[doc] add the gnuplot files.

[hkl.git] / Documentation / hkl.org.in

#+TITLE: Welcome to hkl's @VERSION@ documentation!
#+AUTHOR: Picca Frédéric-Emmanuel
#+EMAIL: picca at synchrotron dash soleil dot fr
#+LANGUAGE: en
#+STYLE: <style>table.center {margin-left:auto; margin- right:auto;}</style>
#+HTML_HEAD: <link href="css/style.css" rel="stylesheet" type="text/css" />
#+HTML_MATHJAX:  path:"https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS_HTML"

* Introduction
  The purpose of the library is to factorize single crystal
  diffraction angles computation for different kind of diffractometer
  geometries. It is used at the SOLEIL, Desy and Alba synchrotron with
  the Tango control system to pilot diffractometers.
** Features
   - mode computation (aka PseudoAxis)
   - item for different diffractometer geometries.
   - UB matrix computation.
     - busing & Levy with 2 reflections
     - simplex computation with more than 2 reflections using the GSL
       library.
     - Eulerians angles to pre-orientate your sample.
   - Crystal lattice refinement
     - with more than 2 reflections you can select which parameter must
       be fitted.
   - Pseudoaxes
     - psi, eulerians, q, ...
** Conventions
   In all this document the next convention will be used to describe
   the diffractometers geometries.
   - right handed convention for all the angles.
   - direct space orthogonal base.
   - description of the diffractometer geometries is done with all
     axes values set to zero.
** Diffraction
*** the crystal

    A periodic crystal is the association of a pattern and a lattice. The
    pattern is located at each points of the lattice node. Positions of
    those nodes are given by:

    \[
    R_{uvw}=u\cdot\vec{a}+v\cdot\vec{b}+w\cdot\vec{c}
    \]

    $\vec{a}$, $\vec{b}$, $\vec{c}$ are the former vector of a base of the
    space. =u=, =v=, =w= are integers. The pattern contain atoms
    associated to each lattice node. the purpose of diffraction is to study
    the interaction of this crystal (pattern+lattice) with X-rays.

    #+CAPTION: Crystal direct lattice.
    [[./figures/crystal.png]]

    this lattice is defined by $\vec{a}$, $\vec{b}$, $\vec{c}$ vectors, and
    the angles $\alpha$, $\beta$, $\gamma$. In general cases this lattice is
    not orthonormal.

    Nevertheless to compute the interaction of this real space lattice and
    the X-Rays, it is convenient to define another lattice called reciprocal
    lattice defined like this:

    \begin{eqnarray*}
    \vec{a}^{\star} & = & \tau\frac{\vec{b}\wedge\vec{c}}{\vec{a}\cdot(\vec{b}\wedge\vec{c})}\\
    \vec{b}^{\star} & = & \tau\frac{\vec{c}\wedge\vec{a}}{\vec{b}\cdot(\vec{c}\wedge\vec{a})}\\
    \vec{c}^{\star} & = & \tau\frac{\vec{a}\wedge\vec{b}}{\vec{c}\cdot(\vec{a}\wedge\vec{b})}
    \end{eqnarray*}

    $\tau=2\pi$ or $\tau=1$ depending on the conventions.

    It is then possible to define theses orthogonal properties:

    \begin{eqnarray*}
    \vec{a}^{\star}\cdot\vec{a}=\tau & \vec{b}^{\star}\cdot\vec{a}=0    & \vec{c}^{\star}\cdot\vec{a}=0\\
    \vec{a}^{\star}\cdot\vec{b}=0    & \vec{b}^{\star}\cdot\vec{b}=\tau & \vec{c}^{\star}\cdot\vec{b}=0\\
    \vec{a}^{\star}\cdot\vec{c}=0    & \vec{b}^{\star}\cdot\vec{c}=0    & \vec{c}^{\star}\cdot\vec{c}=\tau
    \end{eqnarray*}

    This reciprocal space lattice allow to write in a simpler form the
    interaction between the crystal and the X-Rays. We often only know about
    $\vec{a}$, $\vec{b}$, $\vec{c}$ vectors and the angles $\alpha$,
    $\beta$, $\gamma$. Using the previous equations reciprocal, we can
    compute the reciprocal lattice this way:


    \begin{eqnarray*}
    a^{\star} & = & \frac{\sin\alpha}{aD}\\
    b^{\star} & = & \frac{\sin\beta}{bD}\\
    c^{\star} & = & \frac{\sin\gamma}{cD}
    \end{eqnarray*}

    where

    \[
    D=\sqrt{1-\cos^{2}\alpha-\cos^{2}\beta-\cos^{2}\gamma+2\cos\alpha\cos\beta\cos\gamma}
    \]

    To compute the angles between the reciprocal space vectors, it is once
    again possible to use the previous equations reciprocal to obtain the
    sines and cosines of the angles $\alpha^\star$, $\beta^\star$ and
    $\gamma^\star$:

    \begin{eqnarray*}
    \cos\alpha^{\star}=\frac{\cos\beta\cos\gamma-\cos\alpha}{\sin\beta\sin\gamma} & \, & \sin\alpha^{\star}=\frac{D}{\sin\beta\sin\gamma} \\
    \cos\beta^{\star}=\frac{\cos\gamma\cos\alpha-\cos\beta}{\sin\gamma\sin\alpha} & \, & \sin\beta^{\star}=\frac{D}{\sin\gamma\sin\alpha}\\
    \cos\gamma^{\star}=\frac{\cos\alpha\cos\beta-\cos\gamma}{\sin\alpha\sin\beta} & \, & \sin\gamma^{\star}=\frac{D}{\sin\alpha\sin\beta}
    \end{eqnarray*}

    the volume of the lattice can be compute this way:

    \[
    V = abcD
    \]

    or

    \[
    V = \vec{a} \dot (\vec{b} \wedge \vec{c}) = \vec{b} \dot (\vec{c} \wedge \vec{a}) = \vec{c} \dot (\vec{a} \wedge \vec{b})
    \]

*** Diffraction

    Let the incoming X-rays beam whose wave vector is $\vec{k_{i}}$,
    $|k_{i}|=\tau/\lambda$ where $\lambda$ is the wavelength of the signal.
    The $\vec{k_{d}}$ vector wavelength of the diffracted beam. There is
    diffusion if the diffusion vector $\vec{q}$ can be expressed as follows:

    \[
    \vec{q}=\vec{k_{d}}-\vec{k_{i}}=h.\vec{a}^{*}+k.\vec{b}^{*}+l.\vec{c}^{*}
    \]

    where $(h,k,l)\in\mathbb{N}^{3}$ and $(h,k,l)\neq(0,0,0)$. Theses
    indices $(h,k,l)$ are named Miller indices.

    Another way of looking at things has been given by Bragg and that famous
    relationship:

    \[
    n\lambda=2d\sin\theta
    \]

    where $d$ is the inter-plan distance and $n \in \mathbb{N}$.

    The diffusion occurs for an unique $\theta$ angle. Then we got
    $\vec{q}$ perpendicular to the diffraction plan.

    The Ewald construction allow to represent this diffraction in the
    reciprocal space.

*** Quaternions
**** Properties

     The quaternions will be used to describe the diffractometers geometries.
     Theses quaternions can represent 3D rotations. There is different way to
     describe then like complex numbers.

     \[
     q=a+bi+cj+dk
     \]

     or

     \[
     q=[a,\vec{v}]
     \]

     To compute the quaternion's norm, we can proceed like for complex
     numbers

     \[
     \|q\|=\sqrt{a²+b²+c²+d²}
     \]

     Its conjugate is :

     \[
     q^{*}=[a,-\vec{u}]=a-bi-cj-dk
     \]

**** Operations

     The difference with the complex number algebra is about
     non-commutativity.

     \[
     qp \neq pq
     \]

     \[
     \begin{bmatrix}
     ~ & 1 & i  & j  & k \cr
     1 & 1 & i  & j  & k \cr
     i & i & -1 & k  & -j \cr
     j & j & -k & -1 & i \cr
     k & k & j  & -i & -1
     \end{bmatrix}
     \]

     The product of two quaternions can be express by the Grassman product
     Grassman product. So for two quaternions $p$ and $q$:

     \begin{align*}
     q &= a+\vec{u} = a+bi+cj+dk\\
     p &= t+\vec{v} = t+xi+yj+zk
     \end{align*}

     we got

     \[
     pq = at - \vec{u} \cdot \vec{v} + a \vec{v} + t \vec{u} + \vec{v} \times \vec{u}
     \]

     or equivalent

     \[
     pq = (at - bx - cy - dz) + (bt + ax + cz - dy) i + (ct + ay + dx - bz) j + (dt + az + by - cx) k
     \]

**** 3D rotations

     L'ensemble des quaternions unitaires (leur norme est égale à 1) est le
     groupe qui représente les rotations dans l'espace 3D. Si on a un vecteur
     unitaire $\vec{u}$ et un angle de rotation $\theta$ alors le quaternion
     $[\cos\frac{\theta}{2},\sin\frac{\theta}{2}\vec{u]}$ représente la
     rotation de $\theta$ autour de l'axe $\vec{u}$ dans le sens
     trigonométrique. Nous allons donc utiliser ces quaternions unitaires
     pour représenter les mouvements du diffractomètre.

