is much more rich than simply read and write.
+of \ref medloader "MEDLoader" is much more rich than simply read and write.
+
+\ref MEDCouplingMeshesPage "MEDCoupling mesh" is \b not as rich as a MED file mesh, and a \ref MEDCouplingFieldsPage "MEDCoupling field" is \b not as rich as a MED file field.
+But it is possible to emulate with a very good fidelity a MED file mesh and a MED file field with a collection of MEDCoupling instances for each.
+
+\section MEDLoader2Approaches Two approaches are available in MEDLoader : Advanced API, Basic API
+
+\ref medloader "MEDLoader" module offers two different approaches to perform Read/Write from/to MED file.
+
+- \ref MEDLoaderAdvApproach "advanced API approach"
+- \ref MEDLoaderBasicApproach "basic API apprach"
+
+Whatever the approach(es) you choose, it is advisable to know main concepts of MED files \ref MEDLoaderMainC "that are quickly reminded here."
+
+\subsection MEDLoaderAdvApproach Advanced API approach
+
+\subpage MEDLoaderAdvancedAPIPage "A specific page dedicated to the advanced API is available here".
+
+This approach is the most close to MED file. By using this advanced API approach the user will manipulates classes that represents MED file concepts.
+
+It implies that the user should be informed about the \ref MEDLoaderMainC "MED file concepts", that do not exist in \ref medcoupling "MEDCoupling". For example :
+
+- group/family in meshes
+- profiles in fields
+
+This is typically the case for a user that wants to precisely set/get mesh/group/family groups set on different level.
+
+*That's why a set of classes representing a memory representation of MED file concepts are proposed by advanced API approach.*
+
+*So All information contained in file is represented in advanced API class instances.*
+
+The level of coherency check is variable across methods, to let to the user the maximal capacity of modification of its MED file data in memory.
+
+This API is particulary recommended :
+
+1. For users that want to repare a MED file (invalid family ids, invalid mesh dimension, mismatch of family ids, numbering cells/nodes array modification)
+2. For users that want to operate directly on complex MED file objects (split of MED files for example, duplication of nodes).
+
+\subsection MEDLoaderBasicApproach Basic API approach
+
+\subpage MEDLoaderBasicAPIPage "A specific page dedicated to the basic API is available here".
+
+This approach is less close to MED file concepts, but closer to \ref MEDCouplingMainConc "MEDCoupling concepts".
+
+So, basic API, is simpler as show method MEDLoader::WriteUMesh that needs no special knowledge needed of MED file concepts to interact with MED files.
+
+This API is in the form of a list of public static methods a class ParaMEDMEM::MEDLoader.
+
+This simplicity has a cost, the I/O are not (cannot be) optimized.
+
+As MED file concepts are more complex than MEDCoupling concepts, this approach is not the most relevant for specific MED file objects read/write.
+
+- Manipulation of multi level MED file mesh is not easy to manipulate with basic approach
+
+- Manipulation of partial fields in not easy to manipulate too with basic approach
+
+
+\subsection MEDLoaderCohabitationApproach Cohabitation of the two approaches
+
+The two approaches are \b NOT opposed, they are compatible each other so it is possible to mix them.
+
+Typically it it is possible to read rich information of a complex MED file using advanced API in read mode, and write a simpler MED file model
+coming from a post treatement of the complex input MED file data to a simple output MED file using basic API for writing.
+
+\section MEDLoaderMainC Main concepts of MED files
+
+Here we will describes some of basic concepts of MED files in order to
+use the best methods proposed by \ref medloader "MEDLoader API".
+
+\subsection BasicMEDLoaderAPIGen Basics in MED files
+
+First of all **MEDLoader will not read MED files whose version is strictly lower than 2.2.**
+
+For new comers in MED file world some of basics principles are recalled in the following graphic : 
+
+\image html MEDFileConcepts.png "Resumed MED file concepts"
 
-MEDCoupling mesh does \b not fit a MED file mesh, and a MEDCoupling
-field does \b not fit a MED file field. But it is possible to emulate
-with a very good fidelity a MED file mesh and a MED file field with
-a collection of MEDCoupling instances for each.
+Inside the parenthesis, there is multiplicity :
 
