X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/dmems12.git/blobdiff_plain/e73cda1143a6ba97c0904b1811130d22ba7daaa8..8d8c7405f943188a7b597675cc8a23e95430b6d7:/dmems12.tex?ds=inline diff --git a/dmems12.tex b/dmems12.tex index f559661..701ce92 100644 --- a/dmems12.tex +++ b/dmems12.tex @@ -1,5 +1,5 @@ -\documentclass[10pt, conference, compsocconf]{IEEEtran} +\documentclass[10pt, peerreview, compsocconf]{IEEEtran} %\usepackage{latex8} %\usepackage{times} \usepackage[utf8]{inputenc} @@ -26,7 +26,6 @@ \newcommand{\tab}{\ \ \ } - \begin{document} @@ -58,7 +57,7 @@ -\maketitle +%\maketitle \thispagestyle{empty} @@ -66,25 +65,39 @@ -{\it keywords}: FPGA, cantilever, interferometry. + \end{abstract} +\begin{IEEEkeywords} +FPGA, cantilever, interferometry. +\end{IEEEkeywords} + + +\IEEEpeerreviewmaketitle + \section{Introduction} -Cantilevers are used inside atomic force microscope which provides high +Cantilevers are used inside atomic force microscope (AFM) 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 +determine accurately the deflection with different mechanisms. +In~\cite{CantiPiezzo01}, authors used piezoresistor integrated into the +cantilever. Nevertheless this approach suffers from the complexity of the +microfabrication process needed to implement the sensor in the cantilever. +In~\cite{CantiCapacitive03}, authors have presented an cantilever mechanism +based on capacitive sensing. This kind of technic also involves to instrument +the cantiliver which result in a complex fabrication process. + +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 +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 +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 @@ -105,12 +118,54 @@ presented. \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. +In order to develop simple, cost effective and user-friendly cantilever arrays, +authors of ~\cite{AFMCSEM11} have developped a system based of +interferometry. In opposition to other optical based systems, using a laser beam +deflection scheme and sentitive to the angular displacement of the cantilever, +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. + +\begin{figure} +\begin{center} +\includegraphics[width=\columnwidth]{AFM} +\end{center} +\caption{schema of the AFM} +\label{fig:AFM} +\end{figure} + + %% image tirée des expériences. \subsection{Cantilever deflection estimation} @@ -132,7 +187,7 @@ 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 : +The pixels intensity $I$ (in gray level) of each profile is modelized by: \begin{equation} \label{equ:profile} @@ -147,45 +202,158 @@ 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. +to obtain, after unwrapping, the deflection of +cantilevers. Originally, this computation was also done with an +algorithm based on spline. This article proposes a new version based +on a least square method. \subsection{Design goals} \label{sec:goals} +The main goal is to implement a computing unit to estimate the +deflection of about $10\times10$ cantilevers, faster than the stream of +images coming from the camera. The accuracy of results must be close +to the maximum precision ever obtained experimentally on the +architecture, i.e. 0.3nm. Finally, the latency between an image +entering in the unit and the deflections must be as small as possible +(NB: future works plan to add some control on the cantilevers).\\ + 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 +$1024\times 1204$ pixels seems the minimum that can be reached. For +100 cantilevers, 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. - - +E6650 at 2.33GHz, this program reaches an average of 155Mflops. + +%%Itimplies that the phase computation algorithm should not take more than +%%$155\times 12.5 = 1937$ floating operations. For integers, it gives $3000$ operations. + +Obviously, some cache effects and optimizations on +huge amount of computations can drastically increase these +performances: peak efficiency is about 2.5Gflops for the considered +CPU. But this is not the case for phase computation that used only few +tenth of values.\\ + +In order to evaluate the original algorithm, we translated it in C +language. As said further, for 20 pixels, it does about 1550 +operations, thus an estimated execution time of $1550/155 +=$10$\mu$s. For a more realistic evaluation, we constructed a file of +1Mo containing 200 profiles of 20 pixels, equally scattered. This file +is equivalent to an image stored in a device file representing the +camera. We obtained an average of 10.5$\mu$s by profile (including I/O +accesses). It is under are requirements but close to the limit. In +case of an occasional load of the system, it could be largely +overtaken. A solution would be to use a real-time operating system but +another one to search for a more efficient algorithm. + +But the main drawback is the latency of such a solution: since each +profile must be treated one after another, the deflection of 100 +cantilevers takes about $200\times 10.5 = 2.1$ms, which is inadequate +for an efficient control. An obvious solution is to parallelize the +computations, for example on a GPU. Nevertheless, the cost to transfer +profile in GPU memory and to take back results would be prohibitive +compared to computation time. It is certainly more efficient to +pipeline the computation. For example, supposing that 200 profiles of +20 pixels can be pushed sequentially in the pipelined unit cadenced at +a 100MHz (i.e. a pixel enters in the unit each 10ns), all profiles +would be treated in $200\times 20\times 10.10^{-9} =$ 40$\mu$s plus +the latency of the pipeline. This is about 500 times faster than +actual results.