     Alors que dans le plan 2D une simple multiplication entre un nombre
     complex et le nombre $e^{i\theta}$ permet de calculer simplement la
     rotation d'angle $\theta$ autour de l'origine, dans l'espace 3D
     l'expression équivalente est:

     \[
     z'=qzq^{-1}
     \]

     où $q$ est le quaternion de norme 1 représentant la rotation dans
     l'espace et $z$ le quaternion représentant le vecteur qui subit la
     rotation (sa partie réelle est nulle).

     Dans le cas des quaternions de norme 1, il est très facile de calculer
     $q^{-1}$. En effet l'inverse d'une rotation d'angle $\theta$ est la
     rotation d'angle $-\theta$. On a donc directement:

     \[
     q^{-1}=[\cos\frac{-\theta}{2},\sin\frac{-\theta}{2}\vec{u}]=[\cos\frac{\theta}{2},-\sin\frac{\theta}{2}\vec{u}]=q^{*}
     \]

     Le passage aux matrices de rotation se fait par la formule suivante
     $q\rightarrow M$.

     \[
     \begin{bmatrix}
     a{{}^2}+b{{}^2}-c{{}^2}-d{{}^2} & 2bc-2ad & 2ac+2bd\\
     2ad+2bc & a{{}^2}-b{{}^2}+c{{}^2}-d{{}^2} & 2cd-2ab\\
     2bd-2ac & 2ab+2cd & a{{}^2}-b{{}^2}-c{{}^2}+d{{}^2}
     \end{bmatrix}
     \]

     La composition de rotation se fait simplement en multipliant les
     quaternions entre eux. Si l'on à $q$

** Modes de fonctionnement
** Equations fondamentales

   Le problème que nous devons résoudre est de calculer pour une famille de
   plan $(h,k,l)$ donné, les angles de rotation du diffractomètre qui
   permettent de le mettre en condition de diffraction. Il faut donc
   exprimer les relations mathématiques qui lient les différents angles
   entre eux lorsque la condition de Bragg est vérifiée. L'équation
   fondamentale est la suivante:

   \begin{align*}
   \left(\prod_{i}S_{i}\right)\cdot U\cdot B\cdot\vec{h} & =\left(\prod_{j}D_{j}-I\right)\cdot\vec{k_{i}}\\
   R\cdot U\cdot B\cdot\vec{h} & =\vec{Q}
   \end{align*}

   ou $\vec{h}$ est le vecteur $(h,k,l)$, $\vec{k_{i}}$ est le vecteur
   incident, $S_{i}$ les matrices de rotations des mouvements liés à
   l'échantillon, $D_{j}$ les matrices de rotation des mouvements liés au
   détecteur, $I$ la matrice identité, $U$ la matrice d'orientation du
   cristal par rapport au repère de l'axe sur lequel ce dernier est monté
   et $B$ la matrice de passage d'un repère non orthonormé ( celui du
   crystal réciproque) à un repère orthonormé.

*** Calcule de B

    Si l'on connaît les paramètres cristallins du cristal étudié, il est
    très simple de calculer $B$:

    \[
    B=
    \begin{bmatrix}
    a^{\star} & b^{\star}\cos\gamma^{\star} & c^{\star}\cos\beta^{\star}\\
    0 & b^{\star}\sin\gamma^{\star} & -c^{\star}\sin\beta^{\star}\cos\alpha\\
    0 & 0 & 1/c
    \end{bmatrix}
    \]

*** Calcule de U

    Il existe plusieurs façons de calculer $U$. Busing et Levy en a proposé
    plusieurs. Nous allons présenter celle qui nécessite la mesure de
    seulement deux réflections ainsi que la connaissance des paramètres
    cristallins. Cette façon de calculer la matrice d'orientation $U$, peut
    être généralisée à n'importe quel diffractomètre pour peu que la
    description des axes de rotation permette d'obtenir la matrice de
    rotation de la machine $R$ et le vecteur de diffusion $\vec{Q}$.

    Il est également possible de calculer $U$ sans la connaîssance des
    paramètres cristallins. il faut alors faire un affinement des
    paramètres. Cela revient à minimiser une fonction. Nous allons utiliser
    la méthode du simplex pour trouver ce minimum et donc ajuster l'ensemble
    des paramètres cristallins ainsi que la matrice d'orientation.

*** Algorithme de Busing Levy

    L'idée est de se placer dans le repère de l'axe sur lequel est monté
    l'échantillon. On mesure deux réflections $(\vec{h}_{1},\vec{h}_{2})$
    ainsi que leurs angles associés. Cela nous permet de calculer $R$ et
    $\vec{Q}$ pour chacune de ces reflections. nous avons alors ce système:

    \begin{eqnarray*}
    U\cdot B\cdot\vec{h}_{1} & = & \tilde{R}_{1}\cdot\vec{Q}_{1}\\
    U\cdot B\cdot\vec{h}_{2} & = & \tilde{R}_{2}\cdot\vec{Q}_{2}
    \end{eqnarray*}

    De façon à calculer facilement $U$, il est intéressant de définir deux
    trièdres orthonormé $T_{\vec{h}}$ et $T_{\vec{Q}}$ à partir des vecteurs
    $(B\vec{h}_{1},B\vec{h}_{2})$ et
    $(\tilde{R}_{1}\vec{Q}_{1},\tilde{R}_{2}\vec{Q}_{2})$. On a alors très
    simplement:

    \[
    U \cdot T_{\vec{h}} = T_{\vec{Q}}
    \]

    Et donc

    \[
    U = T_{\vec{Q}} \cdot \tilde{T}_{\vec{h}}
    \]

*** Affinement par la méthode du simplex

    Dans ce cas nous ne connaissons pas la matrice $B$, il faut donc mesurer
    plus que deux réflections pour ajuster les 9 paramètres. Six paramètres
    pour le crystal et trois pour la matrice d'orientation $U$. Les trois
    paramètres qui permennt de representer $U$ sont en fait les angles
    d'euler. il faut donc être en mesure de passer d'une représentation
    eulérien à cette matrice :math::U et réciproquement.

    \[
    U = X \cdot Y \cdot Z
    \]

    où $X$ est la matrice rotation suivant l'axe Ox et le premier angle
    d'Euler, $Y$ la matrice de rotation suivant l'axe Oy et le deuxième
    angle d'Euler et $Z$ la matrice du troisième angle d'Euler pour l'axe
    Oz.

    #+ATTR_HTML: class="center"
    | $X$        | $Y$        | $Z$        |
    | <10>       | <10>       | <10>       |
    | $\begin{bmatrix} 1 & 0 & 0\\ 0 & A & -B\\ 0 & B & A \end{bmatrix}$ | $\begin{bmatrix}C & 0 & D\\0 & 1 & 0\\-D & 0 & C\end{bmatrix}$ | $\begin{bmatrix}E & -F & 0\\F & E & 0\\0 & 0 & 1\end{bmatrix}$ |

    et donc:

    \[
    U=
    \begin{bmatrix}
    CE & -CF & D\\
    BDE+AF & -BDF+AE & -BC\\
    -ADE+BF & ADF+BE & AC
    \end{bmatrix}
    \]

    Il est donc facile de passer des angles d'Euler à la matrice
    d'orientation.

    Il faut maintenant faire la transformation inverse de la matrice $U$
    vers les angles d'euler.

* PseudoAxes
  This section describe the calculations done by the library for the
  different kind of pseudo axes.
** General process
*** First Solution
    The hkl library use the gsl library in order to find the first
    valid solution.
*** Multiplication of the solutions.
    Once we have got the first solution different strategies are
    applyed in order to generate more solutions.
**** Geometry Multiplication
     For kappa diffractometers, once you have one solution it is
     possible to générate another one using a property of this
     geometry. (Left arm and right arm).
*** Restrains of the Solutions
    We apply then some constrains to reduce these solutions to only a
    bunch of acceptable ones. Usualy we take the axis range into
    account.
** Eulerians to Kappa angles

   1st solution

   \begin{eqnarray*}
   \kappa_\omega & = & \omega - p + \frac{\pi}{2} \\
   \kappa & = & 2 \arcsin\left(\frac{\sin\frac{\chi}{2}}{\sin\alpha}\right) \\
   \kappa_\phi & = &  \phi - p - \frac{\pi}{2}
   \end{eqnarray*}

   or 2nd one

   \begin{eqnarray*}
   \kappa_\omega & = & \omega - p - \frac{\pi}{2} \\
   \kappa & = & -2 \arcsin\left(\frac{\sin\frac{\chi}{2}}{\sin\alpha}\right) \\
   \kappa_\phi & = &  \phi - p + \frac{\pi}{2}
   \end{eqnarray*}

   where

   \[
   p = \arcsin\left(\frac{\tan\frac{\chi}{2}}{\tan\alpha}\right)
   \]

   and $\alpha$ is the angle of the kappa axis with the $\vec{y}$ axis.

