relecture anglais

[dmems12.git] / dmems12.tex

diff --git a/dmems12.tex b/dmems12.tex
index c5ee6cf6f77386663b9f5a6e2b1737f43f834c72..fb6d7d0a61c8bd5006735c3b81936e6ef0805b1f 100644 (file)
--- a/dmems12.tex
+++ b/dmems12.tex
@@ -63,15 +63,15 @@
 
 \begin{abstract}
 
 
 \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.   This method  was based  on the  spline method  to  interpolate the
-deflection and  the computations were performed  on a PC with  LabView.  In this
-paper, we propose a  new method based on the least square  method and we present
-the implementation that we developped on a FPGA.  Our method can be pipelined on
-a FPGA in order to manipulate image profiles very quickly.  Simulations and real
-tests we have performed showed us that this implementation is very efficient and
-should allow us to control of a cantilevers array in real time.
+Atomics force  microscope (AFM) provide  high resolution images of  surfaces. In
+this paper, 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.  Here,  we propose a new approach  based on the
+least square  methods and its implementation  that we have developed  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}
 
 
 \end{abstract}


@@ -85,31 +85,31 @@ FPGA, cantilever, interferometry.
 
 \section{Introduction}
 
 
 \section{Introduction}
 

-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 different  mechanisms. 
+Cantilevers are  used inside atomic  force microscopes (AFM) which  provide high
+resolution images of surfaces.  Several techniques have been used to measure the
+displacement  of cantilevers  in literature.   For  example, it  is possible  to
+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{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~\cite{CantiCapacitive03},  authors  have  presented a  cantilever  mechanism
+based on capacitive sensing. This  kind of technique also involves to instrument
+the cantilever which results 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
 
 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 cantilever
-which enables to  compute the cantilever displacement.  In  order to analyze the
+by an optic source. The interferometry produces fringes on each cantilever which
+enables  us to compute  the cantilever  displacement.  In  order to  analyze the

 fringes a  high speed camera  is used. Images  need to be processed  quickly and
 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},  authors have  used an algorithm  based on
-spline to estimate the cantilevers' positions.
+then  an estimation method  is required  to determine  the displacement  of each
+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 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  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 bottleneck. In  this paper we
+propose  to use  a  method  based on  least  squares and  to  implement all  the
+computation on a FPGA.

 
 The remainder  of the paper  is organized as  follows. Section~\ref{sec:measure}
 describes  more precisely  the measurement  process. Our  solution based  on the
 
 The remainder  of the paper  is organized as  follows. Section~\ref{sec:measure}
 describes  more precisely  the measurement  process. Our  solution based  on the


@@ -120,44 +120,39 @@ presented.
 
 
 
 
 
 

-%% quelques ref commentées sur les calculs basés sur l'interférométrie
+

 
 \section{Measurement principles}
 \label{sec:measure}
 
 \subsection{Architecture}
 \label{sec:archi}
 
 \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,
 
 In order to develop simple,  cost effective and user-friendly cantilever arrays,

-authors   of    ~\cite{AFMCSEM11}   have   developped   a    system   based   of
+authors   of    ~\cite{AFMCSEM11}   have   developed   a    system   based   on

 interferometry. In opposition to other optical based systems, using a laser beam
 interferometry. In opposition to other optical based systems, using a laser beam

-deflection scheme and  sentitive to the angular displacement  of the cantilever,
+deflection scheme and  sensitive to the angular displacement  of the cantilever,

 interferometry  is sensitive  to  the  optical path  difference  induced by  the
 vertical displacement of the cantilever.
 
 interferometry  is sensitive  to  the  optical path  difference  induced by  the
 vertical displacement of the cantilever.
 

-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.
+The    system   built    by   these    authors   is    based   on    a   Linnick
+interferometer~\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 reach 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}
 
 \begin{figure}    
 \begin{center}


@@ -188,9 +183,9 @@ 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
 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.\\
+can be used to "unwrap" the phase at the tip and to determine the deflection.\\

 
 

-More precisely, segment of pixels are extracted from images taken by
+More precisely, segments 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
 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


@@ -207,10 +202,10 @@ I(x) = ax+b+A.cos(2\pi f.x + \theta)
 where $x$ is the position of a pixel in its associated segment.
 
