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+\documentclass[10pt, conference, compsocconf]{IEEEtran}
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+\usepackage{amsmath}
+\usepackage{url}
+\usepackage{graphicx}
+\usepackage{thumbpdf}
+\usepackage{color}
+\usepackage{moreverb}
+\usepackage{commath}
+\usepackage{subfigure}
+%\input{psfig.sty}
+\usepackage{fullpage}
+\usepackage{fancybox}
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+\usepackage[ruled,lined,linesnumbered]{algorithm2e}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%% LyX specific LaTeX commands.
+\newcommand{\noun}[1]{\textsc{#1}}
+
+\newcommand{\tab}{\ \ \ }
+
+
\begin{document}
-blabla
+
+
+%% \author{\IEEEauthorblockN{Authors Name/s per 1st Affiliation (Author)}
+%% \IEEEauthorblockA{line 1 (of Affiliation): dept. name of organization\\
+%% line 2: name of organization, acronyms acceptable\\
+%% line 3: City, Country\\
+%% line 4: Email: name@xyz.com}
+%% \and
+%% \IEEEauthorblockN{Authors Name/s per 2nd Affiliation (Author)}
+%% \IEEEauthorblockA{line 1 (of Affiliation): dept. name of organization\\
+%% line 2: name of organization, acronyms acceptable\\
+%% line 3: City, Country\\
+%% line 4: Email: name@xyz.com}
+%% }
+
+
+
+\title{Using FPGAs for high speed and real time cantilever deflection estimation}
+\author{\IEEEauthorblockN{Raphaël Couturier\IEEEauthorrefmark{1}, Stéphane Domas\IEEEauthorrefmark{1}, Gwenhaël Goavec-Merou\IEEEauthorrefmark{2} and Michel Lenczner\IEEEauthorrefmark{2}}
+\IEEEauthorblockA{\IEEEauthorrefmark{1}FEMTO-ST, DISC, University of Franche-Comte, Belfort, France\\
+\{raphael.couturier,stephane.domas\}@univ-fcomte.fr}
+\IEEEauthorblockA{\IEEEauthorrefmark{2}FEMTO-ST, Time-Frequency, University of Franche-Comte, Besançon, France\\
+\{michel.lenczner@utbm.fr,gwenhael.goavec@trabucayre.com}
+}
+
+
+
+
+
+
+\maketitle
+
+\thispagestyle{empty}
+
+\begin{abstract}
+
+
+
+{\it keywords}: FPGA, cantilever, interferometry.
+\end{abstract}
+
+\section{Introduction}
+
+Cantilevers are used inside atomic force microscope which provides high
+resolution images of surfaces. Several technics have been used to measure the
+displacement of cantilevers in litterature. For example, it is possible to
+determine accurately the deflection with optic
+interferometer~\cite{CantiOptic89}, pizeoresistor~\cite{CantiPiezzo01} or
+capacitive sensing~\cite{CantiCapacitive03}. In this paper our attention is
+focused on a method based on interferometry to measure cantilevers'
+displacements. In this method cantilevers are illiminated by an optic
+source. The interferometry produces fringes on each cantilevers which enables to
+compute the cantilever displacement. In order to analyze the fringes a high
+speed camera is used. Images need to be processed quickly and then a estimation
+method is required to determine the displacement of each cantilever.
+In~\cite{AFMCSEM11} {\bf verifier ref}, the authors have used an algorithm based
+on spline to estimate the cantilevers' positions. The overall process gives
+accurate results but all the computation are performed on a standard computer
+using labview. Consequently, the main drawback of this implementation is that
+the computer is a bootleneck in the overall process. In this paper we propose to
+use a method based on least square and to implement all the computation on a
+FGPA.
+
+The remainder of the paper is organized as follows. Section~\ref{sec:measure}
+describes more precisely the measurement process. Our solution based on the
+least square method and the implementation on FPGA is presented in
+Section~\ref{sec:solus}. Experimentations are described in
+Section~\ref{sec:results}. Finally a conclusion and some perspectives are
+presented.
+
+
+
+%% quelques ref commentées sur les calculs basés sur l'interférométrie
+
+\section{Measurement principles}
+\label{sec:measure}
+
+\subsection{Architecture}
+\label{sec:archi}
+%% description de l'architecture générale de l'acquisition d'images
+%% avec au milieu une unité de traitement dont on ne précise pas ce
+%% qu'elle est.
+
+%% image tirée des expériences.
