documentation update

AAAlvesJr · AAAlvesJr · commit 61f8a32edfa5 · 2018-11-03T02:41:06.000+01:00
diff --git a/Doxyfile b/Doxyfile
@@ -1,14 +1,14 @@
 #PROJECT_NAME          = "Hydra_examples_and_documentation"
-PROJECT_NUMBER         =  3.1.1
+PROJECT_NUMBER         =  2.2.1
 
-STRIP_FROM_PATH        = /home/augalves/Development/Release/Hydra_Official_Repo/Hydra
+STRIP_FROM_PATH        = /home/augalves/Development/Release/Hydra
  
-INPUT                  = /home/augalves/Development/Release/Hydra_Official_Repo/Hydra/hydra /home/augalves/Development/Release/Hydra_Official_Repo/Hydra/doxydefs /home/augalves/Development/Release/Hydra_Official_Repo/Hydra/examples /home/augalves/Development/Release/Hydra_Official_Repo/Hydra/README.md
+INPUT                  = /home/augalves/Development/Release/Hydra/hydra /home/augalves/Development/Release/Hydra/doxydefs /home/augalves/Development/Release/Hydra/examples /home/augalves/Development/Release/Hydra/README.md
 
 
-USE_MDFILE_AS_MAINPAGE = /home/augalves/Development/Release/Hydra_Official_Repo/Hydra/doxydefs/README.md
-#PROJECT_LOGO          = /home/augalves/Development/Release/Hydra_Official_Repo/Hydra/logo_Hydra.png
-OUTPUT_DIRECTORY       = /home/augalves/Development/Release/Hydra_Official_Repo/EclipseProj/doc
+USE_MDFILE_AS_MAINPAGE = /home/augalves/Development/Release/Hydra/doxydefs/README.md
+#PROJECT_LOGO          = /home/augalves/Development/Release/Hydra/logo_Hydra.png
+OUTPUT_DIRECTORY       = /home/augalves/Development/Release/HydraEclipseProj/doc
 
 # Doxyfile 1.8.11
 
@@ -173,10 +173,10 @@ EXCLUDE                =
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = *detail/external*
 EXCLUDE_SYMBOLS        = 
-EXAMPLE_PATH           = /home/augalves/Development/Release/Hydra_Official_Repo/Hydra/examples
+EXAMPLE_PATH           = /home/augalves/Development/Release/Hydra/examples
 EXAMPLE_PATTERNS       = *
 EXAMPLE_RECURSIVE      = YES
-IMAGE_PATH             = /home/augalves/Development/Release/Hydra_Official_Repo/Hydra, /home/augalves/Development/Release/Hydra_Official_Repo/EclipseProj/plots
+IMAGE_PATH             = /home/augalves/Development/Release/Hydra, /home/augalves/Development/Release/HydraEclipseProj/plots
 INPUT_FILTER           = 
 FILTER_PATTERNS        = 
 FILTER_SOURCE_FILES    = NO
diff --git a/hydra/functions/BifurcatedGaussian.h b/hydra/functions/BifurcatedGaussian.h
@@ -47,6 +47,12 @@
 
 namespace hydra {
 
+/**
+ * \ingroup common_functions
+ * \class BifurcatedGaussian
+ *
+ *
+ */
 template<unsigned int ArgIndex=0>
 class BifurcatedGaussian: public BaseFunctor<BifurcatedGaussian<ArgIndex>, double, 3>
 {
diff --git a/hydra/functions/Chebychev.h b/hydra/functions/Chebychev.h
@@ -51,6 +51,14 @@
 
 namespace hydra {
 
+/**
+ * \ingroup common_functions
+ * \class Chebychev
+ *
+ * The Chebyshev polynomials \f$ T_n \f$ (first kind)
+ *  are polynomials with the largest possible leading coefficient,
+ *   but subject to the condition that their absolute value on the interval [−1,1] is bounded by 1
+ */
 template< unsigned int Order, unsigned int ArgIndex=0>
 class  Chebychev:public BaseFunctor<Chebychev<Order, ArgIndex>, double, Order+1>
 {
diff --git a/hydra/functions/ChiSquare.h b/hydra/functions/ChiSquare.h
@@ -50,7 +50,16 @@
 
 namespace hydra {
 
-
+/**
+ * \ingroup common_functions
+ * \class ChiSquare
+ *
+ * The chi-squared distribution (also chi-square or \f$ \chi^2 \f$ -distribution) with  \f$ k \f$ degrees of freedom is
+ *  the distribution of a sum of the squares of k independent standard normal random variables.
+ *  The chi-square distribution is a special case of the gamma distribution and
+ *  is one of the most widely used probability distributions in inferential statistics,
+ *   notably in hypothesis testing or in construction of confidence intervals.
+ */
 template< unsigned int ArgIndex=0 >
 class ChiSquare: public BaseFunctor< ChiSquare<ArgIndex>, double, 1>
 {
diff --git a/hydra/functions/CosHelicityAngle.h b/hydra/functions/CosHelicityAngle.h
@@ -46,6 +46,7 @@
 namespace hydra {
 