-That's why %MEDLoader module offers two different approaches to perform Read/Write from/to MED
-file.
+- + stands for [1,inf)
+- * stands for [0,inf)
+- ? stands for 0 or 1
 
-- Either the user is close too MEDCoupling concepts. This is the case
-if pieces of information to access or to write are \b directly
-mapped to a MEDCouplingMesh/MEDCouplingFieldDouble in MEDCoupling package. \nIn this case, the \ref MEDLoaderBasicAPI "basic API" is recommended in this case because simpler and faster.
+Each box are **independant in MED file format during read write session.**
 
-- Or the user knows the MED file concept well and if nature of
-information to deal with do not fit exactly the class offered by
-MEDCoupling, the \ref MEDLoaderAdvancedAPI "advanced API" is
-recommended. This is typically the case for a user that wants to precisely set/get
-mesh/group/family groups set on different level lying on a same field defined
-partially...  This API is faster, all information contained in file is represented, but
-less check is performed.\n This API is recommended for users that want to operate directly on MED files (split of MED files for example)
+**Boxes instances are linked each other only by red arrows using string as discriminating key.** It implies that empty names in basic concepts objects of MED file are forbidden.
 
-The two methods are \b not opposed, they are compatible each other so
-it is possible to mix them. But the user should keep in mind that
-behaviour of these two methods can vary. 
+There can be as many instance of boxes as wanted in a MED file.
+
+**As it can be seen in MED file world, fields and meshes are sorted by geometric type**.
+
+This specificity leads to a constraint during writing phase because some mesh operations may modify significantly the organization of geometric types during mesh/field operations.
+\n Here some of operation that can alter the geometric type order of cells :
+
+- aggregation of meshes
+- aggregation of fields
+- extraction of a part of meshes
+- extraction of a part of fields
+- partial polyhedrization of meshes
+- unpolyhedronization of meshes
+
+\section MEDLoaderCommonVoc Vocabulary used in MEDLoader
+
+\subsection Relative mesh dimension
+
+As it has been seen \ref BasicMEDLoaderAPIGen "above", all big arrays in fields and meshes (execpted coordinates) are sorted by geometric type, without any awareness of the dimension.
+
+For example an unstructured mesh in MED file world can lie simultaneously on MED_TRI3, MED_POINT1, MED_POLYHED, MED_TETRA4..., \ref MEDCouplingMeshes "which is impossible in MEDCoupling" for manipulation reasons.
+
+To connect the MED file world to the MEDLoader/MEDCoupling world the notion of **relative mesh dimension** has been introduced in \ref medloader "MEDLoader".
+
+This concept of **relative mesh dimension** is used frequently in the \ref medloader "MEDLoader both APIs" ( \ref MEDLoaderBasicAPIPage "basic" and \ref MEDLoaderAdvancedAPIPage "advanced").
+
+To explain the semantic of **relative mesh dimension** let's take the example of a mesh called \a myMesh in a MED file, containing MED_TRI3, MED_POINT1, MED_POLYHED, MED_TETRA4.
+
+For each geometric type on which \a myMesh is defined the mesh dimension are :
+
+- MED_TRI3 -> mesh dimension=2
+- MED_POINT1 -> mesh dimension=0
+- MED_POLYHED -> mesh dimension=3
+- MED_TETRA4 -> mesh dimension=3
+
+The mesh dimension of \a myMesh is equal to 3 ( \f max(2,0,3,3) ). The **relative mesh dimension** is equal to the difference between mesh dimension of geometic type and the mesh dimension
+of the whole MED file dimension. It leads to the following **relative mesh dimension** :
+
+- MED_TRI3 -> **relative mesh dimension** = -1
+- MED_POINT1 -> **relative mesh dimension** = -3
+- MED_POLYHED -> **relative mesh dimension** = 0
+- MED_TETRA4 -> **relative mesh dimension** = 0
+
+In \ref medloader **MEDLoader** all geometric information are then grouped relative dimension per relative dimension. It leads to the following geometric sorting of 
+MED file data structure of \a myMesh :
+
+- Level 0
+  - MED_TETRA4
+  - MED_POLYHED
+- Level -1
+  - MED_TRI3
+- Level -2
+  - nothing -> level **not** available for \a myMesh
+- Level -3
+  - MED_POINT1
+
+The mesh dimension of \a myMesh is 3. The relative mesh dimension available are [0,-1,-3].
 
