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  <o:Author>Domenico Elia</o:Author>
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  <o:Created>2008-04-30T12:51:00Z</o:Created>
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  <o:Company>INFN Sezione di Bari</o:Company>
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<P LANG="en-US" STYLE="margin-top: 0.42cm; margin-bottom: 0.5cm; page-break-after: avoid">
<FONT FACE="Arial"><FONT SIZE=4 STYLE="font-size: 13pt">============================================================================</FONT></FONT></P>
<P LANG="en-US" STYLE="margin-top: 0.42cm; margin-bottom: 0.5cm; page-break-after: avoid">
<FONT FACE="Arial"><FONT SIZE=4 STYLE="font-size: 13pt">Description
of ALICE Silicon Pixel Detector (SPD) Code (Rev. 1.00 &#8212; May 8, 2008
&#8212; D. Elia)</FONT></FONT></P>
<P LANG="en-US" STYLE="margin-top: 0.42cm; margin-bottom: 0.5cm; page-break-after: avoid">
<FONT FACE="Arial"><FONT SIZE=4 STYLE="font-size: 13pt">============================================================================</FONT></FONT></P>
<P STYLE="margin-bottom: 0cm"><A NAME="Content"></A><STRONG><SPAN LANG="en-US"><FONT SIZE=4 STYLE="font-size: 16pt">Content</FONT></SPAN></STRONG>
</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P STYLE="margin-left: 1.27cm; margin-top: 0.18cm; margin-bottom: 0cm">
<SPAN LANG="en-US">1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN><A HREF="#punto_1"><SPAN LANG="en-US">SPD
module geometrical description</SPAN></A></P>
<P STYLE="margin-left: 1.27cm; margin-top: 0.18cm; margin-bottom: 0cm">
<SPAN LANG="en-US">2.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN><A HREF="#punto_2"><SPAN LANG="en-US">Raw
data format</SPAN></A></P>
<P STYLE="margin-left: 1.27cm; margin-top: 0.18cm; margin-bottom: 0cm">
<SPAN LANG="en-US">3.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN><A HREF="#punto_3"><SPAN LANG="en-US">Simulation</SPAN></A></P>
<P STYLE="margin-left: 1.27cm; margin-top: 0.18cm; margin-bottom: 0cm">
<SPAN LANG="en-US">4.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN><A HREF="#punto_4"><SPAN LANG="en-US">Local
reconstruction</SPAN></A></P>
<P STYLE="margin-left: 1.27cm; margin-top: 0.18cm; margin-bottom: 0cm">
<SPAN LANG="en-US">5.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </SPAN><A HREF="#punto_5"><SPAN LANG="en-US">Calibration
and DAs</SPAN></A></P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P><A NAME="punto_1"></A><A HREF="#Content"><B><SPAN LANG="en-US">SPD
module geometrical description</SPAN></B></A></P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">The SPD module geometrical
description is managed by the <B>AliITSsegmentationSPD</B> class.&nbsp;
</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">This offline module
corresponds to half of a single SPD basic unit (the half-stave which
is made of 2 ladders), so it corresponds to a single SPD ladder. In
total the SPD consists of 240 modules, 80 on the inner layer and 160
on the outer layer. The module is divided into 5 chips with the
corresponding sensor cells connected to 5 independent read-out
matrices. 
</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">The single pixel cell size
is 425 microns (local Z) x 50 microns (local X). Pixels at the
boundary between adjacent chips in the module are 625 microns wide in
Z.</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">The single chip has 32
columns (local Z) x 256 rows (local X).</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">The single module size is
6.96 cm (local Z) x 1.28 cm (local X). The sensor is 200 microns
thick. The read-out chip is 150 microns thick.&nbsp;&nbsp;&nbsp;&nbsp;
</P>
<P STYLE="margin-bottom: 0cm"><SPAN LANG="en-US">The module numbering
and the correspondence between online and offline conventions are
illustrated <A HREF="http://tydes.home.cern.ch/tydes/doc/Numbering5/"><B><FONT COLOR="#0000ff">here</FONT></B></A>.