 The global method consists in two main sequences. The first one aims
 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
+to determine the frequency $f$ of each profile with an algorithm based
+on spline interpolation (see section \ref{sec:algo-spline}). It also

 computes the coefficient used for unwrapping the phase. The second one
 computes the coefficient used for unwrapping the phase. The second one

-is the acquisition loop, while which images are taken at regular time
+is the acquisition loop, during 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. Originally, this computation was also done with an
 steps. For each image, the phase $\theta$ of all profiles is computed
 to obtain, after unwrapping, the deflection of
 cantilevers. Originally, this computation was also done with an


@@ -238,9 +233,9 @@ $1024\times 1204$ pixels seems the minimum that can be reached. For
 that computing the deflection of a single
 cantilever should take less than 25$\mu$s, thus 12.5$\mu$s by phase.\\
 
 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
+In fact, this timing is a very hard constraint. Let us consider a very
+small program that initializes twenty million of doubles in memory
+and then does 1,000,000 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. 
 
 (experimental profiles have about this size). On an intel Core 2 Duo
 E6650 at 2.33GHz, this program reaches an average of 155Mflops. 
 


@@ -250,17 +245,17 @@ E6650 at 2.33GHz, this program reaches an average of 155Mflops.
 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
 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
+CPU. But this is not the case for phase computation that used only a few

 tenth of values.\\
 
 In order to evaluate the original algorithm, we translated it in C
 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
+language. As stated before, for 20 pixels, it does about 1,550
+operations, thus an estimated execution time of $1,550/155

 =$10$\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
 =$10$\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
+accesses). It is under our 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.
 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.


@@ -269,8 +264,8 @@ 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
 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
+computations, for example on a GPU. Nevertheless, the cost of transferring
+profile in GPU memory and of taking 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
 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


@@ -279,7 +274,7 @@ 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.\\
 
 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
+For these reasons, a 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
 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


@@ -291,7 +286,7 @@ some hardware constraints specific to FPGAs.
 
 Project Oscar aims  to provide a hardware and  software architecture to estimate
 and  control the  deflection of  cantilevers. The  hardware part  consists  in a
 
 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
+high-speed camera, linked  on an embedded board hosting FPGAs.  In this 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
 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


@@ -301,47 +296,47 @@ computation, we give some general information about FPGAs and the board we use.
 
 A field-programmable gate  array (FPGA) is an integrated  circuit designed to be
 configured by the customer. FGPAs are composed of programmable logic components,
 
 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
+called  configurable logic  blocks (CLB).  These blocks  mainly  contain 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, ...)
 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
+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
 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
+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
 configuration  is not  obvious at  all, it  can be  done via  a  framework, like

-ISE~\cite{ISE}. Such  a software  can synthetize a  design written in  a hardware
+ISE~\cite{ISE}. Such  a software can synthetize  a design written  in a hardware

 description language  (HDL), map it onto  CLBs, place/route them  for a specific
 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.
+FPGA, and finally produce a bitstream  that is used to configure the FPGA. Thus,
+from  the developer's  point of  view, the  main difficulty  is to  translate an
+algorithm in HDL  code, taking into 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
 
 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
+evolve from state to state. Moreover, HDL instructions can executed
+concurrently. Basic logic operations are used to aggregate signals to

 produce new states and assign it to another signal. States are mainly
 produce new states and assign it to another signal. States are mainly

-expressed as arrays of bits. Fortunaltely, libraries propose some
+expressed as arrays of bits. Fortunately, 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
 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
+operations. A pipeline consists in cutting a process in a 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
 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
+several data concurrently. Whenever possible, the best performance

 is reached using parallelism to handle simultaneously several
 pipelines in order to handle multiple data streams.
 
