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 <book lang="en">
 
 <bookinfo>
  <title>Atlantis Online Documentation
  </title>
  <author>
   <surname>Atlantis Support Group</surname>
  </author>
  <affiliation>
   <address format="linespecific">CERN
   <email>Atlantis.Support@CERN.CH</email></address>
  </affiliation>
  <pubdate>Docbook V1.4 01-may-2007</pubdate>
  <copyright>
   <year>2006-2007</year>
   <holder>ATLAS Collaboration</holder>
  </copyright>
 </bookinfo>
 
 <!--=======================================================================-->
 <chapter id="HelpHowTo">
 <title id="HelpHowTo.title">About the Atlantis Help System</title>
 
 <para>
 The Atlantis event display program has two independent systems for 
 online help, <emphasis>tooltips</emphasis> and 
 <emphasis>online documentation</emphasis>. 
 The tooltips are integrated into the program, 
 the online documentation is placed outside the program, but is shown 
 in a pop-up window when referenced from the program.
 </para>
 
 <para>
 <emphasis>Tooltips</emphasis>
 </para>
 
 <para>
 Tooltip help consists of short text messages associated with practically 
 every graphical component of the user interface. You obtain these messages 
 by stopping the mouse cursor in the area you want to get help for. 
 If a message exists for the component it will appear on the screen after 
 a few moments.
 </para>
 
 <para>
 <emphasis>Online documentation</emphasis>
 </para>
 
 <para>
 The online documentation is a hierarchically organized set of pages, 
 linked to each other by hypertext links. These pages provide much more 
 detailed descriptions than tooltips, but not every graphical component 
 has an associated page. The online documentation is displayed in the 
 help pop-up window 
 (see <xref endterm="HelpWindow.title" linkend="HelpWindow"></xref>)
 that is opened via the 
 <emphasis>Help&rarr;Online Help System</emphasis> menu option of the menu of 
 the Control Window 
 (see <xref endterm="ControlWindow.title" linkend="ControlWindow"></xref>). 
 This window contains the table of contents in the left margin for easy 
 navigation. 
 </para>
 
 <para>
 The hierarchy of pages is reflected in the terms chapter and section.
 </para>
 
 <para>
 In the help pop-up window you can start navigating and use the Table of 
 Contents to directly go to the page you are interested in. 
 </para>
 
 <para>
 An alternative and more direct way to access the online documentation of 
 a graphical component is to <emphasis>right-click</emphasis> on that 
 component. 
 This will show the available help page directly in the help pop-up window.
 </para>
 
 <para>
 The online documentation is also accessible via the  
 <ulink url="http://atlantis.web.cern.ch/atlantis/">
 <emphasis>Atlantis website</emphasis></ulink>, both as webpages and as PDF 
 document (select <emphasis>Documentation</emphasis> in the left margin of 
 a webpage of the Atlantis website).
 </para>
 
 </chapter>
 
 <!--=======================================================================-->
 <chapter id="Introduction">
 <title id="Introduction.title">Introduction</title>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="AboutAtlantis">
 <title id="AboutAtlantis.title">2.1 About Atlantis</title>
 
 <para>
 Atlantis is an event display program for the 
 <ulink url="http://www.cern.ch/atlas/">ATLAS</ulink> experiment at 
 <ulink url="http://www.cern.ch/">CERN</ulink>'s 
 <ulink url="http://www.cern.ch/lhc/">Large Hadron Collider</ulink>. 
 The primary goal of the program is <emphasis>the visual investigation and 
 the understanding of the physics of complete events</emphasis>. 
 Secondary goals are to help develop reconstruction and analysis algorithms, 
 to facilitate debugging during commisioning and to create pictures and 
 animations for publications, presentations and exhibitions.
 </para>
 
 <para>
 Specific features of the program are:
 
 <itemizedlist>
 <listitem>
  <para>
  The use of <emphasis>data oriented projections</emphasis>. 
  See <xref linkend="Projection"></xref>.
  </para>
 </listitem>
 <listitem>
  <para>
  The use of
  <emphasis>subviews within the display area window</emphasis> to be able to
  view various projections simultaneously.
  See <xref endterm="Canvas.title" linkend="Canvas"></xref>.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>2D animations</emphasis> beyond panning and zooming.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>3D synchronous pointers</emphasis> across the various
  projections, so you may pick an object in one projection and see where it is
  located in the other projections.
  </para>
 </listitem>
 <listitem>
  <para>
  A basically <emphasis>mouse driven user interface</emphasis>
  using generally applied
  facilities of modern user interfaces (e.g. pop-up, tooltip).
  See <xref linkend="UserInterface"></xref>.
  </para>
 </listitem>
 </itemizedlist>
 
 Atlantis is based on the 
 <ulink url="http://www.cern.ch/aleph/">ALEPH</ulink> event display 
 <ulink url="http://www.cern.ch/aleph/dali/">DALI</ulink> and is written 
 entirely in <ulink url="http://java.sun.com/j2se/1.4.1/">JAVA</ulink>.
 </para>
 
 <para>
 <emphasis>Leading Principles</emphasis>
 </para>
 
 <para>
 Three leading principles form the base of Atlantis development:
 
 <itemizedlist>
 <listitem>
  <para>
  Atlantis is <emphasis>fast</emphasis>.
  </para>
 </listitem>
 <listitem>
  <para>
  Atlantis is used <emphasis>intuitively</emphasis>.
  </para>
 </listitem>
 <listitem>
  <para>
  Atlantis is used for <emphasis>complete ATLAS events</emphasis>.
  </para>
 </listitem>
 </itemizedlist>
 
 So we try to realize: 
 <emphasis>Everything quickly available for everybody!</emphasis>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="Roadmap">
 <title id="Roadmap.title">2.2 Roadmap of the Atlantis Online Documentation</title>
 
 <para>
 This section gives a short description of the structure of the documentation.
 </para>
 
 <para>
 <xref linkend="Introduction"></xref> describes some basics: 
 see <xref endterm="YZ1.title" linkend="YZ1"></xref> and  
 <xref endterm="PictureNecessities.title" linkend="PictureNecessities"></xref>.
 Information for new users can be found via 
 <xref endterm="DIRinfo.title" linkend="DIRinfo"></xref>.
 </para>
 
 <para>
 <xref linkend="UserInterface"></xref> 
 describes how the user interface is set up and gives 
 short descriptions of its full functionality. 
 Topics include: read events from various sources (details for 
 interactive selection from Athena in <xref linkend="Athena"></xref>, 
 maintain lists of personally selected data, maintain a personal startup 
 configuration file, choose shape and subdivision of the Canvas, 
 reset the program to initial settings, access help information, 
 select and use interactions and projections (details in 
 <xref linkend="Interactions"></xref> and <xref linkend="Projection"></xref>, 
 select data and apply cuts on selected data (details in 
 <xref linkend="DataMain"></xref>, change attributes of detector elements and 
 data (details in <xref linkend="Detector"></xref>. 
 </para>
 
 <para>
 <xref linkend="Interactions"></xref> describes in detail the various 
 interactions that work on the pictures generated on the Canvas. 
 </para>
 
 <para>
 <xref linkend="Projection"></xref> describes in detail the various projections 
 that can be applied to pictures on the Canvas. 
 </para>
 
 <para>
 <xref linkend="DataMain"></xref> 
 describes in detail how to make selections from the availabe data, which 
 cuts can be applied on the selected data and how cuts can be applied. 
 </para>
 
 <para>
 <xref linkend="Detector"></xref> 
 describes in detail the detector and data elements with attributes that 
 can be modified. 
 </para>
 
 <para>
 <xref linkend="Athena"></xref> 
 describes in detail the interactive selection of events from Athena.
 </para>
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="YZ1">
 <title id="YZ1.title">2.3 Which coordinate systems are used?</title>
 
 <para>
 The ATLAS coordinate system (X,Y,Z) is defined as a right-handed 
 system: 
 
 <itemizedlist>
 <listitem>
  <para>
  X = horizontal axis, pointing to the centre of the LHC ring,
  </para>
 </listitem>
 <listitem>
  <para>
  Y = vertical axis, pointing upward,
  </para>
 </listitem>
 <listitem>
  <para>
  Z = horizontal axis, following the beam direction.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 Additionally, the coordinate system (&phi;,&eta;,&rho;) is defined 
 as: 
 
 <itemizedlist>
 <listitem>
  <para>
  &rho; = sqrt(X<superscript>2</superscript>+Y<superscript>2</superscript>),
  </para>
 </listitem>
 <listitem>
  <para>
  &phi; = arctan(Y/X), the azimuthal angle,
  &phi; = 0 corresponds to the positive X-axis,
  </para>
 </listitem>
 <listitem>
  <para>
  &eta; = arctan(&rho;/Z).
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="PictureNecessities">
 <title id="PictureNecessities.title">2.4 What is necessary to draw a picture?</title>
 
 <para>
 In order to draw a picture, parameters must be set and selections must be 
 made. 
 All parameters and selections have default values which are used to draw 
 proper pictures when Atlantis is started.
 </para>
 
 <para>
 <emphasis>However, you probably want more!</emphasis>
 </para>
 
 <para>
 The following list gives an overview of parameters and selections and where 
 they may be changed:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Canvas pad</emphasis> 
  </para>
  <para>
  The place where a picture is drawn. Selection of a canvas pad 
  (see <xref endterm="Window.title" linkend="Window"></xref>)
  and manipulation 
  of the picture in a canvas pad (e.g. copying into another canvas pad) 
  are done via the canvas control
  (see <xref endterm="WindowControl.title" linkend="WindowControl"></xref>) 
  of the Control Window. 
  </para>
  <para>
  A canvas pad is a subview of the Canvas
  (see <xref endterm="Canvas.title" linkend="Canvas"></xref>). 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Interaction</emphasis>
  </para>
  <para>
  The type of interaction (e.g. zooming, picking)
  (see <xref linkend="Interactions"></xref>)
  to manipulate the picture 
  that will be drawn, is selected and controlled via the interaction control
  (see
  <xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>)
  of the Control Window.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Projection</emphasis>
  </para>
  <para>
  The projection (see <xref linkend="Projection"></xref>)
  used to create the picture for the canvas pad. A projection
  is selected via the <emphasis>Proj</emphasis> tab of the parameter control
  (see
  <xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>)
  of the Control Window.
  Specific projection parameters of the selected projection are displayed in
  the parameter control of the Control Display and can be modified now.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Data</emphasis>
  </para>
  <para>
  The data to be used can be selected via the <emphasis>Data</emphasis>
  tab of the parameter control
  (see
  <xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>)
  of the Control Window. 
  See <xref endterm="Data.title" linkend="Data"></xref>
  for a list of data types.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Cuts</emphasis>
  </para>
  <para>
  Cuts (see <xref endterm="Cuts.title" linkend="Cuts"></xref>)
  on physical values of the selected data can be set via the
  <emphasis>Cuts</emphasis> tab of the parameter control
  (see
  <xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>)
  of the Control Window.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Detector colors</emphasis>
  </para>
  <para>
  Detector colors
  (see <xref endterm="Det.title" linkend="Det"></xref>)
  can be set via the <emphasis>Det</emphasis> tab of the parameter control
  (see
  <xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>)
  of the Control Window.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Data colors and symbols</emphasis>
  </para>
  <para>
  Colors and symbols of the detector subsystem data can be set via the
  <emphasis>InDet</emphasis>, <emphasis>Calo</emphasis> and
  <emphasis>MuonDet</emphasis> tabs of the parameter control
  (see
  <xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>)
  of the Control Window.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="DIRinfo">
 <title id="DIRinfo.title">2.5 Download, install and run information</title>
 
 <para>
 Starting November 17, 2005, Atlantis is distributed with the ATLAS software 
 release. 
 It is available as executables "atlantis" (full version) and 
 "atlantis_beginner" (version with a limited set of GUI options).
 </para>
 
 <para>
 <emphasis>N.B.: Note, however, that Atlantis does not depend on any ATLAS 
 software, only JAVA is needed to run it.</emphasis>
 </para>
 
 <para>
 See the Download page of the 
 <ulink url="http://atlantis.web.cern.ch/atlantis/">
 <emphasis>Atlantis website</emphasis></ulink> for directions how to get 
 Atlantis.
 See the Install page for directions to run Atlantis on Linux, Mac and 
 MS-Windows systems.
 </para>
 
 <para>
 A tag is used in the Atlantis run command to indicate normal events (no tag), 
 Fast Simulation events (tag=Fast), Combined Test Beam events (tag=TB) or a 
 beginner's version with a limited set of GUI options (tag=BEGINNER).
 </para>
 
 <para>
 To change the upper limit of the Atlantis internal work memory see 
 <xref endterm="WorkMemoryLimit.title" linkend="WorkMemoryLimit"></xref>.
 </para>
 
 <para>
 <emphasis>N.B.: Atlantis versions require JAVA version 1.4 or higher to run. 
 However, JAVA version 1.5 is preferred and is currently used for 
 development.</emphasis>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="WorkMemoryLimit">
 <title id="WorkMemoryLimit.title">2.6 Work memory limit</title>
 
 <para>
 The default value of the maximum internal work memory to process events in 
 Atlantis is 64MB.
 If you use the option overlay events (see the menu of the Control Window) or 
 if you work with very large events, you may want to increase this limit. 
 In order to 
 increase this limit, a running option can be specified at Atlantis startup. 
 E.g. to change the default value to 128MB: 
 </para>
 
 <para>
 <informalexample>
 <programlisting format="linespecific">
   java -Xmx128m -jar atlantis.jar
 </programlisting>
 </informalexample>
 </para>
 
 </sect1>
 
 </chapter>
 
 <!--=======================================================================-->
 <chapter id="UserInterface">
 <title id="UserInterface.title">User Interface</title>
 
 <para>
 The Atlantis user interface is 
 basically mouse driven and using generally applied facilities of modern user 
 interfaces (e.g. pop-up, tooltip). It consists of a permanent 
 <emphasis>Control Window</emphasis> "Atlantis GUI" 
 (see <xref endterm="ControlWindow.title" linkend="ControlWindow"></xref>), a permanent 
 display area window "Atlantis Canvas" or <emphasis>Canvas</emphasis> 
 (see <xref endterm="Canvas.title" linkend="Canvas"></xref>) 
 and various <emphasis>pop-up windows</emphasis> 
 (see <xref endterm="PopUpWindows.title" linkend="PopUpWindows"></xref>). 
 </para>
 
 <para>
 Besides, <emphasis>modifier keys</emphasis> 
 (see <xref endterm="MouseModifierKeys.title" linkend="MouseModifierKeys"></xref>) 
 are available for quick view and control of parameters and selections.
 </para>
 
 <para>
 The Control Window is used to view and modify parameters and selections 
 that control the pictures on the Canvas. The pop-up windows are available for 
 quick viewing and modification of relevant parameters and selections.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="ControlWindow">
 <title id="ControlWindow.title">3.1 Control Window</title>
 
 <para>
 The Control Window, "Atlantis GUI", is opened when Atlantis is started. 
 It is used to view and modify parameters and selections that control the 
 pictures on the Canvas, the display area of Atlantis. 
 Functionality is grouped into components, namely (listed from top to 
 bottom of the Control Window): 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Menu</emphasis> 
  </para>
  <para>
  Provides functionality for I/O, program customisation and the help system. 
  See <xref endterm="Menu.title" linkend="Menu"></xref>. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Canvas Control</emphasis>  
  </para>
  <para>
  Provides functionality to select a canvas pad and to copy 
  pictures between canvas pads. 
  See <xref endterm="WindowControl.title" linkend="WindowControl"></xref>.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Interaction Control</emphasis> 
  </para>
  <para>
  Provides functionality for user interaction with the program (pick, zoom, 
  transformations, projections). 
  See <xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Parameter Control</emphasis>  
  </para>
  <para>
  Provides functionality for viewing and changing various parameters 
  (data selection, cuts, detector, subdetector systems, projections). 
  See <xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Output Display</emphasis>  
  </para>
  <para>
  Displays specific output of the program (picking output, cuts summary, 
  etc.).  See <xref endterm="OutputDisplay.title" linkend="OutputDisplay"></xref>. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Menu">
 <title id="Menu.title">3.1.1 Menu</title>
 
 <para>
 The Menu is positioned at the very top of the Atlantis Control Window. 
 It contains the items <emphasis>File</emphasis>,
 <emphasis>Preferences</emphasis>, <emphasis>Lists</emphasis>,
 <emphasis>Demo</emphasis>, <emphasis>Reset</emphasis>, 
 <emphasis>Previous</emphasis> (previous event), 
 <emphasis>Next</emphasis> (next event), <emphasis>Help</emphasis>.
 The options of the menu items are briefly described below. 
 </para>
 
 <para>
 <emphasis>File</emphasis>
 </para>
 
 <para>
 The File menu item is used to perform operations on event files and to exit 
 Atlantis. Note that event files are expected to be in XML format (which may 
 also be zipped). The item contains the following options:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Read Event</emphasis>
  </para>
  <para>
  Displays a dialog window where you can choose which event file 
  to read from your local computer.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Read Event From URL</emphasis>
  </para>
  <para>
  Displays a dialog window where you can specify a URL to read events from.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Read Event From Server</emphasis>
  </para>
  <para>
  Displays a dialog window where you can specify a
  server name or IP-address to read events from. This option can be used to
  start e.g. online event monitoring with Atlantis. See
  <xref endterm="EventAccess.title" linkend="EventAccess"></xref> for details.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Interactive Athena</emphasis>
  </para>
  <para>
  Displays a dialog window to select and fetch events interactively
  from Athena. See <xref linkend="Athena"></xref> for further details.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Save Canvas</emphasis>
  </para>
  <para>
  Displays the graphics output format options from which you may select
  the one you want to use to save pictures shown on the Canvas.
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>EPS</emphasis>
   </para>
   <para>
   Encapsulated PostScript. Vector graphics format for posters,
   publications, etc.
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>PNG</emphasis>
   </para>
   <para>
   Portable Network Graphics. A compressed bitmap format to be used in
   Powerpoint presentations, etc.
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>GIF</emphasis>
   </para>
   <para>
   Graphics Interchange Format. Another compressed bitmap format. 
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Animated event</emphasis>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Event Properties</emphasis>
  </para>
  <para>
  Displays a pop-up window with a summary of various properties of the
  selected event.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Overlay Events</emphasis>
  </para>
  <para>
  Pile up events (as they are read from whichever source) and
  display them superimposed. This option is turned off by default, tick the
  box to enable. This feature was implemented for comparing simple low-size
  events (e.g. cosmics single track events).
  </para>
  <para>
  <emphasis>N.B.: Atlantis gets very slow and exhausts available memory
   quickly if this option is enabled when reading in complex, several
   magabytes large event files.
  </emphasis>
  </para>
  <para>
  <emphasis>N.B.: See <xref endterm="WorkMemoryLimit.title"
  linkend="WorkMemoryLimit"></xref>
  to increase the value of the internal work memory.
  </emphasis>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Clear Event Container</emphasis>
  </para>
  <para>
  Clicking this item empties all the events read into
  Atlantis after Overlay Events was enabled, the last event remains.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Read Geometry...</emphasis>
  </para>
  <para>
  Displays a dialog window to select and apply a new
  geometry file in XML format.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Exit</emphasis>
  </para>
  <para>
  Exit Atlantis. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 <emphasis>Preferences</emphasis>
 </para>
 
 <para>
 The Preferences menu item is responsible for customizing the application. 
 It contains the following options:
 
 <itemizedlist>
 <listitem>
  <para>
  Change Canvas Layout - Displays a dialog window that allows the user to
  select a shape and layout set that is applied to the Canvas.
  See <xref endterm="Canvas.title" linkend="Canvas"></xref>.
  </para>
 </listitem>
 <listitem>
  <para>
  Select Color Map - Displays a dialog window which allows the
  user to choose the color set used to draw the pictures.
  There are four color sets:
  <itemizedlist>
  <listitem>
   <para>
   Display - Default color set used for display.
   </para>
  </listitem>
  <listitem>
   <para>
   Printer - The set of colors used when printing.
   </para>
  </listitem>
  <listitem>
   <para>
   Gray - The grayscale set of colors.
   </para>
  </listitem>
  <listitem>
   <para>
   B/W - The black-and-white set of colors. 
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  Color Map Editor - Displays a dialog window that allows the
  user to edit any of the color sets described above.
  </para>
 </listitem>
 <listitem>
  <para>
  Read Color Map - Displays a dialog window that allows the
  user to replace the current colormap with one previously stored on an XML
  file.
  </para>
 </listitem>
 <listitem>
  <para>
  Save Current Color Map - Displays a dialog window that allows the
  user to store the current colormap to an XML file for later use.
  </para>
 </listitem>
 <listitem>
  <para>
  Save Current Configuration - Displays a dialog window that allows the user
  to store the current status (configuration) of the program to an XML file
  for later use.
  </para>
 </listitem>
 <listitem>
  <para>
  Show Pointer Position Window - Displays a dialog window which will
  show the user the position of the pointer when the user right clicks
  while keeping the <emphasis>O</emphasis> key pressed.
  </para>
 </listitem>
 <listitem>
  <para>
  Show Legend Window - Displays a dialog window that shows the color 
  thresholds for the cells of the summed LAr/HEC endcaps when 
  using Calo->LAr/HEC->Color Function->Energy
  </para>
 </listitem>
 <listitem>
  <para>
  Show Canvas Title - Adds or removes the title bar from the top of the
  Canvas.  See <xref endterm="Canvas.title" linkend="Canvas"></xref>. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 <emphasis>Lists</emphasis>
 </para>
 
 <para>
 Creates a Lists pop-up window 
 for the interactive definition and manipulation of subsets of data.
 See <xref endterm="Lists.title" linkend="Lists"></xref>. 
 </para>
 
 <para>
 <emphasis>Reset</emphasis>
 </para>
 
 <para>
 Resets Atlantis to the default initial settings.
 </para>
 
 <para>
 <emphasis>Prev</emphasis>
 </para>
 
 <para>
 Loads and displays the previous event if available.
 </para>
 
 <para>
 <emphasis>Next</emphasis>
 </para>
 
 <para>
 Loads and displays the next event if available.
 </para>
 
 <para>
 <emphasis>Help</emphasis>
 </para>
 
 <para>
 The Help menu item provides a way to get access to help information. 
 It has four options:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Online Help System</emphasis>
  </para>
  <para>
  Starts the help pop-up window with the table of contents. 
  See <xref endterm="HelpWindow.title" linkend="HelpWindow"></xref>.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Modifier Keys</emphasis>
  </para>
  <para>
  Starts the modifier keys pop-up window
  with information about active modifier keys. 
  See <xref endterm="MouseModifiersWindow.title" linkend="MouseModifiersWindow"></xref>.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Current Colors of objects</emphasis>
  </para>
  <para>
  Starts a pop-up window to display the current color
  of some selected objects (eg AOD/track/detector).
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>About</emphasis>
  </para>
  <para>
  Starts the about pop-up window with Atlantis version,
  website address and hypernews email address.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect3 id="EventAccess">
 <title id="EventAccess.title">3.1.1.1 Access to Events</title>
 