In the </SPAN><B><SPAN LANG="en-GB">AliITSRawStreamSPD</SPAN></B>
<SPAN LANG="en-GB">class the raw data is decoded and so-called digits
are extracted. Inside this class a module map matrix
(fgkDDLModuleMap[][]) is used:</SPAN></P>
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<P LANG="en-GB" CLASS="msonormal">This map specifies how the modules
are numbered (the rows of the matrix represent different equipment
ids, the columns have the 2 ladders of hs0, the 2 ladders of hs1, and
so on...). <BR>Then one also needs to take the columns and rows
numbering into account. 
</P>
<P LANG="en-GB" CLASS="msonormal">To make the conversion between
online and offline coordinates there are the following static member
functions in AliITSRawStreamSPD: 
</P>
<P CLASS="msonormal">&nbsp;</P>
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<P CLASS="msonormal" ALIGN=CENTER>&nbsp;</P>
<P CLASS="msonormal" ALIGN=CENTER>&nbsp;</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">=================================================================================================================</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P><A NAME="punto_2"></A><A HREF="#Content"><B><SPAN LANG="en-US">Raw
data format</SPAN></B></A></P>
<P CLASS="msonormal">&nbsp;</P>
<P LANG="en-GB" CLASS="msonormal">The SPD raw data are decoded by the
<B>AliITSRawStreamSPD</B> class.</P>
<P CLASS="msonormal">&nbsp;</P>
<P CLASS="msonormal"><SPAN LANG="en-GB">The SPD has equipment IDs
from 0 to 19, each corresponding to the readout of one half sector.
The geometrical map of the DDLs is illustrated <A HREF="http://tydes.home.cern.ch/tydes/doc/Numbering5/"><B>here</B></A>.</SPAN></P>
<P CLASS="msonormal"><SPAN LANG="en-GB">Each equipment</SPAN> <SPAN LANG="en-GB">starts
with the <I>Equipment Header</I> (15 32-bit words) of which the last
8 words are known as the <I>Common Data Header, CDH</I> (8 32-bit
words). After these headers, sometimes a <I>Calibration Header</I>
appears (for dedicated calibration runs). This extra header has
variable length, depending on the type of calibration scan. Finally,
there is the actual data words, i.e. which pixels are hit in the
event. This part has a variable length depending on the number of
hits. Further details on the various headers and the data word
formats can be found <A HREF="http://tydes.home.cern.ch/tydes/doc/DataFormat/"><B>here</B></A>.</SPAN></P>
<P CLASS="msonormal">&nbsp;</P>
<P CLASS="msonormal">&nbsp;</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">=================================================================================================================</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P><A NAME="punto_3"></A><A HREF="#Content"><B><SPAN LANG="en-US">Simulation</SPAN></B></A></P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">The SPD digitization is
implemented in the <B>AliITSsimulationSPD</B> class and managed via
the <B>AliITSDetTypeSim</B> class.</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">It is based on the
following working scheme:</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm"><B>1) Hits --&gt; SDigits
(AliSimulation::RunSDigitization)</B></P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt; AliITS::Hits2SDigits
</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt;
AliITS::Hits2Predigits 
</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt;
AliITSsimulationSPD::SDigitiseModule</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt;
AliITSsimulationSPD::HitToSDigitFast</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- read hits, gets
parameters for diffusion (temperature, thickness over bias voltage,
asymmetry of gaussian diffusion, etc.) and for electronic coupling
from OCDB</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- apply electron cloud
diffusion (gaussian smearing) along z and r*phi</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- eventually apply the
Lorentz drift to the electron cloud (by default null Lorentz drift) 
</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- apply coupling between
adiacent pixels</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt;
AliITSsimulationSPD::RemoveDeadPixel</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&nbsp; remove dead pixels
as stored in the calibration object</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt;
AliITSsimulationSPD::WriteSDigits</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- write SDigits to file,
basically call AliITS::AddSumDigit (which calls
AliITSDetTypeSim::AddSumDigit) to write SDigits (AliITSpListItem) to
file</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm"><B>2) SDigits --&gt;
Digits (AliSimulation::RunDigitization)</B></P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt;
AliITSDigitizer::Exec</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- load SDigits</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt;
AliITSsimulationSPD::FinishSDigitiseModule</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- call
AliITSsimulationSPD::FrompListToDigits</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- eventually add
electronic baseline and noise, perform the zero suppression and add
