From 14f3554c7b07bb06399bcdecbe309fa82a36f921 Mon Sep 17 00:00:00 2001
From: Jean-Philippe ARGAUD <ahbhhjp@cli23jp.(none)>
Date: Mon, 31 Jan 2011 15:22:00 +0100
Subject: [PATCH] =?utf8?q?Mise=20=C3=A0=20jour=20d'avancement=20de=20la=20?=
 =?utf8?q?doc,=20avec=20un=20premier=20jet=20d'une=20introduction=20m?=
 =?utf8?q?=C3=A9thodologique?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 doc/advanced.rst                            |   4 +-
 doc/conf.py                                 |   2 +-
 doc/examples.rst                            |   4 +-
 doc/index.rst                               |  42 ++--
 doc/ressources/ADAO.png                     | Bin 11797 -> 5479 bytes
 doc/ressources/ADAO_small.png               | Bin 1123 -> 755 bytes
 doc/theory.rst                              | 204 ++++++++++++++++++++
 doc/using.rst                               |  20 +-
 src/daComposant/daCore/AssimilationStudy.py |  34 +++-
 src/daComposant/daCore/Persistence.py       |  46 ++++-
 10 files changed, 316 insertions(+), 40 deletions(-)
 create mode 100644 doc/theory.rst

diff --git a/doc/advanced.rst b/doc/advanced.rst
index 5f48310..8dd33bb 100644
--- a/doc/advanced.rst
+++ b/doc/advanced.rst
@@ -1,3 +1,5 @@
+.. _section_advanced:
+
 ================================================================================
 Advanced usage of ADAO
 ================================================================================
@@ -32,7 +34,7 @@ Running an ADAO calculation scheme in YACS in console mode
 
 This section describes how to execute in console mode a YACS calculation scheme,
 obtained using the ADAO "Export to YACS" function. It uses the standard YACS
-console mode, wich will be briefly recall here (see YACS documentation for more
+console mode, which will be briefly recall here (see YACS documentation for more
 information).
 
 The way to do that is as follows:
diff --git a/doc/conf.py b/doc/conf.py
index dc6a04c..f5e458b 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -22,7 +22,7 @@ import sys, os
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = []
+extensions = ["sphinx.ext.pngmath"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
diff --git a/doc/examples.rst b/doc/examples.rst
index e040bd6..5ac3096 100644
--- a/doc/examples.rst
+++ b/doc/examples.rst
@@ -1,3 +1,5 @@
+.. _section_examples:
+
 ================================================================================
 Examples on using the ADAO module
 ================================================================================
@@ -59,7 +61,7 @@ Using the GUI to build the ADAO case
 First, you have to activate the ADAO module by choosing the appropriate module
 button or menu of SALOME, and you will see:
 
-  .. _adao_activate:
+  .. _adao_activate2:
   .. image:: images/adao_activate.png
     :align: center
   .. centered::
diff --git a/doc/index.rst b/doc/index.rst
index 6816059..0385fcf 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -3,36 +3,37 @@
 ADAO module documentation
 ================================================================================
 
-The ADAO module provides **data assimilation** features [#]_ in SALOME context.
-It is based on an extensible generic underlying data assimilation library, and
-on usage on other SALOME modules, namely YACS and EFICAS.
+The ADAO module provides **data assimilation** features in SALOME context. It is
+based on usage on other SALOME modules, namely YACS and EFICAS, and on an
+extensible generic underlying data assimilation library.
 