 <para>
 Events to display in Atlantis can be fetched in many ways:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>File &rarr; Read Event</emphasis>
  - an XML event file or a ZIP archive of XML event files from a local source
  (i.e. file on the local disk). 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>File &rarr; Read Event From URL</emphasis>
  - from a web server over HTTP protocol.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>File &rarr; Read Event From Server</emphasis>
  - from a server started within 
  the JiveXML algtool (Athena - Atlantis event data converter) running in the 
  Athena framework. The name or the IP address of the remote server where 
  Athena runs must be entered into the dialog. The event data is delivered to 
  Atlantis either after the user clicks the <emphasis>Get Event</emphasis>
  button or automatically (with a specified delay) if the
  <emphasis>timer</emphasis> is enabled.
  </para>
  <para>
  In order to use this feature, the JiveXML server must be started in 
  Athena/JiveXML which is done by
  <emphasis>ToolSvc.EventData2XML.OnlineMode =  True</emphasis>
  (JiveXML job option). Every time Athena reconstructs an event, 
  JiveXML will produce the XML event data for Atlantis. This mechanism can 
  be used for online monitoring and gets rid of the intermediate step of 
  writing the event data into the event files. Nonetheless, if the user spots 
  an interesting event, the data read into Atlantis in this online mode can 
  be stored on the local disk after clicking the
  <emphasis>Save Event</emphasis> button. 
  If not stored, the event data will be lost with reading in the next event.
  </para>
  <para>
  The JiveXML server listens on the high number non-privileged port on the 
  remote server. Should there be any firewall network security restrictions 
  imposed, it might be necessary to communicate via an SSH tunnel between the 
  local computer running Atlantis and the remote machine running Athena/JiveXML.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>File &rarr; Interactive Athena</emphasis>
  - getting the event on demand (<emphasis>Get  Event</emphasis> button)
  while steering the Athena framework from Atlantis through 
  the Athena interactive prompt. Further details in <xref linkend="Athena"></xref>.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 When starting Atlantis, it tries by default to look for a file 
 <emphasis>test_events.zip</emphasis> in the <emphasis>events</emphasis> 
 directory. If not found, Atlantis starts without any event read in. 
 </para>
 
 <para>
 <emphasis>N.B.</emphasis>: When starting Atlantis in the 
 <emphasis>Fast</emphasis> or the <emphasis>TB</emphasis> mode, 
 the event archives <emphasis>test_eventsFast.zip</emphasis>, resp. 
 <emphasis>test_eventsTB.zip</emphasis> are looked for.
 </para>
 
 </sect3>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="WindowControl">
 <title id="WindowControl.title">3.1.2 Canvas Control</title>
 
 <para>
 Pictures are shown in the display area window or Canvas
 (see <xref endterm="Canvas.title" linkend="Canvas"></xref>), 
 which may have one or more subwindows, the <emphasis>canvas pads</emphasis>. 
 So in the case of multiple canvas pads, one may e.g. view event data in 
 different projections on the Canvas. The possible canvas pad 
 configurations are specified in <emphasis>layout sets</emphasis>.
 </para>
 
 <para>
 A layout set is selected via the
 <emphasis>Preferences&rarr;Change Canvas Layout</emphasis> menu 
 option of the Menu 
 (see <xref endterm="Menu.title" linkend="Menu"></xref>) of the 
 Control Window.
 </para>
 
 <para>
 The layouts of the current layout set are displayed in the Control Window as 
 a row of rectangles directly under the menu. A rectangle is divided into one 
 or more boxes, representing the canvas pads. A letter or number in a box 
 represents the canvas pad name. 
 </para>
 
 <para>
 For example, in Landscape Layout the canvas pads are UDR, 123456, SR, W, 
 LMR and in Square Layout they are W, SRB, 123456789, LMRB, UCD369.
 </para>
 
 <para>
 Canvas Control provides functionality for different kinds of operations on 
 the boxes: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Making a canvas pad current</emphasis>
  </para>
  <para>
  The current canvas pad corresponds to the box with the white background. 
  Clicking with the left mouse button into another named box will select 
  another canvas pad to become current. If this is not visible on the 
  Canvas it will be made visible.
  </para>
  <para>
  <emphasis>N.B.:</emphasis>
  </para>
  <para>
  You can also make a canvas pad current by clicking on it in the Canvas 
  (at least, if you can see part of the desired canvas pad).
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Copying the content of one canvas pad into another</emphasis>
  </para>
  <para>
  You can copy the content (picture) of one canvas pad into another by 
  dragging and dropping it into another one. While you are dragging, the cursor 
  will change to let you know that you are dragging. You can copy canvas 
  windows even if they are not current. After the copy finishes the target 
  canvas pad will become current.
  </para>
  <para>
  <emphasis>N.B.:</emphasis>
  </para>
  <para>
  Another possibility to copy is to drag from the Canvas Control into the
  Canvas 
  (if you can see in the Canvas at least a part of the target canvas pad).
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Zooming a region of one canvas pad into another</emphasis>
  </para>
  <para>
  Canvas Control contributes to the process of zooming with a rubber band, 
  however you cannot perform a zoom by using Canvas Control only. Further 
  information about using Canvas Control for zooming is available on the 
  Rubberband page
  (see <xref endterm="Rubberband.title" linkend="Rubberband"></xref>).
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Accessing the pop-up Canvas Pad Menu</emphasis>
  </para>
  <para>
  The pop-up Canvas Pad Menu
  (see <xref endterm="WindowMenu.title" linkend="WindowMenu"></xref>) can be 
  accessed by <emphasis>right-clicking</emphasis> with the mouse in the
  corresponding box. 
  The corresponding canvas pad will become selected. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="InteractionControl">
 <title id="InteractionControl.title">3.1.3 Interaction Control</title>
 
 <para>
 The interaction control part of the Control Window
 (see <xref endterm="ControlWindow.title" linkend="ControlWindow"></xref>) is used to 
 activate an interaction in a canvas pad and to modify interaction specific 
 control options of the activated interaction. Control options are described 
 under the specific interactions (see <xref linkend="Interactions"></xref>.
 </para>
 
 <para>
 Interactions can be invoked in different ways: 
 
 <itemizedlist>
 <listitem>
  <para>
 Via the interaction control of the Control Window: 
  </para>
  <para>
  In the Control Window they are represented as a set of tabs, each 
  representing a specific interaction. Clicking on a tab makes the 
  corresponding interaction available in the current canvas pad and 
  displays control options (if available for the selected interaction) on 
  the panel just below the set of tabs in the Control Window.
  </para>
 </listitem>
 <listitem>
  <para>
  Via a modifier key in a canvas pad: 
  </para>
  <para>
  An alternative representation is obtained by holding the
  <emphasis>I</emphasis> key down and <emphasis>right-clicking</emphasis>
  inside the canvas pad for which you want to change an interaction.
  As result you will get a pop-up menu
  (see <xref endterm="InteractionMenu.title" linkend="InteractionMenu"></xref>)
  with the same set of tabs as in the Control Window.
  You can select the interaction you want. 
  </para>
 </listitem>
 </itemizedlist> 
 
 Since not all interactions are available for all projections, only the 
  available interactions are shown for a specific projection.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="ParametersControl">
 <title id="ParametersControl.title">3.1.4 Parameter Control</title>
 
 <para>
 Atlantis has many parameters. For convenience these parameters are combined 
 into a number of groups that are accessed via the following tabs: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Proj</emphasis>
  </para>
  <para>
  To select a 
  projection and to modify specific parameters of the selected projection. 
  See <xref linkend="Projection"></xref>.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Data</emphasis>
  </para>
  <para>
  To select the 
  <xref endterm="DataTypes.title" linkend="DataTypes"></xref> of which the
  data will be used and to select the order of display 
  (e.g. when using different track reconstructions). See 
  <xref endterm="Data.title" linkend="Data"></xref>. 
  </para>
  <para>
  See the <emphasis>InDet</emphasis>, <emphasis>Calo</emphasis> and
  <emphasis>MuonDet</emphasis> tabs below for the
  appearance of the data in the various subdetector systems.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Cuts</emphasis> 
  </para>
  <para>
  To apply cuts to the physical values of the selected data. 
  See <xref endterm="Cuts.title" linkend="Cuts"></xref>. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>InDet</emphasis>
  </para>
  <para>
  To control the display and appearance of data in the inner detector.
  See <xref endterm="InDet.title" linkend="InDet"></xref>. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Calo</emphasis>
  </para>
  <para>
  To control the display and appearance of data in the calorimeters.
  See <xref endterm="Calo.title" linkend="Calo"></xref>. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>MuonDet</emphasis>
  </para>
  <para>
  To control the display and appearance of data in the muon system. 
  See <xref endterm="MuonDet.title" linkend="MuonDet"></xref>. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>AOD</emphasis>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>ATLAS</emphasis>
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="OutputDisplay">
 <title id="OutputDisplay.title">3.1.5 Output Display</title>
 
 <para>
 The output display is located at the very bottom of the 
 <emphasis>Control Window</emphasis> 
 (see <xref endterm="ControlWindow.title" linkend="ControlWindow"></xref>) 
 and is used as a replacement for standard terminal output. 
 It provides information in a more readable format by using multiple fonts 
 and colors.
 </para>
 
 <para>
 Information is shown e.g. from: 
 
 <itemizedlist>
 <listitem>
  <para>
  Rubberband interaction
  (see <xref endterm="Rubberband.title" linkend="Rubberband"></xref>) 
  </para>
 </listitem>
 <listitem>
  <para>
  Pick interaction
  (see <xref endterm="Pick.title" linkend="Pick"></xref>)
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="Canvas">
 <title id="Canvas.title">3.2 Canvas</title>
 
 <para>
 The display area window or <emphasis>Canvas</emphasis> is the place where 
 Atlantis draws pictures. It is opened when Atlantis is started. 
 </para>
 
 <para>
 <emphasis>Shape, Layout Set and Canvas Pads</emphasis>
 </para>
 
 <para>
 The Canvas has a user selectable <emphasis>shape</emphasis> with associated 
 <emphasis>layout set</emphasis>. A layout set is a set of predefined 
 subwindows within the selected shape. These subwindows are used to draw 
 pictures and are called <emphasis>canvas pads</emphasis>. 
 </para>
 
 <para>
 The different shapes of the Canvas are: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Landscape</emphasis>
  - Using a 3&times;2 grid to define the associated layout set. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Portrait</emphasis>
  - Using a 2&times;3 grid. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Square</emphasis>
  - Using a 3&times;3 grid. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Square B</emphasis>
  - Using a 3&times;3 grid (alternative layout set). 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Two Squares</emphasis>
  - Using a 2&times;1 grid. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 The user may select a shape via the
 <emphasis>Preferences&rarr;Change Canvas Layout</emphasis> menu 
 option of the Menu (see <xref endterm="Menu.title" linkend="Menu"></xref>) 
 of the Control Window. 
 The layout set of the selected shape is displayed in and controlled via the 
 Canvas Control
 (see <xref endterm="WindowControl.title" linkend="WindowControl"></xref>) 
 of the Control Window. 
 </para>
 
 <para>
 Each canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>) 
 has associated with it a <emphasis>projection</emphasis> 
 (see <xref linkend="Projection"></xref>), 
 an <emphasis>interaction</emphasis> (e.g. zooming, copying, see 
 <xref linkend="Interactions"></xref>) 
 and a <emphasis>parameter set</emphasis> (see 
 <xref endterm="ParametersControl.title" linkend="ParametersControl"></xref> 
 of the Control Window).
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Window">
 <title id="Window.title">3.2.1 Canvas Pads</title>
 
 <para>
 Canvas pads are the subwindows of the Canvas into which Atlantis 
 draws pictures (one picture per canvas pad). 
 The selection of the shape and associated layout set 
 of the Canvas determines the available canvas pads  
 (see <xref endterm="Canvas.title" linkend="Canvas"></xref>).
 </para>
 
 <para>
 Selection of the current canvas pad and copying 
 of pictures between canvas pads is performed via the Canvas Control 
 (see <xref endterm="WindowControl.title" linkend="WindowControl"></xref>) 
 of the Control Window.
 </para>
 
 <para>
 Each canvas pad has associated with it a projection 
 (see <xref linkend="Projection"></xref>), an interaction 
 (see <xref linkend="Interactions"></xref>) and a set of 
 parameters, which are controlled via the Interaction Control 
 (see <xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) 
 and the Parameter Control 
 (see <xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>) 
 of the Control Window. 
 </para>
 
 <para>
 Additionally, control is possible via the associated pop-up menus, which are 
 activated by modifier keys in a canvas pad:
 
 <table frame="topbot" pgwide="0">
 <title>Modifier keys and actions of canvas pad</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="modifierkey" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="action"      colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Modifier Key</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>right-click</emphasis> only
   </entry>
   <entry>Interaction pop-up menu
    (see <xref endterm="InteractionMenu.title" linkend="InteractionMenu"></xref>):
    interaction dependent operations (e.g. type of rubberband)
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>I</emphasis> + <emphasis>right-click</emphasis>
   </entry>
   <entry>Interaction pop-up menu
    (see <xref endterm="InteractionMenu.title" linkend="InteractionMenu"></xref>):
    list with available interactions
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>P + <emphasis>right-click</emphasis></emphasis>
   </entry>
   <entry>Projection pop-up menu
    (see <xref endterm="ProjectionMenu.title" linkend="ProjectionMenu"></xref>):
    projection dependent (e.g. restore aspect ratio)
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>W + <emphasis>right-click</emphasis></emphasis>
   </entry>
   <entry>Canvas pad pop-up menu
    (see <xref endterm="WindowMenu.title" linkend="WindowMenu"></xref>):
    restore canvas pad defaults, rotation, flipping, etc.
   </entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="PopUpWindows">
 <title id="PopUpWindows.title">3.3 Pop-up Windows</title>
 
 <para>
 These windows are popped up while running Atlantis, generally by using a 
 modifier key 
 (see <xref endterm="MouseModifierKeys.title" linkend="MouseModifierKeys"></xref>). The pop-up 
 windows contain menus which provide different "one click" operations: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Canvas Pad Menu</emphasis> 
  (see <xref endterm="WindowMenu.title" linkend="WindowMenu"></xref>) 
  - Provides canvas pad related operations (restoring of defaults, rotation 
  and flipping, etc.). 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Projection Menus</emphasis> 
  (see <xref endterm="ProjectionMenu.title" linkend="ProjectionMenu"></xref>) 
  - Provide projection specific operations. Each projection has it's own menu. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Interaction Menus</emphasis> 
  (see <xref endterm="InteractionMenu.title" linkend="InteractionMenu"></xref>) 
  - Provide interaction specific operations. Not all interactions have such a 
  menu. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Lists Window</emphasis> 
  (see <xref endterm="Lists.title" linkend="Lists"></xref>) 
  - Allows the interactive definition and manipulation of subsets of data. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Modifier Keys Window</emphasis> 
  (see <xref endterm="MouseModifiersWindow.title" linkend="MouseModifiersWindow"></xref>) 
  - Shows information about various modifier keys. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Help Window</emphasis> 
  (see <xref endterm="HelpWindow.title" linkend="HelpWindow"></xref>) 
  - To browse the Atlantis Help System pages. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>ZMR Pop-up Menu</emphasis> 
  (see <xref endterm="ZMR.title" linkend="ZMR"></xref>) 
  - Zoom/Move/Rotate control.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Interactive Athena</emphasis> (see <xref linkend="Athena"></xref>).
  - Dialog window for interaction with Athena.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 The menus disappear either after the appropriate action has been selected or 
 when another left-click is performed on the corresponding window.
 </para>
 
 <para>
 See <xref endterm="MouseModifierKeys.title" linkend="MouseModifierKeys"></xref>.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="WindowMenu">
 <title id="WindowMenu.title">3.3.1 Canvas Pad Menu</title>
 
 <para>
 This pop-up menu provides canvas pad related operations such as restoring 
 the defaults, rotation and flipping, etc. This menu is the same for all 
 canvas pads and it is not projection dependent. It can be accessed in 
 two different ways: 
 
 <itemizedlist>
 <listitem>
  <para>
  By applying the <emphasis>W + right-click</emphasis>
  combination in the canvas pad from which you want to get the menu. 
  </para>
 </listitem>
 <listitem>
  <para>
  By <emphasis>right-clicking</emphasis> in one of the canvas
  mini-windows in the Canvas Control of the Control Window. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 In both cases the Window pop-up menu will appear on the screen. 
 The content of the menu is: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Horizontal Flip</emphasis>
  - mirrors the picture w.r.t vertical middle line of the selected canvas pad 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Vertical Flip</emphasis>
  - mirrors the picture w.r.t horizontal middle line of the selected canvas pad 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Rotate by 90</emphasis>
  - rotates the picture by 90<emphasis>&deg;</emphasis> in the
  clockwise direction 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Rotate by -90</emphasis>
  - rotates the picture by 90<emphasis>&deg;</emphasis> in the
  counterclockwise direction 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Toggle Scale</emphasis>
  - toggles <emphasis>on</emphasis> or <emphasis>off</emphasis> the state of 
  the canvas pad scales 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Restore Size and Position</emphasis>
  - restores the size and the position of the 
  picture in the selected canvas pad as it was at the startup of the program 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Freeze</emphasis>
  - Freezes the graphics state of the selected canvas pad 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Unfreeze</emphasis>
  - Unfreezes the graphics state of the selected canvas window 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 Any operation chosen from the Canvas Pad Menu is applied to the currently 
 selected canvas pad.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="ProjectionMenu">
 <title id="ProjectionMenu.title">3.3.2 Projection Menus</title>
 
 <para>
 Each Atlantis projection (see <xref linkend="Projection"></xref>) has a pop-up menu 
 associated with it. This menu contains projection dependent operations. To 
 access the projection menu perform the combination 
 <emphasis>P + right-click</emphasis>. As 
 a result the window in which you have clicked will become selected and the 
 menu will appear on the screen. If you select any of the operations of the 
 projection menu, the operation will be applied to the currently selected 
 window.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 </sect2><sect2 id="InteractionMenu">
 <title id="InteractionMenu.title">3.3.3 Interaction Menus</title>
 
 <para>
 There are two typical pop-up menus for interaction control 
 (see <xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>): 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Interaction list pop-up menu</emphasis>
  </para>
  <para>
  A menu with a list of all available interactions in a canvas pad. This 
  list is dependent on the selected projection in the canvas pad.  The menu 
  is invoked by keeping the <emphasis>I</emphasis> key down and 
  <emphasis>right-clicking</emphasis>. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Interaction pop-up menu</emphasis>
  </para>
  <para>
  Many Atlantis interactions have a pop-up menu with interaction dependent 
  operations associated with the selected projection. To invoke the menu, 
  <emphasis>right-click</emphasis> in the desired canvas pad.
  As a result the canvas 
  window will become selected and the menu will appear on the screen. If you 
  select any of the operations of the interaction menu, the operation will be 
  applied to the currently selected canvas pad. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 The ZMR Pop-up Menu is described in 
 <xref endterm="ZMR.title" linkend="ZMR"></xref>.
 </para>
 
 <para>
 The Fisheye Pop-up Menu is described in 
 <xref endterm="FishEye.title" linkend="FishEye"></xref>. 
 </para>
 
 <para>
 The Skew Pop-up Menu is described in 
 <xref endterm="Skew.title" linkend="Skew"></xref>. 
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Lists">
 <title id="Lists.title">3.3.4 Lists Window</title>
 
 <para>
 The Lists pop-up window allows the interactive definition and manipulation 
 of subsets of data. Lists are kept in the form of a singly-rooted tree and 
 may be manipulated in a way similar to Windows Explorer. 
 </para>
 
 <para>
 <emphasis>Predefined lists</emphasis>
 </para>
 
 <para>
 By default there are four predefined lists, three of which are used for 
 special purposes:
 
 <table frame="topbot" pgwide="0">
 <title>Predefined lists</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="modifierkey" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="action"      colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>List</entry>
   <entry>Purpose</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>Highlight</emphasis></entry>
   <entry>This list should contain at most one item that is to be drawn 
    in a special highlighted color (normally white). This list is controlled
    via the pick interaction (see <xref endterm="Pick.title" linkend="Pick"></xref>).
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Last Drawn</emphasis></entry>
   <entry>This list contains all data which were actually drawn on the 
    screen by the last drawing operation. This list is by its very nature 
    transient and can only be usefully manipulated after it has been copied.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Others</emphasis></entry>
   <entry>May be used to control the color of all data which are drawn 
    in a picture but which are not given a color by any user defined list.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>List 0</emphasis></entry>
   <entry>This is a predefined list which may be manipulated by the user. 
   </entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 <para>
 <emphasis>Nodes</emphasis>
 </para>
 
 <para>
 The current node is indicated in the Lists Window by a purple background 
 region drawn around its text. If no node is current, actions applied to the 
 current list are applied to the root node "Lists". Nodes may be either 
 directories (depicted by rectangles) or data items (depicted by squares). 
 Data items may represent a single item (e.g. STr 5 for simulated track number 
 5) or a group of similar items (e.g. STr(22) for a group of 22 simulated 
 tracks).
 </para>
 
 <para>
 <emphasis>Adding data to the current list</emphasis>
 </para>
 
 <para>
 Single user selected items may be added to the currently selected directory 
 using the pick interaction 
 (see <xref endterm="Pick.title" linkend="Pick"></xref>) 
 of the interaction control of the Control Window 
 (the interaction is described under Interactions). 
 Groups of 
 items are best added by using a rubberband to select and draw them in an 
 unused window temporarily and then by making a copy of the last drawn list.
 </para>
 
 <para>
 <emphasis>Manipulation of lists</emphasis>
 </para>
 
 <para>
 Data items and directories may be moved by dragging them to the desired 
 destination directory. They may be copied by dragging them to the desired 
 destination directory while holding down the <emphasis>ctrl-key</emphasis>. 
 Each node has 
 an associated pop-up menu which may be obtained by right-clicking on its 
 rectangle or square. The contents of the pop-up menu is node specific and 
 may contain standard operations such as:
 
 <table frame="topbot" pgwide="0">
 <title>Options for the manipulation of lists</title>
 <tgroup cols="3">
 <colspec colnum="1" colname="colone"   colwidth="2*" align="left"></colspec>
 <colspec colnum="2" colname="coltwo"   colwidth="3*" align="left"></colspec>
 <colspec colnum="3" colname="colthree" colwidth="6*" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Option</entry>
   <entry>Node Type</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>Remove</emphasis></entry>
   <entry>All (except root)</entry>
   <entry>Remove the node from the tree</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Rename</emphasis></entry>
   <entry>Directories</entry>
   <entry>Rename the node</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>New Parent</emphasis></entry>
   <entry>All (except root)</entry>
   <entry>Add new parent directory (List) above a node</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>New Child</emphasis></entry>
   <entry>Directories</entry>
   <entry>Add new child directory (List) below a node</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Reset</emphasis></entry>
   <entry>Root</entry>
   <entry>Reset the Lists removing any user supplied data</entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 <para>
 or it may contain actions appropiate to the type of data contained by the 
 node, e.g. <emphasis>Vertex</emphasis> to form a secondary vertex from a 
 group of three reconstructed tracks.
 </para>
 
 <para>
 <emphasis>Coloring of lists</emphasis>
 </para>
 
 <para>
 A color may be associated to a user-defined node and it will be applied as 
 the default color for all contained child nodes (which are not themselves 
 given a selected color). Colors are applied by selecting a node as current 
 and then clicking on the corresponding color icon in the color palette on 
 the right of the lists window. Two special "colors" which may be associated 
 are (+) default color or (x) invisible.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="MouseModifiersWindow">
 <title id="MouseModifiersWindow.title">3.3.5 Modifier Keys Window</title>
 
 <para>
 This pop-up window is activated from the menu of the Control Window and 
 shows information about various active modifier keys.
 