 \subsection{The board}
 
 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
+The board we use is designed by the Armadeus company, 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
 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


@@ -370,25 +365,25 @@ 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
 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
+classical least square method which supposes that the frequency is already

 known.
 
 \subsubsection{Spline algorithm (SPL)}
 \label{sec:algo-spline}
 known.
 
 \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
+Let us consider a profile $P$, that is a segment of $M$ pixels with an
+intensity in gray levels. Let us call $I(x)$ the intensity of profile in $x

 \in [0,M[$. 
 
 At first, only $M$ values of $I$ are known, for $x = 0, 1,
 \in [0,M[$. 
 
 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]$. We compute splines that fit at best these normalised
+\ldots,M-1$. A normalization allows to scale known intensities into
+$[-1,1]$. We compute splines that fit at best these normalized

 intensities. Splines are used to interpolate $N = k\times M$ points
 intensities. Splines are used to interpolate $N = k\times M$ points

-(typically $k=4$ is sufficient), within $[0,M[$. Let call $x^s$ the
+(typically $k=4$ is sufficient), within $[0,M[$. Let  $x^s$ be 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
 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.
+computed. Finding intersections of $I^s$ and this line allows us to obtain
+the period and thus the frequency.

 
 The phase is computed via the equation:
 \begin{equation}
 
 The phase is computed via the equation:
 \begin{equation}


@@ -399,9 +394,9 @@ 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.
 \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
+\item frequency of each profile is computed only once, before the

   acquisition loop. Thus, $sin(2\pi f x^s_i)$ and $cos(2\pi f x^s_i)$
   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
+  could also be computed before the loop, which would lead to a much faster

   computation of $\theta$.
 \end{itemize}
 
   computation of $\theta$.
 \end{itemize}
 


@@ -415,7 +410,7 @@ 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.
 
 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
+Fortunately, 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:
 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:


@@ -439,12 +434,15 @@ Then, the least square method to find $\theta$ is reduced to search the minimum
 
 \[\sum_{i=0}^{M-1} \left[ cos(2\pi f.i + \theta) - \frac{I^{corr}(i)}{A} \right]^2\]
 
 
 \[\sum_{i=0}^{M-1} \left[ cos(2\pi f.i + \theta) - \frac{I^{corr}(i)}{A} \right]^2\]
 

-It is equivalent to derivate this expression and to solve the following equation:
+It is equivalent to derivating this expression and to solving the following equation:
+
+
+%\begin{eqnarray*}{l}
+$$2\left[ cos\theta \sum_{i=0}^{M-1} I^{corr}(i).sin(2\pi f.i) \right.$$
+$$\left. + sin\theta \sum_{i=0}^{M-1} I^{corr}(i).cos(2\pi f.i)\right]- $$
+$$ A\left[ cos2\theta \sum_{i=0}^{M-1} sin(4\pi f.i) + sin2\theta \sum_{i=0}^{M-1} cos(4\pi f.i)\right]   = 0$$
+%\end{eqnarray*}

 
 

-\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}
 
 Several points can be noticed:
 \begin{itemize}


@@ -459,7 +457,7 @@ 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
 
 \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
+  result closest to zero. Hence, three other lookup tables can

   also be computed before the loop:
 
 \[ sin \theta, cos \theta, \]
   also be computed before the loop:
 
 \[ sin \theta, cos \theta, \]


@@ -470,13 +468,13 @@ computed.
 
 \end{itemize}
 
 
 \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, this is synthetized in an algorithm (called LSQ in the following) in two parts, one before and one during the acquisition loop:

 \begin{algorithm}[htbp]
 \caption{LSQ algorithm - before acquisition loop.}
 \label{alg:lsq-before}
 
    $M \leftarrow $ number of pixels of the profile\\
 \begin{algorithm}[htbp]
 \caption{LSQ algorithm - before acquisition loop.}
 \label{alg:lsq-before}
 
    $M \leftarrow $ number of pixels of the profile\\

-   I[] $\leftarrow $ intensities of pixels\\
+   I[] $\leftarrow $ intensity of pixels\\

