-\title{Using FPGAs for high speed and real time cantilever deflection estimation}
+\title{A new approach based on least square methods to estimate in real time cantilevers deflection with a FPGA}
\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}
\begin{abstract}
-
+ Atomic force microscope (AFM) provides high resolution images of
+ surfaces. We focus our attention on an interferometry method to
+ estimate the cantilevers deflection. The initial method was based
+ on splines to determine the phase of interference fringes, and thus
+ the deflection. Computations were performed on a PC with LabView.
+ In this paper, we propose a new approach based on the least square
+ methods and its implementation that we developped on a FPGA, using
+ the pipelining technique. Simulations and real tests showed us that
+ this implementation is very efficient and should allow us to control
+ a cantilevers array in real time.
\end{abstract}
In this paper our attention is focused on a method based on interferometry to
measure cantilevers' displacements. In this method cantilevers are illuminated
-by an optic source. The interferometry produces fringes on each cantilevers
+by an optic source. The interferometry produces fringes on each cantilever
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}, the authors have used an algorithm based on
+cantilever. In~\cite{AFMCSEM11}, 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 overall process gives accurate results but all the computations
+are performed on a standard computer using LabView. Consequently, the
+main drawback of this implementation is that the computer is a
+bootleneck. 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
\section{Measurement principles}
\label{sec:measure}
-
-
-
-
-
-
-
\subsection{Architecture}
\label{sec:archi}
%% description de l'architecture générale de l'acquisition d'images
interferometry is sensitive to the optical path difference induced by the
vertical displacement of the cantilever.
-The system build by authors of~\cite{AFMCSEM11} has been developped based on a
-Linnick interferomter~\cite{Sinclair:05}. It is illustrated in
-Figure~\ref{fig:AFM}. A laser diode is first split (by the splitter) into a
-reference beam and a sample beam that reachs the cantilever array. In order to
-be able to move the cantilever array, it is mounted on a translation and
-rotational hexapod stage with five degrees of freedom. The optical system is
-also fixed to the stage. Thus, the cantilever array is centered in the optical
-system which can be adjusted accurately. The beam illuminates the array by a
-microscope objective and the light reflects on the cantilevers. Likewise the
-reference beam reflects on a movable mirror. A CMOS camera chip records the
-reference and sample beams which are recombined in the beam splitter and the
-interferogram. At the beginning of each experiment, the movable mirror is
-fitted manually in order to align the interferometric fringes approximately
-parallel to the cantilevers. When cantilevers move due to the surface, the
-bending of cantilevers produce movements in the fringes that can be detected
-with the CMOS camera. Finally the fringes need to be
-analyzed. In~\cite{AFMCSEM11}, the authors used a LabView program to compute the
-cantilevers' movements from the fringes.
+The system build by these authors is based on a Linnick
+interferomter~\cite{Sinclair:05}. It is illustrated in
+Figure~\ref{fig:AFM}. A laser diode is first split (by the splitter)
+into a reference beam and a sample beam that reachs the cantilever
+array. In order to be able to move the cantilever array, it is
+mounted on a translation and rotational hexapod stage with five
+degrees of freedom. The optical system is also fixed to the stage.
+Thus, the cantilever array is centered in the optical system which can
+be adjusted accurately. The beam illuminates the array by a
+microscope objective and the light reflects on the cantilevers.
+Likewise the reference beam reflects on a movable mirror. A CMOS
+camera chip records the reference and sample beams which are
+recombined in the beam splitter and the interferogram. At the
+beginning of each experiment, the movable mirror is fitted manually in
+order to align the interferometric fringes approximately parallel to
+the cantilevers. When cantilevers move due to the surface, the
+bending of cantilevers produce movements in the fringes that can be
+detected with the CMOS camera. Finally the fringes need to be
+analyzed. In~\cite{AFMCSEM11}, authors used a LabView program to
+compute the cantilevers' deflections from the fringes.
\begin{figure}
\begin{center}
\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.