the digits to the list&nbsp; (by calling AliITS::AddSimDigit)</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P STYLE="margin-bottom: 0cm"><SPAN LANG="en-US">A detailed
description of the SPD response model (in
AliITSsimulationSPD::HitToSDigitFast) can be found <A HREF="https://edms.cern.ch/document/888905/1"><B>here</B></A>
(ALICE-INT-2008-003 and references therein). The model parameters are
stored in two OCDB files under $ALICE_ROOT/ITS/Calib:</SPAN></P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">1) RespSPD: contains 1
AliITSresponseSPD object with parameters common to all the modules
(coupling type and diffusion asymmetry)</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">2) SPDDead: contains 1
TOjArray with 240 AliITSCalibrationSPD objects, i.e. 1
AliITSCalibrationSPD object for each module with the list of dead
pixels (see calibration section below) and the other parameters
needed to the response model (threshold, noise, coupling strength,
bias-over-voltage) 
</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">========================================================================================================================</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P><A NAME="punto_4"></A><A HREF="#Content"><B><SPAN LANG="en-US">Local
Reconstruction</SPAN></B></A></P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">The SPD local
reconstruction is implemented in <B>AliITSClusterFinderV2SPD </B>class
and managed via the <B>AliITSDetTypeRec</B> class.</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">It is based on the
following working scheme:</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm"><B>Cluster Finding
(AliReconstruction::RunLocalEventReconstruction)</B></P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt;
AliITSReconstructor::Reconstruct</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt;
AliITSDetTypeRec::DigitsToRecPoints 
</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- Based on the input data
(simulation digits or simulation/real raw data), there are two
possibilities:</P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">A)
<U>RECONSTRUCTION FROM DIGITS</U></SPAN></P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">-&gt;
AliITSClusterFinderV2SPD::FindRawClusters</SPAN></P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">- call
AliITSClusterFinderV2SPD::FindClustersSPD</SPAN></P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">- build
AliBin array from digit tree</SPAN></P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">- call
AliITSClusterFinderV2SPD::ClustersSPD</SPAN></P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">B)
<U>RECONSTRUCTION FROM RAW DATA </U></SPAN>
</P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">-&gt;
AliITSClusterFinderV2SPD::RawdataToClusters</SPAN></P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">-
instantiate AliITSRawStreamSPD object</SPAN></P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">- call
AliITSClusterFinderV2SPD::FindClustersSPD</SPAN></P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">- build
AliBin array from raw data</SPAN></P>
<P STYLE="margin-bottom: 0cm">&nbsp;&nbsp; <SPAN LANG="en-US">- call
AliITSClusterFinderV2SPD::ClustersSPD</SPAN></P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">-&gt; AliITS
ClusterFinderV2SPD::ClustersSPD</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- loop on dead pixels as
stored in the calibration objects and reset them (corresponding
AliBin elements)</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">- loop on AliBin elements
and:</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">1) find cluster
(FindCluster)</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">2) unfold cluster if
allowed (this is set via AliITSRecoParam, the default is unfolding
off)</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">3) calculate cluster
coordinates and sigmas</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">4) add cluster to cluster
array</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P LANG="en-US" STYLE="margin-bottom: 0cm">===============================================================================================================================</P>
<P STYLE="margin-bottom: 0cm">&nbsp;</P>
<P><A NAME="punto_5"></A><A HREF="#Content"><B><SPAN LANG="en-US">Calibration
and DAs</SPAN></B></A></P>
<P LANG="en-GB">For the SPD there are two types of processes, called
<I>Detector Algoritms (DAs)</I>, running on the <I>DAQ</I> network to
produce output transported via the <I>File Exchange Server (FXS)</I>
to the <I>Offline</I> and <I>Detector Control System (DCS)</I>
networks. The following picture illustrates how the Online
Calibration scheme works:</P>
<P ALIGN=CENTER><SPAN LANG="en-GB"><BR><!--[if gte vml 1]><v:shape id="_x0000_i1027" type="#_x0000_t75" alt=""
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<P>&nbsp;</P>
<P><SPAN LANG="en-GB">In case <I>a</I> the calibration is performed
as a <B>standalone scan</B>. The raw data collected on the <I>Local
Data Concentrators (LDCs)</I> are analyzed. In case <I>b</I> the
calibration is performed on a regular <B>physics run</B> and the data
is analyzed online through the <I>DATE</I> monitoring functionality.