    $f \leftarrow $ frequency of the profile\\
    $s4i \leftarrow \sum_{i=0}^{M-1} sin(4\pi f.i)$\\
    $c4i \leftarrow \sum_{i=0}^{M-1} cos(4\pi f.i)$\\
    $f \leftarrow $ frequency of the profile\\
    $s4i \leftarrow \sum_{i=0}^{M-1} sin(4\pi f.i)$\\
    $c4i \leftarrow \sum_{i=0}^{M-1} cos(4\pi f.i)$\\


@@ -559,9 +557,9 @@ Finally, the whole summarizes in an algorithm (called LSQ in the following) in t
 
 We compared the two algorithms on the base of three criteria:
 \begin{itemize}
 
 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 precision of results on a cosines profile, distorted by noise,

 \item number of operations,
 \item number of operations,

-\item complexity to implement an FPGA version.
+\item complexity of implementating an FPGA version.

 \end{itemize}
 
 For the first item, we produced a matlab version of each algorithm,
 \end{itemize}
 
 For the first item, we produced a matlab version of each algorithm,


@@ -570,9 +568,9 @@ 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
 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
+M. Favre's experiments show a ratio of 50 between the variation of a phase and

 the deflection of a lever. Thus, the maximal error due to
 the deflection of a lever. Thus, the maximal error due to

-discretization correspond to an error of 0.15nm on the lever
+discretization corresponds to an error of 0.15nm on the lever

 deflection, which is smaller than the best precision they achieved,
 i.e. 0.3nm.
 
 deflection, which is smaller than the best precision they achieved,
 i.e. 0.3nm.
 


@@ -581,10 +579,11 @@ 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
 (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 percentage. That is: $err =

 100\times \frac{|\theta_{ref} - \theta_{comp}|}{2\pi}$.
 
 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 $N$.
+Table  \ref{tab:algo_prec}  gives  the   maximum  and  average  error  for  both
+algorithms and increasing values of $N$.

 
 \begin{table}[ht]
   \begin{center}
 
 \begin{table}[ht]
   \begin{center}


@@ -601,15 +600,15 @@ Table \ref{tab:algo_prec} gives the maximum and average error for the two algori
   30 & 17.06 & 2.6 & 13.94 & 2.45 \\ \hline
 
 \end{tabular}
   30 & 17.06 & 2.6 & 13.94 & 2.45 \\ \hline
 
 \end{tabular}

-\caption{Error (in \%) for cosinus profiles, with noise.}
+\caption{Error (in \%) for cosines profiles, with noise.}

 \label{tab:algo_prec}
 \end{center}
 \end{table}
 
 These results show that the two algorithms are very close, with a
 \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
+slight advantage for LSQ. Furthermore, both behave very well against

 noise. Assuming the experimental ratio of 50 (see above), an error of
 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
+1 percent on the phase corresponds 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
 deflection, which is very close to the best precision.
 
 Obviously, it is very hard to predict which level of noise will be


@@ -617,8 +616,8 @@ 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
 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,
+close to experiments. Figure \ref{fig:noise60}
+shows a sample of worst profile for $N=30$. It is completely distorted,

 largely beyond the worst experimental ones. 
 
 \begin{figure}[ht]
 largely beyond the worst experimental ones. 
 
 \begin{figure}[ht]


@@ -639,13 +638,13 @@ largely beyond the worst experimental ones.
 