 Briefly stated, Data Assimilation is a methodological framework to compute the
-optimal estimate of the inaccesible true value of a system state over time. It
+optimal estimate of the inaccessible true value of a system state over time. It
 uses information coming from experimental measurements or observations, and from
 numerical *a priori* models, including information about their errors. Parts of
 the framework are also known as *parameter estimation*, *inverse problems*,
-*bayesian estimation*, *optimal interpolation*, etc.
-
-The documentation of this module is divided in 4 parts, the first one being an
-introduction. The second part describes how to use the module ADAO. The third
-part focuses on advanced usages of the module, how to get more information, or
-how to use it without the graphical user interface (GUI). The last part gives
-examples on ADAO usage.
-
-Users interested in quick use of the module can jump to the last part, but a
-valuable use of the module requires to read and come back regularly the second
-part.
+*bayesian estimation*, *optimal interpolation*, etc. More details can be found
+in the section :ref:`section_theory`.
+
+The documentation of this module is divided in 5 parts, the first one being an
+introduction. The second part briefly introduces data assimilation and concepts.
+The third part describes how to use the module ADAO. The fourth part focuses on
+advanced usages of the module, how to get more information, or how to use it
+without the graphical user interface (GUI). The last part gives examples on ADAO
+usage. Users interested in quick use of the module can jump to the section
+:ref:`section_examples`, but a valuable use of the module requires to read and
+come back regularly the section :ref:`section_using`.
 
 In all this documentation, we use standard notations of data assimilation.
-Vectors are written horizontally or vertically without difference. Matrices are
-written either normally, either with a condensed notation, consisting in the
-use of a "``;``" to separate the rows in a continuous line.
+Moreover, vectors are written horizontally or vertically without difference.
+Matrices are written either normally, either with a condensed notation,
+consisting in the use of a "``;``" to separate the rows in a continuous line.
 
 .. toctree::
    :maxdepth: 2
 
    intro
+   theory
    using
    advanced
    examples
@@ -42,8 +43,3 @@ Indices and tables
 