 <table frame="topbot" pgwide="0">
 <title>Modifier keys</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="modifierkey" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="action"      colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Modifier Key</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>I + right-click</emphasis></entry>
   <entry>Interaction Manager pops up</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>P + right-click</emphasis></entry>
   <entry>Projection Menu pops up</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>W + right-click</emphasis></entry>
   <entry>Canvas Pad Menu pops up</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>right-click</emphasis></entry>
   <entry>Interaction Menu pops up</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>&nbsp;</emphasis></entry>
   <entry>Zoom</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>C</emphasis></entry>
   <entry>Change position Central Point</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>F</emphasis></entry>
   <entry>Fast zoom</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>H</emphasis></entry>
   <entry>Horizontal zoom</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>M</emphasis></entry>
   <entry>Move (pan)</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>R</emphasis></entry>
   <entry>Rotate</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>V</emphasis></entry>
   <entry>Vertical zoom</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Z</emphasis></entry>
   <entry>Zoom</entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="HelpWindow">
 <title id="HelpWindow.title">3.3.6 Help Window</title>
 
 <para>
 The help window is a pop-up window that is used to browse the online 
 documentation pages of the Atlantis Help System
 (see <xref linkend="HelpHowTo"></xref>).
 </para>
 
 <para>
 The window may be opened via the <emphasis>Help&rarr;Help Content</emphasis> 
 menu option of the menu 
 (see <xref endterm="Menu.title" linkend="Menu"></xref>) 
 of the Control Window.  It starts by showing the Table of Contents.
 </para>
 
 <para>
 The window may also be opened by <emphasis>right-clicking</emphasis> on a 
 graphical component. 
 If the component has a help page attached, this page is shown.
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="MouseModifierKeys">
 <title id="MouseModifierKeys.title">3.4 Modifier Keys</title>
 
 <para>
 Modifier keys are combinations of a keyboard key and a mouse key that are 
 used to generate pop-up menus or to perform interactions. Generally a 
 keyboard key is kept pressed and during this pressing, a mouse key is 
 clicked (e.g. to get a pop-up menu) or kept pressed (e.g. zooming).
 </para>
 
 <para>
 A list of available modifier keys with conditions and actions:
 
 <table frame="topbot" pgwide="0">
 <title>Modifier keys and actions</title>
 <tgroup cols="3">
 <colspec colnum="1" colname="colone"   colwidth="2*" align="left"></colspec>
 <colspec colnum="2" colname="coltwo"   colwidth="6*" align="left"></colspec>
 <colspec colnum="3" colname="colthree" colwidth="6*" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Modifier Key</entry>
   <entry>Condition</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>left-press</emphasis> only</entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Zoom with respect to the central point (horizontal zoom in the 
    &phi;/&rho; projection (see <xref endterm="FR.title" linkend="FR"></xref>))
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>left-press</emphasis> only</entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>),
    3DBox projection active (see <xref endterm="3DBox.title" linkend="3DBox"></xref>)
   </entry>
   <entry>Change the volume of the box</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>right-click</emphasis> only</entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Interaction pop-up menu
    (see <xref endterm="InteractionMenu.title" linkend="InteractionMenu"></xref>):
    interaction dependent operations (e.g. type of rubberband)
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>A</emphasis> + <emphasis>left-click</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>),
    pick interaction active (see <xref endterm="Pick.title" linkend="Pick"></xref>)
   </entry>
   <entry>Add the data item to be picked to the currently selected list node
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>C</emphasis> + <emphasis>left-click</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>),
    pick interaction active (see <xref endterm="Pick.title" linkend="Pick"></xref>)
   </entry>
   <entry>Clear the highlight list node</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>C</emphasis> + <emphasis>left-click</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Change position of central point</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>F</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Fast zoom with respect to the central point (horizontal zoom 
    in the &phi;/&rho; projection (see <xref endterm="FR.title" linkend="FR"></xref>));
    data are not shown during the zoom
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>H</emphasis> + <emphasis>left-click</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>),
    pick interaction active (see <xref endterm="Pick.title" linkend="Pick"></xref>)
   </entry>
   <entry>Highlight, place the data item to be picked in the highlight 
    list node, causing it to be drawn in white
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>H</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Horizontal zoom with respect to the central point
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>H</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>),
    3DBox projection active (see <xref endterm="3DBox.title" linkend="3DBox"></xref>)
   </entry>
   <entry>Change the length of the box</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>I</emphasis> + <emphasis>right-click</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Interaction list pop-up menu
    (see <xref endterm="InteractionMenu.title" linkend="InteractionMenu"></xref>):
    list with available interactions
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>M</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Move (panning)</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>P</emphasis> + <emphasis>right-click</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Projection pop-up menu
    (see <xref endterm="ProjectionMenu.title" linkend="ProjectionMenu"></xref>);
    projection dependent (e.g. restore aspect ratio)
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>P</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>),
    synchro cursors active
    (see <xref endterm="SynchroCursors.title" linkend="SynchroCursors"></xref>)
   </entry>
   <entry>Change splitting angle &phi; and copy it to &rho;/Z projection</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>R</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Rotate (projection dependent)</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>R</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>),
    3DBox projection active (see <xref endterm="3DBox.title" linkend="3DBox"></xref>)
   </entry>
   <entry>Rotate the tracks around the direction of flight of the decaying particle
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>V</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Vertical zoom with respect to the central point</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>V</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>),
    3DBox projection active (see <xref endterm="3DBox.title" linkend="3DBox"></xref>)
   </entry>
   <entry>Change the width of the box</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>W</emphasis> + <emphasis>right-click</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Canvas pad pop-up menu
    (see <xref endterm="WindowMenu.title" linkend="WindowMenu"></xref>):
    restore canvas pad defaults, rotation, flipping, etc.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Z</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>)
   </entry>
   <entry>Zoom with respect to the central point (horizontal zoom in the
    &phi;/&rho; projection
    (see <xref endterm="FR.title" linkend="FR"></xref>))
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Z</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry>in canvas pad (see <xref endterm="Window.title" linkend="Window"></xref>),
    3DBox projection active (see <xref endterm="3DBox.title" linkend="3DBox"></xref>)
   </entry>
   <entry>Change the volume of the box</entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 </sect1>
 
 </chapter>
 
 <!--=======================================================================-->
 <chapter id="Interactions">
 <title id="Interactions.title">Interactions</title>
 
 <para>
 It is very important to understand how interactions work, so you may use the 
 full power of each. There are two sets of interactions, the interactions that 
 are sensible for all projections (<emphasis>global interactions</emphasis>) 
 and the interactions which are only sensible for some specific projections 
 (<emphasis>projection dependent interactions</emphasis>). As a consequence, 
 each projection has a specific set of associated interactions represented by 
 the set of tabs in the Control Window.
 </para>
 
 <para>
 <emphasis>N.B.:</emphasis> See the detailed information about available 
 projections in <xref linkend="Projection"></xref>.
 </para>
 
 <para>
 <emphasis>Global Interactions</emphasis>
 </para>
 
 <para>
 Interactions that are available in all projections: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>ZMR</emphasis> 
  (see <xref endterm="ZMR.title" linkend="ZMR"></xref>)
  - Zoom, move and/or rotate a picture in a canvas pad. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Rubberband</emphasis> 
  (see <xref endterm="Rubberband.title" linkend="Rubberband"></xref>) - 
  Different kinds of rubberband selections. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Pick</emphasis> 
  (see <xref endterm="Pick.title" linkend="Pick"></xref>) - Used to pick 
  an object in one projection and find it in another. Also used to display 
  information about hits, tracks or detectors. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>SC</emphasis> 
  (see <xref endterm="SynchroCursors.title" linkend="SynchroCursors"></xref>) - Synchronised 
  cursors, used to see the same cursor position in different projections. 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>Projection Dependent Interactions</emphasis>
 </para>
 
 <para>
 Interactions that perform operations which only make sense in specific 
 projections: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Fisheye</emphasis> 
  (see <xref endterm="FishEye.title" linkend="FishEye"></xref>) - Available in 
  Y/X  (see <xref endterm="YX.title" linkend="YX"></xref>), 
  &rho;/Z  (see <xref endterm="RZ.title" linkend="RZ"></xref>), 
  &phi;/&rho;  (see <xref endterm="FR.title" linkend="FR"></xref>), 
  &phi;/Z  (see <xref endterm="FZ.title" linkend="FZ"></xref>), 
  X'/Z  (see <xref endterm="XZ.title" linkend="XZ"></xref>), 
  Y'/Z  (see <xref endterm="YZ.title" linkend="YZ"></xref>) and 
  3D  (see <xref endterm="3D.title" linkend="3D"></xref>). 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Clock</emphasis> 
  (see <xref endterm="Clock.title" linkend="Clock"></xref>) - Available in 
  Y/X (see <xref endterm="YX.title" linkend="YX"></xref>) only. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Skew</emphasis> 
  (see <xref endterm="Skew.title" linkend="Skew"></xref>) - Available in 
  &rho;/Z (see <xref endterm="RZ.title" linkend="RZ"></xref>), 
  &phi;/&rho; (see <xref endterm="FR.title" linkend="FR"></xref>)
  and &phi;/Z (see <xref endterm="FZ.title" linkend="FZ"></xref>). 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Scale</emphasis>
  (see <xref endterm="ScaleCopy.title" linkend="ScaleCopy"></xref>) - Available in 
  Y/X (see <xref endterm="YX.title" linkend="YX"></xref>), 
  &phi;/&eta; (see <xref endterm="VP.title" linkend="VP"></xref>), 
  &rho;/Z (see <xref endterm="RZ.title" linkend="RZ"></xref>), 
  &phi;/&rho; (see <xref endterm="FR.title" linkend="FR"></xref>), 
  &phi;/Z (see <xref endterm="FZ.title" linkend="FZ"></xref>), 
  X'/Z (see <xref endterm="XZ.title" linkend="XZ"></xref>), 
  Y'/Z (see <xref endterm="YZ.title" linkend="YZ"></xref>) and 
  3D (see <xref endterm="3D.title" linkend="3D"></xref>). 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>Interaction Control</emphasis>
 </para>
 
 <para>
 Interactions are selected and interaction parameters are modified via the 
 interaction control 
 (see <xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) of the 
 Control Window. 
 </para>
 
 <para>
 <emphasis>Interaction Pop-up Menus</emphasis>
 </para>
 
 <para>
 Many interactions have an associated pop-up menu that is invoked for a 
 picture by <emphasis>right-clicking</emphasis> in the canvas pad.  
 See  <xref endterm="InteractionMenu.title" linkend="InteractionMenu"></xref>.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="ZMR">
 <title id="ZMR.title">4.1 Zoom/Move/Rotate (ZMR)</title>
 
 <para>
 The ZMR interaction allows the user to perform zooming, moving and rotation 
 of the picture content in a canvas pad 
 (<xref endterm="Window.title" linkend="Window"></xref>). It is 
 activated for the current canvas pad by clicking on the ZMR tab of the 
 interaction control
 (<xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) 
 in the Control Window. 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Zoom</emphasis> 
  </para>
  <para>
  Zooming is always done with respect to a <emphasis>central point</emphasis>
  (<xref endterm="CentralPoint.title" linkend="CentralPoint"></xref>) which 
  the user can specify. The central point is represented by a small red circle 
  superimposed on the picture. 
  </para>
  <para>
  If you want to perform a zoom operation just drag a point of the picture 
  inside or outside, increasing or decreasing its distance to the central
  point. 
  </para>
  <para>
  See the <emphasis>Modifier Key Summary</emphasis> for the different types
  of zoom that can be applied.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Move</emphasis>
  </para>
  <para>
  You can move (pan) the picture by dragging a point of the picture while 
  keeping the <emphasis>M</emphasis> key pressed.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Rotate</emphasis> 
  </para>
  <para>
  Rotation is also done with respect to a <emphasis>central point</emphasis>
  (<xref endterm="CentralPoint.title" linkend="CentralPoint"></xref>) which 
  the user can specify. To obtain a rotation of the picture you drag a point of 
  the picture around while keeping the <emphasis>R</emphasis> key pressed. 
  </para>
  <para>
  Note that rotation is a projection dependent operation: 
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>Y/X</emphasis> (<xref endterm="YX.title" linkend="YX"></xref>)
   - It performs a real rotation around the central point. 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>  &rho;/Z (<xref endterm="RZ.title" linkend="RZ"></xref>), 
   X'/Z (<xref endterm="XZ.title" linkend="XZ"></xref>), 
   Y'/Z</emphasis> (<xref endterm="YZ.title" linkend="YZ"></xref>)
   - It performs a rotation of splitting angle &phi; or the viewing angle
   &phi;<subscript>
   VIEW</subscript>, respectively. 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>  &phi;/&rho; (<xref endterm="FR.title" linkend="FR"></xref>), 
   &phi;/Z (<xref endterm="FZ.title" linkend="FZ"></xref>), &phi;/&eta;
   (<xref endterm="VP.title" linkend="VP"></xref>)</emphasis>
   - It performs a shift (up or down) of the &phi; scale. 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>The ZMR Pop-up Menu</emphasis>
 </para>
 
 <para>
 The ZMR pop-up menu can be accessed by <emphasis>right-clicking</emphasis> in 
 a canvas window with ZMR applied. It contains the following utility 
 operations: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>To Center of Detector</emphasis> - Sets the 
  <emphasis>central point</emphasis>
  (<xref endterm="CentralPoint.title" linkend="CentralPoint"></xref>) to 
  the geometrical center of the detector. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Center the Picture</emphasis> - Shifts the picture
  in such a way that the 
  center of the detector coincides with the center of the canvas pad. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Unzoom Full</emphasis> - Restores the window to its initial 
  zoomed state.
 </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>Modifier Key Summary</emphasis>
 
 <table frame="topbot" pgwide="0">
 <title>Modifier key summary</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="colone" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="coltwo" colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Modifier Key</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry>None</entry>
   <entry><emphasis>Zoom</emphasis> with respect to the central point
    (horizontal zoom in the &phi;/&rho; projection
    (<xref endterm="FR.title" linkend="FR"></xref>))
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>F</emphasis></entry>
   <entry><emphasis>Fast Zoom</emphasis> with respect to the central point 
    (horizontal zoom in the &phi;/&rho; projection 
    (<xref endterm="FR.title" linkend="FR"></xref>)); 
    data are not updated during the zoom
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>H</emphasis></entry>
   <entry><emphasis>Horizontal Zoom</emphasis> with respect to the central point
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>V</emphasis></entry>
   <entry><emphasis>Vertical Zoom</emphasis> with respect to the central point
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>M</emphasis></entry>
   <entry><emphasis>Move</emphasis> (panning)</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>R</emphasis></entry>
   <entry><emphasis>Rotate</emphasis> (projection dependent)</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>C</emphasis></entry>
   <entry>Change position of <emphasis>central point</emphasis></entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="CentralPoint">
 <title id="CentralPoint.title">4.1.1 Central Point</title>
 
 <para>
 The central point is used by the ZMR interaction for zooming (all projections) 
 and rotation (Y/X projection) in a canvas pad. It is represented as a small 
 <emphasis>red circle</emphasis> superimposed on the picture.
 </para>
 
 <para>
 By default the central point is in the center of the detector (0, 0, 0). 
 There are different ways to change it's position: 
 
 <itemizedlist>
 <listitem>
  <para>
  By pressing the <emphasis>C</emphasis> key on the keyboard and the
  <emphasis>left</emphasis> mouse button to specify the new center position. 
  </para>
 </listitem>
 <listitem>
  <para>
  By selecting "<emphasis>To Center of Detector</emphasis>" in the ZMR Pop-up
  Menu to set the center back to it's initial position (center of the detector).
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="Rubberband">
 <title id="Rubberband.title">4.2 Rubberband</title>
 
 <para>
 The rubberband interaction provides an alternative way of zooming in 
 Atlantis. Unlike the ZMR interaction 
 (<xref endterm="ZMR.title" linkend="ZMR"></xref>) you may 
 exactly specify the region you are interested in by simply drawing a 
 rubberband around that region. The interaction is activated for the current 
 canvas pad by clicking on the Rubberband tab of the interaction control 
 (<xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) in the 
 Control Window.
 </para>
 
 <para>
 If rubberbanding is activated, the panel below the rubberband tab shows a 
 box from which you may select a rubberband type: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Rectangle</emphasis>
  </para>
  <para>
  Rectangle is specified by two opposite corners. Sides run parallel to the 
  projection axes. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Rotated Rectangle</emphasis>
  </para>
  <para>
  Rectangle is specified by two middle points of opposite sides. These points 
  can be moved to change the orientation of the rectangle and the corners can 
  be moved to increase or decrease the width of the rectangle. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Parallelogram</emphasis>
  </para>
  <para>
  Parallelogram is specified by two middle points of opposite sides. These 
  points can be moved to change the orientation of the parallelogram (the side 
  with the opposite point remains fixed) and the corners can be moved both to 
  change the orientation and to increase or decrease the width of the
  parallelogram (the two middle points remain fixed). 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Square</emphasis>
  </para>
  <para>
  Square is specified by the central point and by a corner. Preserves the 
  aspect ratio of the picture. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>X Skew</emphasis>
  </para>
  <para>
  As parallelogram but with base side horizontally fixed. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Y Skew</emphasis>
  </para>
  <para>
  As parallelogram but with base side vertically fixed. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>X Slice</emphasis>
  </para>
  <para>
  Vertical slice is specified by points on left and right side. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Y Slice</emphasis>
  </para>
  <para>
  Horizontal slice is specified by points on left and right side. 
  </para>
 </listitem>
 </itemizedlist> 
 
 Draw a rubberband in the current canvas pad by clicking and then 
 dragging with the left mouse button on the picture. When you release the 
 mouse button a pop-up menu will appear near your mouse. 
 </para>
 
 <para>
 Now you may re-adjust the rubberband by moving any of its corners or (if 
 applicable) middle points.
 </para>
 
 <para>
 There are two options to apply the current rubberband: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Zoom in the same canvas pad</emphasis>
  - Just click the Zoom button of the pop-up menu.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Zoom in some other canvas pad</emphasis> - Two options: 
  <itemizedlist>
  <listitem>
   <para>
   Drag the Zoom button of the pop-up menu into one of the
   canvas pads shown in the canvas control
   (<xref endterm="WindowControl.title" linkend="WindowControl"></xref>) of the 
   Control Window. 
   </para>
  </listitem>
  <listitem>
   <para>
   Drag the Zoom button of the pop-up menu into the target
   canvas pad directly (in the Canvas). This only works if at least some part
   of the target canvas pad is visible on the Canvas. 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>Rubberband Pop-up Menu</emphasis>
 
 <table frame="topbot" pgwide="0">
 <title>Options of rubberband pop-up menu</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="colone" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="coltwo" colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Option</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>Zoom</emphasis></entry>
   <entry>Zooms the selected region.</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>New List</emphasis></entry>
   <entry>Shows the Lists pop-up window (<xref endterm="Lists.title" linkend="Lists"></xref>).
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Summarize</emphasis></entry>
   <entry>Information about the selected objects is displayed in the
    output display (<xref endterm="OutputDisplay.title" linkend="OutputDisplay"></xref>)
    of the Control Window.
   </entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 <para>
 <emphasis>Unzoom</emphasis>
 </para>
 
 <para>
 After a rubberband has been applied, you may right-click 
 in the canvas pad to get a pop-up Unzoom button. Click to undo the zoom. 
 This works recursively. 
 </para>
 
 <para>
 <emphasis>Unzoom Full</emphasis>
 </para>
 
 <para>
 After any number of rubberbands have been applied, you may right-click 
 in the canvas pad to get a pop-up Unzoom Full button. Click to restore 
 the window to its initial zoomed state.
 </para>
 
 <para>
 <emphasis>Rubberbanding in YX</emphasis>
 </para>
 
 <para>
 In the YX (<xref endterm="YX.title" linkend="YX"></xref>) projection 
 the rectangular rubberband has additional functionality, which is 
 described in Rubberband in YX Projection 
 (<xref endterm="RubberbandYX.title" linkend="RubberbandYX"></xref>).
 </para>
 
 <para>
 <emphasis>Rubberbanding in &phi;/&eta;</emphasis>
 </para>
 
 <para>
 In the &phi;/&eta; (<xref endterm="VP.title" linkend="VP"></xref>) projection 
 only the rectangular rubberband is available. However in this projection 
 the rubberbanding has additional functionality, which is described in 
 Rubberband in &phi;/&eta; Projection 
 (<xref endterm="VPSelection.title" linkend="VPSelection"></xref>).
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="RubberbandYX">
 <title id="RubberbandYX.title">4.2.1 Rubberband in YX Projection</title>
 
 <para>
 In the YX projection (<xref endterm="YX.title" linkend="YX"></xref>) 
 the normal rubberband options exist
 (<xref endterm="Rubberband.title" linkend="Rubberband"></xref>) 
 except for the rectangle rubberband. In this projection the rectangle rubberband 
 has additional functionality which is available as extra options in the pop-up 
 menu which appears when a rubberbanding operation is complete. These extra options 
 are described in the following table:
 
 <table frame="topbot" pgwide="0">
 <title>Additional rubberbanding options</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="colone" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="coltwo" colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Option</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>Zoom Summed Endcaps</emphasis></entry>
   <entry>Zooms the currently selected region, showing the summed data over each 
    of layers of the endcaps LAr-, LAr+, HEC-, and HEC+ being shown in canvas pads 
    1-4, respectively.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Zoom Endcap Layers -</emphasis></entry>
   <entry>Zooms the currently selected region, showing the 8 individual layers of 
    the LAr and HEC Endcap in the - z region, shown in canvas pads 1-8 with the 
    zoomed in region of the &rho;Z view in canvas pad 9.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Zoom Endcap Layers +</emphasis></entry>
   <entry>As <emphasis>Zoom Endcap Layers -</emphasis>, but for the +z region 
    of the Endcap.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Zoom Endcap Layers both</emphasis></entry>
   <entry>As <emphasis>Zoom Endcap Layers -</emphasis>, but shows hits for both 
    the +z region and -z region of the Endcap.
   </entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 <para>
 <emphasis>Unzoom Features</emphasis>
 </para>
 
 <para>
 After a rubberband has been applied, you may right-click in the canvas pad 
 to get a pop-up menu which will have the normal rubberband features 
 (<xref endterm="Rubberband.title" linkend="Rubberband"></xref>). There are 
 also <emphasis>Unzoom Summed</emphasis> and <emphasis>Unzoom Layers</emphasis>.
 </para>
 
 <para>
 <emphasis>Unzoom Summed</emphasis>
 </para>
 
 <para>
 After <emphasis>Zoom Summed Endcaps</emphasis> has been applied, you may 
 right-click in the canvas pad to get a pop-up Unzoom Summed button. Click 
 to undo the <emphasis>Zoom Summed Endcaps</emphasis>. This works recursively. 
 </para>
 
