From 21d9e7947ce5203b5f9a8745d557cee6c49ad943 Mon Sep 17 00:00:00 2001
From: Jean-Philippe ARGAUD <jean-philippe.argaud@edf.fr>
Date: Wed, 27 Feb 2019 18:59:40 +0100
Subject: [PATCH] Update various configurations

---
 doc/en/conf.py                        |  5 +++--
 doc/fr/conf.py                        |  5 +++--
 src/daComposant/daAlgorithms/3DVAR.py | 23 ++++++++++++++++++++++-
 test/CTestTestfileInstall.cmake.in    |  2 +-
 4 files changed, 29 insertions(+), 6 deletions(-)

diff --git a/doc/en/conf.py b/doc/en/conf.py
index d8cfa7d..d1c9d94 100644
--- a/doc/en/conf.py
+++ b/doc/en/conf.py
@@ -57,7 +57,8 @@ except:
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ["sphinx.ext.pngmath"]
+extensions = ["sphinx.ext.imgmath"]
+# extensions = ["sphinx.ext.pngmath"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -201,7 +202,7 @@ htmlhelp_basename = 'ADAOdoc'
 # -- Options for LaTeX output --------------------------------------------------
 
 # The paper size ('letter' or 'a4').
-latex_paper_size = 'letter'
+latex_elements = {'papersize':'letterpaper'}
 
 # The font size ('10pt', '11pt' or '12pt').
 latex_font_size = '10pt'
diff --git a/doc/fr/conf.py b/doc/fr/conf.py
index b1e250f..2f76da9 100644
--- a/doc/fr/conf.py
+++ b/doc/fr/conf.py
@@ -57,7 +57,8 @@ except:
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ["sphinx.ext.pngmath"]
+extensions = ["sphinx.ext.imgmath"]
+# extensions = ["sphinx.ext.pngmath"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -201,7 +202,7 @@ htmlhelp_basename = 'ADAOdoc'
 # -- Options for LaTeX output --------------------------------------------------
 
 # The paper size ('letter' or 'a4').
-latex_paper_size = 'a4'
+latex_elements = {'papersize':'a4paper'}
 
 # The font size ('10pt', '11pt' or '12pt').
 latex_font_size = '10pt'
diff --git a/src/daComposant/daAlgorithms/3DVAR.py b/src/daComposant/daAlgorithms/3DVAR.py
index 0dc21b0..597352e 100644
--- a/src/daComposant/daAlgorithms/3DVAR.py
+++ b/src/daComposant/daAlgorithms/3DVAR.py
@@ -91,6 +91,9 @@ class ElementaryAlgorithm(BasicObjects.Algorithm):
                 "IndexOfOptimum",
                 "Innovation",
                 "InnovationAtCurrentState",
+                "JacobianMatrixAtBackground",
+                "JacobianMatrixAtOptimum",
+                "KalmanGainAtOptimum",
                 "MahalanobisConsistency",
                 "OMA",
                 "OMB",
@@ -161,6 +164,11 @@ class ElementaryAlgorithm(BasicObjects.Algorithm):
         if max(Y.shape) != max(HXb.shape):
             raise ValueError("The shapes %s of observations Y and %s of observed calculation H(X) are different, they have to be identical."%(Y.shape,HXb.shape))
         #
+        if self._toStore("JacobianMatrixAtBackground"):
+            HtMb = HO["Tangent"].asMatrix(ValueForMethodForm = Xb)
+            HtMb = HtMb.reshape(Y.size,Xb.size) # ADAO & check shape
+            self.StoredVariables["JacobianMatrixAtBackground"].store( HtMb )
+        #
         # Précalcul des inversions de B et R
         # ----------------------------------
         BI = B.getI()
@@ -320,11 +328,18 @@ class ElementaryAlgorithm(BasicObjects.Algorithm):
         # Calcul de la covariance d'analyse
         # ---------------------------------
         if self._toStore("APosterioriCovariance") or \
-           self._toStore("SimulationQuantiles"):
+            self._toStore("SimulationQuantiles") or \
+            self._toStore("JacobianMatrixAtOptimum") or \
+            self._toStore("KalmanGainAtOptimum"):
             HtM = HO["Tangent"].asMatrix(ValueForMethodForm = Xa)
             HtM = HtM.reshape(Y.size,Xa.size) # ADAO & check shape
+        if self._toStore("APosterioriCovariance") or \
+            self._toStore("SimulationQuantiles") or \
+            self._toStore("KalmanGainAtOptimum"):
             HaM = HO["Adjoint"].asMatrix(ValueForMethodForm = Xa)
             HaM = HaM.reshape(Xa.size,Y.size) # ADAO & check shape
+        if self._toStore("APosterioriCovariance") or \
+            self._toStore("SimulationQuantiles"):
             HessienneI = []
             nb = Xa.size
             for i in range(nb):
@@ -346,6 +361,12 @@ class ElementaryAlgorithm(BasicObjects.Algorithm):
                     raise ValueError("The %s a posteriori covariance matrix A is not symmetric positive-definite. Please check your a priori covariances and your observation operator."%(self._name,))
         if self._toStore("APosterioriCovariance"):
             self.StoredVariables["APosterioriCovariance"].store( A )
+        if self._toStore("JacobianMatrixAtOptimum"):
+            self.StoredVariables["JacobianMatrixAtOptimum"].store( HtM )
+        if self._toStore("KalmanGainAtOptimum"):
+            if   (Y.size <= Xb.size): KG  = B * HaM * (R + numpy.dot(HtM, B * HaM)).I
+            elif (Y.size >  Xb.size): KG = (BI + numpy.dot(HaM, RI * HtM)).I * HaM * RI
+            self.StoredVariables["KalmanGainAtOptimum"].store( KG )
         #
         # Calculs et/ou stockages supplémentaires
         # ---------------------------------------
diff --git a/test/CTestTestfileInstall.cmake.in b/test/CTestTestfileInstall.cmake.in
index 618bb41..da05965 100644
--- a/test/CTestTestfileInstall.cmake.in
+++ b/test/CTestTestfileInstall.cmake.in
@@ -22,7 +22,7 @@
 SET(SALOME_TEST_DRIVER "@CMAKE_INSTALL_PREFIX@/bin/salome/appliskel/salome_test_driver.py")
 
 SET(COMPONENT_NAME ADAO)
-SET(TIMEOUT         500)
+SET(TIMEOUT        500)
 
 # Add all test subdirs
 SUBDIRS(
-- 
2.39.2