** Kappa to Eulerians angles

   1st solution

   \begin{eqnarray*}
   \omega & = & \kappa_\omega + p - \frac{\pi}{2} \\
   \chi   & = & 2 \arcsin\left(\sin\frac{\kappa}{2} \sin\alpha\right) \\
   \phi   & = & \kappa_\phi + p + \frac{\pi}{2}
   \end{eqnarray*}

   or 2nd one

   \begin{eqnarray*}
   \omega & = & \kappa_\omega + p + \frac{\pi}{2} \\
   \chi   & = & -2 \arcsin\left(\sin\frac{\kappa}{2} \sin\alpha\right) \\
   \phi   & = & \kappa_\phi + p - \frac{\pi}{2}
   \end{eqnarray*}

   where

   \[
   p = \arctan\left(\tan\frac{\kappa}{2} \cos\alpha\right)
   \]

   #+CAPTION: $\omega = 0$, $\chi = 0$, $\phi = 0$, 1st solution
   [[./figures/e2k_1.png]]

   #+CAPTION: $\omega = 0$, $\chi = 0$, $\phi = 0$, 2nd solution
   [[./figures/e2k_2.png]]

   #+CAPTION: $\omega = 0$, $\chi = 90$, $\phi = 0$, 1st solution
   [[./figures/e2k_3.png]]

   #+CAPTION: $\omega = 0$, $\chi = 90$, $\phi = 0$, 2nd solution
   [[./figures/e2k_4.png]]

** Qper and Qpar
   [[./figures/qper_qpar.png]]

   this pseudo axis engine compute the perpendicular
   ($\left|\left|\vec{Q_\text{per}}\right|\right|$) and parallel
   ($\left|\left|\vec{Q_\text{par}}\right|\right|$) contribution of
   $\vec{Q}$ relatively to the surface of the sample defined by the
   $\vec{n}$ vector.

   \begin{eqnarray*}
   \vec{q} & = & \vec{k_\text{f}} - \vec{k_\text{i}} \\
   \vec{q} & = & \vec{q_\text{per}} + \vec{q_\text{par}} \\
   \vec{q_\text{per}} & = & \frac{\vec{q} \cdot \vec{n}}{\left|\left|\vec{n}\right|\right|} \frac{\vec{n}}{\left|\left|\vec{n}\right|\right|}
   \end{eqnarray*}
* Diffractometers
  #+BEGIN_QUOTE
  *warning*

  This section is automatically generating by introspecting the hkl library.
  #+END_QUOTE

#+BEGIN_SRC python :exports results :results value raw
  from gi.repository import Hkl

  def bold(l):
      return ["\"*" + _ + "*\"" for _ in l]

  def level(indent=1, s=None):
      return "  "*indent + s

  diffractometers = Hkl.factories().iterkeys()

  output = ''
  for diffractometer in sorted(diffractometers):
      factory = Hkl.factories()[diffractometer]
      output += "** " + diffractometer + "\n\n"
      detector = Hkl.Detector.factory_new(Hkl.DetectorType(0))
      sample = Hkl.Sample.new("toto")
      geometry = factory.create_new_geometry()
      engines = factory.create_new_engine_list()
      engines.init(geometry, detector, sample)

      output += "*** Axes: \n"
      for axis in geometry.axis_names_get():
          axis_v = geometry.axis_get(axis).axis_v_get().data
          output += level(2, "+ \"*" + axis + "*\": rotation around the *" + repr(axis_v) + "* axis\n")

      output += "*** Engines: \n"
      for engine in engines.engines_get():
          output += "**** \"*" + engine.name_get() + "*\":\n\n"
          output += level(3, "* pseudo axes:\n")
          for pseudo in engine.pseudo_axis_names_get():
              p = engine.pseudo_axis_get(pseudo)
              description = p.description_get()
              output += level(4, "* \"*" + pseudo + "*\" : " + description + '\n\n')
          output += "\n"
          for mode in engine.modes_names_get():
              output += level(3, "+ mode: \"*" + mode + "*\"\n")
              engine.current_mode_set(mode)
              axes_r = engine.axis_names_get(Hkl.EngineAxisNamesGet.READ)
              axes_w = engine.axis_names_get(Hkl.EngineAxisNamesGet.WRITE)
              output += level(4, "+ axes (read) : " + ", ".join(bold(axes_r)) + "\n")
              output += level(4, "+ axes (write): " + ", ".join(bold(axes_w)) + "\n")
              parameters = engine.parameters_names_get()
              output += level(4, "+ parameters: ")
              if parameters:
                  output += "\n"
                  for parameter in parameters:
                      p = engine.parameter_get(parameter)
                      description = p.description_get()
                      value = p.value_get(Hkl.UnitEnum.USER)
                      output += level(5, "+ *" + parameter + "* [" + str(value) + "]: " + description + "\n")
              else:
                  output += "No parameter\n"

  return output
#+END_SRC
* Developpement
** Getting hkl

   To get hkl, you can download the last stable version from sourceforge or
   if you want the latest development version use
   [[http://git.or.cz/][git]] or
   [[http://code.google.com/p/msysgit/downloads/list][msysgit]] on windows
   system and do:

   #+BEGIN_SRC sh
git clone git://repo.or.cz/hkl.git
   #+END_SRC

   or:

   #+BEGIN_SRC sh
    git clone http://repo.or.cz/r/hkl.git (slower)
   #+END_SRC

   then checkout the next branch like this:

   #+BEGIN_SRC sh
    cd hkl
    git checkout -b next origin/next
   #+END_SRC

** Building hkl

   To build hkl you need [[http://www.python.org][Python 2.3+]] the
   [[http://www.gnu.org/software/gsl/][GNU Scientific Library 1.12]] and
   [[https://developer.gnome.org/glib/][GLib-2.0 >= 2.3.4]]:

   #+BEGIN_SRC sh
    ./configure --disable-gui
    make
    sudo make install
   #+END_SRC

   you can also build a GUI interfaces which use
   [[http://www.gtk.org][gtk]]:

   #+BEGIN_SRC sh
    ./configure
    make
    sudo make install
   #+END_SRC

   optionnaly you can build an experimental /libhkl3d/ library (no public
   API for now) which is used by the GUI to display and compute
   diffractometer collisions (only the /K6C/ model). To build it you need
   also [[https://projects.gnome.org/gtkglext/][gtkglext]] and
   [[http://bulletphysics.org/wordpress/][bullet 2.82]]:

   #+BEGIN_SRC sh
    ./configure --enable-hkl3d
    make
    sudo make install
   #+END_SRC

   if you want to work on the documentation you need the extra

   - [[http://www.gtk.org/gtk-doc/][gtk-doc]] for the api
   - [[http://sphinx.pocoo.org/][sphinx]] for the html and latex doc.
   - [[http://asymptote.sourceforge.net/][asymptote]] for the figures
   - [[http://www.gnu.org/software/emacs/][emacs]] the well known editor
   - [[https://github.com/emacsmirror/htmlize][htmlize]] used to highlight the source code
   - [[http://orgmode.org][org-mode]] litteral programming

   On Debian/Ubuntu you just need to install

   #+BEGIN_SRC sh
    sudo apt-get install emacs dvipng emacs-goodies-el org-mode
   #+END_SRC

   #+BEGIN_SRC sh
    ./configure --enable-gtk-doc
    make
    make html
#+END_SRC

   nevertheless if you do not want to build the documentation you can do:

   #+BEGIN_SRC sh
   ./configure --disable-hkl-doc
   #+END_SRC

** Hacking hkl
*** Bug reporting

    You can find the bug tracker here
    [[https://bugs.debian.org/cgi-bin/pkgreport.cgi?repeatmerged=no&src=hkl][libhkl]]

-  Debian/Ubuntu:

   #+BEGIN_SRC sh
       reportbug hkl
   #+END_SRC

-  Other OS

   You just need to send an [[mailto:submit@bugs.debian.org?subject=%20My%20problem%20with%20hkl...&body=Package:%20hkl%0AVersion:%20@VERSION@%0A%0AI%20found%20this%20problem%20in%20hkl][email]]

*** Providing patches

    you can send your patch to [[mailto:picca@synchrotron-soleil.fr][Picca Frédéric-Emmanuel]] using =git=

    Here a minimalist example of the workflow to prepare and send
    patches for integration into the hkl library. Suppose you wan to
    add a new feature, you need first to create a new branch from the
    =next= one:

    #+BEGIN_SRC sh
    git checkout -b my-next next
    #+END_SRC

    hack, hack:

    #+BEGIN_SRC sh
    git commit -a
    #+END_SRC

    more hacks:

    #+BEGIN_SRC sh
    git commit -a
    #+END_SRC

    now that your new feature is ready, you can send by email your
    work using =git format-patch= for review:

    #+BEGIN_SRC sh
    git format-patch origin/next
    #+END_SRC

    which will generate a bunch of ~0001\_xxx~, ~0002\_xxx~,
    ... patches

    Then you can configure =git send-email= in order to send the
    patches for review.