 <para>
 <emphasis>Unzoom Layers</emphasis>
 </para>
 
 <para>
 As <emphasis>Unzoom Summed</emphasis> but for when any of 
 <emphasis>Zoom Endcap Layers -</emphasis>, <emphasis>Zoom Endcap Layers +</emphasis>, 
 or <emphasis>Zoom Endcap Layers both</emphasis> have been applied.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="VPSelection">
 <title id="VPSelection.title">4.2.2 Rubberband in &phi;/&eta; Projection</title>
 
 <para>
 In the &phi;/&eta; projection (<xref endterm="VP.title" linkend="VP"></xref>) 
 only the rectangular rubberband 
 (<xref endterm="Rubberband.title" linkend="Rubberband"></xref>) 
 is available. 
 However in this projection the rubberbanding has additional functionality 
 which is available as extra options in the pop-up menu which appears when a 
 rubberbanding operation is complete. These extra options are described in 
 the following table:
 
 <table frame="topbot" pgwide="0">
 <title>Additional rubberbanding options</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="colone" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="coltwo" colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Option</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>Zoom LAr</emphasis></entry>
   <entry>Zooms the currently selected region, with the four samplings 
    of the LAr calorimeter being shown in canvas pads 1-4, respectively.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Zoom Calorimeters</emphasis></entry>
   <entry>As <emphasis>Zoom LAr</emphasis>, with additionally the four
    samplings of the hadronic calorimeters being shown in canvas
    pads 5-8, respectively.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Cut</emphasis></entry>
   <entry>Switch on the &phi; and &eta; cuts, with the cut region set to 
    that defined by the rubberband. 
    If this <emphasis>Cut</emphasis> is dragged into another canvas pad the
    projection in that canvas pad is not changed.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Whole Window</emphasis></entry>
   <entry>Sets the current zoom region to correspond to the whole canvas window.
   </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Print Contents</emphasis></entry>
   <entry>A short summary describing the tracks and the calorimetric energy
    inside the rubberband region is displayed in the output display 
    (<xref endterm="OutputDisplay.title" linkend="OutputDisplay"></xref>) of the 
    Control Window.
   </entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 <para>
 <emphasis>Unzoom Features</emphasis>
 </para>
 
 <para>
 After a rubberband has been applied, you may right-click in the canvas pad 
 to get a pop-up menu which will have the normal rubberband features 
 (<xref endterm="Rubberband.title" linkend="Rubberband"></xref>). There are 
 also <emphasis>Unzoom LAr</emphasis> and <emphasis>Unzoom Calorimeters</emphasis>.
 </para>
 
 <para>
 <emphasis>Unzoom LAr</emphasis>
 </para>
 
 <para>
 After <emphasis>Zoom LAr</emphasis> has been applied, you may 
 right-click in the canvas pad to get a pop-up Unzoom LAr button. Click 
 to undo the <emphasis>Zoom LAr</emphasis>. This works recursively. 
 </para>
 
 <para>
 <emphasis>Unzoom Calorimeters</emphasis>
 </para>
 
 <para>
 As <emphasis>Unzoom LAr</emphasis> but for when  
 <emphasis>Zoom Calorimeters</emphasis> has been applied.
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="Pick">
 <title id="Pick.title">4.3 Pick</title>
 
 <para>
 The pick interaction has two modes, allowing the selection of either hits 
 and tracks or detectors. The desired mode is selected from the box on the 
 panel of the Pick tab in the interaction control 
 (<xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) 
 of the Control Window. 
 </para>
 
 <para>
 <emphasis>Hits and Tracks</emphasis>
 </para>
 
 <para>
 If the picking mode is set to hits and tracks: 
 
 <itemizedlist>
 <listitem>
  <para>
  Clicking the <emphasis>left mouse button</emphasis> in a
  canvas pad will move the cursor to the nearest data item in the window and
  will show information about the picked data item on the output display
  (<xref endterm="OutputDisplay.title" linkend="OutputDisplay"></xref>) of the 
  Control Window. 
  </para>
 </listitem>
 <listitem>
  <para>
  Clicking the <emphasis>right mouse button</emphasis> will
  move the cursor to the nearest appearance of the previously picked data
  item in the canvas pad where the mouse button is pressed. In the case of 
  <itemizedlist>
  <listitem>
   <para>
   a hit, which is drawn once on a canvas pad, the cursor is
   moved to that hit, 
   </para>
  </listitem>
  <listitem>
   <para>
   a hit, which is drawn twice on a canvas pad (V-plot) the
   cursor is moved to the closer of the two, 
   </para>
  </listitem>
  <listitem>
   <para>
   a track, the cursor is moved to that point on the track
   which is closest to the current cursor position.
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 </itemizedlist> 
 
 Any canvas pad in which a mouse button is clicked, is automatically 
 popped up. 
 </para>
 
 <para>
 <emphasis>Detectors</emphasis>
 </para>
 
 <para>
 If the picking mode is set to detectors:
 
 <itemizedlist>
 <listitem>
  <para>
  Clicking the <emphasis>left mouse button</emphasis> in a
  canvas pad on a detector element will print the name of the element on the 
  output display (<xref endterm="OutputDisplay.title" linkend="OutputDisplay"></xref>)
  of the Control Window.
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>Lists and Picking</emphasis>
 </para>
 
 <para>
 The pick interaction may be used for the interactive manipulation of lists 
 (<xref endterm="Lists.title" linkend="Lists"></xref>) by using a 
 modifier key while performing the pick. The available modifier keys are:
 
 <table frame="topbot" pgwide="0">
 <title>Modifier keys for pick interaction</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="colone" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="coltwo" colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Modifier Key</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>A</emphasis> + <emphasis>left-click</emphasis></entry>
   <entry><emphasis>Add</emphasis> the data item to be picked to the currently
    selected list node
   </entry>
  </row>
 
  <row rowsep="1">
   <entry><emphasis>C</emphasis> + <emphasis>left-click</emphasis></entry>
   <entry><emphasis>Clear highlighted</emphasis>, colours the previously picked
       data item with its default colour
   </entry>
  </row>
 
  <row rowsep="1">
   <entry><emphasis>I</emphasis> + <emphasis>left-click</emphasis></entry>
   <entry><emphasis>Ignore</emphasis>, picked item is moved into the
       <emphasis>invisible</emphasis> list under List manager and is ignored
       unless removed from this list or list manager is re-set, useful to mask
       hot calo cells for instance
   </entry>
  </row>
 
  <row rowsep="1">
   <entry><emphasis>V</emphasis> + <emphasis>left-click</emphasis></entry>
   <entry><emphasis>Set primary vertex</emphasis>, if picked item is simulated
       vertex (SimVertex) or reconstructed vertex (RecVertex), the position of
       the picked vertex is considered by Atlantis the primary vertex 
       (see Projections&rarr;&eta;/&phi; projection menu)
   </entry>
  </row>
 
 </tbody>
 </tgroup>
 </table>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="SynchroCursors">
 <title id="SynchroCursors.title">4.4 Synchro Cursors</title>
 
 <para>
 If different projections are visible simultaneously in separate canvas 
 windows, then synchro cursors show the same cursor position in all 
 projections. Syncro cursors are activated by clicking on the SC tab of 
 the interaction control in the Control Window.
 </para>
 
 <para>
 Now simply click in a canvas pad with the left mouse key and, while 
 keeping the key pressed, move around in the canvas pad to see the 
 synchro cursor follow the cursor position. The synchro cursors in the 
 other canvas pads follow the leading synchro cursor. The synchro cursor 
 in any canvas pad may be used as leading cursor.
 </para>
 
 <para>
 The concept is simple: a 3D point defined by (&phi;,&eta;,&rho;) in one 
 projection is shown in all other projections by conversion to the appropriate 
 coordinates. This is rigorously applied if the pointer is moved in the 
 &phi;/&eta; projection. Otherwise only those coordinates are shown, 
 which are modified in the projection according to the table below:
 
 <table frame="topbot" pgwide="0">
 <title>Coordinates affected by synchro cursors</title>
 <tgroup cols="7">
 <colspec colnum="1" colname="colone"   colwidth="60" align="left"></colspec>
 <colspec colnum="2" colname="coltwo"   colwidth="50" align="left"></colspec>
 <colspec colnum="3" colname="colthree" colwidth="50" align="left"></colspec>
 <colspec colnum="4" colname="colfour"  colwidth="50" align="left"></colspec>
 <colspec colnum="5" colname="colfive"  colwidth="50" align="left"></colspec>
 <colspec colnum="6" colname="colsix"   colwidth="50" align="left"></colspec>
 <colspec colnum="7" colname="colseven" colwidth="50" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Pointer</entry>
   <entry>Displayed</entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry>moved in</entry>
   <entry>&rho;/Z (<xref endterm="RZ.title" linkend="RZ"></xref>)</entry>
   <entry>Y/X (<xref endterm="YX.title" linkend="YX"></xref>)</entry>
   <entry>&phi;/&rho; (<xref endterm="FR.title" linkend="FR"></xref>)</entry>
   <entry>&phi;/Z (<xref endterm="FZ.title" linkend="FZ"></xref>)</entry>
   <entry>&phi;/&eta; (<xref endterm="VP.title" linkend="VP"></xref>)</entry>
   <entry>X'/Z (<xref endterm="XZ.title" linkend="XZ"></xref>)</entry>
  </row>
  <row rowsep="1">
   <entry>&rho;/Z (<xref endterm="RZ.title" linkend="RZ"></xref>)</entry>
   <entry>&rho;,Z,&eta;</entry>
   <entry>&rho;</entry>
   <entry>&rho;</entry>
   <entry>Z</entry>
   <entry>&eta;</entry>
   <entry>Z</entry>
  </row>
  <row rowsep="1">
   <entry>Y/X (<xref endterm="YX.title" linkend="YX"></xref>)</entry>
   <entry>&rho;</entry>
   <entry>&phi;,&rho;</entry>
   <entry>&phi;,&rho;</entry>
   <entry>&phi;</entry>
   <entry>&phi;</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>&phi;/&rho; (<xref endterm="FR.title" linkend="FR"></xref>)</entry>
   <entry>&rho;</entry>
   <entry>&phi;,&rho;</entry>
   <entry>&phi;,&rho;</entry>
   <entry>&phi;</entry>
   <entry>&phi;</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>&phi;/Z (<xref endterm="FZ.title" linkend="FZ"></xref>)</entry>
   <entry>Z</entry>
   <entry>&phi;</entry>
   <entry>&phi;</entry>
   <entry>&phi;,Z</entry>
   <entry>&phi;</entry>
   <entry>Z</entry>
  </row>
  <row rowsep="1">
   <entry>&phi;/&eta; (<xref endterm="VP.title" linkend="VP"></xref>)</entry>
   <entry>Z,&rho; <superscript>*</superscript></entry>
   <entry>&phi;,&rho;<superscript>*</superscript></entry>
   <entry>&phi;,&rho;<superscript>*</superscript></entry>
   <entry>&phi;,Z<superscript>**</superscript></entry>
   <entry>&phi;,&eta;</entry>
   <entry>?</entry>
  </row>
  <row rowsep="1">
   <entry>X'/Z (<xref endterm="XZ.title" linkend="XZ"></xref>)</entry>
   <entry>Z</entry>
   <entry></entry>
   <entry></entry>
   <entry>Z</entry>
   <entry></entry>
   <entry>Z</entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 
 <superscript>*</superscript> Current &rho; is used. 
 </para>
 
 <para>
 <superscript>**</superscript> Current &rho; is used to calculate Z. 
 </para>
 
 <para>
 <emphasis>Setting the splitting angle in &rho;/Z</emphasis>
 </para>
 
 <para>
 A special feature of the synchro cursors interaction is to set the angle 
 <emphasis>&phi;<subscript>&rho;Z</subscript></emphasis> of the &rho;/Z 
 (<xref endterm="RZ.title" linkend="RZ"></xref>) projection from any 
 other projection which defines &phi;. This transfer of &phi; information is 
 performed by keeping modifier key <emphasis>P</emphasis> pressed while the 
 cursor is being moved in a &phi; defining projection. This is particularly 
 useful when the &phi; defining projection is taken to be Y/X 
 (<xref endterm="YX.title" linkend="YX"></xref>) as in this case 
 all data in one Y/X hemisphere are shown on the upper half of the &rho;/Z 
 projection while all data in the other Y/X hemisphere are shown on the lower 
 half of the &rho;/Z projection.
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="FishEye">
 <title id="FishEye.title">4.5 Fisheye</title>
 
 <para>
 If the calorimeters and the muon detectors are drawn in, e.g. the 
 Y/X projection 
 (<xref endterm="YX.title" linkend="YX"></xref>), the inner 
 tracking chambers are so small that track recognition may suffer. 
 This problem may be partially solved by applying a fisheye transformation, 
 which allows a relative magnification of the inner chambers without 
 increasing the outer radius. Besides, since the outer parts of the detector 
 are in sight, tracks are still completely visible.
 </para>
 
 <para>
 A fisheye transformation is available in most projections:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Y/X, &phi;/&rho; and &rho;/Z projections</emphasis>
  </para>
  <para>
  When &rho; (&radic;(X<superscript>2</superscript>+Y<superscript>2</superscript>))
  is known in a projection (namely Y/X 
  (<xref endterm="YX.title" linkend="YX"></xref>), &phi;/&rho; 
  (<xref endterm="FR.title" linkend="FR"></xref>) and &rho;/Z 
  (<xref endterm="RZ.title" linkend="RZ"></xref>)), it is modified as:
  </para>
  <para>
  &rho;<subscript>new</subscript> = &rho; &times; 
  (1+<emphasis>d</emphasis>&times;<emphasis>&rho;<subscript>max</subscript></emphasis>) /
  (1+<emphasis>d</emphasis>&times;&rho;)
  </para>
  <para>
  where <emphasis>&rho;<subscript>max</subscript></emphasis> is the outer 
  radius and <emphasis>d</emphasis> the fisheye distortion factor.
  </para>
  <para>
  In Y/X (<xref endterm="YX.title" linkend="YX"></xref>) the
  azimuthal angle is unchanged and  X<subscript>new</subscript>, Y<subscript>new</subscript>
  are calculated from &phi; and &rho;<subscript>new</subscript>, in &phi;/&rho;
  (<xref endterm="FR.title" linkend="FR"></xref>) 
  the azimuthal angle &phi; is unchanged.
  </para>
  <para>
  In the case of the &rho;/Z
  (<xref endterm="RZ.title" linkend="RZ"></xref>) projection the 
  value of Z is changed according to the formula: 
  </para>
  <para>
  Z<subscript>new</subscript> = Z &times; 
  (1+<emphasis>d</emphasis>&times;<emphasis>Z<subscript>max</subscript></emphasis>) /
  (1+<emphasis>d</emphasis>&times;Z)
  </para>
  <para>
  where <emphasis>Z<subscript>max</subscript></emphasis> is the outer Z range.
  In this projection, radial tracks are slightly curved by the fisheye.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Other projections</emphasis>
  </para>
  <para>
  In all other projections where the fisheye is available, the axes 
  representing distance are transformed with the formula used to transform Z 
  in the &rho;/Z (<xref endterm="RZ.title" linkend="RZ"></xref>) projection.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 <emphasis>Applying the Fisheye Transformation</emphasis>
 </para>
 
 <para>
 The fisheye interaction is selected for the current canvas pad by 
 clicking on the Fisheye tab of the interaction control 
 (<xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) 
 in the Control Window. The label of the tab contains a toggle to activate 
 and deactivate the fisheye and a box with the value of the distortion factor 
 <emphasis>d</emphasis>. This value is modified by clicking the left mouse 
 button and dragging the cursor over the picture. If the <emphasis>F</emphasis> 
 modifier key is pressed while dragging, the data will not be updated, thus 
 allowing for better response. 
 </para>
 
 <para>
 <emphasis>The Fisheye Pop-up Menu</emphasis>
 </para>
 
 <para>
 The Fisheye Pop-up Menu can be accessed by right-clicking into the desired 
 canvas pad. It contains the following set of utility operations: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Set no Fisheye</emphasis>
  - Switch off the fisheye interaction. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>To Window Radius</emphasis>
  - Not implemented yet. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="Clock">
 <title id="Clock.title">4.6 Clock</title>
 
 <para>
 The clock transformation is an angular fisheye transformation which allows a 
 selected azimuthal region to be shown in detail while still displaying the 
 full 360&deg;. It is only available in the Y/X projection 
 (<xref endterm="YX.title" linkend="YX"></xref>).
 </para>
 
 <para>
 Under a clock transformation about an axis &phi;<subscript>0</subscript>, 
 &phi; transforms to &phi;<subscript>new</subscript> with: 
 </para>
 
 <para>
 &phi;<subscript>new</subscript> = &phi;<subscript>0</subscript> + 
 ((&pi;/<emphasis>d</emphasis>)&times;&Delta;&phi;) /
 ((&pi;/<emphasis>d</emphasis>)+&pi;-&verbar;&Delta;&phi;&verbar;)
 </para>
 
 <para>
 where <emphasis>d</emphasis> is the clock distortion factor and 
 &Delta;&phi;=&phi;-&phi;<subscript>0</subscript>. 
 The clock transformation does not change &rho;. 
 The values of X<subscript>new</subscript>, Y<subscript>new</subscript> are 
 calculated from &rho; and &phi;<subscript>new</subscript>. 
 </para>
 
 <para>
 <emphasis>Applying the Clock Transformation</emphasis>
 </para>
 
 <para>
 The clock interaction is selected for the current canvas pad by 
 clicking on the Clock tab of the interaction control 
 (<xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) 
 in the Control Window. The label of the tab contains a toggle to activate 
 and deactivate the interaction. Upon activation the distortion factor 
 <emphasis>d</emphasis> is modified by clicking on a point at a selected 
 opening angle with respect to the &phi;<subscript>0</subscript> direction 
 and dragging it to a larger or smaller opening angle.
 </para>
 
 <para>
 When the clock interaction is selected, a white line appears over the picture 
 representing the selected &phi;<subscript>0</subscript> direction around 
 which to perform the angular fisheye. This &phi; axis may be rotated by 
 dragging it with the mouse.
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="Skew">
 <title id="Skew.title">4.7 Skew</title>
 
 <para>
 The skew interaction is activated for the current canvas pad by 
 clicking on the Skew tab of the interaction control 
 (<xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) 
 in the Control Window. It is available in the 
 &rho;/Z (<xref endterm="RZ.title" linkend="RZ"></xref>), 
 &phi;/&rho; (<xref endterm="FR.title" linkend="FR"></xref>) and 
 &phi;/Z (<xref endterm="FZ.title" linkend="FZ"></xref>) 
 projections. 
 However, in the &phi;/&rho;, &phi;/Z it is only available when a small 
 region of the total azimuthal angle has been selected. 
 </para>
 
 <para>
 <emphasis>The Skew Pop-up Menu</emphasis>
 </para>
 
 <para>
 The Skew Pop-up Menu can be accessed by right-clicking into the desired 
 canvas pad. It contains the following set of utility operations: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Set no skew</emphasis>
  - Switch off the skew interaction.
  (doesn't work for &rho;/Z: BUG!)
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="ScaleCopy">
 <title id="ScaleCopy.title">4.8 Scale</title>
 
 <para>
 The skew interaction is activated for the current canvas pad by 
 clicking on the Scale tab of the interaction control 
 (<xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) 
 in the Control Window.
 </para>
 
 <para>
 The scale interaction allows the copying of &phi; or Z scales between 
 projections. After activating the scale interaction, a scale may be copied 
 by dragging it from the source window into the target window. A &phi;-scale 
 copy will only work between two projections which have their vertical axes 
 representing &phi;. A Z-scale copy will only work between two projections 
 which have their horizontal axes representing Z.
 </para>
 
 <para>
 The scale interaction does not have a pop-up menu.
 </para>
 
 </sect1>
 
 </chapter>
 
 <!--=======================================================================-->
 <chapter id="Projection">
 <title id="Projection.title">Projections</title>
 
 <para>
 <emphasis>Available Projections</emphasis>
 </para>
 
 <para>
 The projections that are available in Atlantis are data oriented, that is, 
 they are adapted to the cylindrical structure of helices and of the ATLAS 
 detector. The following projections are available:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Linear projections</emphasis> 
  <itemizedlist>
  <listitem>
   <para>
   The <emphasis>Y/X projection</emphasis> (<xref endterm="YX.title" linkend="YX"></xref>) 
   looking along the beam axis. 
   </para>
  </listitem>
  <listitem>
   <para>
   The <emphasis>X'/Z projection</emphasis>
   (<xref endterm="XZ.title" linkend="XZ"></xref>)  
   looking perpendicular to the beam axis. The angle around the axis may 
   be changed. 
   </para>
  </listitem>
  <listitem>
   <para>
   The <emphasis>Y'/Z projection</emphasis>
   (<xref endterm="YZ.title" linkend="YZ"></xref>) 
   looking perpendicular to the beam axis and perpendicular to X'Z. 
   The angle around the axis may be changed. 
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Non-linear projections</emphasis> 
  <itemizedlist>
  <listitem>
   <para>
   The <emphasis>&rho;/Z projection</emphasis>
   (<xref endterm="RZ.title" linkend="RZ"></xref>), 
   which is intuitively understandable. 
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Expert non-linear projections</emphasis> 
  <itemizedlist>
  <listitem>
   <para>
   The <emphasis>&phi;/&rho; projection</emphasis>
   (<xref endterm="FR.title" linkend="FR"></xref>). 
   </para>
  </listitem>
  <listitem>
   <para>
   The <emphasis>&phi;/Z projection</emphasis>
   (<xref endterm="FZ.title" linkend="FZ"></xref>). 
   </para>
  </listitem>
  <listitem>
   <para>
   The <emphasis>&phi;/&eta; projection</emphasis>
   (<xref endterm="VP.title" linkend="VP"></xref>), 
   of which the V-plot is a special form. 
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Special projections</emphasis> 
  <itemizedlist>
  <listitem>
   <para>
   The <emphasis>3D projection</emphasis>
   (<xref endterm="3D.title" linkend="3D"></xref>). 
   </para>
  </listitem>
  <listitem>
   <para>
   The <emphasis>3DBox projection</emphasis>
   (<xref endterm="3DBox.title" linkend="3DBox"></xref>). 
   </para>
  </listitem>
  <listitem>
   <para>
   The <emphasis>Lego Plot</emphasis>
   (<xref endterm="LegoPlot.title" linkend="LegoPlot"></xref>). 
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 <emphasis>Selection of Projections</emphasis>
 </para>
 
 <para>
 A projection is selected via the Parameter Control
 (<xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>) of the 
 Control Window or via the projection pop-up menu
 (<xref endterm="ProjectionMenu.title" linkend="ProjectionMenu"></xref>). 
 </para>
 
 <para>
 <emphasis>Projections and Data</emphasis>
 </para>
 
 <para>
 In the program a distinction is made for data in 3D space between 
 <emphasis>space points</emphasis> (e.g. silicon hits) and 
 <emphasis>space lines</emphasis> (e.g. straws from the TRT).
 </para>
 
 <para>
 All projections may be used for both types of data. 
 However, space lines are best viewed in the following projections:
 