+
+\subsection{Cantilever deflection estimation}
+\label{sec:deflest}
+
+As shown on image \ref{img:img-xp}, each cantilever is covered by
+interferometric fringes. The fringes will distort when cantilevers are
+deflected. Estimating the deflection is done by computing this
+distortion. For that, (ref A. Meister + M Favre) proposed a method
+based on computing the phase of the fringes, at the base of each
+cantilever, near the tip, and on the base of the array. They assume
+that a linear relation binds these phases, which can be use to
+"unwrap" the phase at the tip and to determine the deflection.\\
+
+More precisely, segment of pixels are extracted from images taken by a
+high-speed camera. These segments are large enough to cover several
+interferometric fringes and are placed at the base and near the tip of
+the cantilevers. They are called base profile and tip profile in the
+following. Furthermore, a reference profile is taken on the base of
+the cantilever array.
+
+The pixels intensity $I$ (in gray level) of each profile is modelized by :
+
+\begin{equation}
+\label{equ:profile}
+I(x) = ax+b+A.cos(2\pi f.x + \theta)
+\end{equation}
+
+where $x$ is the position of a pixel in its associated segment.
+
+The global method consists in two main sequences. The first one aims
+to determin the frequency $f$ of each profile with an algorithm based
+on spline interpolation (see section \ref{algo-spline}). It also
+computes the coefficient used for unwrapping the phase. The second one
+is the acquisition loop, while which images are taken at regular time
+steps. For each image, the phase $\theta$ of all profiles is computed
+to obtain, after unwrapping, the deflection of cantilevers.
+
+\subsection{Design goals}
+\label{sec:goals}
+
+If we put aside some hardware issues like the speed of the link
+between the camera and the computation unit, the time to deserialize
+pixels and to store them in memory, ... the phase computation is
+obviously the bottle-neck of the whole process. For example, if we
+consider the camera actually in use, an exposition time of 2.5ms for
+$1024\times 1204$ pixels seems the minimum that can be reached. For a
+$10\times 10$ cantilever array, if we neglect the time to extract
+pixels, it implies that computing the deflection of a single
+cantilever should take less than 25$\mu$s, thus 12.5$\mu$s by phase.\\
+
+In fact, this timing is a very hard constraint. Let consider a very
+small programm that initializes twenty million of doubles in memory
+and then does 1000000 cumulated sums on 20 contiguous values
+(experimental profiles have about this size). On an intel Core 2 Duo
+E6650 at 2.33GHz, this program reaches an average of 155Mflops. It
+implies that the phase computation algorithm should not take more than
+$240\times 12.5 = 1937$ floating operations. For integers, it gives
+$3000$ operations.
+
+%% to be continued ...
+
+%% � faire : timing de l'algo spline en C avec atan et tout le bordel.
+
+
+
+
+\section{Proposed solution}
+\label{sec:solus}
+
+
+\subsection{FPGA constraints}
+
+%% contraintes imposées par le FPGA : algo pipeline/parallele, pas d'op math complexe, ...
+
+
+\subsection{Considered algorithms}
+
+Two solutions have been studied to achieve phase computation. The
+original one, proposed by A. Meister and M. Favre, is based on
+interpolation by splines. It allows to compute frequency and
+phase. The second one, detailed in this article, is based on a
+classical least square method but suppose that frequency is already
+known.
+
+\subsubsection{Spline algorithm}
+\label{sec:algo-spline}
+Let consider a profile $P$, that is a segment of $M$ pixels with an
+intensity in gray levels. Let call $I(x)$ the intensity of profile in $x
+\in [0,M[$.
+
+At first, only $M$ values of $I$ are known, for $x = 0, 1,
+\ldots,M-1$. A normalisation allows to scale known intensities into
+$[-1,1]$. We compute splines that fit at best these normalised
+intensities. Splines are used to interpolate $N = k\times M$ points
+(typically $k=4$ is sufficient), within $[0,M[$. Let call $x^s$ the
+coordinates of these $N$ points and $I^s$ their intensities.
+
+In order to have the frequency, the mean line $a.x+b$ (see equation \ref{equ:profile}) of $I^s$ is
+computed. Finding intersections of $I^s$ and this line allow to obtain
+the period thus the frequency.
+
+The phase is computed via the equation :
+\begin{equation}
+\theta = atan \left[ \frac{\sum_{i=0}^{N-1} sin(2\pi f x^s_i) \times I^s(x^s_i)}{\sum_{i=0}^{N-1} cos(2\pi f x^s_i) \times I^s(x^s_i)} \right]
+\end{equation}
+
+Two things can be noticed :
+\begin{itemize}
+\item the frequency could also be obtained using the derivates of
+ spline equations, which only implies to solve quadratic equations.