 /**
+ * \ingroup common_functions
  * \class CosTheta
  *
  *  This functor calculates the cosine of the helicity angle of the particle with four-vector D,
diff --git a/hydra/functions/DeltaDMassBackground.h b/hydra/functions/DeltaDMassBackground.h
@@ -52,7 +52,10 @@
 
 namespace hydra {
 
-
+/**
+ * \ingroup common_functions
+ * \class DeltaDMassBackground
+ */
 template<unsigned int ArgIndex=0>
 class DeltaDMassBackground: public BaseFunctor<DeltaDMassBackground<ArgIndex>, double, 4>
 {
diff --git a/hydra/functions/Exponential.h b/hydra/functions/Exponential.h
@@ -46,7 +46,12 @@
 #include <utility>
 
 namespace hydra {
-
+/**
+ * \ingroup common_functions
+ * \class Exponential
+ * https://en.wikipedia.org/wiki/Exponential_function
+ *
+ */
 template<unsigned int ArgIndex=0>
 class Exponential:public BaseFunctor<Exponential<ArgIndex>, double, 1>
 {
diff --git a/hydra/functions/Gaussian.h b/hydra/functions/Gaussian.h
@@ -47,6 +47,16 @@
 
 namespace hydra {
 
+/**
+ * \ingroup common_functions
+ * \class Gaussian
+ *
+ * Gaussian functions are often used to represent the probability density function of a normally distributed random variable with
+ * expected value \f$ \mu \f$ and variance \f$ \sigma \f$. In this case, the Gaussian is of the form:
+
+\f[ g(x) = \frac{1}{\sigma\sqrt{2\pi}} e^{ -\frac{1}{2}\left(\frac{x-\mu}{\sigma}\right)^2 }. \f]
+ *
+ */
 template<unsigned int ArgIndex=0>
 class Gaussian: public BaseFunctor<Gaussian<ArgIndex>, double, 2>
 {
diff --git a/hydra/functions/GaussianKDE.h b/hydra/functions/GaussianKDE.h
@@ -48,6 +48,10 @@
 
 namespace hydra {
 
+/**
+ *  \ingroup common_functions
+ *  \class GaussianKDE
+ */
 template< size_t NBins, size_t ArgIndex=0>
 class GaussianKDE: public BaseFunctor<GaussianKDE<NBins, ArgIndex>, double, 0>
 {
diff --git a/hydra/functions/GeneralizedGamma.h b/hydra/functions/GeneralizedGamma.h
@@ -53,6 +53,9 @@ namespace hydra {
 
 
 /**
+ * \ingroup common_functions
+ * \class GeneralizedGamma
+ *
  * The Gamma distribution is often used to describe variables bounded on one side. An even
 more flexible version of this distribution is obtained by adding a third parameter giving
 the so called generalized Gamma distribution :
diff --git a/hydra/functions/JohnsonSUShape.h b/hydra/functions/JohnsonSUShape.h
@@ -53,7 +53,9 @@ namespace hydra {
 
 
 /**
- * @class JohnsonSUShape
+ * \ingroup common_functions
+ * \class JohnsonSUShape
+ *
  * Implementation the JohnsonSU line shape.
  * https://en.wikipedia.org/wiki/Johnson%27s_SU-distribution
  *
diff --git a/hydra/functions/LogNormal.h b/hydra/functions/LogNormal.h
@@ -51,6 +51,13 @@
 
 namespace hydra {
 
+/**
+ * \ingroup common_functions
+ * \class LogNormal
+ *
+ * In probability theory, a log-normal (or lognormal) distribution is a continuous probability distribution of a random
+ * variable whose logarithm is normally distributed. Thus, if the random variable X is log-normally distributed, then Y = ln(X) has a normal distribution.
+ */
 template<unsigned int ArgIndex=0>
 class LogNormal: public BaseFunctor<LogNormal<ArgIndex>, double, 2>
 {
diff --git a/hydra/functions/M12PhaseSpaceLineShape.h b/hydra/functions/M12PhaseSpaceLineShape.h
@@ -49,6 +49,7 @@
 namespace hydra {
 
 /**
+ * \ingroup common_functions
  * @class M12PhaseSpaceLineShape
  *
  * Two-body phase-space distribution for \f$ m_{12}\f$:
diff --git a/hydra/functions/M12SqPhaseSpaceLineShape.h b/hydra/functions/M12SqPhaseSpaceLineShape.h
@@ -49,6 +49,7 @@
 namespace hydra {
 
 /**
+ * \ingroup common_functions
  * @class M12SqPhaseSpaceLineShape
  *
  * Two-body phase-space distribution for \f$ m_{12}^2\f$:
diff --git a/hydra/functions/PlanesDeltaAngle.h b/hydra/functions/PlanesDeltaAngle.h
@@ -47,6 +47,7 @@
 namespace hydra {
 