 * :ref:`genindex`
 * :ref:`search`
-
-.. _ECMWF: http://www.ecmwf.int/newsevents/training/rcourse_notes/DATA_ASSIMILATION/ASSIM_CONCEPTS/Assim_concepts.html
-.. _Wikipedia/Data_assimilation: http://en.wikipedia.org/wiki/Data_assimilation
-
-.. [#] If you are not familiar with data assimilation concepts in general, an introductory on-line training course can be found at ECMWF_, along with other materials coming from geosciences applications. See also for example `Wikipedia/Data_assimilation`_. Note that data assimilation is not restricted to meteorology or geosciences, but is widely used in other scientific domains.
diff --git a/doc/ressources/ADAO.png b/doc/ressources/ADAO.png
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diff --git a/doc/theory.rst b/doc/theory.rst
new file mode 100644
index 0000000..bb465cb
--- /dev/null
+++ b/doc/theory.rst
@@ -0,0 +1,204 @@
+.. _section_theory:
+
+================================================================================
+A brief introduction to Data Assimilation
+================================================================================
+
+**Data Assimilation** is a general framework for computing the optimal estimate
+of the true state of a system, over time if necessary. It uses values obtained
+both from observations and *a priori* models, including information about their
+errors.
+
+In other words, data assimilation merges measurement data, the observations,
+with *a priori* physical and mathematical knowledge, embedded in numerical
+models, to obtain the best possible estimate of the true state and of its
+stochastic properties. Note that this true state can not be reached, but can
+only be estimated. Moreover, despite the fact that used information are
+stochastic by nature, data assimilation provides deterministic techniques in
+order to realize the estimation.
+
+Two main types of applications exist in data assimilation being covered by the
+same formalism: **parameters identification** and **fields reconstruction**.
+Before introducing the `Simple description of the data assimilation framework`_
+in a next section, we describe briefly these two types. At the end, some
+references allow `Going further in the data assimilation framework`_.
+
+Fields reconstruction or measures interpolation
+-----------------------------------------------
+
+Fields reconstruction consists in finding, from a restricted set of real
+measures, the physical field which is the most *consistent* with these measures.
+
+This consistency is to understand in terms of interpolation, that is to say that
+the field, we want to reconstruct using data assimilation on measures, has to
+fit at best the measures, while remaining constrained by the overall
+calculation. The calculation is thus an *a priori* estimation of the field that
+we seek to identify.
+
+If the system evolves in time, the reconstruction has to be established on every
+time step, as a whole. The interpolation process in this case is more
+complicated since it is temporal, not only in terms of instantaneous values of
+the field.
+
+A simple example of fields reconstruction comes from of meteorology, in which we
+look for value of variables such as temperature or pressure in all points of the
+spatial domain. We have instantaneous measurements of these quantities at
+certain points, but also a history set of these measures. Moreover, these
+variables are constrained by evolution equations for the state of the
+atmosphere, which indicates for example that the pressure at a point can not
+take any value independently of the value at this same point in previous time.
+We must therefore make the reconstruction of a field at any point in space, in
+order "consistent" with the evolution equations and measures of the previous
+time steps.
+
+Parameters identification or calibration
+----------------------------------------
+
+The identification of parameters by data assimilation is a form of calibration
+which uses both the measurement and an *a priori* estimation (called the
+"*background*") of the state that one seeks to identify, as well as a
+characterization of their errors. From this point of view, it uses all available
+information on the physical system (even if assumptions about errors are
+relatively restrictive) to find the "*optimal*" estimation from the true state.
+We note, in terms of optimization, that the background realizes a mathematical
+regularization of the main problem of identification.
+
+In practice, the two gaps "*calculation-background*" and
+"*calculation-measures*" are added to build the calibration correction of
+parameters or initial conditions. The addition of these two gaps requires a
+relative weight, which is chosen to reflect the trust we give to each piece of
+information. This confidence is measured by the covariance of the errors on the
+background and on the observations. Thus the stochastic aspect of information,
+measured or *a priori*, is essential for building the calibration error
+function.
+
+Simple description of the data assimilation framework
+-----------------------------------------------------
+
+We can write these features in a simple manner. By default, all variables are
+vectors, as there are several parameters to readjust.
+
+According to standard notations in data assimilation, we note
+:math:`\mathbf{x}^a` the optimal unknown parameters that is to be determined by
+calibration, :math:`\mathbf{y}^o` the observations (or experimental
+measurements) that we must compare the simulation outputs, :math:`\mathbf{x}^b`
+the background (*a priori* values, or regularization values) of searched
+parameters, :math:`\mathbf{x}^t` unknown ideals parameters that would give as
+output exactly the observations (assuming that the errors are zero and the model
+exact).
+
+In the simplest case, static, the steps of simulation and of observation can be
+combined into a single operator noted :math:`H` (linear or nonlinear), which
+transforms the input parameters :math:`\mathbf{x}` to results :math:`\mathbf{y}`
+to be compared to observations :math:`\mathbf{y}^o`. Moreover, we use the
+linearized operator :math:`\mathbf{H}` to represent the effect of the full
+operator :math:`H` around a linearization point (and we omit thereafter to
+mention :math:`H` even if it is possible to keep it). In reality, we have already
+indicated that the stochastic nature of variables is essential, coming from the