+\item frequency of each profile is computed a single time, before the
+ acquisition loop. Thus, $sin(2\pi f x^s_i)$ and $cos(2\pi f x^s_i)$
+ could also be computed before the loop, which leads to a much faster
+ computation of $\theta$.
+\end{itemize}
+
+\subsubsection{Least square algorithm}
+
+Assuming that we compute the phase during the acquisition loop,
+equation \ref{equ:profile} has only 4 parameters :$a, b, A$, and
+$\theta$, $f$ and $x$ being already known. Since $I$ is non-linear, a
+least square method based an Gauss-newton algorithm must be used to
+determine these four parameters. Since it is an iterative process
+ending with a convergence criterion, it is obvious that it is not
+particularly adapted to our design goals.
+
+Fortunatly, it is quite simple to reduce the number of parameters to
+only $\theta$. Let $x^p$ be the coordinates of pixels in a segment of
+size $M$. Thus, $x^p = 0, 1, \ldots, M-1$. Let $I(x^p)$ be their
+intensity. Firstly, we "remove" the slope by computing :
+
+\[I^{corr}(x^p) = I(x^p) - a.x^p - b\]
+
+Since linear equation coefficients are searched, a classical least
+square method can be used to determine $a$ and $b$ :
+
+\[a = \frac{covar(x^p,I(x^p))}{var(x^p)} \]
+
+Assuming an overlined symbol means an average, then :
+
+\[b = \overline{I(x^p)} - a.\overline{{x^p}}\]
+
+Let $A$ be the amplitude of $I^{corr}$, i.e.
+
+\[A = \frac{max(I^{corr}) - min(I^{corr})}{2}\]
+
+Then, the least square method to find $\theta$ is reduced to search the minimum of :
+
+\[\sum_{i=0}^{M-1} \left[ cos(2\pi f.i + \theta) - \frac{I^{corr}(i)}{A} \right]^2\]
+
+It is equivalent to derivate this expression and to solve the following equation :
+
+\begin{eqnarray*}
+2\left[ cos\theta \sum_{i=0}^{M-1} I^{corr}(i).sin(2\pi f.i) + sin\theta \sum_{i=0}^{M-1} I^{corr}(i).cos(2\pi f.i)\right] \\
+- A\left[ cos2\theta \sum_{i=0}^{M-1} sin(4\pi f.i) + sin2\theta \sum_{i=0}^{M-1} cos(4\pi f.i)\right] = 0
+\end{eqnarray*}
+
+Several points can be noticed :
+\begin{itemize}
+\item As in the spline method, some parts of this equation can be
+ computed before the acquisition loop. It is the case of sums that do
+ not depend on $\theta$ :
+
+\[ \sum_{i=0}^{M-1} sin(4\pi f.i), \sum_{i=0}^{M-1} cos(4\pi f.i) \]
+
+\item Lookup tables for $sin(2\pi f.i)$ and $cos(2\pi f.i)$ can also be
+computed.
+
+\item The simplest method to find the good $\theta$ is to discretize
+ $[-\pi,\pi]$ in $nb_s$ steps, and to search which step leads to the
+ result closest to zero. By the way, three other lookup tables can
+ also be computed before the loop :
+
+\[ sin \theta, cos \theta, \]
+
+\[ \left[ cos 2\theta \sum_{i=0}^{M-1} sin(4\pi f.i) + sin 2\theta \sum_{i=0}^{M-1} cos(4\pi f.i)\right] \]
+
+\item This search can be very fast using a dichotomous process in $log_2(nb_s)$
+
+\end{itemize}
+
+Finally, the whole summarizes in an algorithm (called LSQ in the following) in two parts, one before and one during the acquisition loop :
+\begin{algorithm}[h]
+\caption{LSQ algorithm - before acquisition loop.}
+\label{alg:lsq-before}
+
+ $M \leftarrow $ number of pixels of the profile\\
+ I[] $\leftarrow $ intensities of pixels\\
+ $f \leftarrow $ frequency of the profile\\
+ $s4i \leftarrow \sum_{i=0}^{M-1} sin(4\pi f.i)$\\