+\begin{figure}
+\begin{center}
+\includegraphics[width=\columnwidth]{lever-xp}
+\end{center}
+\caption{Portion of an image picked by the camera}
+\label{fig:img-xp}
+\end{figure}
+
+As shown on image \ref{fig:img-xp}, each cantilever is covered by
+several interferometric fringes. The fringes will distort when
+cantilevers are deflected. Estimating the deflection is done by
+computing this distortion. For that, authors of \cite{AFMCSEM11}
+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
+the camera. These segments are large enough to cover several
+interferometric fringes. As said above, they 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:
tunnel. By default, the WEIM interface provides a clock signal at
100MHz that is connected to dedicated FPGA pins.
-The Spartan6 is an LX100 version. It has 15822 slices, equivalent to
-101261 logic cells. There are 268 internal block RAM of 18Kbits, and
-180 dedicated multiply-adders (named DSP48), which is largely enough
-for our project.
+The Spartan6 is an LX100 version. It has 15822 slices, each slice
+containing 4 LUTs and 8 flip/flops. It is equivalent to 101261 logic
+cells. There are 268 internal block RAM of 18Kbits, and 180 dedicated
+multiply-adders (named DSP48), which is largely enough for our
+project.
Some I/O pins of Spartan6 are connected to two $2\times 17$ headers
that can be used as user wants. For the project, they will be
classical least square method but suppose that frequency is already
known.
-\subsubsection{Spline algorithm}
+\subsubsection{Spline algorithm (SPL)}
\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 (SPL in the
-following) 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.
+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
computation of $\theta$.
\end{itemize}
-\subsubsection{Least square algorithm}
+\subsubsection{Least square algorithm (LSQ)}
Assuming that we compute the phase during the acquisition loop,
equation \ref{equ:profile} has only 4 parameters: $a, b, A$, and
\subsection{VHDL implementation}
+From the LSQ algorithm, we have written a C program that uses only
+integer values. We use a very simple quantization by multiplying
+double precision values by a power of two, keeping the integer
+part. For example, all values stored in lut$_s$, lut$_c$, $\ldots$ are
+scaled by 1024. Since LSQ also computes average, variance, ... to
+remove the slope, the result of implied euclidian divisions may be
+relatively wrong. To avoid that, we also scale the pixel intensities
+by a power of two. Futhermore, assuming $nb_s$ is fixed, these
+divisions have a known denominator. Thus, they can be replaced by
+their multiplication/shift counterpart. Finally, all other
+multiplications or divisions by a power of two have been replaced by
+left or right bit shifts. By the way, the code only contains
+additions, substractions and multiplications of signed integers, which
+is perfectly adapted to FGPAs.
+
+As said above, hardware constraints have a great influence on the VHDL
+implementation. Consequently, we searched the maximum value of each
+variable as a function of the different scale factors and the size of
+profiles, which gives their maximum size in bits. That size determines
+the maximum scale factors that allow to use the least possible RAMs
+and DSPs. Actually, we implemented our algorithm with this maximum
+size but current works study the impact of quantization on the results
+precision and design complexity. We have compared the result of the
+LSQ version using integers and doubles and observed that the precision
+of both were similar.
+
+Then we built two versions of VHDL codes: one directly by hand coding
+and the other with Matlab using the Simulink HDL coder
+feature~\cite{HDLCoder}. Although the approach is completely different
+we obtained VHDL codes that are quite comparable. Each approach has
+advantages and drawbacks. Roughly speaking, hand coding provides
+beautiful and much better structured code while Simulink allows to
+produce a code faster. In terms of throughput and latency,
+simulations shows that the two approaches are close with a slight
+advantage for hand coding. We hope that real experiments will confirm
+that.
+\subsection{Simulation}
-% - ecriture d'un code en C avec integer
-% - calcul de la taille max en bit de chaque variable en fonction de la quantization.
-% - tests de quantization : équilibre entre précision et contraintes FPGA
-% - en parallèle : simulink et VHDL à la main
+Before experimental tests on the board, we simulated our two VHDL
+codes with GHDL and GTKWave (two free tools with linux). For that, we
+build a testbench based on profiles taken from experimentations and
+compare the results to values given by the SPL algorithm. Both
+versions lead to correct results.