\\ + +For these reasons, an FPGA as the computation unit is the best choice +to achieve the required performance. Nevertheless, passing from +a C code to a pipelined version in VHDL is not obvious at all. As +explained in the next section, it can even be impossible because of +some hardware constraints specific to FPGAs. \section{Proposed solution} \label{sec:solus} - -\subsection{FPGA constraints} - -%% contraintes imposées par le FPGA : algo pipeline/parallele, pas d'op math complexe, ... - +Project Oscar aims to provide a hardware and software architecture to estimate +and control the deflection of cantilevers. The hardware part consists in a +high-speed camera, linked on an embedded board hosting FPGAs. By the way, the +camera output stream can be pushed directly into the FPGA. The software part is +mostly the VHDL code that deserializes the camera stream, extracts profile and +computes the deflection. Before focusing on our work to implement the phase +computation, we give some general information about FPGAs and the board we use. + +\subsection{FPGAs} + +A field-programmable gate array (FPGA) is an integrated circuit +designed to be configured by the customer. FGPAs are composed of +programmable logic components, called configurable logic blocks +(CLB). These blocks mainly contains look-up tables (LUT), flip/flops +(F/F) and latches, organized in one or more slices connected +together. Each CLB can be configured to perform simple (AND, XOR, ...) +or complex combinational functions. They are interconnected by +reconfigurable links. Modern FPGAs contain memory elements and +multipliers which enable to simplify the design and to increase the +performance. Nevertheless, all other complex operations, like +division, trigonometric functions, $\ldots$ are not available and must +be done by configuring a set of CLBs. Since this configuration is not +obvious at all, it can be done via a framework, like ISE. Such a +software can synthetize a design written in an hardware description +language (HDL), map it onto CLBs, place/route them for a specific +FPGA, and finally produce a bitstream that is used to configre the +FPGA. Thus, from the developper point of view, the main difficulty is +to translate an algorithm in HDL code, taking account FPGA resources +and constraints like clock signals and I/O values that drive the FPGA. + +Indeed, HDL programming is very different from classic languages like +C. A program can be seen as a state-machine, manipulating signals that +evolve from state to state. By the way, HDL instructions can execute +concurrently. Basic logic operations are used to agregate signals to +produce new states and assign it to another signal. States are mainly +expressed as arrays of bits. Fortunaltely, libraries propose some +higher levels representations like signed integers, and arithmetic +operations. + +Furthermore, even if FPGAs are cadenced more slowly than classic +processors, they can perform pipeline as well as parallel +operations. A pipeline consists in cutting a process in sequence of +small tasks, taking the same execution time. It accepts a new data at +each clock top, thus, after a known latency, it also provides a result +at each clock top. However, using a pipeline consumes more logics +since the components of a task are not reusable by another +one. Nevertheless it is probably the most efficient technique on +FPGA. Because of its architecture, it is also very easy to process +several data concurrently. When it is possible, the best performance +is reached using parallelism to handle simultaneously several +pipelines in order to handle multiple data streams. + +\subsection{The board} + +The board we use is designed by the Armadeus compagny, under the name +SP Vision. It consists in a development board hosting a i.MX27 ARM +processor (from Freescale). The board includes all classical +connectors: USB, Ethernet, ... A Flash memory contains a Linux kernel +that can be launched after booting the board via u-Boot. + +The processor is directly connected to a Spartan3A FPGA (from Xilinx) +via its special interface called WEIM. The Spartan3A is itself +connected to a Spartan6 FPGA. Thus, it is possible to develop programs +that communicate between i.MX and Spartan6, using Spartan3 as a +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. + +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 +connected to the interface card of the camera. \subsection{Considered algorithms} @@ -202,23 +370,23 @@ 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. +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. 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 : +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 : +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. @@ -231,9 +399,9 @@ Two things can be noticed : \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 +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 +least square method based on a Gauss-newton algorithm can 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. @@ -241,16 +409,16 @@ 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 : +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 $b$ : +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 : +Assuming an overlined symbol means an average, then: \[b = \overline{I(x^p)} - a.