 */
 
 /*!
-\page MEDLoaderBasicAPI Basic MEDLoader API.
+\page MEDLoaderBasicAPIPage Basic MEDLoader API.
+
+[TOC]
 
 The aim of this page is to present basic API of MEDLoader. The goal of
 this basic API is to perform a read or a write in one shot without any
@@ -48,9 +171,10 @@ character in capital. You are intended to use these methods. The following
 chapters will try to describe in details some of important ones.
 
 The basic idea of MEDLoader is to exploite as much as possible MED
-file capabilities to store MEDCoupling data file in a MED file and 
+ file capabilities to store MEDCoupling data file in a MED file and 
 reversely to load from a MED file into a MEDCoupling data structure.
 Basically, the info on components of ParaMEDMEM::DataArrayDouble
+
 instances are stores into components and units into MED files. The
 name of meshes and fields are used by MEDLoader to use it as this into
 MED file. A field f with \ref ParaMEDMEM::MEDCouplingTimeDiscretization
@@ -62,26 +186,9 @@ are limited.
 That's why the user should be aware of these constaints when trying to read/write a MED file using MEDLoader. 
 MEDLoader tries to manage that by protecting the user by throwing exceptions when the rules are not followed.
 
-\section MEDLoaderMainC Main concepts of MED files
-
-Here we will describes some of basic concepts of MED files in order to
-use the best methods proposed by MEDLoader API.
-
-\subsection BasicMEDLoaderAPIGen Basics in MED files
-
-First of all MEDLoader \b will \b not read MED files whose version is
-\b lower \b than \b 2.2. The MEDLoader::CheckFileForRead will perform
-the check of that before any attempt of read.
-
-
-For new comers in MED file world some of basics principles are
-recalled here. Let's recall basic principles that explains some of the aspect of MEDLoade API.
-\anchor MEDLoaderMeshNameConstraint MED file can contain several meshes. These meshes are
-discriminated by their names (two meshes could not have the same
-names). By the same way a MED file can contain several fields in MED.
-So MEDLoader propose to you the MEDLoader::GetMeshNames method to
-discover all the mesh names contained in your file.
+\section BasicMEDLoaderBasicAPIGlobalInfo Retrieving tiny global information from MED files using basic API
 
+The MEDLoader::CheckFileForRead method will perform the check of that before any attempt of read.
 A field is also discriminated by its name. The method MEDLoader::GetCellFieldNamesOnMesh and MEDLoader::GetNodeFieldNamesOnMesh are available to know all fields
 respectively on cells and on nodes lying on a specified mesh.
 
@@ -96,11 +203,16 @@ each respectively iteration and order.
 A time step of a field lyies on one \b or \b more mesh(es) specified by its \b or \b their name. A time step of a field in
 MED file could be defined on point \b and on cell \b and, \b or on gauss points \b and, \b or on point per element.
 
-This recalled specificities of MED file explains that it is necessary to specify
-each time, at field-read time, the type of field, the iteration and order
-number the mesh you are interested in.  
+This recalled specificities of MED file explains that it is necessary to specify each time, at field-read time, the type of field, the iteration and order number the mesh you are interested in.
 
-\subsection BasicMEDLoaderAPIMesh Meshes in MED files
+Let's recall basic principles that explains some of the aspect of MEDLoade API.
+\anchor MEDLoaderMeshNameConstraint MED file can contain several meshes. These meshes are
+discriminated by their names (two meshes could not have the same
+names). By the same way a MED file can contain several fields in MED.
+So MEDLoader propose to you the MEDLoader::GetMeshNames method to
+discover all the mesh names contained in your file.
+
+\section BasicMEDLoaderBasicAPIMesh Reading and writing meshes in MED files using basic API
 
 In MED file meshes could combine in one unstructured mesh cells that
 have different dimension. For example it is possible to mix
@@ -389,7 +501,9 @@ is not needed here.
 */
 
 /*!
-\page MEDLoaderAdvancedAPI Advanced %MEDLoader API.
+\page MEDLoaderAdvancedAPIPage Advanced %MEDLoader API.
+
+[TOC]
 
 This method is much closer to MED file organization than \ref
 MEDLoaderBasicAPI "basic MEDLoader API". All MED file
-- 
2.39.2