    #+BEGIN_SRC sh
    git config sendemail.to "picca@synchrotron-soleil.fr"
    #+END_SRC

    and send then with this command:

    #+BEGIN_SRC sh
    git send-email 0001-xxx.patch, 0002-xxx.patch, ...
    #+END_SRC

    If it does not work you can use your usually email software and
    send these generated patches to the [[mailto:picca@synchrotron-soleil.fr][author]].

** Howto's
*** Add a diffractometer
    To add a new diffractometer, you just need to copy the
    ~hkl/hkl-engine-template.c~ into
    ~hkl/hkl-engine-INSTITUT-BEAMLINE-INSTRUMENT.c~ where you replace
    the upper case with the appropriate values.

    The template file is compiled during the build process to ensure
    that it is always valid.

    Then you just need to follow the instruction found in the
    template. If you need some precision about the process, do not
    hesitate to contact the main author.

    do not forgot also to add this new file into ~hkl/Makefile.am~
    with other diffractometers in the hkl_c_sources variable (please
    keep the alphabetic order).
*** Work on the documentation
    The documentation system is written with [[http://orgmode.org/][org-mode]], and the [[http://orgmode.org/worg/org-contrib/babel/][babel]]
    extension which allow to introspect the library and generate part
    of the doc using the hkl library. Python code is executed during
    the build process to generate the Diffractometer section of the
    documentation. To work on the doc and test the embedded python
    code it is necessary to setup a few environment variables and
    start emacs with the right LD_LIBRARY_PATH. In order to simplify
    the process a make target was written. You just need to type:
    #+BEGIN_SRC sh
      cd Documentation
      make doc-edit
    #+END_SRC
    and start to contribute.

    If you do not have emacs, you can nevertheless contribute by
    editing the ~Documentation/hkl.org.in~ file which is text only.

    The most expected contributions are for now:
    * english correctness
    * a nicer css
* Bindings

  The hkl library use the gobject-introspection to provide automatic
  binding for a few languages.

** Python

   You can test the binding directly from the source directory with
   these commandes if ipython is installed.

    #+BEGIN_SRC sh
      cd tests/bindings
      make ipython
    #+END_SRC

   then you have the Hkl module preloaded into the ipython environment.

   hkl computation:

   has you can see there is 4 available solutions.

   let's compute an hkl trajectory and select the first solution.

   if we look at the 3 other solutions we can see that there is a problem
   of continuity at the begining of the trajectory.

   hey what's happend with theses solutions ! let's look closely to real
   numbers. the last column is the distance to the diffractometer current
   position. This distance is for now express like this:

   $\sum_{axes} \left|\text{current position} - \text{target position}\right|$

   #+BEGIN_EXAMPLE
    [0.0, 119.99999999999999, 0.0, -90.0, 0.0, 59.99999999999999] 0.0
    [0.0, -119.99999999999999, 0.0, -90.0, 0.0, -59.99999999999999] 6.28318530718
    [0.0, -60.00000000000005, 0.0, 90.0, 0.0, 59.99999999999999] 6.28318530718
    [0.0, 60.00000000000001, 0.0, 90.0, 0.0, -59.99999999999999] 6.28318530718

    [0.0, 117.7665607657826, 7.456826294401656, -92.39856410531434, 0.0, 60.33024982425957] 0.216753826612
    [0.0, -57.436310940366894, -7.456826294401656, 92.39856418853617, 0.0, 60.33024982425957] 6.41621345188
    [0.0, 62.2334392342174, -7.456826294401656, 92.39856410531434, 0.0, -60.33024982425957] 6.42197739723
    [0.0, -122.5636890596331, 7.456826294401656, -92.3985641885362, 0.0, -60.33024982425957] 6.50570308205

    [0.0, 115.89125602137928, 14.781064139466098, -94.7660423112577, 0.0, 61.314597086440706] 0.219062698235
    [0.0, -125.42334103772737, 14.781064139466098, -94.7660427050904, 0.0, -61.314597086440706] 6.53671995288
    [0.0, -54.57665896227262, -14.781064139466098, 94.76604270509038, 0.0, 61.314597086440706] 6.67989976726
    [0.0, 64.10874397862072, -14.781064139466098, 94.7660423112577, 0.0, -61.314597086440706] 6.71437170098

    [0.0, 114.39338605351007, 21.85448296702796, -97.074145033719, 0.0, 62.93506298693471] 0.218163667981
    [0.0, -128.54167683157993, 21.85448296702796, -97.07414574435087, 0.0, -62.93506298693471] 6.59846359365
    [0.0, -51.45832316842005, -21.85448296702796, 97.07414574435087, 0.0, 62.93506298693471] 6.93673746356
    [0.0, 65.60661394648993, -21.85448296702796, 97.074145033719, 0.0, -62.93506298693471] 7.03385205725

    [0.0, 113.28316795475283, 28.583837575232764, -99.29953499008337, 0.0, 65.16540747008955] 0.21459359225
    [0.0, -131.88223933078322, 28.583837575232764, -99.29953638594702, 0.0, -65.16540747008955] 6.69038531388
    [0.0, -48.11776066921677, -28.583837575232764, 99.29953638594702, 0.0, 65.16540747008955] 7.18296350386
    [0.0, 66.71683204524717, -28.583837575232764, 99.29953499008337, 0.0, -65.16540747008955] 7.37556986959

    [0.0, 112.56286877075006, 34.90573305321372, -101.42496979586187, 0.0, 67.97568017857415] 0.209053830457
    [0.0, -135.4128111996365, 34.90573305321372, -101.42497263302461, 0.0, -67.97568017857415] 6.81174779784
    [0.0, -44.58718880036348, -34.90573305321372, 101.4249726330246, 0.0, 67.97568017857415] 7.41581162393
    [0.0, 67.43713122924994, -34.90573305321372, 101.42496979586187, 0.0, -67.97568017857415] 7.7353201851

    [0.0, 112.2291126083182, 40.78594007247402, -103.43941832567457, 0.0, 71.33706722449408] 0.202280147961
    [0.0, -139.10795451001587, 40.78594007247402, -103.43942357602316, 0.0, -71.33706722449408] 6.96173845391
    [0.0, -40.89204548998411, -40.78594007247402, 103.43942357602312, 0.0, 71.33706722449408] 7.63358787543
    [0.0, 67.7708873916818, -40.78594007247402, 103.43941832567457, 0.0, -71.33706722449408] 8.10986069093

    [0.0, 112.27578927291766, 46.214916130901734, -105.33741042812996, 0.0, 75.22640762217479] 0.196576175748
    [0.0, -142.95061850160724, 46.214916130901734, -105.3374188005596, 0.0, -75.22640762217479] 7.13962155618
    [0.0, -37.04938149839278, -46.214916130901734, 105.33741880055959, 0.0, 75.22640762217479] 7.83557762281
    [0.0, 67.72421072708234, -46.214916130901734, 105.33741042812996, 0.0, -75.22640762217479] 8.49706672677

    [0.0, 112.697137434232, 51.201667684695856, -107.11797492933192, 0.0, 79.63023536264535] 0.202327153157
    [0.0, -146.9330984641471, 51.201667684695856, -107.11798610058318, 0.0, -79.63023536264535] 7.34491897177
    [0.0, -33.0669015358529, -51.201667684695856, 107.11798610058317, 0.0, 79.63023536264535] 8.02185610877
    [0.0, 67.30286256576798, -51.201667684695856, 107.11797492933192, 0.0, -79.63023536264535] 8.89597005568

    [0.0, 113.49085964586432, 55.76762791023837, -108.78347437395287, 0.0, 84.54867879242364] 0.208455586312
    [0.0, -151.05782007465257, 55.76762791023837, -108.78348605483542, 0.0, -84.54867879242364] 7.57761473366
    [0.0, -28.942179925347414, -55.76762791023837, 108.78348605483538, 0.0, 84.54867879242364] 8.19307323084
    [0.0, 66.50914035413568, -55.76762791023837, 108.78347437395287, 0.0, -84.54867879242364] 9.30675279514

    [0.0, 114.6614608037443, 59.941489465646214, -110.3385360479293, 0.0, 90.00000081324956] 0.215562935229
    [0.0, -155.33854118146962, 59.941489465646214, -110.33854432979601, 0.0, -89.99999918675044] 7.83839602383
    [0.0, -24.661458818530395, -59.941489465646214, 110.33854432979601, 0.0, 90.00000081324956] 8.3502621071
    [0.0, 65.3385391962557, -59.941489465646214, 110.3385360479293, 0.0, -89.99999918675044] 9.7307712883
   #+END_EXAMPLE

   as you can see for the first point of the trajectory, the 2nd, 3rd and
   4th solutions have identical distances to the current position of the
   diffractometer so they are un-ordered:

   #+BEGIN_EXAMPLE
    [0.0, 119.99999999999999, 0.0, -90.0, 0.0, 59.99999999999999] 0.0
    [0.0, -119.99999999999999, 0.0, -90.0, 0.0, -59.99999999999999] 6.28318530718
    [0.0, -60.00000000000005, 0.0, 90.0, 0.0, 59.99999999999999] 6.28318530718
    [0.0, 60.00000000000001, 0.0, 90.0, 0.0, -59.99999999999999] 6.28318530718
   #+END_EXAMPLE

   then the problem arise with the second and third solution. you can see a
   sort of reorganisation of the solution. 2 -> 3, 3 -> 4 and 4 -> 2 then
   the order will stick unchanged until the end of the trajectory. this is
   because the distance is computed relatively to the current position of
   the diffractometer.:

   #+BEGIN_EXAMPLE
    [0.0, 117.7665607657826, 7.456826294401656, -92.39856410531434, 0.0, 60.33024982425957] 0.216753826612
    [0.0, -57.436310940366894, -7.456826294401656, 92.39856418853617, 0.0, 60.33024982425957] 6.41621345188
    [0.0, 62.2334392342174, -7.456826294401656, 92.39856410531434, 0.0, -60.33024982425957] 6.42197739723
    [0.0, -122.5636890596331, 7.456826294401656, -92.3985641885362, 0.0, -60.33024982425957] 6.50570308205

    [0.0, 115.89125602137928, 14.781064139466098, -94.7660423112577, 0.0, 61.314597086440706] 0.219062698235
    [0.0, -125.42334103772737, 14.781064139466098, -94.7660427050904, 0.0, -61.314597086440706] 6.53671995288
    [0.0, -54.57665896227262, -14.781064139466098, 94.76604270509038, 0.0, 61.314597086440706] 6.67989976726
    [0.0, 64.10874397862072, -14.781064139466098, 94.7660423112577, 0.0, -61.314597086440706] 6.71437170098
   #+END_EXAMPLE

   #+BEGIN_QUOTE
   *warning*

   when you compute a trajectory, start from a valid position (the
   starting point must be the real first point of your trajectory) then
   use only the closest solution for the next points of the trajectory.
   (first solution of the geometries list)
   #+END_QUOTE
* Releases
** @VERSION@
*** DONE add emergence on all e4c diffractometers <2017-03-16 Thu>
    The emergence pseudo axis is was added to =SOLEIL MARS= and =E4CV=
*** DONE Fix for multiarch (headers) <2016-05-04 mer.>
    The =ccan_config.h= generated file is arch specific. It is then
    necessary to install this file under /usr/include/<triplet> on
    Debian like systems. This way it will be possible to co-installa
    32/64 bit version of hkl, or to do cross-compilation (arm on
    x86_64, etc...)
*** DONE Fix the FTBFS with the new bullet 2.86.1 version <2017-08-13 dim.>
    In order to update the internal structures of =Hkl3DObject= (the
    =is-colliding= member), we were using a callback which became
    un-effectiv with this new version of bullet. The logic was
    rewritten in order to be much more efficent using the manifold
    informations. Now we iterate on =Hkl3DObject= object only once
    (n) complexity instead of (n²) with the previous one.
** 5.0.0.2080 <2016-04-27 mer.>
*** DONE =HklEngine= <2016-01-20 mer.>
    emergence_fixed for the SOLEIL SIX MED 2+2 geometry.
*** DONE =HklVector= <2016-02-09 mar.>
    The hkl_vector_init method is now public.
*** DONE =HklParameter= <2016-02-25 Thu>
    at the end of the computation all solutions are filtered in order
    to check that they are valid (min < value < range). BUT for a
    rotation axis this check was instead (min < value % 2pi < max).
*** DONE =HklGeometry= <2016-04-20 mer.>
    Add hkl_geometry_[sample/detector]_rotation_get method. It is now
    possible to get the sample or the detector rotation expressed as a
    =HklQuaternion=.
#+BEGIN_SRC python :export code
  qr = geometry.sample_rotation_get(sample)
  qd = geometry.detector_rotation_get(detector)
#+END_SRC
*** DONE =HklQuaternion= <2016-04-20 mer.>
    Add hkl_quaternion_to_matrix in order to convert a =HklQuaternion=
    into a =HklMatrix=. Then you just need to convert this HklMatrix
    into a numpy array when used from the python binding
#+BEGIN_SRC python :export code
  def hkl_matrix_to_numpy(m):
      M = empty((3, 3))
      for i in range(3):
          for j in range(3):
              M[i, j] = m.get(i, j)
      return M


  M = hkl_matrix_to_numpy(q.to_matrix())
#+END_SRC
*** DONE Soleil Sirius Turret <2016-04-26 mar.>
    Add the =basepitch= axis which rotate around $\vec{y}$ in mrad.
** 4.99.99.1955 <2015-07-15 mer.>
   Add the ccan_config.h public header. This header is generated with
   the ccan configurator program.
** 4.99.99.1950 <2015-07-07 mar.>
   Fix an FTBFS observed on the sparc arch
** 4.99.99.1949 <2015-07-03 ven.>
*** DONE =HklInterval= <2015-07-03 ven.>
    =hkl_interval_cmp= was wrong. Now the comparison is done between
    =HKL_EPSILON= and the distance between minimum and maximum. This
    problem was triggered first on ppc64el architecture.
*** DONE PATH_MAX <2015-07-03 ven.>
    Replace getcwd called by get_current_dir_path instead in order to
    avoid PATH_MAX which is not available on hurd.
** 4.99.99.1946 <2015-06-30 mar.>
*** DONE =HklEngine=
**** "emergence" <2015-06-22 lun.>
     Add a new emergence engine which contain only one pseudo axis.
     + =emergence= the outgoing beam emergence from the sample's surface.
     + =azimuth= the sample's surface azimuth.
** 4.99.99.1940 <2015-05-04 lun.>
*** DONE =HklLattice= add an =hkl_lattice_volume_get=
#+BEGIN_SRC c
  volume = hkl_lattice_volume_get(lattice);
#+END_SRC
*** DONE =HklEngine=
**** "nrj, sample, ...  dependencies" <2015-03-24 mar.>
     Add the =hkl_engine_dependencies_get= method which return if the
     =HklEngine= depends of the axes, the energy, or the sample. the
     possible values are stored in the =HklEngineDependencies= enum.

#+BEGIN_SRC c
  dependencies = hkl_engine_dependencies_get(engine);
  if (dependencies & HKL_ENGINE_DEPENDENCIES_ENERGY) {
          ...
  }
  if (dependencies & HKL_ENGINE_DEPENDENCIES_SAMPLE) {
          ...
  }
  ...
#+END_SRC
**** "tth2" <2015-04-03 ven>
     Add a new hkl engine which contain two pseudo axes.
     + =tth=  two times the diffraction angle $\theta$
     + =alpha= the azimuth of q in the zOy plan.
**** "incidence" <2015-04-21 mar.>
     Add a new incidence engine which contain only one pseudo axis.
     + =incidence= the incoming beam incidence on the sample surface.
     + =azimuth= the sample surface azimuth.
**** =hkl_engine_parameter_set= <2015-05-04 lun.>
     Fix a bug and expose the method in the binding.
**** general
     - use #define AXIS "axis_name" in all the code to set the axes
       names at only one place. <2015-04-23 jeu.>
*** DONE =HklLattice= expose in the binding the _x_get/set methods <2015-03-24 mar.>
    Now you can use hkl_lattice_x_get where x=a, b, c, alpha, beta,
    gamma in the bindings.
#+BEGIN_SRC python :export code
  a = lattice.a_get()
  lattice.a_set(a)
#+END_SRC
*** DONE =HklSampleReflection= expose the flag_get/set and geometry_get/set method <2015-03-24 mar.>
    It is now possible to change the geometry stored in a reflection
    via the bindings.
#+BEGIN_SRC python :export code
  flag = reflection.flag_get()
  reflection.flag_set(flag)

  geometry = reflection.geometry_get()
  geometry.axes_values_set([omega, chi, phi, ...])
  reflection.geometry_set(geometry)
#+END_SRC
* Todo
** hkl
*** TODO [#A] =HklEngine= *q/q2*
    Fix all these engines... This engine takes into account only the
    *gamma* and *delta* axes.  so diffractometers with 3 axes for the
    detector are wrong.  It would be nice to take into account all the
    detector holder AND the position of the detecteor on the
    diffractometer arms (for now the detector is always on the last
    axis).
*** TODO [#A] HklSource
    Create a parameter for the wavelength. This is just internally for
    the futur trajectory system, so no need to change the signature of
    hkl_geometry_vawelength get/set
*** TODO [#A] SOLEIL SIRIUS KAPPA
    Investigation of a problem saw on Sirius Kappa geometry. The idea
    is to compute a trajectory from $[0, 0, 1]$ to $[0, 0, 6]$ on a
    $GaAs$ sample.