 <table frame="topbot" pgwide="0">
 <title>Display of space lines</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="colone" colwidth="130"  align="left"></colspec>
 <colspec colnum="2" colname="coltwo" colwidth="300" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Projection</entry>
   <entry>Space line</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry>Y/X (<xref endterm="YX.title" linkend="YX"></xref>)</entry>
   <entry>TRT, LAr and TILE barrels, RPC &phi;-strips, vertex region (intuitive view)
   </entry>
  </row>
  <row rowsep="1">
   <entry>&phi;/&rho; (<xref endterm="FR.title" linkend="FR"></xref>)</entry>
   <entry>TRT, LAr and TILE barrels, RPC &phi;-strips, tracks are straight lines
   </entry>
  </row>
  <row rowsep="1">
   <entry>&rho;/Z (<xref endterm="RZ.title" linkend="RZ"></xref>)</entry>
   <entry>Barrel and endcap calorimeters; approximate extrapolation to all
    MDT, RPC z-strips and TGC &rho;-strips superimposed
   </entry>
  </row>
  <row rowsep="1">
   <entry>X'/Z (<xref endterm="XZ.title" linkend="XZ"></xref>)</entry>
   <entry>MDT, RPC z-strips and TGC &rho;-strips, vertex region (intuitive view)</entry>
  </row>
  <row rowsep="1">
   <entry>Y'/Z (<xref endterm="YZ.title" linkend="YZ"></xref>)</entry>
   <entry>Vertex region, orthogonal view with respect to X'/Z projection</entry>
  </row>
  <row rowsep="1">
   <entry>&phi;/Z (<xref endterm="FZ.title" linkend="FZ"></xref>)</entry>
   <entry>TRT endcaps, calorimeter endcaps and TGC &phi;-strips</entry>
  </row>
  <row rowsep="1">
   <entry>&phi;/&eta; (<xref endterm="VP.title" linkend="VP"></xref>)</entry>
   <entry>Calorimeters, and their association to tracks and S3D hits</entry>
  </row>
  <row rowsep="1">
   <entry>3DBox (<xref endterm="3DBox.title" linkend="3DBox"></xref>)</entry>
   <entry>Shows tracks near the primary vertex to investigate secondary vertices
    </entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 <para>
 <emphasis>Projections and Magnetic Field</emphasis>
 </para>
 
 <para>
 Depending on the projection and the type of magnetic field, tracks of charged 
 particles will be more or less straight. The following table gives an overview:
 
 <table frame="topbot" pgwide="0">
 <title>Shape of trajectories in magnetic fields</title>
 <tgroup cols="5">
 <colspec colnum="1" colname="colone"   colwidth="70" align="left"></colspec>
 <colspec colnum="2" colname="coltwo"   colwidth="80" align="left"></colspec>
 <colspec colnum="3" colname="colthree" colwidth="80" align="left"></colspec>
 <colspec colnum="4" colname="colfour"  colwidth="80" align="left"></colspec>
 <colspec colnum="5" colname="colfive"  colwidth="80" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry></entry>
   <entry>Y/X</entry>
   <entry>&phi;/&rho;</entry>
   <entry>&phi;/Z</entry>
   <entry>&rho;/Z</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry>Solenoidal</entry>
   <entry>curved</entry>
   <entry>curved</entry>
   <entry>curved</entry>
   <entry>&thksim;straight</entry>
  </row>
  <row rowsep="1">
   <entry>Toroidal</entry>
   <entry>&thksim;straight</entry>
   <entry>&thksim;straight</entry>
   <entry>&thksim;straight</entry>
   <entry>curved</entry></row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 <para>
 <emphasis>Checking the Tracking</emphasis>
 </para>
 
 <para>
 In the Y/X (<xref endterm="YX.title" linkend="YX"></xref>), 
 &phi;/&rho; (<xref endterm="FR.title" linkend="FR"></xref>) and 
 &phi;/Z (<xref endterm="FZ.title" linkend="FZ"></xref>) 
 projections tracks are seen from the side of maximum curvature. In the 
 &rho;/Z (<xref endterm="RZ.title" linkend="RZ"></xref>) projection 
 they are seen from the "orthogonal" side, i.e. the side of minimum curvature. 
 Therefore &rho;/Z is said to be orthogonal to Y/X, &phi;/&rho; and &phi;/Z.
 </para>
 
 <para>
 In order to check in space if a track passes through a set of 3D hits or 
 if it points to a set of calorimeter hits the hits and the track must be 
 displayed in at least two 2-dimensional projections which are orthogonal 
 to each other i.e. in &rho;/Z and in one of the projections Y/X, 
 &phi;/&rho; or &phi;/Z.
 </para>
 
 <para>
 Instead of using a pair of projections the 3-dimensional 
 V-plot (<xref endterm="RZ.title" linkend="RZ"></xref>) 
 is sufficient to check pattern recognition and track extrapolation.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="YX">
 <title id="YX.title">5.1 Y/X Projection</title>
 
 <para>
 The Y/X projection presents an intuitively understandable picture of data 
 with a precise Y/X measurement. This projection may be used to view 3D 
 tracks and hits and to associate them to data in the TRT, LAr and TILE 
 barrels, and to the RPC &phi;-strips. All other data would appear as lines. 
 In this projection the momentum of tracks may be estimated form the curvature. 
 This projection also provides an intuitively understandable view of the 
 region around the primary vertex.
 </para>
 
 <para>
 In the standard view of the Y/X projection, data from the calorimeter and 
 muon detector endcaps are <emphasis>not</emphasis> displayed (in order not to 
 complicate the picture) as they would fall on top of data from the 
 tracking chambers or data from the calorimeter barrel. 
 </para>
 
 <para>
 Alternatively, the <emphasis>view</emphasis> parameter may be used to select 
 a single layer of the muon detector endcaps 
 (<xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>). 
 In this case, the <emphasis>TGC Gas Gap</emphasis> parameter may be used 
 to further select data from only a given sublayer of the detector.
 </para>
 
 <para>
 The Y/X projection is special in that it allows both the particle's charge 
 and P<subscript>
 t</subscript> to be estimated from the track curvature. 
 </para>
 
 <para>
 Even with <emphasis>fisheye</emphasis> 
 (<xref endterm="FishEye.title" linkend="FishEye"></xref>) the inner 
 layers of the pixel detector fall on rather small circles, which do not 
 take into account the high resolution of the pixel detector. 
 The pixel data are better visualised in the &phi;/&rho; projection 
 (<xref endterm="FR.title" linkend="FR"></xref>).
 </para>
 
 <para>
 The orthogonal projection to Y/X is the &rho;/Z projection 
 (<xref endterm="RZ.title" linkend="RZ"></xref>). 
 </para>
 
 <para>
 <emphasis>The Y/X Projection Menu 
 (see <xref endterm="ProjectionMenu.title" linkend="ProjectionMenu"></xref>)</emphasis>
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Aspect Ratio 1</emphasis>
  - Sets the aspect ratio (width/height) of the 
  picture to 1. The operation ensures that the original picture which was 
  in the window does not go outside the window.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 <emphasis>Parameters</emphasis>
 
 <itemizedlist>
 <listitem>
  <para><emphasis>View</emphasis></para>
  <para>Select the data type, choice between:
  <itemizedlist>
  <listitem>
   <para><emphasis>Standard</emphasis> (default)</para>
  </listitem>
  <listitem>
   <para><emphasis>TGC Inner 1</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>TGC Middle 1</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>TGC Middle 2</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>TGC Middle 3</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>MDT/CSC Inner</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>MDT Extension</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>MDT Middle</emphasis></para>
  </listitem>
   <listitem>
   <para><emphasis>FCAL EM</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>FCAL HAD 1</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>FCAL HAD 2</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>LAr Endcap Presampler</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>LAr Endcap 1 (outer wheel 1)</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>LAr Endcap 2 (outer wheel 2, inner wheel 1)</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>LAr Endcap 3 (outer wheel 3, inner wheel 2)</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>HEC 1</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>HEC 2</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>HEC 3</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>HEC 4</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>LAr Summed</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>HEC Summed</emphasis></para>
  </listitem> 
  <listitem>
   <para><emphasis>MBTS</emphasis></para>
  </listitem> 
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para><emphasis>Summed LAr binning</emphasis></para>
  <para>Select the data type, choice between:
  <itemizedlist>
  <listitem>
   <para><emphasis>0.1x0.1</emphasis> (default)</para>
  </listitem>
  <listitem>
   <para><emphasis>0.2x0.2</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>split</emphasis></para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para><emphasis>Summed HEC binning</emphasis></para>
  <para>Select the data type, choice between:
  <itemizedlist>
  <listitem>
   <para><emphasis>0.1x0.1</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>0.2x0.2</emphasis> (default)</para>
  </listitem>
  <listitem>
   <para><emphasis>split</emphasis></para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para><emphasis>Eta of split binning</emphasis></para>
 </listitem>
 <listitem>
  <para><emphasis>Draw FCAL inside HEC</emphasis></para>
 </listitem>
 <listitem>
  <para><emphasis>CSC Gas Gap</emphasis></para>
  <para>Select value, choice between:
  <itemizedlist>
  <listitem>
   <para><emphasis>1</emphasis> (default)</para>
  </listitem>
  <listitem>
   <para><emphasis>2</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>3</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>4</emphasis></para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para><emphasis>TGC Gas Gap</emphasis></para>
  <para>Select value, choice between:
  <itemizedlist>
  <listitem>
   <para><emphasis>1</emphasis> (default)</para>
  </listitem>
  <listitem>
   <para><emphasis>2</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>3</emphasis></para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
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 <sect2 id="YXEndCap">
 <title id="YXEndCap.title">5.1.1 Muon Detector Endcaps in Y/X Projection</title>
 
 <para>
 In order to display the muon detector endcaps and the respective hits 
 (drawn as points or lines) single stations must be selected: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>TGC</emphasis>
  - Inner 1, Middle 1, Middle 2 and Middle 3. The TGC data may belong to 
  different sublayers selected by the TGC Gas Gap parameter. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>MDT</emphasis>
  - Inner 1, Extension, Middle and Outer.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 These pictures show best the structure of the layers. 
 Their position can be seen best from 
 &rho;/Z (<xref endterm="RZ.title" linkend="RZ"></xref>).
 The name of a specific module may be obtained by 
 picking (<xref endterm="Pick.title" linkend="Pick"></xref>).
 </para>
 
 <para>
 In the standard Y/X view (<xref endterm="YX.title" linkend="YX"></xref>) the 
 inner detector and the calorimeter and muon barrel are displayed.
 </para>
 
 </sect2>
 
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 <sect2 id="YXEndCapLArHEC">
 <title id="YXEndCapLArHEC.title">5.1.2 LAr and HEC Endcaps in Y/X Projection</title>
 
 <para>
 In order to display the LAr and HEC endcaps there are several options:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Individual layers</emphasis>
  - Shows the hits in both endcaps unless a cut on &eta; is applied.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Summed layers</emphasis>
  - Takes the sum of all the layers in the endcap, as with the individual
  layers this takes the hits in both endcaps unless a cut on &eta; is applied.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Multiple layers</emphasis>
  - These projections can also be used by using the rectangle selection on 
  the rubberband menu (<xref endterm="RubberbandYX.title" linkend="RubberbandYX"></xref>).
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 In the standard Y/X view (<xref endterm="YX.title" linkend="YX"></xref>) the 
 LAr and HEC Endcaps are not displayed.
 </para>
 
 </sect2>
 
 </sect1>
 
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 <sect1 id="VP">
 <title id="VP.title">5.2 &phi;/&eta; Projection</title>
 
 <para>
 Calorimeter data from a single sampling are best shown in a &phi;/&eta; 
 projection, where the energy deposits may be shown through Lego towers or 
 other methods. There are also methods to show several samplings superimposed.
 </para>
 
 <para>
 Data from 3D tracking chambers may be shown in this projection with optimal 
 separation of tracks. However one faces the problem, that charge, track 
 momentum and the distance of hits from the beam axis cannot be recognised.
 </para>
 
 <para>
 One way out is the V-plot, which preserves all the features of the 
 &phi;/&eta; projection. It may be applied to both tracks and hits. 
 The latter without using any hit to track association.
 </para>
 
 <para>
 For a point in space (with coordinates &phi;, &eta;, &rho;) a pair of 
 points is displayed on the V-plot picture. In the case of particles moving 
 in a solenoidal field the two displayed points get the same &phi; as 
 vertical position and get two different horizontal positions namely 
 </para>
 
 <para>
 &eta; &plusmn; k &times; (&rho;<subscript>max</subscript>-&rho;)
 </para>
 
 <para>
 The value of the parameter k (gradient) is set by default but may be changed 
 interactively. The parameter &rho;<subscript>max</subscript> is set 
 automatically depending on the selected view. 
 As k and &rho;<subscript>max</subscript> are known, &phi;, &eta; and &rho; 
 may be recalculated from the coordinates of a pair of displayed points, 
 which means that the V-plot is a true 3-dimensional image.
 </para>
 
 <para>
 The position ZVTx of the primary vertex along the beam axis must be known to 
 calculate &eta;.
 </para>
 
 <para>
 The following rules apply to interpret the V-plot: 
 
 <itemizedlist>
 <listitem>
  <para>
  Helices transform into a V like pattern. 
  </para>
 </listitem>
 <listitem>
  <para>
  For helices pointing to the origin with not too low
  P<subscript>t</subscript> the arms of the V's are straight. 
  </para>
 </listitem>
 <listitem>
  <para>
  For helices not pointing to the origin the arms of the V's
  are curved: 
  <itemizedlist>
  <listitem>
   <para>
   with the same sign of curvature for tracks separated from
   the origin in z,
   </para>
  </listitem>
  <listitem>
   <para>
   with opposite sign of curvature for tracks separated in &rho;. 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 <listitem>
  <para>
  Positive tracks give V's pointing down. 
  </para>
 </listitem>
 <listitem>
  <para>
  Negative tracks give V's pointing up. 
  </para>
 </listitem>
 <listitem>
  <para>
  The gradient of the V arms is proportional to
  1/P<subscript>t</subscript>: 
  <itemizedlist>
  <listitem>
   <para>
   high P<subscript>t</subscript> tracks give V's with large opening angle, 
   </para>
  </listitem>
  <listitem>
   <para>
   low P<subscript>t</subscript> tracks give V's with
   small opening angle.
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>View's</emphasis>
 </para>
 
 <para>
 In the standard view the energy deposits in the calorimeters are represented 
 by boxes with the area of the box proportional to the energy deposited. 
 All samplings and all calorimeters are drawn superimposed. Furthermore, 
 all energies are given a color according to which of six predefined energy 
 ranges they belong. The cells belonging to each energy range are drawn 
 sequentally with the most energetic range being drawn first. 
 This provides a view of the jet structure of the event where energetic 
 isolated particles may be distinguished from jets. Tracks and S3D hits 
 may be drawn superimposed on the calorimeters with the apex of the V 
 corresponding to the exit of the track from the S3D detectors. 
 </para>
 
 <para>
 In the S3D and TRT views the apex of the V corresponds to the exit of 
 the track from the S3D and TRT detectors, respectively. 
 </para>
 
 <para>
 In the other views the calorimeters data corresponding to a single sampling 
 are drawn according to their actual cell structure and the tracks which are 
 superimposed are drawn with the apex of the V corresponding to the 
 intersection of the track with the selected sampling of the calorimeters. 
 </para>
 
 <para>
 <emphasis>Selecting data from a single jet</emphasis>
 </para>
 
 <para>
 Data corresponding to a single jet or isolated particle may be selected 
 using the special rubberband options (see 
 <xref endterm="InteractionControl.title" linkend="InteractionControl"></xref>) 
 available in the &phi;/&eta; projection. 
 </para>
 
 <para>
 <emphasis>Data selection</emphasis>
 </para>
 
 <para>
 For convenience the data to be viewed in the V-plot (S3D, STr, RTr and SNP) 
 may be selected directly in the &phi;/&eta; projection. 
 </para>
 
 <para>
 <emphasis>Options</emphasis>
 </para>
 
 <para>
 By default all &eta; values used in this projection are calculated taking 
 into account the z offset of the primary vertex (ZVtx). 
 However, if &eta; vertex is deselected &eta; will be calculated from z=0.
 </para>
 
 <para>
 The apex of a V may be drawn to a cylinder smaller than the default 
 associated with a view by setting the &rho;Max and zMax parameters.
 </para>
 
 <para>
 When tracks are being shown without the corresponding S3D hits, it may 
 be useful to draw only the outermost portion of the V as determined by 
 the Short V parameter.
 </para>
 
 <para>
 The VPlot Island parameter is used to set the color of the island drawn 
 to allow easier comparison of the relative locations of the hit cells 
 from different samplings which are being displayed in different windows. 
 </para>
 
 <para>
 The Draw Apex parameter is used to draw an additional symbol at the apex 
 of the V. This is useful for high momentum tracks where it may otherwise 
 be difficult to distinguish the exact location of the apex. 
 </para>
 
 <para>
 In the V-plot where the S3D hits are normally nearby it is useful to have 
 them represented by a symbol of a smaller size than in the other projections. 
 This difference in symbol size is determined by the S3D &Delta; 
 Size parameter.
 </para>
 
 </sect1>
 
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 <sect1 id="EG">
 <title id="EG.title">5.3 &phi;/&lambda; Projection</title>
 
 <para>
 To be filled!
 </para>
 
 </sect1>
 
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 <sect1 id="RZ">
 <title id="RZ.title">5.4 &rho;/Z Projection</title>
 
 <para>
 The &rho;/Z projection may be used to view 3D tracks and hits and to 
 associate them to data in the calorimeters. It may also be used to provide 
 a rough association of tracks to the MDT, RPC z-strips and TGC &rho;-strips 
 data from all sectors superimposed. To make this possible the muon data 
 are not drawn at &rho; but rather at &rho;' determined by projecting &rho; 
 onto the &phi;-axis of the corresponding sector. 
 </para>
 
 <para>
 Although not a linear projection, the &rho;/Z projection is intuitively 
 understandable. Circles (projections of helices) which pass through the 
 origin are recognised as approximately straight lines: 
 </para>
 
 <para>
 &rho; &thkap; 
 (P<subscript>t</subscript>/P<subscript>z</subscript>)&times;(-Z<subscript>vertex</subscript>)
 </para>
 
 <para>
 The picture of the detector is the same as if a cut through the beam axis 
 would have been applied. For a point with coordinates &rho; and &phi;, 
 this is achieved by defining: 
 </para>
 
 <para>
 &rho; = +&radic;(X<superscript>2</superscript>+Y<superscript>2</superscript>) 
 &nbsp; &nbsp; if &nbsp; &nbsp;
 &phi;<subscript>&rho;Z</subscript>-90&deg; 
 &lt; &phi; &lt; 
 &phi;<subscript>&rho;Z</subscript>+90&deg;
 </para>
 
 <para>
 and 
 </para>
 
 <para>
 &rho; = -&radic;(X<superscript>2</superscript>+Y<superscript>2</superscript>)
 &nbsp; &nbsp; otherwise.
 </para>
 
 <para>
 Due to the cylindrical structure of ATLAS, the &rho;/Z projection is the 
 only one, where all main detector units may be displayed without overlapping. 
 The different radial sub-elements of the muon detectors do overlap, 
 but may be shown separately in the X'/Z projection 
 (see <xref endterm="XZ.title" linkend="XZ"></xref>). 
 </para>
 
 <para>
 In the Y/X (see <xref endterm="YX.title" linkend="YX"></xref>), 
 &phi;/&rho; (see <xref endterm="FR.title" linkend="FR"></xref>) 
 and &phi;/Z (see <xref endterm="FZ.title" linkend="FZ"></xref>) 
 projections tracks are seen from the side of maximum curvature. 
 In the &rho;/Z projection (see <xref endterm="RZ.title" linkend="RZ"></xref>) 
 they are seen from the "orthogonal" side, i.e. the side of minimum 
 curvature. Therefore &rho;/Z is said to be orthogonal to Y/X, &phi;/&rho; 
 and &phi;/Z.
 </para>
 
 <para>
 In order to check in space if a track passes through a set of 3D hits, 
 or if it points to a set of calorimeter hits, the hits and the track 
 must be displayed in at least two 2-dimensional projections which are 
 orthogonal to each other i.e. in &rho;/Z and in one of the projections Y/X, 
 &phi;/&rho; or &phi;/Z. 
 Instead of using a pair of projections the 3-dimensional 
 V-plot (see <xref endterm="VP.title" linkend="VP"></xref>) 
 is sufficient to check pattern recognition and track extrapolation.
 </para>
 
 <para>
 Charge and momentum cannot be estimated in &rho;/Z. 
 </para>
 
 <para>
 <emphasis>TRT</emphasis> data cannot be shown, unless very few TRT straws can 
 be selected, which appear as lines, as neither Z in the barrel nor &rho; in 
 the endcap are known.
 </para>
 
 <para>
 The inner detectors may be enlarged without enlarging the outer ones by 
 using the fisheye interaction 
 (see <xref endterm="FishEye.title" linkend="FishEye"></xref>). 
 </para>
 
 <para>
 The angle <emphasis>&phi;<subscript>
 &rho;Z</subscript></emphasis> may be 
 modified in any &phi; defining projection while simultaneously being viewed 
 in the &rho;/Z projection as described in the Synchro Cursors interaction 
 (see <xref endterm="SynchroCursors.title" linkend="SynchroCursors"></xref>). 
 </para>
 
 <para>
 <emphasis>The &rho;/Z Projection Menu 
 (see <xref endterm="ProjectionMenu.title" linkend="ProjectionMenu"></xref>)</emphasis>
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Aspect Ratio 1</emphasis>
  - Sets the aspect ratio (width/height) of the picture to 1.
  The operation ensures that the original picture which was 
  in the window does not go outside the window.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect1>
 
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 <sect1 id="FR">
 <title id="FR.title">5.5 &phi;/&rho; Projection</title>
 
 <para>
 The &phi;/&rho; projection may be regarded as a modified 
 Y/X projection (see <xref endterm="YX.title" linkend="YX"></xref>). 
 The same data are displayed in both. This projection may be used to view 
 3D tracks and hits and to associate them to data in the TRT, LAr and TILE 
 barrels, and to the RPC &phi;-strips.
 </para>
 
 <para>
 The &phi;/&rho; projection is not intuitively understandable, but allows to 
 get a better angular separation of data from the innermost detectors. 
 It has a singularity at &rho;=0, so that the primary vertex cannot be 
 displayed. Circles (projections of helices) which pass through the origin, 
 transform into approximately straight lines, with a gradient inversely 
 proportional to P<subscript>t</subscript>: 
 </para>
 
 <para>
 &rho; &nbsp;&nbsp; &prop; &nbsp;&nbsp; P<subscript>t</subscript> &times; 
 sin(&phi;-&phi;<subscript>0</subscript>) &nbsp;&nbsp; &thkap; &nbsp;&nbsp; 
 P<subscript>t</subscript> &times; (&phi;-&phi;<subscript>0</subscript>) 
 </para>
 
 <para>
 where the constant of proportionality depends on the strength of the 
 solenoidal magnetic field. For large path lengths, &phi; will increase 
 (decrease) with increasing path length for negatively (positively) charged 
 tracks. Tracks not pointing exactly to the origin 
 (d<subscript>0</subscript>&ne;0) 
 show a distinct non linearity when approaching &rho;=0. Low momentum tracks 
 curve far from the origin, due to the approximation in the above formula. 
 </para>
 