+ $c4i \leftarrow \sum_{i=0}^{M-1} cos(4\pi f.i)$\\
+ $nb_s \leftarrow $ number of discretization steps of $[-\pi,\pi]$\\
+
+ \For{$i=0$ to $nb_s $}{
+ $\theta \leftarrow -\pi + 2\pi\times \frac{i}{nb_s}$\\
+ lut$_s$[$i$] $\leftarrow sin \theta$\\
+ lut$_c$[$i$] $\leftarrow cos \theta$\\
+ lut$_A$[$i$] $\leftarrow cos 2 \theta \times s4i + sin 2 \theta \times c4i$\\
+ lut$_{sfi}$[$i$] $\leftarrow sin (2\pi f.i)$\\
+ lut$_{cfi}$[$i$] $\leftarrow cos (2\pi f.i)$\\
+ }
+\end{algorithm}
+
+\begin{algorithm}[ht]
+\caption{LSQ algorithm - during acquisition loop.}
+\label{alg:lsq-during}
+
+ $\bar{x} \leftarrow \frac{M-1}{2}$\\
+ $\bar{y} \leftarrow 0$, $x_{var} \leftarrow 0$, $xy_{covar} \leftarrow 0$\\
+ \For{$i=0$ to $M-1$}{
+ $\bar{y} \leftarrow \bar{y} + $ I[$i$]\\
+ $x_{var} \leftarrow x_{var} + (i-\bar{x})^2$\\
+ }
+ $\bar{y} \leftarrow \frac{\bar{y}}{M}$\\
+ \For{$i=0$ to $M-1$}{
+ $xy_{covar} \leftarrow xy_{covar} + (i-\bar{x}) \times (I[i]-\bar{y})$\\
+ }
+ $slope \leftarrow \frac{xy_{covar}}{x_{var}}$\\
+ $start \leftarrow y_{moy} - slope\times \bar{x}$\\
+ \For{$i=0$ to $M-1$}{
+ $I[i] \leftarrow I[i] - start - slope\times i$\\
+ }
+
+ $I_{max} \leftarrow max_i(I[i])$, $I_{min} \leftarrow min_i(I[i])$\\
+ $amp \leftarrow \frac{I_{max}-I_{min}}{2}$\\
+
+ $Is \leftarrow 0$, $Ic \leftarrow 0$\\
+ \For{$i=0$ to $M-1$}{
+ $Is \leftarrow Is + I[i]\times $ lut$_{sfi}$[$i$]\\
+ $Ic \leftarrow Ic + I[i]\times $ lut$_{cfi}$[$i$]\\
+ }
+
+ $\delta \leftarrow \frac{nb_s}{2}$, $b_l \leftarrow 0$, $b_r \leftarrow \delta$\\
+ $v_l \leftarrow -2.I_s - amp.$lut$_A$[$b_l$]\\
+
+ \While{$\delta >= 1$}{
+
+ $v_r \leftarrow 2.[ Is.$lut$_c$[$b_r$]$ + Ic.$lut$_s$[$b_r$]$ ] - amp.$lut$_A$[$b_r$]\\
+
+ \If{$!(v_l < 0$ and $v_r >= 0)$}{
+ $v_l \leftarrow v_r$ \\
+ $b_l \leftarrow b_r$ \\
+ }
+ $\delta \leftarrow \frac{\delta}{2}$\\
+ $b_r \leftarrow b_l + \delta$\\
+ }
+ \uIf{$!(v_l < 0$ and $v_r >= 0)$}{
+ $v_l \leftarrow v_r$ \\
+ $b_l \leftarrow b_r$ \\
+ $b_r \leftarrow b_l + 1$\\
+ $v_r \leftarrow 2.[ Is.$lut$_c$[$b_r$]$ + Ic.$lut$_s$[$b_r$]$ ] - amp.$lut$_A$[$b_r$]\\
+ }
+ \Else {
+ $b_r \leftarrow b_l + 1$\\
+ }
+
+ \uIf{$ abs(v_l) < v_r$}{
+ $b_{\theta} \leftarrow b_l$ \\
+ }
+ \Else {
+ $b_{\theta} \leftarrow b_r$ \\
+ }
+ $\theta \leftarrow \pi\times \left[\frac{2.b_{ref}}{nb_s}-1\right]$\\
+
+\end{algorithm}
+
+\subsubsection{Comparison}
+
+We compared the two algorithms on the base of three criterions :
+\begin{itemize}
+\item precision of results on a cosinus profile, distorted with noise,
+\item number of operations,
+\item complexity to implement an FPGA version.
+\end{itemize}
+
+For the first item, we produced a matlab version of each algorithm,
+running with double precision values. The profile was generated for
+about 34000 different values of period ($\in [3.1, 6.1]$, step = 0.1),
+phase ($\in [-3.1 , 3.1]$, step = 0.062) and slope ($\in [-2 , 2]$,
+step = 0.4). For LSQ, $nb_s = 1024$, which leads to a maximal error of
+$\frac{\pi}{1024}$ on phase computation. Current A. Meister and
+M. Favre experiments show a ratio of 50 between variation of phase and
+the deflection of a lever. Thus, the maximal error due to
+discretization correspond to an error of 0.15nm on the lever
+deflection, which is smaller than the best precision they achieved,
+i.e. 0.3nm.