    #+BEGIN_SRC sh
      Geometry SOLEIL SIRIUS KAPPA (Source 1.4586370000000007e-9 m) (fromList [-0.5193202,40.795148838481424,134.08834052117254,-55.57809067120416,-2.23369e-2,14.824478553649875]) (Just [Parameter "mu" (-0.5193202) (Range (-180.0) 180.0),Parameter "komega" 40.795148838481424 (Range (-180.0) 180.0),Parameter "kappa" 134.08834052117254 (Range (-180.0) 180.0),Parameter "kphi" (-55.57809067120416) (Range (-180.0) 180.0),Parameter "delta" (-2.23369e-2) (Range (-180.0) 180.0),Parameter "gamma" 14.824478553649875 (Range (-180.0) 180.0)])
      [Engine "hkl" [Parameter "h" 2.1481674408578524e-8 (Range (-1.0) 1.0),Parameter "k" 6.392014061803081e-8 (Range (-1.0) 1.0),Parameter "l" 1.0000000132413767 (Range (-1.0) 1.0)] (Mode "bissector_vertical" []),Engine "eulerians" [Parameter "omega" 7.412239314132745 (Range (-180.0) 180.0),Parameter "chi" 89.72020738176312 (Range (-180.0) 180.0),Parameter "phi" 91.03899980444716 (Range (-180.0) 180.0)] (Mode "eulerians" [Parameter "solutions" 1.0 (Range 0.0 1.0)]),Engine "psi" [Parameter "psi" 154.5513657893786 (Range (-180.0) 180.0)] (Mode "psi_vertical_soleil_sirius_kappa" [Parameter "h2" 1.0 (Range (-1.0) 1.0),Parameter "k2" 1.0 (Range (-1.0) 1.0),Parameter "l2" 1.0 (Range (-1.0) 1.0)]),Engine "q2" [Parameter "q" 1.1114190632688228 (Range 0.0 1.0),Parameter "alpha" 89.91560430137815 (Range (-180.0) 180.0)] (Mode "q2" []),Engine "qper_qpar" [Parameter "qper" 1.1114162413072137 (Range (-1.0) 1.0),Parameter "qpar" 2.5045470426602284e-3 (Range (-1.0) 1.0)] (Mode "qper_qpar" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "tth2" [Parameter "tth" 14.824495004588014 (Range (-180.0) 180.0),Parameter "alpha" 89.91560430137815 (Range (-180.0) 180.0)] (Mode "tth2" []),Engine "incidence" [Parameter "incidence" 7.414401593159588 (Range (-180.0) 180.0),Parameter "azimuth" 89.78541978058817 (Range (-180.0) 180.0)] (Mode "incidence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "emergence" [Parameter "emergence" 7.410055570443473 (Range (-180.0) 180.0),Parameter "azimuth" 89.78541978058817 (Range (-180.0) 180.0)] (Mode "emergence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)])]
      Geometry SOLEIL SIRIUS KAPPA (Source 1.4586370000000007e-9 m) (fromList [-0.5193202,47.97247473743512,134.654265266118,124.92415016158583,-2.23369e-2,29.904632884360968]) (Just [Parameter "mu" (-0.5193202) (Range (-180.0) 180.0),Parameter "komega" 47.97247473743512 (Range (-180.0) 180.0),Parameter "kappa" 134.654265266118 (Range (-180.0) 180.0),Parameter "kphi" 124.92415016158583 (Range (-180.0) 180.0),Parameter "delta" (-2.23369e-2) (Range (-180.0) 180.0),Parameter "gamma" 29.904632884360968 (Range (-180.0) 180.0)])
      [Engine "hkl" [Parameter "h" (-1.3839931497468412e-9) (Range (-1.0) 1.0),Parameter "k" (-4.913404854447784e-10) (Range (-1.0) 1.0),Parameter "l" 2.000000003360829 (Range (-1.0) 1.0)] (Mode "bissector_vertical" []),Engine "eulerians" [Parameter "omega" 14.95231642186499 (Range (-180.0) 180.0),Parameter "chi" 89.9575990161042 (Range (-180.0) 180.0),Parameter "phi" 271.9039918460157 (Range (-180.0) 180.0)] (Mode "eulerians" [Parameter "solutions" 1.0 (Range 0.0 1.0)]),Engine "psi" [Parameter "psi" (-26.325999847139332) (Range (-180.0) 180.0)] (Mode "psi_vertical_soleil_sirius_kappa" [Parameter "h2" 1.0 (Range (-1.0) 1.0),Parameter "k2" 1.0 (Range (-1.0) 1.0),Parameter "l2" 1.0 (Range (-1.0) 1.0)]),Engine "q2" [Parameter "q" 2.2228381008394895 (Range 0.0 1.0),Parameter "alpha" 89.96116221471468 (Range (-180.0) 180.0)] (Mode "q2" []),Engine "qper_qpar" [Parameter "qper" 2.222832456913507 (Range (-1.0) 1.0),Parameter "qpar" (-5.009095284686147e-3) (Range (-1.0) 1.0)] (Mode "qper_qpar" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "tth2" [Parameter "tth" 29.90464045486422 (Range (-180.0) 180.0),Parameter "alpha" 89.96116221471468 (Range (-180.0) 180.0)] (Mode "tth2" []),Engine "incidence" [Parameter "incidence" 14.952081490954424 (Range (-180.0) 180.0),Parameter "azimuth" 90.09480115642252 (Range (-180.0) 180.0)] (Mode "incidence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "emergence" [Parameter "emergence" 14.952481262345229 (Range (-180.0) 180.0),Parameter "azimuth" 90.09480115642252 (Range (-180.0) 180.0)] (Mode "emergence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)])]
      Geometry SOLEIL SIRIUS KAPPA (Source 1.4586370000000007e-9 m) (fromList [-0.5193202,56.25907471532187,133.92128004831832,-55.45556970293517,-2.23369e-2,45.53873596992208]) (Just [Parameter "mu" (-0.5193202) (Range (-180.0) 180.0),Parameter "komega" 56.25907471532187 (Range (-180.0) 180.0),Parameter "kappa" 133.92128004831832 (Range (-180.0) 180.0),Parameter "kphi" (-55.45556970293517) (Range (-180.0) 180.0),Parameter "delta" (-2.23369e-2) (Range (-180.0) 180.0),Parameter "gamma" 45.53873596992208 (Range (-180.0) 180.0)])
      [Engine "hkl" [Parameter "h" 8.37724528421826e-9 (Range (-1.0) 1.0),Parameter "k" 2.018612859089285e-8 (Range (-1.0) 1.0),Parameter "l" 2.999999983141756 (Range (-1.0) 1.0)] (Mode "bissector_vertical" []),Engine "eulerians" [Parameter "omega" 22.76936798418434 (Range (-180.0) 180.0),Parameter "chi" 89.64969149765572 (Range (-180.0) 180.0),Parameter "phi" 91.0547235659273 (Range (-180.0) 180.0)] (Mode "eulerians" [Parameter "solutions" 1.0 (Range 0.0 1.0)]),Engine "psi" [Parameter "psi" 154.50191592522592 (Range (-180.0) 180.0)] (Mode "psi_vertical_soleil_sirius_kappa" [Parameter "h2" 1.0 (Range (-1.0) 1.0),Parameter "k2" 1.0 (Range (-1.0) 1.0),Parameter "l2" 1.0 (Range (-1.0) 1.0)]),Engine "q2" [Parameter "q" 3.334257126919726 (Range 0.0 1.0),Parameter "alpha" 89.97807925598289 (Range (-180.0) 180.0)] (Mode "q2" []),Engine "qper_qpar" [Parameter "qper" 3.334248661038927 (Range (-1.0) 1.0),Parameter "qpar" 7.513639271725189e-3 (Range (-1.0) 1.0)] (Mode "qper_qpar" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "tth2" [Parameter "tth" 45.53874024285007 (Range (-180.0) 180.0),Parameter "alpha" 89.97807925598289 (Range (-180.0) 180.0)] (Mode "tth2" []),Engine "incidence" [Parameter "incidence" 22.771374111123095 (Range (-180.0) 180.0),Parameter "azimuth" 89.8380685773065 (Range (-180.0) 180.0)] (Mode "incidence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "emergence" [Parameter "emergence" 22.767244039797937 (Range (-180.0) 180.0),Parameter "azimuth" 89.8380685773065 (Range (-180.0) 180.0)] (Mode "emergence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)])]