+fact that model, background and observations are incorrect. We therefore
+introduce errors of observations additively, in the form of a random vector
+:math:`\mathbf{\epsilon}^o` such that:
+
+.. math:: \mathbf{y}^o = \mathbf{H} \mathbf{x}^t + \mathbf{\epsilon}^o
+
+The errors represented here are not only those from observation, but also from
+the simulation. We can always consider that these errors are of zero mean. We
+can then define a matrix :math:`\mathbf{R}` of the observation error covariance
+by:
+
+.. math:: \mathbf{R} = E[\mathbf{\epsilon}^o.{\mathbf{\epsilon}^o}^T]
+
+The background can also be written as a function of the true value, by
+introducing the error vector :math:`\mathbf{\epsilon}^b`:
+
+.. math:: \mathbf{x}^b = \mathbf{x}^t + \mathbf{\epsilon}^b
+
+where errors are also assumed of zero mean, in the same manner as for
+observations. We define the :math:`\mathbf{B}` matrix of background error
+covariances by:
+
+.. math:: \mathbf{B} = E[\mathbf{\epsilon}^b.{\mathbf{\epsilon}^b}^T]
+
+The optimal estimation of the true parameters :math:`\mathbf{x}^t`, given the
+background :math:`\mathbf{x}^b` and the observations :math:`\mathbf{y}^o`, is
+then the "*analysis*" :math:`\mathbf{x}^a` and comes from the minimisation of an
+error function (in variational assimilation) or from the filtering correction (in
+assimilation by filtering).
+
+In **variational assimilation**, one classically attempts to minimize the
+following function :math:`J`:
+
+.. math:: J(\mathbf{x})=(\mathbf{x}-\mathbf{x}^b)^T.\mathbf{B}^{-1}.(\mathbf{x}-\mathbf{x}^b)+(\mathbf{y}^o-\mathbf{H}.\mathbf{x})^T.\mathbf{R}^{-1}.(\mathbf{y}^o-\mathbf{H}.\mathbf{x})
+
+which is usually designed as the "*3D-VAR*" function. Since covariance matrices
+are proportional to the variances of errors, their presence in both terms of the
+function :math:`J` can effectively weight the differences by confidence in the
+background or observations. The parameters :math:`\mathbf{x}` realizing the
+minimum of this function therefore constitute the analysis :math:`\mathbf{x}^a`.
+It is at this level that we have to use the full panoply of function
+minimization methods otherwise known in optimization. Depending on the size of
+the parameters vector :math:`\mathbf{x}` to identify and ot the availability of
+gradient and Hessian of :math:`J`, it is appropriate to adapt the chosen
+optimization method (gradient, Newton, quasi-Newton ...).
+
+In **assimilation by filtering**, in this simple case usually referred to as
+"*BLUE*"(for "*Best Linear Unbiased Estimator*"), the :math:`\mathbf{x}^a`
+analysis is given as a correction of the background :math:`\mathbf{x}^b` by a
+term proportional to the difference between observations :math:`\mathbf{y}^o`
+and calculations :math:`\mathbf{H}\mathbf{x}^b`:
+
+.. math:: \mathbf{x}^a = \mathbf{x}^b + \mathbf{K}(\mathbf{y}^o - \mathbf{H}\mathbf{x}^b)
+
+where :math:`\mathbf{K}` is the Kalman gain matrix, which is expressed using
+covariance matrices in the following form:
+
+.. math:: \mathbf{K} = \mathbf{B}\mathbf{H}^T(\mathbf{H}\mathbf{B}\mathbf{H}^T+\mathbf{R})^{-1}
+
+The advantage of filtering is to explicitly calculate the gain, to produce then
+the *a posteriori* covariance analysis matrix.
+
+In this simple static case, we can show, under the assumption of Gaussian error
+distributions, that the two *variational* and *filtering* approaches are
+equivalent.
+
+It is indicated here that these methods of "*3D-VAR*" and "*BLUE*" may be
+extended to dynamic problems, called respectively "*4D-VAR*" and "*Kalman
+filter*". They can take account of the evolution operator to establish an
+analysis at the right time steps of the gap between observations and simulations,
+and to have, at every moment, the propagation of the background through the
+evolution model. Many other variants have been developed to improve the
+numerical quality or to take into account computer requirements such as
+calculation size and time.
+
+Going further in the data assimilation framework
+++++++++++++++++++++++++++++++++++++++++++++++++
+
+To get more information about all the data assimilation techniques, the reader
+can consult introductory documents like [Argaud09], on-line training courses or
+lectures like [Bouttier99] and [Bocquet04] (along with other materials coming
+from geosciences applications), or general documents like [Talagrand97],
+[Tarantola87], [Kalnay03] and [WikipediaDA].
+
+Note that data assimilation is not restricted to meteorology or geo-sciences, but
+is widely used in other scientific domains. There are several fields in science
+and technology where the effective use of observed but incomplete data is
+crucial.
+
+Some aspects of data assimilation are also known as *parameter estimation*,
+*inverse problems*, *bayesian estimation*, *optimal interpolation*,
+*mathematical regularisation*, *data smoothing*, etc. These terms can be used in
+bibliographical searches.
+
+.. [Argaud09] Argaud J.-P., Bouriquet B., Hunt J., *Data Assimilation from Operational and Industrial Applications to Complex Systems*, Mathematics Today, pp.150-152, October 2009
+
+.. [Bouttier99] Bouttier B., Courtier P., *Data assimilation concepts and methods*, Meteorological Training Course Lecture Series, ECMWF, 1999, http://www.ecmwf.int/newsevents/training/rcourse_notes/pdf_files/Assim_concepts.pdf
+
+.. [Bocquet04] Bocquet M., *Introduction aux principes et méthodes de l'assimilation de données en géophysique*, Lecture Notes, 2004-2008, http://cerea.enpc.fr/HomePages/bocquet/assim.pdf
+
+.. [Tarantola87] Tarantola A., *Inverse Problem: Theory Methods for Data Fitting and Parameter Estimation*, Elsevier, 1987
+
+.. [Talagrand97] Talagrand O., *Assimilation of Observations, an Introduction*, Journal of the Meteorological Society of Japan, 75(1B), pp. 191-209, 1997
+
+.. [Kalnay03] Kalnay E., *Atmospheric Modeling, Data Assimilation and Predictability*, Cambridge University Press, 2003
+
+.. [WikipediaDA] Wikipedia/Data_assimilation: http://en.wikipedia.org/wiki/Data_assimilation
diff --git a/doc/using.rst b/doc/using.rst
index 9d8c4a3..71b23d6 100644
--- a/doc/using.rst
+++ b/doc/using.rst
@@ -1,3 +1,5 @@
+.. _section_using:
+
 ================================================================================
 Using the module ADAO
 ================================================================================
@@ -5,7 +7,7 @@ Using the module ADAO
 This section presents the usage of the ADAO module in SALOME.
 