+
+For each test, we add some noise to the profile : each group of two
+pixels has its intensity added to a random number picked in $[-N,N]$
+(NB: it should be noticed that picking a new value for each pixel does
+not distort enough the profile). The absolute error on the result is
+evaluated by comparing the difference between the reference and
+computed phase, out of $2\pi$, expressed in percents. That is : $err =
+100\times \frac{|\theta_{ref} - \theta_{comp}|}{2\pi}$.
+
+Table \ref{tab:algo_prec} gives the maximum and average error for the two algorithms and increasing values of $N$.
+
+\begin{table}[ht]
+ \begin{center}
+ \begin{tabular}{|c|c|c|c|c|}
+ \hline
+ & \multicolumn{2}{c|}{SPL} & \multicolumn{2}{c|}{LSQ} \\ \cline{2-5}
+ noise & max. err. & aver. err. & max. err. & aver. err. \\ \hline
+ 0 & 2.46 & 0.58 & 0.49 & 0.1 \\ \hline
+ 2.5 & 2.75 & 0.62 & 1.16 & 0.22 \\ \hline
+ 5 & 3.77 & 0.72 & 2.47 & 0.41 \\ \hline
+ 7.5 & 4.72 & 0.86 & 3.33 & 0.62 \\ \hline
+ 10 & 5.62 & 1.03 & 4.29 & 0.81 \\ \hline
+ 15 & 7.96 & 1.38 & 6.35 & 1.21 \\ \hline
+ 30 & 17.06 & 2.6 & 13.94 & 2.45 \\ \hline
+
+\end{tabular}
+\caption{Error (in \%) for cosinus profiles, with noise.}
+\label{tab:algo_prec}
+\end{center}
+\end{table}
+
+These results show that the two algorithms are very close, with a
+slight advantage for LSQ. Furthemore, both behave very well against
+noise. Assuming the experimental ratio of 50 (see above), an error of
+1 percent on phase correspond to an error of 0.5nm on the lever
+deflection, which is very close to the best precision.
+
+Obviously, it is very hard to predict which level of noise will be
+present in real experiments and how it will distort the
+profiles. Nevertheless, we can see on figure \ref{fig:noise20} the
+profile with $N=10$ that leads to the biggest error. It is a bit
+distorted, with pikes and straight/rounded portions, and relatively
+close to most of that come from experiments. Figure \ref{fig:noise60}
+shows a sample of worst profile for $N=30$. It is completly distorted,
+largely beyond the worst experimental ones.
+
+\begin{figure}[ht]
+\begin{center}
+ \includegraphics[width=9cm]{intens-noise20-spl}
+\end{center}
+\caption{Sample of worst profile for N=10}
+\label{fig:noise20}
+\end{figure}
+
+\begin{figure}[ht]
+\begin{center}
+ \includegraphics[width=9cm]{intens-noise60-lsq}
+\end{center}
+\caption{Sample of worst profile for N=30}
+\label{fig:noise60}
+\end{figure}
+
+The second criterion is relatively easy to estimate for LSQ and harder
+for SPL because of $atan$ operation. In both cases, it is proportional
+to numbers of pixels $M$. For LSQ, it also depends on $nb_s$ and for
+SPL on $N = k\times M$, i.e. the number of interpolated points.
+
+We assume that $M=20$, $nb_s=1024$, $k=4$, all possible parts are
+already in lookup tables and only arithmetic operations (+, -, *, /)
+are taken account. Translating the two algorithms in C code, we obtain
+about 400 operations for LSQ and 1340 (plus the unknown for $atan$)
+for SPL. Even if the result is largely in favor of LSQ, we can notice
+that executing the C code (compiled with \tt{-O3}) of SPL on an
+2.33GHz Core 2 Duo only takes 6.5µs in average, which is under our
+desing goals. The final decision is thus driven by the third criterion.\\
+
+The Spartan 6 used in our architecture has hard constraint : it has no
+floating point units. Thus, all computations have to be done with
+integers.
+
+
+
+\subsection{VHDL design paradigms}
+
+\subsection{VHDL implementation}
+
+\section{Experimental results}
+\label{sec:results}
+
+
+
+
+\section{Conclusion and perspectives}
+
+
+\bibliographystyle{plain}
+\bibliography{biblio}
+
\end{document}