      Geometry SOLEIL SIRIUS KAPPA (Source 1.4586370000000007e-9 m) (fromList [-0.5193202,64.64191214924969,133.78682078017752,-55.41938838621407,-2.23369e-2,62.132688461209455]) (Just [Parameter "mu" (-0.5193202) (Range (-180.0) 180.0),Parameter "komega" 64.64191214924969 (Range (-180.0) 180.0),Parameter "kappa" 133.78682078017752 (Range (-180.0) 180.0),Parameter "kphi" (-55.41938838621407) (Range (-180.0) 180.0),Parameter "delta" (-2.23369e-2) (Range (-180.0) 180.0),Parameter "gamma" 62.132688461209455 (Range (-180.0) 180.0)])
      [Engine "hkl" [Parameter "h" 9.177457430250849e-9 (Range (-1.0) 1.0),Parameter "k" 2.5693823994163015e-8 (Range (-1.0) 1.0),Parameter "l" 3.9999999929703476 (Range (-1.0) 1.0)] (Mode "bissector_vertical" []),Engine "eulerians" [Parameter "omega" 31.06634423136446 (Range (-180.0) 180.0),Parameter "chi" 89.5927920859556 (Range (-180.0) 180.0),Parameter "phi" 91.00504369590071 (Range (-180.0) 180.0)] (Mode "eulerians" [Parameter "solutions" 1.0 (Range 0.0 1.0)]),Engine "psi" [Parameter "psi" 154.51996903181714 (Range (-180.0) 180.0)] (Mode "psi_vertical_soleil_sirius_kappa" [Parameter "h2" 1.0 (Range (-1.0) 1.0),Parameter "k2" 1.0 (Range (-1.0) 1.0),Parameter "l2" 1.0 (Range (-1.0) 1.0)]),Engine "q2" [Parameter "q" 4.44567618639551 (Range 0.0 1.0),Parameter "alpha" 89.9881895320358 (Range (-180.0) 180.0)] (Mode "q2" []),Engine "qper_qpar" [Parameter "qper" 4.445664898550648 (Range (-1.0) 1.0),Parameter "qpar" 1.0018187400499787e-2 (Range (-1.0) 1.0)] (Mode "qper_qpar" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "tth2" [Parameter "tth" 62.13269076337942 (Range (-180.0) 180.0),Parameter "alpha" 89.9881895320358 (Range (-180.0) 180.0)] (Mode "tth2" []),Engine "incidence" [Parameter "incidence" 31.068363501362125 (Range (-180.0) 180.0),Parameter "azimuth" 89.83747231179481 (Range (-180.0) 180.0)] (Mode "incidence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "emergence" [Parameter "emergence" 31.064152026450454 (Range (-180.0) 180.0),Parameter "azimuth" 89.83747231179481 (Range (-180.0) 180.0)] (Mode "emergence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)])]
      Geometry SOLEIL SIRIUS KAPPA (Source 1.4586370000000007e-9 m) (fromList [-0.5193202,73.83399863752925,133.64586701159254,-55.35712475482595,-2.23369e-2,80.33702663350934]) (Just [Parameter "mu" (-0.5193202) (Range (-180.0) 180.0),Parameter "komega" 73.83399863752925 (Range (-180.0) 180.0),Parameter "kappa" 133.64586701159254 (Range (-180.0) 180.0),Parameter "kphi" (-55.35712475482595) (Range (-180.0) 180.0),Parameter "delta" (-2.23369e-2) (Range (-180.0) 180.0),Parameter "gamma" 80.33702663350934 (Range (-180.0) 180.0)])
      [Engine "hkl" [Parameter "h" 2.7577312257761425e-9 (Range (-1.0) 1.0),Parameter "k" 7.650403950118726e-9 (Range (-1.0) 1.0),Parameter "l" 4.999999999622215 (Range (-1.0) 1.0)] (Mode "bissector_vertical" []),Engine "eulerians" [Parameter "omega" 40.168513316578995 (Range (-180.0) 180.0),Parameter "chi" 89.53300638651663 (Range (-180.0) 180.0),Parameter "phi" 90.9773899242238 (Range (-180.0) 180.0)] (Mode "eulerians" [Parameter "solutions" 1.0 (Range 0.0 1.0)]),Engine "psi" [Parameter "psi" 154.50326819560394 (Range (-180.0) 180.0)] (Mode "psi_vertical_soleil_sirius_kappa" [Parameter "h2" 1.0 (Range (-1.0) 1.0),Parameter "k2" 1.0 (Range (-1.0) 1.0),Parameter "l2" 1.0 (Range (-1.0) 1.0)]),Engine "q2" [Parameter "q" 5.557095242340622 (Range 0.0 1.0),Parameter "alpha" 89.99619673890915 (Range (-180.0) 180.0)] (Mode "q2" []),Engine "qper_qpar" [Parameter "qper" 5.557081132533362 (Range (-1.0) 1.0),Parameter "qpar" 1.2522734784728349e-2 (Range (-1.0) 1.0)] (Mode "qper_qpar" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "tth2" [Parameter "tth" 80.33702737486469 (Range (-180.0) 180.0),Parameter "alpha" 89.99619673890915 (Range (-180.0) 180.0)] (Mode "tth2" []),Engine "incidence" [Parameter "incidence" 40.17045932119529 (Range (-180.0) 180.0),Parameter "azimuth" 89.82724901343079 (Range (-180.0) 180.0)] (Mode "incidence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "emergence" [Parameter "emergence" 40.16632251480728 (Range (-180.0) 180.0),Parameter "azimuth" 89.82724901343079 (Range (-180.0) 180.0)] (Mode "emergence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)])]
      Geometry SOLEIL SIRIUS KAPPA (Source 1.4586370000000007e-9 m) (fromList [-0.5193202,84.086619565407,134.11156620489382,125.37371040144704,-2.23369e-2,101.43713587367031]) (Just [Parameter "mu" (-0.5193202) (Range (-180.0) 180.0),Parameter "komega" 84.086619565407 (Range (-180.0) 180.0),Parameter "kappa" 134.11156620489382 (Range (-180.0) 180.0),Parameter "kphi" 125.37371040144704 (Range (-180.0) 180.0),Parameter "delta" (-2.23369e-2) (Range (-180.0) 180.0),Parameter "gamma" 101.43713587367031 (Range (-180.0) 180.0)])
      [Engine "hkl" [Parameter "h" 8.392762843275724e-10 (Range (-1.0) 1.0),Parameter "k" 2.459154264227675e-9 (Range (-1.0) 1.0),Parameter "l" 6.0000000015375905 (Range (-1.0) 1.0)] (Mode "bissector_vertical" []),Engine "eulerians" [Parameter "omega" 50.718567936651276 (Range (-180.0) 180.0),Parameter "chi" 89.72999512595882 (Range (-180.0) 180.0),Parameter "phi" 272.0056587726913 (Range (-180.0) 180.0)] (Mode "eulerians" [Parameter "solutions" 1.0 (Range 0.0 1.0)]),Engine "psi" [Parameter "psi" (-26.58708882570157) (Range (-180.0) 180.0)] (Mode "psi_vertical_soleil_sirius_kappa" [Parameter "h2" 1.0 (Range (-1.0) 1.0),Parameter "k2" 1.0 (Range (-1.0) 1.0),Parameter "l2" 1.0 (Range (-1.0) 1.0)]),Engine "q2" [Parameter "q" 6.668514293021504 (Range 0.0 1.0),Parameter "alpha" 90.00451897705055 (Range (-180.0) 180.0)] (Mode "q2" []),Engine "qper_qpar" [Parameter "qper" 6.6684973612522915 (Range (-1.0) 1.0),Parameter "qpar" (-1.5027281967821613e-2) (Range (-1.0) 1.0)] (Mode "qper_qpar" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "tth2" [Parameter "tth" 101.43713499280318 (Range (-180.0) 180.0),Parameter "alpha" 90.00451897705055 (Range (-180.0) 180.0)] (Mode "tth2" []),Engine "incidence" [Parameter "incidence" 50.71877816056822 (Range (-180.0) 180.0),Parameter "azimuth" 90.20844936572345 (Range (-180.0) 180.0)] (Mode "incidence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)]),Engine "emergence" [Parameter "emergence" 50.71800112341318 (Range (-180.0) 180.0),Parameter "azimuth" 90.20844936572345 (Range (-180.0) 180.0)] (Mode "emergence" [Parameter "x" 0.0 (Range (-1.0) 1.0),Parameter "y" 1.0 (Range (-1.0) 1.0),Parameter "z" 0.0 (Range (-1.0) 1.0)])
    #+END_SRC