 Logical procedure to build an ADAO test case
---------------------------------------------------------------------------------
+--------------------------------------------
 
 The construction of an ADAO case follows a simple approach to define the set of
 input data, either static or dynamic data, and then generates a complete block
@@ -26,16 +28,16 @@ data assimilation study. These data can be in SALOME or not.
 Each step will be detailed later in the next section.
 
 Detailed procedure to build an ADAO test case
---------------------------------------------------------------------------------
+---------------------------------------------
 
 Activate the ADAO module and use the editor GUI
-++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++
 
 As always for a module, it has to be activated by choosing the appropriate
 module button (or menu) in the toolbar of SALOME. A popup appears, allowing to
 choose between creating a new study, or opening an already existing one:
 
-  .. _adao_activate:
+  .. _adao_activate1:
   .. image:: images/adao_activate.png
     :align: center
   .. centered::
@@ -64,7 +66,7 @@ You will be prompted for a location in your file tree and a name, that will be
 completed by a "*.comm*" extension used for JDC EFICAS files.
 
 Build and modify the ADAO case and save it
-++++++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++
 
 To build a case using EFICAS, you have to go through a series of steps for
 selecting a keyword and then filling in its value. The structured editor
@@ -79,16 +81,16 @@ incorrect keywords are identified by a visual error red flag.
 At the end, you have to save your ADAO case.
 
 Export the ADAO case as a YACS scheme
-++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++
 
 
 
 Modify and supplement the YACS scheme and save it
-++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++
 
 
 Execute the YACS case and obtain the results
-++++++++++++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++++
 
 
 
@@ -96,7 +98,7 @@ Execute the YACS case and obtain the results
 
 
 Reference description of the commands and keywords available throught the GUI
---------------------------------------------------------------------------------
+-----------------------------------------------------------------------------
 
 --TODO--
 
diff --git a/src/daComposant/daCore/AssimilationStudy.py b/src/daComposant/daCore/AssimilationStudy.py
index 5587dd5..8a69181 100644
--- a/src/daComposant/daCore/AssimilationStudy.py
+++ b/src/daComposant/daCore/AssimilationStudy.py
@@ -648,8 +648,8 @@ class AssimilationStudy:
             Scheduler      = None,
             ):
         """
-        Permet d'associer un observer à une variable nommée gérée en interne,
-        activable selon des règles définies dans le Scheduler.
+        Permet d'associer un observer à une ou des variables nommées gérées en
+        interne, activable selon des règles définies dans le Scheduler.
         """
         # 
         if type( self.__algorithm ) is dict:
@@ -676,6 +676,36 @@ class AssimilationStudy:
                 HookParameters = HookParameters,
                 )
 