 The second criterion is relatively easy to estimate for LSQ and harder
 for SPL because of $atan$ operation. In both cases, it is proportional
 
 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
+to the 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 a limited set of operations (+, -, *, /,
 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 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
+$<$, $>$) is taken into account. Translating both algorithms in C code, we
+obtain about 430 operations for LSQ and 1,550 (plus a 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
 $atan$) 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


@@ -653,26 +652,26 @@ and their
 ordering. The final decision is thus driven by the third criterion.\\
 
 The Spartan 6 used in our architecture has a hard constraint: it has no built-in
 ordering. The final decision is thus driven by the third criterion.\\
 
 The Spartan 6 used in our architecture has a 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
+floating  point  units.   Obviously,  it   is  possible  to  use  some  existing
+"black-boxes"  for double  precision operations.   But  they have  quite a  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
 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
-a varying  number of  clock cycles  to complete. Even  multiplications can  be a
-problem:  DSP48 take  inputs of  18  bits maximum.  For larger  multiplications,
+single or  few clock  cycles. Divisions fall  into that category  and, moreover,
+they need a varying number of clock cycles to complete. Even multiplications can
+be a problem: a DSP48 takes 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
 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.
+but from  the algorithms.  Their VHDL implementation  will be efficient  only if
+they can be fully (or near) pipelined.  Thus, the choice is quickly made: only a
+small  part  of  SPL  can  be  pipelined.  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 latest 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 at 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
 
 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


@@ -680,7 +679,7 @@ 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
 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
+routing the design  on the Spartan6. Thus,  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
 there must be idle times between two profiles entering into the pipeline.
 
 %%Before obtaining the least bitstream, the crucial question is: how to


@@ -691,77 +690,83 @@ there must be idle times between two profiles entering into the pipeline.
 
 \section{Experimental tests}
 
 
 \section{Experimental tests}
 

-In this section we explain what  we have done yet. Until now, we could not perform
-real experiments  since we just have  received the FGPA  board. Nevertheless, we
-will include real experiments in the final version of this paper.
+%In this section we explain what  we have done yet. Until now, we could not perform
+%real experiments  since we just have  received the FGPA  board. Nevertheless, we
+%will include real experiments in the final version of this paper.

 
 \subsection{VHDL implementation}
 
 
 \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
-
-

 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
 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
+scaled by 1,024. Since LSQ also computes average, variance, ... to
+remove the slope, the result of implied Euclidean divisions may be

 relatively wrong. To avoid that, we also scale the pixel intensities
 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 knonw denominator. Thus, they can be replaced by
+by a power of two. Furthermore, 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
 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.
+left or right bit shifts. Thus, the code only contains
+additions, subtractions and multiplications of signed integers, which
+are perfectly adapted to FGPAs.
+
+As  mentioned 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
 
 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
+beautiful and much better structured code while Simulink enables us to

 produce a code faster.  In terms of throughput and latency,
 produce a code faster.  In terms of throughput and latency,

-simulations shows that the two approaches are close with a slight
+simulations show that the two approaches are close with a slight

 advantage for hand coding.  We hope that real experiments will confirm
 that.
 
 \subsection{Simulation}
 
 advantage for hand coding.  We hope that real experiments will confirm
 that.
 
 \subsection{Simulation}
 

-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.
+Before experimental tests on the board, we simulated our two VHDL
+codes with GHDL and GTKWave (two free tools with linux). For that, we
+built a testbench based on profiles taken from experimentations and
+compared the results to values given by the SPL algorithm. Both
+versions lead to correct results.
+
+Our first codes 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 15,000 estimations by second.
+

 \subsection{Bitstream creation}
 
 \subsection{Bitstream creation}
 

-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.
+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 other components. It is mainly used
+to start to flush profiles and to retrieve the computed phases in RAM.
+
+Unfortunately, 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. So, 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.
+
+This bitstream has been successfully tested on the board.
+

 
 

-% pas fait mais prévision d'une sortie tous les 480ns avec une latence de 1120

 
 \label{sec:results}
 
 
 \label{sec:results}
 


@@ -769,16 +774,18 @@ could accept new profiles of pixel each 48 cycles, i.e. 480$n$s.
 
 
 \section{Conclusion and perspectives}
 
 
 \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
-studied  the  quantization  of this  algorithm  and  have  implemented it  on  a
-FPGA. Our method gives comparable  results compared to the initial version based
-on splines.   Our solution has been be  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.
+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 plan to study  the quantization. Then we want  to couple our
+algorithm with a high speed camera and we plan to control the whole AFM system.

 
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