 <para>
 Checking of pattern recognition is easier in the &phi;/&rho; projection, 
 where helices are approximately straight lines, than in the 
 Y/X projection (see <xref endterm="YX.title" linkend="YX"></xref>). 
 In particular a Y-Skew rubber-band can be used to optimally select the 
 region around a track for closer inspection. This would correspond to a - 
 non-existent - curved rubber-band pattern in the Y/X projection.
 </para>
 
 <para>
 If the standard view is selected, data from the calorimeter endcaps and the 
 muon endcaps are not displayed, in order not to complicate the picture, as 
 they may fall on top of data from the tracking chambers or data from the 
 calorimeter barrel. 
 </para>
 
 <para>
 Alternatively, the view parameter may be used to select a single layer of 
 the muon endcap detectors 
 (see <xref endterm="YXEndCap.title" linkend="YXEndCap"></xref>). 
 In this case, the TGC Gas Gap parameter may be used to further select 
 data from only a given sublayer of the detector. The view parameter may also 
 be used to select layers from the FCAL, LAr and HEC Endcaps and MBTS, it 
 can also display the summed LAr and HEC Endcaps.
 </para>
 
 <para>
 The &phi;/&rho; projection is special in that it allows both the 
 particle's charge and P<subscript>t</subscript> to be estimated from the 
 track slope. 
 </para>
 
 <para>
 The projection orthogonal to &phi;/&rho; is the &rho;/Z projection 
 (see <xref endterm="RZ.title" linkend="RZ"></xref>).
 </para>
 
 </sect1>
 
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 <sect1 id="FZ">
 <title id="FZ.title">5.6 &phi;/Z Projection</title>
 
 <para>
 The &phi;/Z projection may be used to view 3D tracks and hits and to 
 associate them to data in the TRT endcaps, the LAr endcaps, the HEC and to 
 the TGC &phi;-strips. Indeed it is the only projection in which the TRT 
 endcap straws may be viewed.
 </para>
 
 <para>
 It is not intuitively understandable, but allows to get a good angular 
 separation of data from the innermost detectors. Circles (projections of 
 helices) which pass through the origin, transform into straight lines, 
 with a gradient inversely proportional to P<subscript>z</subscript>: 
 </para>
 
 <para>
 z-z<subscript>v</subscript> &nbsp;&nbsp; &prop; &nbsp;&nbsp; 
 P<subscript>z</subscript> &times; (&phi;-&phi;<subscript>0</subscript>)
 </para>
 
 <para>
 where the constant of proportionality depends on the strength of the 
 solenoidal magnetic field. For large path lengths, &phi; will increase 
 (decrease) with increasing path length for negatively (positively) charged 
 tracks. 
 </para>
 
 <para>
 Checking of pattern recognition is easier in the &phi;/Z projection than 
 in the Y/X projection (see <xref endterm="YX.title" linkend="YX"></xref>). 
 In particular a Y-Skew rubber-band can be used to optimally select the region 
 around a track for closer inspection. Ideal helices passing through the 
 origin appear as a sequence of parallel lines, one for each turn. Even 
 helices with slowly changing radius can be identified as such. For simulated 
 and reconstructed tracks only the first half turn of the helix is drawn. 
 </para>
 
 <para>
 If the standard view is selected, data from the calorimeter barrel are not 
 displayed (in order not to complicate the picture) as they fall on top of 
 data either from the tracking chambers or from the calorimeter endcaps. 
 </para>
 
 <para>
 Alternatively, the view parameter may be used to select a single layer of the 
 muon barrel detectors. In the case of RPC layers, the RPC Gas Gap parameter 
 may be used to further select data from only a given sublayer of the detector.
 </para>
 
 <para>
 The projection orthogonal to &phi;/Z is the &rho;/Z projection 
 (see <xref endterm="RZ.title" linkend="RZ"></xref>).
 </para>
 
 </sect1>
 
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 <sect1 id="XZ">
 <title id="XZ.title">5.7 X'/Z Projection</title>
 
 <para>
 If one views an event perpendicular to the beam axis, some tracks are 
 curved and some are straight, depending on the azimuthal angle 
 <emphasis>&phi;<subscript>
 VIEW</subscript></emphasis> of the viewing 
 direction. 
 Such a projection is of use only if a sufficiently narrow jet is selected, 
 which may even consist of a single track. In this case a jet based Cartesian 
 coordinate system is optimal, which depends on the direction of the jet axis: 
 
 <itemizedlist>
 <listitem>
  <para>
  Y' = perpendicular to the beam axis and the jet axis, 
  </para>
 </listitem>
 <listitem>
  <para>
  X' = perpendicular to the Z and Y' axis, i.e. it lies in the
  plane containing the beam axis and the jet axis, 
  </para>
 </listitem>
 <listitem>
  <para>
  Z = beam-axis.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 In the X'/Z projection a single track has minimum curvature and maximum 
 angle to the Z axis. It lies in the display screen. The track is seen 
 from the orthogonal side as compared to the Y/X projection 
 (see <xref endterm="YX.title" linkend="YX"></xref>). 
 The jet image is similar to the one in the &rho;/Z projection 
 (see <xref endterm="RZ.title" linkend="RZ"></xref>), 
 which is however not limited to single jets. This projection provides a 
 second intuitively understandable view of the region around the primary 
 vertex orthogonal to that of the Y'/Z projection 
 (see <xref endterm="YZ.title" linkend="YZ"></xref>). The momentum 
 of tracks may not be estimated form their curvature in this projection. 
 </para>
 
 <para>
 Due to the maximum angle between jet and Z axis in the X'/Z projection the 
 sub detector sectors lying in the jet direction can be displayed for the 
 barrel and the endcap. This is specially interesting for the MDT tubes. 
 If only one <emphasis>MDT sector</emphasis> is displayed and the viewing 
 direction is perpendicular to the sector angle, the MDT tubes can be 
 represented as small circles. 
 </para>
 
 <para>
 <emphasis>The X'/Z Projection Menu 
 (see <xref endterm="ProjectionMenu.title" linkend="ProjectionMenu"></xref>)</emphasis>
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Aspect Ratio 1</emphasis>
  - Sets the aspect ratio (width/height) of the picture to 1.
  The operation ensures that the original picture which was in 
  the window does not go outside the window. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="YZ">
 <title id="YZ.title">5.8 Y'/Z Projection</title>
 
 <para>
 If one views an event perpendicular to the beam axis, some tracks are 
 curved and some are straight, depending on the azimuthal angle 
 <emphasis>&phi;<subscript>
 VIEW</subscript></emphasis> of the viewing 
 direction. Such a projection 
 is of use only if a sufficiently narrow jet is selected, which may even 
 consist of a single track. In this case a jet based Cartesian coordinate 
 system is optimal, which depends on the direction of the jet axis: 
 
 <itemizedlist>
 <listitem>
  <para>
  Y' = perpendicular to the beam axis and the jet axis, 
  </para>
 </listitem>
 <listitem>
  <para>
  X' = perpendicular to the Z and Y' axis, i.e. it lies in the
  plane containing the beam axis and the jet axis, 
  </para>
 </listitem>
 <listitem>
  <para>
  Z = beam axis. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 In the Y'/Z projection a single track has maximal curvature and minimum 
 angle to the Z axis. Seen with stereo it would leave the plane towards 
 the observer or opposite. The track is seen from the same side as in the 
 Y/X projection 
 (see <xref endterm="YX.title" linkend="YX"></xref>) only rotated 
 around the Y' axis. This projection provides a second intuitively 
 understandable view of the region around the primary vertex orthogonal 
 to that of the X'/Z projection 
 (see <xref endterm="XZ.title" linkend="XZ"></xref>). 
 The momentum of tracks may not be estimated form their curvature 
 in this projection. 
 </para>
 
 <para>
 The calorimeters and the muon chamber barrels cannot be displayed as they 
 would overlap the inner tracking detectors. The endcaps can be drawn. 
 </para>
 
 <para>
 An alternative to Y'/Z is the expert &phi;/Z projection 
 (see <xref endterm="FZ.title" linkend="FZ"></xref>), 
 which is not limited to single jets. 
 </para>
 
 <para>
 <emphasis>The Y'/Z Projection Menu (see 
 <xref endterm="ProjectionMenu.title" linkend="ProjectionMenu"></xref>)</emphasis>
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Aspect Ratio 1</emphasis>
  - Sets the aspect ratio (width/height) of the picture to 1.
  The operation ensures that the original picture which was 
  in the window does not go outside the window. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="3D">
 <title id="3D.title">5.9 3D Projection</title>
 
 <para>
 The 3D projection is a linear projection of the data such that a given axis 
 is transformed into a straight horizontal line through the center of the 
 window. It allows the user to perform rotations about an arbitrary axis in 
 space. The unit vector of this axis is defined by <emphasis>(xAxis, yAxis, 
 zAxis)</emphasis>. The center of rotation is taken to be the reconstructed 
 primary vertex of the event. 
 </para>
 
 <para>
 Rotations about the selected axis by an angle &phi; are performed by 
 dragging with the <emphasis>R</emphasis> modifier key pressed down in the 
 ZMR interaction (see <xref endterm="ZMR.title" linkend="ZMR"></xref>). 
 </para>
 
 <para>
 The axis of rotation will by default be set to the line joining the 
 primary vertex to the last secondary vertex to be reconstructed.
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="3DBox">
 <title id="3DBox.title">5.10 3DBox Projection</title>
 
 <para>
 The 3DBox projection allows the user to investigate a small 3D region 
 around a newly formed secondary vertex. 
 Every time a new secondary vertex is formed from a list 
 (see <xref endterm="Lists.title" linkend="Lists"></xref>), the direction of 
 flight of the incoming particle is calculated as the vector joining the 
 primary vertex to the reconstructed vertex. A 3D box of default size 
 2 mm x 2 mm x 4 cm is formed around this axis. The box has three vertically 
 oriented planes and transparent front and top faces. The left hand plane 
 contains the primary vertex, which is represented by the red point. 
 The axis of the direction of flight of the decaying particle lies 
 horizontally on the screen. The middle and right hand plane are at decay 
 distances of 2 cm and 4 cm, respectively. Tracks fully contained withing 
 the box are represented as straight lines and their intersections with 
 the three planes are shown as ellipses representing the correlated impact 
 parameter errors of the track. The dashed sections of tracks correspond 
 to regions where they pass behind behind a plane. 
 </para>
 
 <para>
 The user may interact with the region shown in the box via the 3DBox 
 interaction.  When the 3D box interaction is selected the size of the box 
 may be adjusted in a manner analogous to the zooming performed in the 
 ZMR (see <xref endterm="ZMR.title" linkend="ZMR"></xref>) interaction.
 </para>
 
 <para>
 There are two operations which may be performed:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Changing the volume contained by the box</emphasis> 
  </para>
  <para>
  The volume contained by the box is changed by dragging any point of the 
  picture towards or away from the central point represented by a small 
  <emphasis>red circle</emphasis> superimposed on the picture.
  Dragging towards the central 
  point will increase the volume of the box. Dragging away from the central 
  point will decrease the volume of the box. The length of the box may be 
  changed independently of the width by holding down the <emphasis>H</emphasis>
  key of the 
  keyboard. The width of the box may be changed independently of the length 
  by holding down the <emphasis>V</emphasis> key of the keyboard.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Rotation</emphasis> 
  </para>
  <para>
  In order to obtain a rotation of the tracks around the horizontal axis 
  corresponding to the direction of flight of the decaying particle you 
  drag any point on the picture while keeping the <emphasis>R</emphasis>
  key of your keyboard pressed.
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>The 3D Box Pop-up Menu</emphasis>
 </para>
 
 <para>
 The 3DBox Pop-up Menu can be accessed by right-clicking into the desired 
 canvas pad while keeping the <emphasis>R</emphasis> key of your keyboard 
 pressed.  
 It contains the following set of utility operations: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Default box Volume</emphasis>
  - reset the volume of the box to correspond to the default values. 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>Modifier Key Summary</emphasis>
 
 <table frame="topbot" pgwide="0">
 <title>Modifier key summary</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="colone" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="coltwo" colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Modifier Key</entry>
   <entry>Action</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>left-press</emphasis> only</entry>
   <entry><emphasis>Change</emphasis> the volume of the box</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Z</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry><emphasis>Change</emphasis> the volume of the box</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>H</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry><emphasis>Change</emphasis> the length of the box</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>V</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry><emphasis>Change</emphasis> the width of the box</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>R</emphasis> + <emphasis>left-press</emphasis></entry>
   <entry><emphasis>Rotate</emphasis> the tracks around the direction of
    flight of the decaying particle
   </entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="LegoPlot">
 <title id="LegoPlot.title">5.11 Lego Plot</title>
 
 <para>
 The lego plot shows stacks of energy seen in the calorimeter towers. 
 The stacks are positioned on the surface spanned by &eta; (in radians) and 
 &phi; (in degrees). 
 </para>
 
 <para>
 <emphasis>Parameters</emphasis>
 
 <itemizedlist>
 <listitem>
  <para><emphasis>View</emphasis></para>
  <para>Select the data type, choice between:
  <itemizedlist>
  <listitem>
   <para><emphasis>Calo</emphasis> (default)</para>
  </listitem>
  <listitem>
   <para><emphasis>LVL1TriggerTower</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>LVL1JetElement</emphasis></para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para><emphasis>ET Axis Height</emphasis></para>
  <para>Set the maximum height of the ET axis in GeV.</para>
  <para>0 = auto sets height to height of tallest calo tower or if no calo
  information is present then the tallest AOD tower is used.</para>
 </listitem>
 <listitem>
  <para><emphasis>&phi; Cells</emphasis></para>
  <para>Set the number of bins in &phi;.</para>
 </listitem>
 <listitem>
  <para><emphasis>&eta; Cells</emphasis></para>
  <para>Set the number of bins in &eta;.</para>
 </listitem>
 <listitem>
  <para><emphasis>Lego Cut</emphasis></para>
  <para>Set the minimum energy for lego bars to be drawn.</para>
 </listitem>
 <listitem>
  <para><emphasis>Jet Circle Radius</emphasis></para>
  <para>Set the jet circle radius.</para>
 </listitem>
 <listitem>
  <para><emphasis>Scale</emphasis></para>
  <para>
  Set the scale type, choice between:
  <itemizedlist>
  <listitem>
   <para><emphasis>standard</emphasis> (default)</para>
  </listitem>
  <listitem>
   <para><emphasis>logarithmic</emphasis></para>
  </listitem>
  <listitem>
   <para><emphasis>square root</emphasis></para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para><emphasis>Reverse</emphasis></para>
  <para>Toggle to select reverse &eta; or not.</para>
 </listitem>
 <listitem>
  <para><emphasis>Fill</emphasis></para>
  <para>Set the background fill color.</para>
 </listitem>
 <listitem>
  <para><emphasis>Draw Lego</emphasis></para>
  <para>Toggle to draw selected parts of lego plot or not.
  <itemizedlist>
  <listitem>
   <para><emphasis>Draw Legend</emphasis></para>
   <para>Toggle to draw selected parts of legend or not.
   <itemizedlist>
   <listitem>
    <para><emphasis>Main</emphasis></para>
    <para>Toggle to draw main legend or not.</para>
   </listitem>
   <listitem>
    <para><emphasis>L1 ET</emphasis></para>
    <para>Toggle to draw ET info or not.</para>
   </listitem>
   <listitem>
    <para><emphasis>Item list</emphasis></para>
    <para>Toggle to draw item list or not.</para>
   </listitem>
   </itemizedlist>
   </para>
  </listitem>
  <listitem>
   <para><emphasis>Draw Plot</emphasis></para>
   <para>Toggle to draw plot or not.</para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 </itemizedlist>
 
 <para>
 <emphasis>The Lego Projection Menu (see 
 <xref endterm="ProjectionMenu.title" linkend="ProjectionMenu"></xref>)</emphasis>
 <para>
 These options are to aid with selecting useful rotations which can also be
 achieved by using the rotation option in ZMR 
 (<xref endterm="ZMR.title" linkend="ZMR"></xref>).
 </para>
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>View normal</emphasis>
  - Sets the viewing angle to the default.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>View from above</emphasis>
  - Sets the viewing angle to view from above so reduces the Et axis size.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>View ET v &eta;</emphasis>
  - Sets the viewing angle so that the plot is ET v &eta;.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>View ET v &phi;</emphasis>
  - Sets the viewing angle so that the plot is ET v &phi;.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 </para>
 
 </sect1>
 
 </chapter>
 
 <!--=======================================================================-->
 <chapter id="DataMain">
 <title id="DataMain.title">Data</title>
 
 <para>
 The <emphasis>data types</emphasis> that are available in Atlantis are listed 
 in section Data Types 
 (<xref endterm="DataTypes.title" linkend="DataTypes"></xref>).
 The graphical repesentation of data types in the different projections on 
 the Canvas is listed in section Data Representation in Projections 
 (<xref endterm="DataRep.title" linkend="DataRep"></xref>).
 </para>
 
 <para>
 <emphasis>Control of data to be displayed</emphasis> on the Atlantis Canvas 
 is done by making a selection of available data and by applying cuts to the 
 selected data:  
 
 <itemizedlist>
 <listitem>
  <para>
  The <emphasis>selection of data</emphasis> is found via the
  <emphasis>Data</emphasis> tab of the parameter control
  (<xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>) 
  of the Control Window. 
  See Data Selection  (<xref endterm="Data.title" linkend="Data"></xref>) for a 
  description of the various selections. 
  Order of drawing, data representation by projection and commands are listed 
  here. 
  </para>
 </listitem>
 <listitem>
  <para>
  The <emphasis>cuts that can be applied</emphasis> are found
  via the <emphasis>Cuts</emphasis> tab of the parameter control
  (<xref endterm="ParametersControl.title" linkend="ParametersControl"></xref>) 
  of the Control Window. 
  See Cuts (<xref endterm="Cuts.title" linkend="Cuts"></xref>) for a 
  description of the various cuts that can be applied. 
  </para>
 </listitem>
 </itemizedlist>
 
 <emphasis>Control of attributes of data types</emphasis> is described in  
 <xref linkend="Detector"></xref>.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="DataTypes">
 <title id="DataTypes.title">6.1 Data Types</title>
 
 <para>
 The table below contains a list of names and short descriptions of the 
 data types available in Atlantis.  The names are in alphabetical order. 
 
 <table frame="topbot" pgwide="0">
 <title>Available data types</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="colone" colwidth="80"  align="left"></colspec>
 <colspec colnum="2" colname="coltwo" colwidth="350" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Data Type</entry>
   <entry>Description</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>BJet</emphasis></entry>
   <entry>(AOD) B-tagged Jet</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>CSC</emphasis></entry>
   <entry>(MuonDet) Cathode Strip Chambers </entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Electron</emphasis></entry>
   <entry>(AOD) Electron</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>EmTauROI</emphasis></entry>
   <entry>(Calo) Electromagnetic/Tau Region of Interest</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>ETMis Collections</emphasis></entry>
   <entry>(ATLAS) Missing ET Collections</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>FCAL</emphasis></entry>
   <entry>(Calo) Forward Calorimeter</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>HEC</emphasis></entry>
   <entry>(Calo) Hadronic End Cap</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Jet</emphasis></entry>
   <entry>(ATLAS) ESD Jet</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>JetROI</emphasis></entry>
   <entry>(Calo) Jet Region of Interest</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>LAr</emphasis></entry>
   <entry>(Calo) Liquid Argon Calorimeter</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>MDT</emphasis></entry>
   <entry>(MuonDet) Monitored Drift Tube Chambers</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>MSeg</emphasis></entry>
   <entry>(MuonDet) Segments of Muon Tracks</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Muon</emphasis></entry>
   <entry>(AOD) Muon</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Photon</emphasis></entry>
   <entry>(AOD) Photon</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>RecVertex</emphasis></entry>
   <entry>(InDet) Reconstructed Vertices</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>RMTr</emphasis></entry>
   <entry>(MuonDet) Reconstructed Muon Tracks</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>RPC</emphasis></entry>
   <entry>(MuonDet) Resistive Plate Chamber</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>SiCluster</emphasis></entry>
   <entry>(InDet) Silicon Cluster</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>SiHit</emphasis></entry>
   <entry>(InDet) Geant Silicon Hits</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>SimVertex</emphasis></entry>
   <entry>(InDet) Simulated Vertices (Truth Vertex)</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>SMTr</emphasis></entry>
   <entry>(MuonDet) Simulated Muon Tracks</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>SpacePoint</emphasis></entry>
   <entry>(InDet) Silicon 3D Space Points</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>SNP</emphasis></entry>
   <entry>(Calo) Simulated Neutral Particles in Calorimeter (Neutral Truth)</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>STr</emphasis></entry>
   <entry>(InDet) Simulated Tracks (Charged Truth)</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>TauJet</emphasis></entry>
   <entry>(AOD) Tau</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>TGC</emphasis></entry>
   <entry>(MuonDet) Thin Gap Chambers</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>TILE</emphasis></entry>
   <entry>(Calo) Tile Calorimeter</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>Track Collections</emphasis></entry>
   <entry>(InDet) Reconstructed Track Collections</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>TrigSiSpacePoint</emphasis></entry>
   <entry>(InDet) Online Silicon 3D Space Points</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>TRT_DriftCircle</emphasis></entry>
   <entry>(InDet) TRT_DriftCircle Hits</entry>
  </row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="DataRep">
 <title id="DataRep.title">6.2 Data Representation in Projections</title>
 
 <para>
 The following table shows if and how data are displayed in the 
 different projections. 
 