 /**
+ * \ingroup common_functions
  * \class PlanesDeltaAngle
  *
  *  This functor calculates the delta angle between decay plane of the particle with four-vector d2 and d3 (same plane)
diff --git a/hydra/functions/Polynomial.h b/hydra/functions/Polynomial.h
@@ -48,6 +48,30 @@
 
 namespace hydra {
 
+/**
+ * \ingroup common_functions
+ * \class  Polynomial
+ *
+ * From :  https://en.wikipedia.org/wiki/Polynomial
+ *
+ * A polynomial is an expression
+ * that can be built from constants and
+ *  symbols called indeterminates or variables by means of addition, multiplication and
+ *  exponentiation to a non-negative integer power.
+ *  Two such expressions that may be transformed, one to the other,
+ *  by applying the usual properties of commutativity,
+ *  associativity and distributivity of
+ *   addition and multiplication are considered as defining the same polynomial.
+ *   A polynomial in a single indeterminate \f$ x \f$ can always be written (or rewritten) in the form
+\f[ a_n x^n + a_{n-1}x^{n-1} + \dotsb + a_2 x^2 + a_1 x + a_0, \f]
+where \f$ a_0, \ldots, a_n \f$ are constants and \f$ x \f$ is the indeterminate. The word "indeterminate" means that
+\f$ x \f$ represents no particular value, although any value may be substituted for it.
+The mapping that associates the result of this substitution to the substituted value is a function, called a ''polynomial function''.
+
+This can be expressed more concisely by using summation notation:
+\f$ \sum_{k=0}^n a_k x^k \f$.
+ *
+ */
 template< unsigned int Order, unsigned int ArgIndex=0>
 class  Polynomial:public BaseFunctor<Polynomial<Order, ArgIndex>, double, Order+1>
 {
diff --git a/hydra/functions/ThreeBodyMassThresholdBackground.h b/hydra/functions/ThreeBodyMassThresholdBackground.h
@@ -45,8 +45,11 @@
 #include <utility>
 
 namespace hydra {
-
-
+/**
+ * \ingroup common_functions
+ * \class ThreeBodyMassThresholdBackground
+ *
+ */
 template<unsigned int ArgIndex=0>
 class ThreeBodyMassThresholdBackground: public BaseFunctor<ThreeBodyMassThresholdBackground<ArgIndex>, double, 4>
 {
diff --git a/hydra/functions/TrapezoidalShape.h b/hydra/functions/TrapezoidalShape.h
@@ -48,6 +48,7 @@
 
 namespace hydra {
 /**
+ * \ingroup common_functions
  * \class TrapezoidalShape
  *
  * In probability theory and statistics, the trapezoidal distribution is a continuous probability distribution the graph
diff --git a/hydra/functions/TriangularShape.h b/hydra/functions/TriangularShape.h
@@ -48,6 +48,7 @@
 
 namespace hydra {
 /**
+ * \ingroup common_functions
  * \class TriangularShape
  * From: https://en.wikipedia.org/wiki/Triangular_distribution
  *
diff --git a/hydra/functions/UniformShape.h b/hydra/functions/UniformShape.h
@@ -49,6 +49,7 @@
 
 namespace hydra {
 /**
+ * \ingroup common_functions
  * \class UniformShape
  * From: https://en.wikipedia.org/wiki/Uniform_distribution_(continuous)
  *
diff --git a/hydra/functions/Utils.h b/hydra/functions/Utils.h
@@ -39,6 +39,7 @@
 namespace hydra {
 
 /**
+ *  \ingroup common_functions
  * Orbital angular momentum tags.
  */
 enum Wave{ SWave=0, PWave, DWave, FWave, GWave, HWave };
diff --git a/hydra/functions/WignerDMatrix.h b/hydra/functions/WignerDMatrix.h
@@ -52,7 +52,8 @@
 namespace hydra {
 
 /**
- * \class WignerD
+ *  \ingroup common_functions
+ * \class WignerDMatrix
  *
  *  Calculates the beta-term
  *                   \f[ d^j_{mn}(beta) \f]
diff --git a/hydra/functions/ZemachFunctions.h b/hydra/functions/ZemachFunctions.h
@@ -47,6 +47,8 @@ namespace hydra {
 
 
 /**
+ * \ingroup common_functions
+ *
  * @class ZemachFunction
  *
  * Zemach's angular probability distribution for 3-body decays of spinless particle into spinless final

Original file line number	Diff line number	Diff line change
`@@ -46,6 +46,7 @@`
`46`	`46`	`namespace hydra {`
`47`	`47`
`48`	`48`	`/**`
	`49`	`+ * \ingroup common_functions`
`49`	`50`	`* \class CosTheta`
`50`	`51`	`*`
`51`	`52`	`* This functor calculates the cosine of the helicity angle of the particle with four-vector D,`
Original file line number	Diff line number	Diff line change
`@@ -48,6 +48,10 @@`
`48`	`48`
`49`	`49`	`namespace hydra {`
`50`	`50`
	`51`	`+/**`
	`52`	`+ * \ingroup common_functions`
	`53`	`+ * \class GaussianKDE`
	`54`	`+ */`
`51`	`55`	`template< size_t NBins, size_t ArgIndex=0>`
`52`	`56`	`class GaussianKDE: public BaseFunctor<GaussianKDE<NBins, ArgIndex>, double, 0>`
`53`	`57`	`{`