\overline{{x^p}}\] @@ -258,22 +426,22 @@ 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 : +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 : +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 : +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 $\theta$ : + not depend on $\theta$: \[ \sum_{i=0}^{M-1} sin(4\pi f.i), \sum_{i=0}^{M-1} cos(4\pi f.i) \] @@ -283,7 +451,7 @@ 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 : + also be computed before the loop: \[ sin \theta, cos \theta, \] @@ -293,7 +461,7 @@ computed. \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 : +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} @@ -380,7 +548,7 @@ Finally, the whole summarizes in an algorithm (called LSQ in the following) in t \subsubsection{Comparison} -We compared the two algorithms on the base of three criterions : +We compared the two algorithms on the base of three criteria: \begin{itemize} \item precision of results on a cosinus profile, distorted with noise, \item number of operations, @@ -399,12 +567,12 @@ 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 +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 = +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 $N$. @@ -446,7 +614,7 @@ largely beyond the worst experimental ones. \begin{figure}[ht] \begin{center} - \includegraphics[width=9cm]{intens-noise20-spl} + \includegraphics[width=\columnwidth]{intens-noise20} \end{center} \caption{Sample of worst profile for N=10} \label{fig:noise20} @@ -454,7 +622,7 @@ largely beyond the worst experimental ones. \begin{figure}[ht] \begin{center} - \includegraphics[width=9cm]{intens-noise60-lsq} + \includegraphics[width=\columnwidth]{intens-noise60} \end{center} \caption{Sample of worst profile for N=30} \label{fig:noise60} @@ -466,25 +634,76 @@ 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. +already in lookup tables and a limited set of operations (+, -, *, /, +$<$, $>$) is taken account. Translating the two algorithms in C code, we +obtain about 430 operations for LSQ and 1550 (plus few tenth for +$atan$) for SPL. This result is largely in favor of LSQ. Nevertheless, +considering the total number of operations is not really pertinent for +an FPGA implementation: it mainly depends on the type of operations +and their +ordering. The final decision is thus driven by the third criterion.\\ + +The Spartan 6 used in our architecture has hard constraint: it has no +built-in floating point units. Obviously, it is possible to use some +existing "black-boxes" for double precision operations. But they have +a quite long latency. It is much simpler to exclusively use integers, +with a quantization of all double precision values. Obviously, this +quantization should not decrease too much the precision of +results. Furthermore, it should not lead to a design with a huge +latency because of operations that could not complete during a single +or few clock cycles. Divisions are in this case and, moreover, they +need an varying number of clock cycles to complete. Even +multiplications can be a problem: DSP48 take inputs of 18 bits +maximum. For larger multiplications, several DSP must be combined, +increasing the latency. + +Nevertheless, the hardest constraint does not come from the FPGA +characteristics but from the algorithms. Their VHDL implentation will +be efficient only if they can be fully (or near) pipelined. By the +way, the choice is quickly done: only a small part of SPL can be. +Indeed, the computation of spline coefficients implies to solve a +tridiagonal system $A.m = b$. Values in $A$ and $b$ can be computed +from incoming pixels intensity but after, the back-solve starts with +the lastest values, which breaks the pipeline. Moreover, SPL relies on +interpolating far more points than profile size. Thus, the end +of SPL works on a larger amount of data than the beginning, which +also breaks the pipeline. + +LSQ has not this problem: all parts except the dichotomial search +work on the same amount of data, i.e. the profile size. Furthermore, +LSQ needs less operations than SPL, implying a smaller output +latency. Consequently, it is the best candidate for phase +computation. Nevertheless, obtaining a fully pipelined version +supposes that operations of different parts complete in a single clock +cycle. It is the case for simulations but it completely fails when +mapping and routing the design on the Spartan6. By the way, +extra-latency is generated and there must be idle times between two +profiles entering into the pipeline. + +%%Before obtaining the least bitstream, the crucial question is: how to +%%translate the C code the LSQ into VHDL ? + + +%\subsection{VHDL design paradigms} + +\section{Experimental tests} +\subsection{VHDL implementation} +% - 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 +% +\subsection{Simulation} -\subsection{VHDL design paradigms} +% ghdl + gtkwave +% au mieux : une phase tous les 33 cycles, latence de 95 cycles. +% mais routage/placement impossible. +\subsection{Bitstream creation} -\subsection{VHDL implementation} +% pas fait mais prévision d'une sortie tous les 480ns avec une latence de 1120 -\section{Experimental results} \label{sec:results}