 <table frame="topbot" pgwide="0">
 <title>Display of data in different projections</title>
 <tgroup cols="7">
 <colspec colnum="1" colname="colone"   colwidth="70" align="left"></colspec>
 <colspec colnum="2" colname="coltwo"   colwidth="50" align="left"></colspec>
 <colspec colnum="3" colname="colthree" colwidth="50" align="left"></colspec>
 <colspec colnum="4" colname="colfour"  colwidth="50" align="left"></colspec>
 <colspec colnum="5" colname="colfive"  colwidth="50" align="left"></colspec>
 <colspec colnum="6" colname="colsix"   colwidth="50" align="left"></colspec>
 <colspec colnum="7" colname="colseven" colwidth="50" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Data</entry>
   <entry>&rho;/Z (<xref endterm="RZ.title" linkend="RZ"></xref>)</entry>
   <entry>Y/X (<xref endterm="YX.title" linkend="YX"></xref>)</entry>
   <entry>&phi;/&rho; (<xref endterm="FR.title" linkend="FR"></xref>)</entry>
   <entry>&phi;/Z (<xref endterm="FZ.title" linkend="FZ"></xref>)</entry>
   <entry>&phi;/&eta; (<xref endterm="VP.title" linkend="VP"></xref>)</entry>
   <entry>X'/Z (<xref endterm="XZ.title" linkend="XZ"></xref>)</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry>BJet</entry>
   <entry>&nbsp;</entry>
   <entry>&nbsp;</entry>
   <entry>&nbsp;</entry>
   <entry>&nbsp;</entry>
   <entry>Circle</entry>
   <entry>&nbsp;</entry>
  </row>
  <row rowsep="1">
   <entry>Electron</entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>Circle</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>FCAL</entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>Square/cell</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>HEC</entry>
   <entry>Cell</entry>
   <entry></entry>
   <entry></entry>
   <entry>Cell</entry>
   <entry>Square/cell</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>LAr</entry>
   <entry>Cell</entry>
   <entry>Cell</entry>
   <entry>Cell</entry>
   <entry>Cell</entry>
   <entry>Square/cell</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>MDT</entry>
   <entry>Circle</entry>
   <entry>Line</entry>
   <entry>Line</entry>
   <entry>Line</entry>
   <entry></entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>Muon (AOD)</entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>Circle</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>Photon</entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>Circle</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>R3D</entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>Box</entry>
   <entry>Box</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>RecVertex</entry>
   <entry>Point</entry>
   <entry>Ellipse</entry>
   <entry>Point</entry>
   <entry>Point</entry>
   <entry></entry>
   <entry>Ellipse</entry>
  </row>
  <row rowsep="1">
   <entry>RPC</entry>
   <entry>Box</entry>
   <entry>Box</entry>
   <entry>Box</entry>
   <entry>Box</entry>
   <entry></entry>
   <entry>Box</entry>
  </row>
  <row rowsep="1">
   <entry>SimVertex</entry>
   <entry>Point</entry>
   <entry>Point</entry>
   <entry>Point</entry>
   <entry>Point</entry>
   <entry></entry>
   <entry>Point</entry>
  </row>
  <row rowsep="1">
   <entry>SNP</entry>
   <entry>Line</entry>
   <entry>Line</entry>
   <entry>Line</entry>
   <entry>Line</entry>
   <entry>Point</entry>
   <entry>Line</entry>
  </row>
  <row rowsep="1">
   <entry>SpacePoint</entry>
   <entry>Point</entry>
   <entry>Point</entry>
   <entry>Point</entry>
   <entry>Point</entry>
   <entry>Points</entry>
   <entry>Point</entry>
  </row>
  <row rowsep="1">
   <entry>STr</entry>
   <entry>S.line</entry>
   <entry>Circle</entry>
   <entry>S.line</entry>
   <entry>S.line</entry>
   <entry>V</entry>
   <entry>Helix</entry>
  </row>
  <row rowsep="1">
   <entry>T3D</entry>
   <entry>Box</entry>
   <entry>Box</entry>
   <entry>Box</entry>
   <entry></entry>
   <entry>Box</entry>
   <entry>Box</entry>
  </row>
  <row rowsep="1">
   <entry>TauJet</entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>Circle</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>TGC</entry>
   <entry></entry>
   <entry>Box</entry>
   <entry>Box</entry>
   <entry>Box</entry>
   <entry></entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>TILE</entry>
   <entry>Cell</entry>
   <entry>Cell</entry>
   <entry>Cell</entry>
   <entry></entry>
   <entry>Square/cell</entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>Track</entry>
   <entry>S.line</entry>
   <entry>Circle</entry>
   <entry>S.line</entry>
   <entry>S.line</entry>
   <entry>V</entry>
   <entry>Helix</entry>
  </row>
  <row rowsep="1">
   <entry>TRT_DriftCircle barrel</entry>
   <entry>Line</entry>
   <entry>Line</entry>
   <entry>Line</entry>
   <entry></entry>
   <entry></entry>
   <entry></entry>
  </row>
  <row rowsep="1">
   <entry>TRT_DriftCircle endcap</entry>
   <entry>Line</entry>
   <entry></entry>
   <entry></entry>
   <entry>Line</entry>
   <entry></entry>
   <entry></entry></row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="Data">
 <title id="Data.title">6.3 Data Selection</title>
 
 <para>
 Selection of data is made available via the <emphasis>Data</emphasis> tab of 
 the parameter control section in the Control Window. 
 The various selection options are described below.
 The data types that are available in Atlantis are listed under 
 Data Types (<xref endterm="DataTypes.title" linkend="DataTypes"></xref>). 
 The graphical representation of data types in the available projections 
 is listed under Data Representation in Projections 
 (<xref endterm="DataRep.title" linkend="DataRep"></xref>). 
 </para>
 
 <para>
 <emphasis>Order</emphasis>
 </para>
 
 <para>
 The order of drawing of simulated tracks (<emphasis>STr</emphasis>), 
 reconstructed tracks (<emphasis>RTr</emphasis>) and hits 
 (<emphasis>Hits</emphasis>) is set by selecting one of the following options: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>STr RTr Hits</emphasis> (default) 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>STr Hits RTr</emphasis> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Rtr Hits STr</emphasis>
  </para>
 </listitem>
 </itemizedlist>
 
 For the default option the simulated tracks are drawn first, then the 
 reconstructed tracks (so with perfect reconstruction you will only see the 
 reconstructed tracks) and finally the hits. 
 </para>
 
 <para>
 <emphasis>Assoc Hits To Track</emphasis>
 
 The track type to which hits are assigned to:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>xKalTrack</emphasis> (default)
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>iPatTrack</emphasis>
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 <emphasis>SpacePoint Order</emphasis>
 </para>
 
 <para>
 The order of drawing of spacepoints:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>SpacePoint TrigSiSpacePoint</emphasis> (default)
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TrigSiSpacePoint SpacePoint</emphasis>
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 <emphasis>Status</emphasis>
 </para>
 
 <para>
 Hierarchical lists to make data types active/inactive for drawing. 
 </para>
 
 <para>
 See <xref endterm="DataTypes.title" linkend="DataTypes"></xref> 
 for a short description of the data types. 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>InDet</emphasis>
  <itemizedlist>
   <listitem>
   <para>
   <emphasis>Spacepoint</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>TrigSiSpacePoint</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>SiHit</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>SiCluster</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>TRT_DriftCircle</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>STr</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Track Collections</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>SimVertex</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>RecVertex</emphasis>
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Calo</emphasis>
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>LAr</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>TILE</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>HEC</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>FCAL</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>SNP</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>EmTauROI</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>JetROI</emphasis>
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>MuonDet</emphasis>
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>MDT</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>CSC</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>RPC</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>TGC</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>MSeg</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>RMTr</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>SMTr</emphasis>
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>AOD</emphasis>
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>BJet</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Electron</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Muon</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Photon</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>TauJet</emphasis>
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>ATLAS</emphasis>
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>Jet</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>ETMis Collections</emphasis>
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 <emphasis>Cuts</emphasis>
 </para>
 
 <para>
 Finally, different cuts can be applied to the selected data. See 
 <xref endterm="Cuts.title" linkend="Cuts"></xref>.
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="Cuts">
 <title id="Cuts.title">6.4 Cuts</title>
 
 <para>
 Cuts may be applied to select the data to be displayed. 
 They are grouped (InDet 
 (<xref endterm="CutsInDet.title" linkend="CutsInDet"></xref>), Calo 
 (<xref endterm="CutsCalo.title" linkend="CutsCalo"></xref>), MuonDet 
 (<xref endterm="CutsMuon.title" linkend="CutsMuon"></xref>), AOD 
 (<xref endterm="CutsAOD.title" linkend="CutsAOD"></xref>) and 
 ATLAS (<xref endterm="CutsATLAS.title" linkend="CutsATLAS"></xref>)) 
 and are accessible via the <emphasis>Cuts</emphasis> tab of the parameter 
 control section in the Control Window. 
 </para>
 
 <para>
 Cuts can be made on tracks, track associations, hits, calorimeter cells, 
 TRT straws, angular regions. 
 </para>
 
 <para>
 Each cut can be switched on or off by clicking on the small check-box on the 
 left hand side. 
 The value of each cut is displayed in the white field and is modified by 
 changing the value in the field, followed by pressing the 
 <emphasis>Enter</emphasis> key on the keyboard. 
 </para>
 
 <para>
 Cuts which act on real numbers may select values either &lt; or &gt; 
 the cut value. The selection of &lt; or &gt; is 
 toggled by clicking on them with the left mouse button. 
 </para>
 
 <para>
 For cuts applied to integer values a left-click causes a pull down menu to 
 appear where you may select according to the C/JAVA syntax: 
 =, != (not equal), &lt;, &lt;=, &gt; or &gt;=.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="CutsInDet">
 <title id="CutsInDet.title">6.4.1 Cuts for Inner Detector (InDet)</title>
 
 <para>
 Most cuts are applied to tracks. 
 </para>
 
 <para>
 If the track association of hits or calorimeter cells is known, they may be 
 selected according to the tracks - with their cuts - they are associated to. 
 See <emphasis>Hits By STr</emphasis> and <emphasis>Hits By Track</emphasis>.
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>&verbar;Pt&verbar;</emphasis> :
  (tracks) transverse momentum [GeV/c] 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;d0&verbar;</emphasis> :
  (tracks) distance of closest approach to the beam axis [cm] 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;z0&verbar;</emphasis> :
  (tracks) distance in Z from nominal origin at d0 [cm] 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;d0 Loose&verbar;</emphasis> :
  (tracks) outer loose d0 cut [cm] 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;z0-ZVtx&verbar;</emphasis> :
  (tracks) distance in Z from primary vertex at d0 [cm] 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Num SpacePoint</emphasis> :
  (tracks) number of associated silicon space points 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;STr (code)&verbar;</emphasis> :
  (tracks) code of simulated track 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>STr (barcode)</emphasis> :
  (tracks) kine number of simulated track 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>STr type</emphasis> :
  (tracks) type of simulated track
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>charged hadron</emphasis> (default) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>tau</emphasis> 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>electron</emphasis> 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>muon</emphasis> 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>neutral hadron</emphasis> 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>photon</emphasis> 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>neutrino</emphasis> 
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>SimVertex</emphasis>
  : (tracks) originating simulated vertex (0=primary) 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>SCT/Pixel</emphasis> : ...
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>All</emphasis> (default) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Endcap-</emphasis>: ... 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Barrel</emphasis>: ... 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Endcap+</emphasis>: ... 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TRT_DriftCircle</emphasis> : ...
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>All</emphasis> (default) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Barrel-</emphasis>: ... 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Barrel+</emphasis>: ... 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Track Index</emphasis>
  : (tracks) identifier of reconstructed track 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Hits By STr</emphasis> : 
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>All</emphasis> (default) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Connected</emphasis>
   : hits connected to simulated tracks 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Unconnected</emphasis>
   : hits unconnected to simulated tracks 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Hits By Track</emphasis> : 
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>All</emphasis> (default) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Connected</emphasis>
   : hits connected to reconstructed tracks 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Unconnected</emphasis>
   : hits unconnected to reconstructed tracks 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Hit type</emphasis>: 
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>noise</emphasis> : noise hits (other hits) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>good</emphasis>
   : good hits (associated to tracks, or passing the filter
   (<xref endterm="Fil.title" linkend="Fil"></xref>)) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>all</emphasis> (default) 
   </para>
  </listitem>
  </itemizedlist>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Group</emphasis>
  : group number of silicon hit: 0 = noise. See 
  <xref endterm="Fil.title" linkend="Fil"></xref>. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TRT Threshold</emphasis>: threshold for TRT Straws
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>high</emphasis> (default) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>low</emphasis> 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="CutsCalo">
 <title id="CutsCalo.title">6.4.2 Cuts for Calorimeters (Calo)</title>
 
 <para>
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>&verbar;Jet Et&verbar;</emphasis>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;LAr Energy&verbar;</emphasis>: energy deposit [MeV] 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;Tile Energy&verbar;</emphasis>: energy deposit [MeV] 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;HEC Energy&verbar;</emphasis>: energy deposit [MeV] 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;FCAL Energy&verbar;</emphasis>: energy deposit [MeV] 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>FCAL</emphasis>
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>All</emphasis> (default) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Endcap-</emphasis> 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Endcap+</emphasis> 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>LAr</emphasis>
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>All</emphasis> (default) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Endcap-</emphasis> 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Endcap+</emphasis> 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>HEC</emphasis>
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>All</emphasis> (default) 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Endcap-</emphasis> 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Endcap+</emphasis> 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;Cluster ET&verbar;</emphasis>
  : cluster to which the cell is associated 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Cluster</emphasis>
  </para>
  <para>Cluster to which the cell is associated 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;LVL1 Trigger Energy&verbar;</emphasis>
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="CutsMuon">
 <title id="CutsMuon.title">6.4.3 Cuts for Muon Detector (MuonDet)</title>
 
 <para>
 No cuts available yet.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="CutsAOD">
 <title id="CutsAOD.title">6.4.4 Cuts for Analysis Object Data (AOD)</title>
 
 <para>
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>&verbar;BJet Pt&verbar;</emphasis>
  : B-tagged Jet transverse momentum
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>BJet lhSig</emphasis>
  : B-tagged Jet likelihood significance, combined B-tagging algorithms.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>BJet weight</emphasis>
  : B-tagged Jet B-tagging algorithm's weight
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;Electron Pt&verbar;</emphasis>
  : Electron transverse momentum
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Electron isEM (*)</emphasis>
  : Electron electromagnetic criteria passed (bitmap)
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Electron eOverp</emphasis>
  : Electron ratio of energy over momentum
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;Muon Pt&verbar;</emphasis>
  : Muon transverse momentum
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Muon chi2</emphasis> : Muon fit chi2
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;Photon Pt&verbar;</emphasis>
  : Photon transverse momentum
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Photon isEM (*)</emphasis>
  : Photon electromagnetic criteria passed (bitmap)
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;TauJet Pt&verbar;</emphasis>
  : Tau transverse momentum
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&verbar;TauJet Charge&verbar;</emphasis>
  : Tau total charge
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TauJet NumTrack</emphasis>
  : Tau number of tracks
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TauJet isolFrac</emphasis>
  : Tau isolation fraction
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TauJet logLhRatio</emphasis>
  : Tau log-likelihood ratio between tau and jet
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 <emphasis>N.B.</emphasis>
 </para>
 
 <para>
 <emphasis>(*)</emphasis> Cut-logic for isEM: int required.
 Logic in bitmap: "1" means "do not care". Non-passing of algorithm is allowed.
 "0" means: "is required to be passed". E.g. 16 (binary: 1000) means that
 algorithm encoded into fourth bit is allowed to have failed.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="CutsATLAS">
 <title id="CutsATLAS.title">6.4.5 Cuts for whole Detector (ATLAS)</title>
 
 <para>
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Index</emphasis>
  : (tracks) in the range 0 to numTracks-1 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Module</emphasis> : ... 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Layer</emphasis> : ... 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Cut &phi;</emphasis>
  : (angular region) hits and tracks in the range 
  &phi;&plusmn;&phi;<subscript>cut</subscript> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&phi;</emphasis>
  : (angular region) ... 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Cut &eta;</emphasis>
  : (angular region) hits and tracks in the range 
  &eta;&plusmn;&eta;<subscript>cut</subscript> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>&eta;</emphasis>
  : (angular region) ... 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>ByList</emphasis>
  : (list) only data in the currently selected list
  (<xref endterm="Lists.title" linkend="Lists"></xref>) are shown 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Summary</emphasis>
  : a summary of the effects of the currently applied cuts
  is shown in the
  output window (<xref endterm="OutputDisplay.title" linkend="OutputDisplay"></xref>). 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect2>
 
 </sect1>
 
 </chapter>
 
 <!--=======================================================================-->
 <chapter id="Detector">
 <title id="Detector.title">Detector</title>
 
 <para>
 This chapter describes specific elements, data and their attributes of the 
 Whole Detector (ATLAS) 
 (<xref endterm="ATLAS.title" linkend="ATLAS"></xref>) and 
 its subsystems Inner Detector (InDet) 
 (<xref endterm="InDet.title" linkend="InDet"></xref>), 
 Calorimeters (Calo) (<xref endterm="Calo.title" linkend="Calo"></xref>) and 
 Muon Detector (Muon) (<xref endterm="MuonDet.title" linkend="MuonDet"></xref>). 
 </para>
 
 <para>
 Section Analysis Object Data (AOD) 
 (<xref endterm="AOD.title" linkend="AOD"></xref>) 
 describes data and their attributes from AOD collections. 
 </para>
 
 <para>
 Section General Information 
 (<xref endterm="GenInfo.title" linkend="GenInfo"></xref>) 
 contains information about generally used attributes.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="InDet">
 <title id="InDet.title">7.1 Inner Detector (InDet)</title>
 
 <para>
 Elements, attributes and control are grouped into:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>SpacePoint</emphasis>
  (<xref endterm="S3D.title" linkend="S3D"></xref>)
  : silicon space points 
  </para>
  <para>
  SpacePoint hits may be cleaned with the Silicon hit filter
  (<xref endterm="Fil.title" linkend="Fil"></xref>).
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>PixelRDO</emphasis>
  (<xref endterm="PixelRDO.title" linkend="PixelRDO"></xref>)
  : Pixel Raw Data Object
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TrigSiSpacePoint</emphasis>
  (<xref endterm="TrigS3D.title" linkend="TrigS3D"></xref>)
  : Online Silicon 3D Space Points
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>SiHit</emphasis>
  (<xref endterm="SiHit.title" linkend="SiHit"></xref>)
  : Geant Silicon Hits
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>SiCluster</emphasis>
  (<xref endterm="SiCluster.title" linkend="SiCluster"></xref>) :
  Silicon Cluster 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>SiClusterRDO</emphasis>
  (<xref endterm="SiClusterRDO.title" linkend="SiClusterRDO"></xref>) :
  Silicon Cluster Raw Data Object
  </para>
 </listitem>
 <listitem>
 <para>
  <emphasis>TRT_DriftCircle</emphasis>
  (<xref endterm="TRT.title" linkend="TRT"></xref>) : TRT straws
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>STr</emphasis>
  (<xref endterm="STr.title" linkend="STr"></xref>)
  : simulated tracks 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Segment</emphasis>
  (<xref endterm="InDetSegment.title" linkend="InDetSegment"></xref>)
  : Reconstructed InDet Segment Collections
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Track</emphasis>
  (<xref endterm="InDetTrack.title" linkend="InDetTrack"></xref>)
  : Reconstructed Track Collections 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>SimVertex</emphasis>
  (<xref endterm="SVx.title" linkend="SVx"></xref>)
  : simulated vertices 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>RecVertex</emphasis>
  (<xref endterm="RVx.title" linkend="RVx"></xref>)
  : reconstructed vertices 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Hit Filter</emphasis>
  (<xref endterm="Fil.title" linkend="Fil"></xref>)
  : Hit Filter Setup
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="S3D">
 <title id="S3D.title">7.1.1 Silicon 3D SpacePoints (SpacePoint)</title>
 
 <para>
 Space points from silicon pixel 
 (<xref endterm="SiliconPixels.title" linkend="SiliconPixels"></xref>) 
 clusters and calculated from the low angle stereo silicon strips 
 (<xref endterm="SiliconStrips.title" linkend="SiliconStrips"></xref>) 
 are called S3D hits. 
 </para>
 
 <para>
 The following element and attribute items are available and can be controlled:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Color Function</emphasis>
  </para>
  <para>
  The color of each hit is defined by the color function selected from the 
  following options: 
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>Constant</emphasis> (default)
   </para>
   <para>
   in which case the color defined by item <emphasis>Constant</emphasis> is
   used for all hits 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Simulated Track</emphasis>
   </para>
   <para>
   the colors of unconnected and shared hits can be selected by items
   <emphasis>Unconnected</emphasis> and <emphasis>Shared</emphasis> 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Reconstructed Track</emphasis>
   </para>
   <para>
   the colors of unconnected and shared hits can be selected 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>SubDetector</emphasis>
   </para>
   <para>
   (Barrel, Endcap+, Endcap-), 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Group</emphasis>
   </para>
   <para>
   as determined by the filter
   (<xref endterm="Fil.title" linkend="Fil"></xref>),
   the color of ungrouped hits can be selected 
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>Layer</emphasis>.
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Constant</emphasis>
  </para>
  <para>
  The color of all hits, used for the <emphasis>Constant</emphasis> color
  function. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Unconnected</emphasis>
  </para>
  <para>
  The color used for unconnected hits. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Shared</emphasis>
  </para>
  <para>
  The color used for shared hits. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Ungrouped</emphasis>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Symbol Size</emphasis>
  </para>
  <para>
  The size in pixels of the symbol used to represent hits. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Symbol</emphasis>
  </para>
  <para>
  The type of symbol used to represent hits. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Frame</emphasis>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Frame Width</emphasis>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Noise Size</emphasis>
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Noise</emphasis>
  </para>
 </listitem>
 </itemizedlist>
 
 See Graphics Attributes of Hits 
 (<xref endterm="Attributes.title" linkend="Attributes"></xref>) 
 for a description of graphics parameters related to hits.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect3 id="SiliconPixels">
 <title id="SiliconPixels.title">7.1.1.1 Silicon Pixels</title>
 
 <para>
 Silicon pixels give directly 3D positions. From each cluster of pixels a 
 space point is calculated. The pixel dimensions are 
 50&micro;m&times;400&micro;m. The barrel of the pixel detector has three 
 layers at 4, 11 and 15 cm, respectively, which provide position measurements 
 with a resolution of 12 &micro;m in &rho;-&phi; and 66 &micro;m in Z. 
 The endcap has four layers at &plusmn;35, &plusmn;67, &plusmn;95 and 
 &plusmn;115 cm, respectively, which provide position measurements with a 
 resolution of 12 &micro;m in &rho;-&phi; and 77 &micro;m in &rho;.
 </para>
 
 </sect3>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect3 id="SiliconStrips">
 <title id="SiliconStrips.title">7.1.1.2 Silicon Strips</title>
 
 <para>
 To be filled.
 </para>
 
 </sect3>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="PixelRDO">
 <title id="PixelRDO.title">7.1.2 Pixel Raw Data Object (PixelRDO)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="TrigS3D">
 <title id="TrigS3D.title">7.1.3 Online Silicon 3D Space Points (TrigSiSpacePoint)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="SiHit">
 <title id="SiHit.title">7.1.4 Geant Silicon Hits (SiHit)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="SiCluster">
 <title id="SiCluster.title">7.1.5 Silicon Cluster (SiCluster)</title>
 
 <para>
 Silicon clusters are formed from groups of neighbouring silicon strips. 
 In the barrel these silicon strips are either parallel to the beam axis 
 (&phi;-strips) or inclined by either +0.04 radians = 2.3&deg; (u-strips) 
 or by -0.04 radians (v-strips). In the endcaps the &phi;-strips are 
 perpendicular to the cylinder axis. Each layer contains &phi;-strips and 
 either u-strips or v-strips (alternating between neighbouring layers) to 
 allow for low angle stereo. If both such strips fire, when a charged 
 particle traverses the layer, a space point can be calculated. If more 
 than one particle traverse the same layer in close proximity ghost space 
 points are produced. 
 </para>
 
 <para>
 For barrel layers the &phi;-&rho; position of a space point is taken 
 from the position of the &phi; strip. Z is calculated through low angle 
 stereo. 
 For endcap the &phi;-Z position is taken from the &phi;-strip and &rho; is 
 calculated through low angle stereo. Each barrel space point is measured 
 with a precision of 16&micro;m in &rho;-&phi; and 580 &micro;m in Z, 
 respectively. Two tracks can be distinguished if separated by more than 
 &thkap;200 &micro;m. 
 </para>
 
 <para>
 The distance between &phi; strips and the u- or v- strips in the same 
 module is 400 &micro;m. The calculated value of Z for the barrel and &rho; 
 for the endcap depends of the direction of the track passing through the 
 module. As this is normally unknown, most space point calculations assume 
 particles of infinite momentum coming from X, Y, Z=0. 
 </para>
 