    As we can see the phi and kphi motor switch from time to time to
    another solution which is at around 180° of the other solutions.

    #+CAPTION: plot the [0,0,1] -> [0,0,6] trajectory from two different starting point and different step size.
    [[./figures/sirius-s.svg]]

    #+CAPTION: plot the [0,0,1] -> [0,0,6] idem previous figure but move the diffractometer.
    [[./figures/sirius-m.svg]]

    #+CAPTION: zoom on the 2 solutions.
    [[./figures/sirius-m-zoom.svg]]

    #+CAPTION: plot the [0,0,1] -> [0,0,6]  for different number of steps
    [[./figures/traj_n.svg]]

*** TODO [0/2] PetraIII
**** TODO computation problem
     Dear Teresa,

     Using the prruptest.txt ubmatrix I see that the value of psi is
     offset by 45 degrees. I expect it to be 0 degrees when azimuth
     reference vector is 0 0 1 that is along the beam. See below
     thereturned numbers. This might have to do with the definition of
     the beam axis in the controller.  Otherwise now when I change
     reference vector by 90 degrees the computed value is changed by
     90 degrees. That is a progress. Can you contact Frederic and ask
     him about this ?

     Best regards,

     Sonia

     See below
     p09/door/haspp09.01 [9]: setaz 1 0 0

     p09/door/haspp09.01 [10]: wh

     Engine: hkl

     Mode: psi_constant_vertical

     H K L =    0.00000   3.00605  -0.00000
     Ref   =    1.00000   0.00000   0.00000
     Azimuth (Psi - calculated) =  -45.00005
     Azimuth (Psi - set) =  0.00000
     Wavelength =  2.07957

     Delta       Theta          Chi         Phi         Mu       Gamma
     45.77575    22.88783     90.00000   182.85400    0.00000    -0.00000

     p09/door/haspp09.01 [11]: setaz 0 0 1

     p09/door/haspp09.01 [12]: wh

     Engine: hkl

     Mode: psi_constant_vertical

     H K L =    0.00000   3.00605  -0.00000
     Ref   =    0.00000   0.00000   1.00000
     Azimuth (Psi - calculated) =  -135.00005
     Azimuth (Psi - set) =  0.00000
     Wavelength =  2.07957

     Delta       Theta          Chi         Phi         Mu       Gamma
     45.77575    22.88783     90.00000   182.85400    0.00000    -0.00000

     where:

     Azimuth (Psi - calculated) is the value of the pseudomotor psi.
     Azimuth (Psi - set) is the value set in the parameter psi of the current mode.

   Hi Frederic,

   This is the UB matrix:

   Best regards,

   Sonia

   Created at 2015-01-21 12:35

   Crystal    prruptest

   Wavelength 2.07957463938

   A 8.03656 B 8.03656 C 8.03656
   Alpha 90.0 Beta 90.0 Gamma 90.0

   R0 0 0.0 1.0 0.0 0 1 0.0 14.8979 90.0 182.854 0.0 29.7959
   R1 1 1.0 0.0 1.0 0 1 0.0 14.8979 0.0 182.854 0.0 29.7959

   Mode psi_constant_vertical

   PsiRef 0.0 0.0 1.0

   U00 -0.580 U01 0.000 U02 0.525
   U10 0.000 U11 0.782 U12 -0.000
   U20 -0.525 U21 -0.000 U22 -0.580

   Ux 179.999952315 Uy 42.14605 Uz -179.999932647

   SaveDirectory /home/p09user/crystals/

**** TODO another question
     J'ai un probleme avec la position que le controlleur calcule avec la
     matrice UB que nous t'avons envoye.
     See sequence of emails echanges avec Teresa.

     >>>> I am at 0 3.00605 0 with phi -182 and psi calculated is -135
     >>>> When I freeze psi at -135  and type ca 0 3.00605 0 the controller
     >> should return to me the positions at which I am. But no he tells me
     that I
     >> have to go to 178 degrees in  phi that is turning by 360 degrees.

     Est-ce un probleme avec la trajectoire selectionnee ?
     Est-ce qu'il est possible de definir des cut-points comme dans spec avec
     ta librairie ?
*** TODO [2/4] HklParameter
    - [X] method to use min/max to check for the validity
    - [X] add a method to get the axis_v and quaternion of the HklAxis
      this method will return NULL if this is not relevant.
      hkl_parameter_axis_v_get and hkl_parameter_quaternion_get
    - [ ] degenerated an axis is degenerated if its position have no
      effect on the HklPseudoAxis calculus. Add a degenerated member
      to the axis. that way it would be possible to check a posteriori
      for this degenerescencence.
    - [ ] Add a description for each parameters.
*** TODO This will help for the documentation and the gui.
*** TODO HklGeometryList different method to help select a solution.
    this select solution can depend on the geometry
    for example the kappa axis must be in one side of the plane.
*** TODO add a fit on the Hklaxis offsets.
*** TODO API to put a detector and a sample on the Geometry.
*** TODO HklSample
**** TODO [#B] unit test: hkl_sample_affine.
     Check this:
     lattice=1.540000;1.540000;1.540000;90.000000;90.000000;90.000000;0;0;0;0;0;0
     uxuyuz=0.000000;0.000000;0.000000
     reflection=1.540000;0.159010;1.256718;0.796660;1;0.000000;0.000000;0.000000;0.000000;0.000000
     reflection=1.540000;0.206208;0.342357;-0.080346;1;0.000000;0.000000;0.000000;0.000000;0.000000
     reflection=1.540000;0.206208;0.342357;-0.080346;1;0.000000;0.000000;0.000000;0.000000;0.000000

     A,  B, C, Alpha,  Beta, Gamma, Ux, Uy, Uy:
     17764892.133, 5793679.092, 15733785.198,  179.997,  179.999,452408725.23,  -575727594.04,  -1913661011.01 (affine) 1rst finetness

     all the reflections are non collinear the affine method should
     warn the user about this.
*** TODO HklEngine "zone"
*** TODO HklEngine "custom"
    for now this pseudoaxis let you select the axis you
    want to use for the computation.
*** TODO HklEngine "q/q2" add a "reflectivity" mode
    This mode should have the surface as parameters and the incident
    angle is equal to the emergence angle.
*** TODO create a macro to help compare two real the right way
    fabs(a-b) < epsilon * max(1, abs(a), abs(b))
*** TODO add an hkl_sample_set_lattice_unit()
*** TODO SOLEIL SIXS
**** DONE find the right solutions.                                   :zaxis:
     The cosinus and sinus properties are not enough to find the solution expected by the users.
     The idea is to use the Ewalds construction to generate a valid solution from the first one
     obtain numerically. The basic idea is to rotate the hkl vector around the last axis of the
     sample holder until it intersect again the Ewalds sphere. Then we just need to fit the
     detector position. This way the solution can be entirely generic (not geometry specific).
     Nevertheless it is necessary to propose this only for the hkl pseudo axes. I will add this
     special feature in the Mode. So it will be possible to add thoses special cases easily.
**** TODO Add the DEP diffractometer geometry
     This diffractometer is a Newport one based on the kappa 6 circles ones.
     But instead of a kappa head, they use an Hexapod head.
     This head can be put horizontally or vertically.
*** TODO generalisation of the z-axis hkl solver
    first we need the degenerated member of the Axis. thaht way it could be possible
    to find the last non degenerated axis for the detector fit.
*** TODO investigate the prigo geometry.
*** TODO augeas/elektra for the plugin configure part.
*** TODO logging
**** TODO [1/2] add in a few methods.
     + [X] hkl_pseudo_axes_values_set
     + [ ] hkl_sample_affine
**** TODO gir logging
     It would be nice to generate the library logging using the .gir
     information. So instead of writing the logging code for each
     method, it would be better to have a generic method for this
     purpose.
**** TODO parsable logging information.
     A parsable logging format would help to setup some re-play unit
     test. This way it could help during the developpement process
     (modification of the hkl internals) to be confident that
     computation are ok.
*** TODO performances
    + Investigate [[http://liboil.freedesktop.org/wiki/][liboil]] to speed calculation (in HklVector, HklMatrix
      and HklQuaternion)
    + Avoid to call =hkl_engine_prepare_internal= at each computation.

** documentation
*** TODO [1/6] rewrite documentation in org-mode
    - [-] embedding code into the org file
      - [-] [1/4] python
        - [X] auto generation of the diffractometer descriptions
        - [ ] trajectories explanations
        - [ ] trajectories tests.
        - [ ] unit tests output ?
      - [ ] asymptote
    - [X] need to check if templates could be generated using the hkl
      python binding for all diffractometer geometries.
    - [ ] need to add a description for the diffractometer, the mode, the parameters.
    - [ ] need a nice css for the generated doc.
    - [ ] check if org-info.js could be usefull
    - [ ] add documentation explaining the sector-cuts a la hkl
** [0/3] gui
   - [ ] change the color of fitparameter cells if they differ from
     the current sample values
   - [ ] check if a [[https://github.com/jonathanslenders/python-prompt-toolkit/tree/master/examples/tutorial][REPL]] could be integrated to provide an autocad
      like interface.
   - [ ] add tooltips using hkl_parameter_description_get for the
     pseudo axes and the mode parameters.
** hkl3d
*** TODO add a method to find the 3D models in the right directories.

** packaging
*** TODO add a .spec file for rpm generation.