+    def removeDataObserver(self,
+            VariableName   = None,
+            HookFunction   = None,
+            ):
+        """
+        Permet de retirer un observer à une ou des variable nommée.
+        """
+        # 
+        if type( self.__algorithm ) is dict:
+            raise ValueError("No observer can be removed before choosing an algorithm.")
+        #
+        # Vérification du nom de variable et typage
+        # -----------------------------------------
+        if type( VariableName ) is str:
+            VariableNames = [VariableName,]
+        elif type( VariableName ) is list:
+            VariableNames = map( str, VariableName )
+        else:
+            raise ValueError("The observer requires a name or a list of names of variables.")
+        #
+        # Association interne de l'observer à la variable
+        # -----------------------------------------------
+        for n in VariableNames:
+            if not self.__algorithm.has_key( n ):
+                raise ValueError("An observer requires to be removed on a variable named %s which does not exist."%n)
+        else:
+            self.__algorithm.StoredVariables[ n ].removeDataObserver(
+                HookFunction   = HookFunction,
+                )
+
     def prepare_to_pickle(self):
         self.__algorithmFile = None
         self.__diagnosticFile = None
diff --git a/src/daComposant/daCore/Persistence.py b/src/daComposant/daCore/Persistence.py
index 79dae99..b8d100d 100644
--- a/src/daComposant/daCore/Persistence.py
+++ b/src/daComposant/daCore/Persistence.py
@@ -538,6 +538,32 @@ class Persistence:
         # -----------------------------------------------
         self.__dataobservers.append( [HookFunction, HookParameters, Schedulers] )
 
+    def removeDataObserver(self,
+        HookFunction   = None,
+        ):
+        """
+        Méthode de suppression d'un observer sur la variable.
+        
+        On peut donner dans HookFunction la meme fonction que lors de la
+        définition, ou un simple string qui est le nom de la fonction.
+        
+        """
+        if hasattr(HookFunction,"func_name"):
+            name = str( HookFunction.func_name )
+        elif type(HookFunction) is str:
+            name = str( HookFunction )
+        else:
+            name = None
+        #
+        i = -1
+        index_to_remove = []
+        for [hf, hp, hs] in self.__dataobservers:
+            i = i + 1
+            if name is hf.func_name: index_to_remove.append( i )
+        index_to_remove.reverse()
+        for i in index_to_remove:
+                self.__dataobservers.pop( i )
+
 # ==============================================================================
 class OneScalar(Persistence):
     """
@@ -1005,21 +1031,35 @@ if __name__ == "__main__":
         print "  ---> Mise en oeuvre de l'observer"
         print "       var  =",var.valueserie(-1)
         print "       info =",info
+    def obs_bis(var=None,info=None):
+        print "  ---> Mise en oeuvre de l'observer"
+        print "       var  =",var.valueserie(-1)
+        print "       info =",info
     OBJET_DE_TEST = Persistence("My object", unit="", basetype=list)
     D = OBJET_DE_TEST
     D.setDataObserver(
         HookFunction   = obs,
         Scheduler      = [2, 4],
-        HookParameters = "Second observer",
+        HookParameters = "Premier observer",
         )
     D.setDataObserver(
         HookFunction   = obs,
         Scheduler      = xrange(1,3),
+        HookParameters = "Second observer",
+        )
+    D.setDataObserver(
+        HookFunction   = obs_bis,
+        Scheduler      = range(1,3)+range(7,9),
         HookParameters = "Troisième observer",
         )
     for i in range(5):
-        # print
-        print "Action de 2 observers sur la variable observée, étape :",i
+        print "Action de 3 observers sur la variable observée, étape :",i
+        D.store( [i, i, i] )
+    D.removeDataObserver(
+        HookFunction   = obs,
+        )
+    for i in range(5,10):
+        print "Action d'un seul observer sur la variable observée, étape :",i
         D.store( [i, i, i] )
     del OBJET_DE_TEST
     print
-- 
2.39.2