Further details on the types of runs and scans and a global overview
of the SPD calibration can be found <A HREF="http://tydes.home.cern.ch/tydes/doc/CalibrationOverview/"><B>here</B></A>.</SPAN></P>
<P LANG="en-GB" CLASS="msonormal">The so-called <I>Shuttle</I> brings
the output files from the <I>FXS</I> to <I>DCS</I> and <I>Offline</I>
networks. Here the data go through a second level of processing,
generally called preprocessing. Finally, the <I>Offline Calibration
Database (OCDB)</I> and the <I>DCS Configuration Database</I> are
updated. 
</P>
<P LANG="en-GB" CLASS="msonormal">The procedures also produce
so-called <I>Reference Data</I>, basically raw data summaries, which
can later be used offline to reconstruct the calibration output. This
may be useful for instance for debugging purposes. A <I>Reference
Data Displayer</I> (GUI) program has been developed to simplify the
analysis of the Reference Data.</P>
<P LANG="en-GB" STYLE="margin-bottom: 0cm">The two top level classes
corresponding to Standalone Calibration Runs and Physics Runs are
<B>ITSSPDSCANda</B> and <B>ITSSPDPHYSda</B> respectively. The <I>Offline
Preprocessing</I> is implemented in the <B>AliITSPreprocessorSPD</B>
class. It takes care of saving the reference data and put information
relevant for the offline reconstruction (lists of dead and noisy
pixels) in the OCDB.</P>
<P LANG="en-GB" STYLE="margin-bottom: 0cm">The calibration files in
the OCDB are stored in two directories under $ALICE_ROOT/ITS/Calib:</P>
<P STYLE="margin-bottom: 0cm"><SPAN LANG="en-GB">1</SPAN><SPAN LANG="en-US">)
SPDDead: contains 1 TOjArray with 240 AliITSCalibrationSPD objects,
i.e. 1 AliITSCalibrationSPD object for each module with the list of
dead pixels and some parameters needed to the response model </SPAN>
</P>
<P STYLE="margin-bottom: 0cm"><SPAN LANG="en-GB">2) SPDNoisy:
conatins </SPAN><SPAN LANG="en-US">1 TOjArray with 240
AliITSCalibrationSPD objects, i.e. 1 AliITSCalibrationSPD object for
each module with the list of noisy pixels</SPAN></P>
<P STYLE="margin-bottom: 0cm"><SPAN LANG="en-GB">The noisy pixel
search is always based on one run only. There is a minimum number of
events required to do the search which is basically performed at the
level of one read-out chip (8192 pixels). The dead pixel search may
span several runs, in order to collect more statistics (which is
mandatory for the p-p runs). Also here there is a minimum number of
events required to even try to perform the search. The search
requires that a noisy pixel search has been done first. The noisy
pixels are then removed from the hit-maps before the dead pixel
search. Also the dead pixel search is basically performed on the
level of one read-out chip. For further details on the dead and noisy
pixel search see <A HREF="http://tydes.home.cern.ch/tydes/doc/CalibrationOverview/CalibrationAlgorithms/noisydead/"><B>here</B></A>.</SPAN></P>
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