+Our first code were highly optimized : the pipeline could compute a
+new phase each 33 cycles and its latency was equal to 95 cycles. Since
+the Spartan6 is clocked at 100MHz, it implies that estimating the
+deflection of 100 cantilevers would take about $(95 + 200\times 33).10
+= 66.95\mu$s, i.e. nearly 15000 estimations by second.
-From the LSQ algorithm, we have written a C program which uses only integer
-values that have been previously scaled. The quantization of doubles into
-integers has been performed in order to obtain a good trade-off between the
-number of bits used and the precision. We have compared the result of
-the LSQ version using integers and doubles. We have observed that the results of
-both versions were similar.
+\subsection{Bitstream creation}
-Then we have built two versions of VHDL codes: one directly by hand coding and
-the other with Matlab using the Simulink HDL coder
-feature~\cite{HDLCoder}. Although the approach is completely different we have
-obtain VHDL codes that are quite comparable. Each approach has advantages and
-drawbacks. Roughly speaking, hand coding provides beautiful and much better
-structured code while HDL coder provides code faster. In terms of speed of
-code, we think that both approaches will be quite comparable with a slightly
-advantage for hand coding. We hope that real experiments will confirm that. In
-the LSQ algorithm, we have replaced all the divisions by multiplications by
-constants since divisions are performed with constants depending of the number
-of pixels in the profile (i.e. $M$).
+In order to test our code on the SP Vision board, the design was
+extended with a component that keeps profiles in RAM, flushes them in
+the phase computation component and stores its output in another
+RAM. We also added a wishbone : a component that can "drive" signals
+to communicate between i.MX and others components. It is mainly used
+to start to flush profiles and to retrieve the computed phases in RAM.
-\subsection{Simulation}
+Unfortunatly, the first designs could not be placed and route with ISE
+on the Spartan6 with a 100MHz clock. The main problems came from
+routing values from RAMs to DSPs and obtaining a result under 10ns. By
+the way, we needed to decompose some parts of the pipeline, which adds
+some cycles. For example, some delays have been introduced between
+RAMs output and DSPs. Finally, we obtained a bitstream that has a
+latency of 112 cycles and computes a new phase every 40 cycles. For
+100 cantilevers, it takes $(112 + 200\times 40).10 = 81.12\mu$s to
+compute their deflection.
-Currently, we have only simulated our VHDL codes with GHDL and GTKWave (two free
-tools with linux). Both approaches led to correct results. At the beginning of
-our simulations, our pipiline could compute a new phase each 33 cycles and the
-length of the pipeline was equal to 95 cycles. When we tried to generate the
-corresponding bitsream with ISE environment we had many problems because many
-stages required more than the 10$n$s required by the clock frequency. So we
-needed to decompose some part of the pipeline in order to add some cycles and
-simplify some parts between a clock top.
-% ghdl + gtkwave
-% au mieux : une phase tous les 33 cycles, latence de 95 cycles.
-% mais routage/placement impossible.
-\subsection{Bitstream creation}
+This bitstream has been successfully tested on the board TODAY ! YEAAHHHHH
-Currently both approaches provide synthesable bitstreams with ISE. We expect
-that the pipeline will have a latency of 112 cycles, i.e. 1.12$\mu$s and it
-could accept new profiles of pixel each 48 cycles, i.e. 480$n$s.
-% pas fait mais prévision d'une sortie tous les 480ns avec une latence de 1120
\label{sec:results}
\section{Conclusion and perspectives}
-
+In this paper we have presented a new method to estimate the
+cantilevers deflection in an AFM. This method is based on least
+square methods. We have used quantization to produce an algorithm
+based exclusively on integer values, which is adapted to a FPGA
+implementation. We obtained a precision on results similar to the
+initial version based on splines. Our solution has been implemented
+with a pipeline technique. Consequently, it enables to handle a new
+profile image very quickly. Currently we have performed simulations
+and real tests on a Spartan6 FPGA.
+
+In future work, we want to couple our algorithm with a high speed camera
+and we plan to control the whole AFM system.
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\bibliography{biblio}