 <para>
 There are four layers in the barrel between 35, and 115 cm, and nine layers in 
 the endcap between &plusmn;82 and &plusmn;276 cm. 
 </para>
 
 <para>
 <emphasis>Graphical Representation</emphasis>
 </para>
 
 <para>
 The clusters are represented graphically as a line segment joining their 
 two endpoints. 
 </para>
 
 <para>
 The color of each hit is defined by the <emphasis>color function</emphasis> 
 which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  constant, in which case the <emphasis>constant</emphasis>
  color is used for all hits, 
  </para>
 </listitem>
 </itemizedlist>
 
 or it may vary with each hit being given the color of its associated 
 
 <itemizedlist>
 <listitem>
  <para>
  simulated track.
  The colors of <emphasis>unconnected</emphasis> and
  <emphasis>shared</emphasis> hits can be selected. 
  </para>
 </listitem>
 <listitem>
  <para>
  reconstructed track.
  The colors of <emphasis>unconnected</emphasis> and
  <emphasis>shared</emphasis> hits can be selected. 
  </para>
 </listitem>
 <listitem>
  <para>
  subdetector. (Barrel,Endcap+,Endcap-) 
  </para>
 </listitem>
 <listitem>
  <para>
  layer. 
  </para>
 </listitem>
 <listitem>
  <para>
  orientation. (&phi;-strips, u-strips or v-strips) 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="SiClusterRDO">
 <title id="SiClusterRDO.title">7.1.6 Silicon Cluster Raw Data Object (SiClusterRDO)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="TRT">
 <title id="TRT.title">7.1.7 Transition Radiation Tracker (TRT_DriftCircle)</title>
 
 <para>
 The TRT barrel has straws parallel to the beam axis in the barrel and 
 straws perpendicular to the beam axis in the endcap. The data from each 
 TRT straw is best represented as a circle, however, in practice the radius 
 of each straw (2mm) is so small compared to the length of a track segment 
 (55cm) that when looking at such a track segment the circle can be 
 adequately approximated as a straight line with a length given by twice 
 the drift radius. The barrel straws are represented as lines perpendicular 
 to a radial line in the 
 &phi;/&rho; (<xref endterm="FR.title" linkend="FR"></xref>) and 
 Y/X (<xref endterm="YX.title" linkend="YX"></xref>) projections. 
 The endcap straws are represented as lines perpendicular to the z-axis in the 
 &phi;/Z (<xref endterm="FZ.title" linkend="FZ"></xref>) 
 projection. 
 The drift radius is measured with a precision of around 170&micro;m. 
 </para>
 
 <para>
 <emphasis>Transition radiation hits</emphasis>
 </para>
 
 <para>
 Each straw provides an indication of whether a hit passes a second higher 
 <emphasis>threshold</emphasis> associated with transition radiation. 
 This transition radiation is associated with the passage of electrons and 
 such hits may be used in electron identification. These hits can be viewed 
 on their own by selecting the high <emphasis>threshold</emphasis> in the 
 Cuts (<xref endterm="Cuts.title" linkend="Cuts"></xref>). 
 </para>
 
 <para>
 On the Y/X projection (<xref endterm="YX.title" linkend="YX"></xref>) if the 
 data contains drift signs and if zoomed in far enough the line showing the 
 TRT data will change to an arrow to represent the drift.
 </para>
 
 <para>
 <emphasis>Graphical Representation</emphasis>
 </para>
 
 <para>
 The color of each hit is defined by the <emphasis>color function</emphasis> 
 which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all hits, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each hit being given the color of its associated 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>simulated track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and <emphasis>shared</emphasis> hits can be
  selected, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>reconstructed track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and 
  <emphasis>shared</emphasis> hits can be selected, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>subdetector</emphasis>
  (Endcap-,Barrel-,Barrel+,Endcap+). 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="STr">
 <title id="STr.title">7.1.8 Simulated Tracks (STr)</title>
 
 <para>
 Simulated particles may be either charged STr or neutral SNP, and may 
 be defined by: 
 
 <itemizedlist>
 <listitem>
  <para>
  the 3D position of the vertex, from which the particle
  originated, 
  </para>
 </listitem>
 <listitem>
  <para>
  the 3D momentum vector at the vertex position, 
  </para>
 </listitem>
 <listitem>
  <para>
  the particle type. 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 For charged particles, these parameters may be used to derive helix 
 parameters (perigee parameters), extended by a further value, which gives 
 the vertex position on the helix. 
 </para>
 
 <para>
 The paths travelled by simulated particles are defined in 3D and can 
 therefore be seen in all projections. These paths do not reflect multiple 
 scattering. Furthermore, for charged particles the helix approximation 
 used is only valid inside the homogeneous solenoidal magnetic field and 
 assuming negligible energy loss. 
 </para>
 
 <para>
 The color of each simulated particle is defined by the <emphasis>color 
 function</emphasis> which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all particles, 
  </para>
 </listitem>
 </itemizedlist>
 
 or it may vary with each particle being given the color of its 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>index</emphasis>: in the range 0 to numSTr-1 or 0
  to numSNP-1, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>particle type</emphasis>: 
  <itemizedlist>
  <listitem>
   <para>
   cyan - charged hadrons, 
   </para>
  </listitem>
  <listitem>
   <para>
   yellow - electrons, 
   </para>
  </listitem>
  <listitem>
   <para>
   green - muons, 
   </para>
  </listitem>
  <listitem>
   <para>
   magenta - neutral hadrons, 
   </para>
  </listitem>
  <listitem>
   <para>
   red - photons, 
   </para>
  </listitem>
  <listitem>
   <para>
   orange - neutrinos. 
   </para>
  </listitem>
  </itemizedlist> 
  </para>
 </listitem>
 </itemizedlist> 
 
 The radius (<emphasis>radius Tr</emphasis>) and length (<emphasis>Z 
 Tr</emphasis>) of the cylinder to which the particles are drawn can be 
 changed. 
 </para>
 
 <para>
 Track images are easier recognised if tracks get a black 
 <emphasis>frame</emphasis> with a small <emphasis>frame width</emphasis>, 
 especially in the V-plot if calorimeters are displayed as well. 
 </para>
 
 <para>
 In the V-plot simulated neutral particles SNP are drawn as a 
 <emphasis>symbol</emphasis> with a given <emphasis>symbol size</emphasis>. 
 In the other projections simulated neutral particles are drawn as lines. 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="InDetSegment">
 <title id="InDetSegment.title">7.1.9 Reconstructed InDet Segment Collections (Segment)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="InDetTrack">
 <title id="InDetTrack.title">7.1.10 Reconstructed Track Collections (Track)</title>
 
 <para>
 Reconstructed tracks are described by helix parameters (perigee parameters). 
 The reconstructed tracks are defined in 3D and can therefore be seen in all 
 projections. The helix approximation used is only valid inside the 
 homogeneous solenoidal magnetic field and assuming negligible energy loss 
 and no multiple scattering. 
 </para>
 
 <para>
 The color of each reconstructed track is defined by the <emphasis>color 
 function</emphasis> which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all tracks, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each track being given the color of its 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>index</emphasis>: in the range 0 to numRTr-1, 
  </para>
 </listitem>
 <listitem>
  <para>
  associated <emphasis>simulated track</emphasis> 
  </para>
 </listitem>
 <listitem>
  <para>
  associated <emphasis>E/Gamma reconstucted object</emphasis> 
  </para>
 </listitem>
 </itemizedlist> 
 
 The radius (<emphasis>radius Tr</emphasis>) and length
 (<emphasis>Z Tr</emphasis>) of the cylinder
 to which the tracks are drawn can be changed. 
 </para>
 
 <para>
 Track images are easier recognised if tracks get a black 
 <emphasis>frame</emphasis> with a small <emphasis>frame width</emphasis>, 
 especially in the V-plot if calorimeters are displayed as well. 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="SVx">
 <title id="SVx.title">7.1.11 Simulated Vertices (SimVertex)</title>
 
 <para>
 Simulated vertices from the Monte Carlo truth. Currently only the start 
 vertices of simulated particles are available and there should be at 
 least one simulated particle originating from each simulated vertex.
 </para>
 
 <para>
 The <emphasis>constant</emphasis> color of the simulated vertices may be 
 changed.
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="RVx">
 <title id="RVx.title">7.1.12 Reconstructed Vertices (RecVertex)</title>
 
 <para>
 Reconstructed vertices may be formed interactively inside Atlantis from 
 Lists (<xref endterm="Lists.title" linkend="Lists"></xref>) of 
 reconstructed tracks. 
 These reconstructed vertices are best represented by their error 
 ellipsoids. These representations are currently available only in the 
 Y/X (<xref endterm="YX.title" linkend="YX"></xref>), 
 X'/Z (<xref endterm="XZ.title" linkend="XZ"></xref>) and 
 Y'/Z (<xref endterm="YZ.title" linkend="YZ"></xref>) projections. 
 The error ellipses shown represent <emphasis>Num Sigma</emphasis> standard 
 deviations which may be modified. 
 </para>
 
 <para>
 The <emphasis>constant</emphasis> color of these reconstructed vertices may 
 be changed. 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Fil">
 <title id="Fil.title">7.1.13 Hit Filter Setup (Hit Filter)</title>
 
 <para>
 In the case of normal simulated events and of the real events to be expected, 
 it is difficult if not impossible to recognise tracks, etc., due to ghost 
 hits, delta electrons, hits from the pile up and noise.
 </para>
 
 <para>
 A filter is available to clean the events. In the case of fairly clean 
 events, the V-plot may still help out. For the V-plot as for the filter, 
 the Z-position of the primary vertex of the "triggering event" is required, 
 so that &eta; can be calculated. 
 </para>
 
 <para>
 <emphasis>Single filter</emphasis>
 </para>
 
 <para>
 The filter is based on the simple requirement, that a 3D hit passes the 
 filter if at least N<subscript>H</subscript> 
 (N<subscript>H</subscript>=<emphasis>NumHits</emphasis>) hits on 
 different layers lie in the same direction, as seen from the primary vertex.
 </para>
 
 <para>
 In a &phi;&eta; histogram with cell size 
 &Delta;&phi;&times;&Delta;&eta;, 
 the hits of a given helix with sufficiently high P<subscript>
 t</subscript> lie 
 in one cell or in its direct neighbours due to rounding or measuring errors.
 </para>
 
 <para>
 In a first loop over all hits the histogram is filled, however counting 
 layers and not just hits. This is done using bit patterns. In a second 
 loop over all hits each hit is accepted or rejected depending on the sum 
 of different layers in its histogram bin and its neighbours.
 </para>
 
 <para>
 The second loop can be combined with a clustering algorithm, so that hits 
 falling into isolated clusters get a <emphasis>group</emphasis> number, 
 which varies with different clusters. The subsets of S3D hits belonging to 
 the different <emphasis>groups</emphasis> passing the filter may selected 
 using the <emphasis>group</emphasis> parameter.
 </para>
 
 <para>
 The strength and P<subscript>t</subscript> acceptance of the filter is 
 defined by &Delta;&eta; and &Delta;&phi;: 
 
 <itemizedlist>
 <listitem>
  <para>
  The value of &Delta;&eta;=2&times;<emphasis>&eta;
  Range</emphasis>/<emphasis>Num&eta;</emphasis> 
  reflects measuring &eta; precision and should be as small as possible 
  without loosing hits. 
  </para>
 </listitem>
 <listitem>
  <para>
  The value of &Delta;&phi;=360&deg;/<emphasis>Num&phi;</emphasis> 
  defines the 
  P<subscript>t</subscript> range in which tracks are accepted and the strength 
  of the filter. A small &Delta;&phi; (strong filter) rejects much noise
  but also low P<subscript>t</subscript> tracks.
  </para>
 </listitem>
 </itemizedlist>
 
 In the same way one can filter tracks in a given P<subscript>t</subscript> 
 range through a &phi;'&eta; histogram, where &phi;' is defined as 
 &phi;'=&phi;-c&times;s&times;&rho;, where c depends on the magnetic field. 
 Hits of tracks with P<subscript>t</subscript>=1/s have the same 
 &phi;'<subscript>,</subscript> and pass the filter. Depending on 
 &Delta;&phi; also hits of tracks with close P<subscript>t</subscript> do 
 pass. The sign of P<subscript>t</subscript> is equal to the particle charge. 
 </para>
 
 <para>
 <emphasis>Filter loop</emphasis>
 </para>
 
 <para>
 In order to have a strong filter with also low P<subscript>t</subscript> 
 tracks passing, the filter is executed N times in a loop where s is varied 
 between 
 -1/<emphasis>P<subscript>t<subscript>MIN</subscript></subscript></emphasis> 
 and 
 +1/<emphasis>P<subscript>t<subscript>MIN</subscript></subscript></emphasis> 
 with N=1+2&times;<emphasis>NumSteps</emphasis>. 
 Hits, which pass at least one of the single filters, are accepted. 
 An accepted hit may have different group numbers from different filters. 
 Different clusters, which contain the same hit, get the same new group 
 number. Due to measuring errors, some tracks above 
 <emphasis>P<subscript>t<subscript>MIN</subscript></subscript></emphasis> 
 may get lost, so that 
 <emphasis>P<subscript>t<subscript>MIN</subscript></subscript></emphasis> 
 should be sufficiently low.
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="Calo">
 <title id="Calo.title">7.2 Calorimeters (Calo)</title>
 
 <para>
 Control of the attributes of data from the various calorimeters is described 
 in: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>LAr</emphasis> (<xref endterm="LAr.title" linkend="LAr"></xref>)
  : Liquid Argon Calorimeter 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TILE</emphasis> (<xref endterm="TILE.title" linkend="TILE"></xref>)
  : Tile Calorimeter 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>HEC</emphasis> (<xref endterm="HEC.title" linkend="HEC"></xref>)
  : Hadronic Endcap Calorimeter 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>FCAL</emphasis> (<xref endterm="FCAL.title" linkend="FCAL"></xref>)
  : Forward Calorimeter 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Cluster</emphasis>
  (<xref endterm="Cluster.title" linkend="Cluster"></xref>)
  : Clusters
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>SNP</emphasis> (<xref endterm="SNP.title" linkend="SNP"></xref>)
  : Simulated Neutral Particles
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>EmTauROI</emphasis>
  (<xref endterm="EmTauROI.title" linkend="EmTauROI"></xref>)
  : Electromagnetic/Tau Region of Interest
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>JetROI</emphasis>
  (<xref endterm="JetROI.title" linkend="JetROI"></xref>)
  : Jet Region of Interest
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>LVL1TriggerTower</emphasis> 
  (<xref endterm="LVL1TriggerTower.title" linkend="LVL1TriggerTower"></xref>)
  : Level-1 Calorimeter Trigger Input Data: E/Gamma, tau/had
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>LVL1JetElement</emphasis>
  (<xref endterm="LVL1JetElement.title" linkend="LVL1JetElement"></xref>)
  : Level-1 Calorimeter Trigger Input Data: jet, ET-Miss/ET-Sum
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="LAr">
 <title id="LAr.title">7.2.1 Liquid Argon Electromagnetic Calorimeter (LAr)</title>
 
 <para>
 The Liquid Argon Electromagnetic Calorimeter consists of a barrel and two 
 endcaps. The barrel inner and outer radii are 150 and 198 cm, respectively. 
 The end caps start at 315 and end at 450 cm. Each of the barrel and two 
 end caps are made up from four samplings with separate readout. The first 
 sampling (sampling 0) is called the presampler. Each of the four samplings 
 is split in a large number of separate measuring cells in &phi; and in &eta;. 
 The cell geometry is projective in &phi; and &eta;. The thickness of the 
 different samplings varies with &eta; in order to make the thickness of 
 the two middle samplings to be a roughly constant number of radiation lengths. 
 </para>
 
 <para>
 A detailed description of the parameters which are common to all 
 calorimeters may be found at 
 <xref endterm="Calorimeter.title" linkend="Calorimeter"></xref>. 
 </para>
 
 <para>
 The granularity &Delta;&eta;&times;&Delta;&phi; of the LAr varies over a 
 large range depending on the sampling and pseudorapidity:
 
 <table frame="topbot" pgwide="0">
 <title>Granularity of LAr</title>
 <tgroup cols="5">
 <colspec colnum="1" colname="colone"   colwidth="70" align="left"></colspec>
 <colspec colnum="2" colname="coltwo"   colwidth="80" align="left"></colspec>
 <colspec colnum="3" colname="colthree" colwidth="80" align="left"></colspec>
 <colspec colnum="4" colname="colfour"  colwidth="80" align="left"></colspec>
 <colspec colnum="5" colname="colfive"  colwidth="80" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry></entry>
   <entry>Barrel</entry>
   <entry></entry>
   <entry>Endcap</entry>
   <entry></entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>Sampling</emphasis></entry>
   <entry>
 &Delta;&eta;&times;&Delta;&phi;</entry>
   <entry>
 &verbar;&eta;&verbar; range</entry>
   <entry>
 &Delta;&eta;&times;&Delta;&phi;</entry>
   <entry>
 &verbar;&eta;&verbar; range</entry>
  </row>
  <row rowsep="1">
   <entry>0 (pre)</entry>
   <entry>0.025&times;0.1</entry>
   <entry>&verbar;&eta;&verbar;&lt;1.52</entry>
   <entry>0.025&times;0.1</entry>
   <entry>1.5&lt;&verbar;&eta;&verbar;&lt;1.8</entry>
  </row>
  <row rowsep="1">
   <entry>1</entry>
   <entry>0.003&times;0.1</entry>
   <entry>&verbar;&eta;&verbar;&lt;1.475</entry>
   <entry>0.025&times;0.1</entry>
   <entry>1.375&lt;&verbar;&eta;&verbar;&lt;1.5</entry>
  </row>
  <row rowsep="1">
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>0.003&times;0.1</entry>
   <entry>1.5&lt;&verbar;&eta;&verbar;&lt;1.8</entry>
  </row>
  <row rowsep="1">
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>0.004&times;0.1</entry>
   <entry>1.8&lt;&verbar;&eta;&verbar;&lt;2.0</entry>
  </row>
  <row rowsep="1">
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>0.006&times;0.1</entry>
   <entry>2.0&lt;&verbar;&eta;&verbar;&lt;2.5</entry>
  </row>
  <row rowsep="1">
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>0.1&times;0.1</entry>
   <entry>2.5&lt;&verbar;&eta;&verbar;&lt;3.2</entry>
  </row>
  <row rowsep="1">
   <entry>2</entry>
   <entry>0.025&times;0.025</entry>
   <entry>&verbar;&eta;&verbar;&lt;1.475</entry>
   <entry>0.025&times;0.025</entry>
   <entry>1.375&lt;&verbar;&eta;&verbar;&lt;2.5</entry>
  </row>
  <row rowsep="1">
   <entry></entry>
   <entry></entry>
   <entry></entry>
   <entry>0.1&times;0.1</entry>
   <entry>2.5&lt;&verbar;&eta;&verbar;&lt;3.2</entry>
  </row>
  <row rowsep="1">
   <entry>3</entry>
   <entry>0.05&times;0.025</entry>
   <entry>&verbar;&eta;&verbar;&lt;1.475</entry>
   <entry>0.05&times;0.025</entry>
   <entry>1.5&lt;&verbar;&eta;&verbar;&lt;2.5</entry></row>
 </tbody>
 </tgroup>
 </table>
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="TILE">
 <title id="TILE.title">7.2.2 Tile Calorimeter (TILE)</title>
 
 <para>
 The TILE calorimeter is a sampling calorimeter using iron as the absorber 
 and scintillating tiles as the active material. It is used to measure the 
 hadronic energy of particles moving at small pseudorapidities. The total 
 &eta; coverage of the TILE is &verbar;&eta;&verbar;&lt;1.7. The TILE is split 
 mechanically into three parts: barrel and left and right extended barrels. 
 The barrel region has a pseudorapidity coverage of &verbar;&eta;&verbar;&lt;1.0. 
 The extended barrel region covers the pseudorapidity range 
 0.8&lt;&verbar;&eta;&verbar;&lt;1.7. The inner radius of the calorimeter is 
 2.28 m and the outer radius is 4.25 m. It is longitudinally segmented into 
 three samplings. The cells are arranged in a pseudo-projective geometry 
 with a granularity of 0.1&times;0.1 in &Delta;&eta;&times;&Delta;&phi; for 
 the inner two samplings and 0.2&times;0.1 in &Delta;&eta;&times;&Delta;&phi; 
 for the outer sampling. 
 </para>
 
 <para>
 A detailed description of the parameters which are common to all 
 calorimeters may be found at 
 <xref endterm="Calorimeter.title" linkend="Calorimeter"></xref>. 
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="HEC">
 <title id="HEC.title">7.2.3 Hadronic Endcap Calorimeter (HEC)</title>
 
 <para>
 The HEC is a liquid argon based hadronic endcap calorimeter. It is used to 
 measure the hadronic energy of particles in the pseudorapidity range 
 1.5&lt;&verbar;&eta;&verbar;&lt;3.2. 
 Each endcap consists of two independent 
 wheels which are longitudinally segmented into four samplings. The cell 
 geometry is fully projective in azimuth and pseudo-projective in 
 pseudorapidity with a granularity of 0.1&times;0.1 in 
 &Delta;&eta;&times;&Delta;&phi; in the pseudorapidity range 
 1.5&lt;&verbar;&eta;&verbar;&lt;2.5 and 0.2&times;0.2 in 
 &Delta;&eta;&times;&Delta;&phi; in the pseudorapidity range 
 2.5&lt;&verbar;&eta;&verbar;&lt;3.2.
 </para>
 
 <para>
 A detailed description of the parameters which are common to all 
 calorimeters may be found at 
 <xref endterm="Calorimeter.title" linkend="Calorimeter"></xref>. 
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="FCAL">
 <title id="FCAL.title">7.2.4 Forward Calorimeter (FCAL)</title>
 
 <para>
 The FCAL is a liquid argon based calorimeter providing coverage in the 
 pseudorapidity range 
 3.2&nbsp;&lt;&nbsp;&verbar;&eta;&verbar;&nbsp;&lt;&nbsp;4.9.
 It is longitudinally 
 segmented into three samplings. The innermost sampling uses copper as the 
 absorbing material and is primarily used to measure electromagnetic energy. 
 The outer two samplings use tungsten as the absorbing material and are used 
 to measure hadronic energy. The cells have a granularity of 
 &thksim;0.2&times;0.2 in &Delta;&eta;&times;&Delta;&phi;. 
 The FCAL is situated at a distance in Z 
 of between 4.7 and 6.1 m from the interaction point and at a radial distance 
 between 7 and 46 cm from the beam axis. 
 </para>
 
 <para>
 A detailed description of the parameters which are common to all 
 calorimeters may be found at 
 <xref endterm="Calorimeter.title" linkend="Calorimeter"></xref>. 
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Cluster">
 <title id="Cluster.title">7.2.5 Clusters (Cluster)</title>
 
 <para>
 Clusters are formed from energy deposits in the cells of the 
 liquid argon calorimeter 
 (<xref endterm="LAr.title" linkend="LAr"></xref>). 
 Clusters may not currently be viewed, however, cells in the 
 liquid argon calorimeter may be colored according to their associated cluster. 
 </para>
 
 <para>
 The color of each cluster is defined by the <emphasis>color 
 function</emphasis> which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all clusters, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each cluster being given the color of its 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>index</emphasis>: in the range 0 to numClusters-1, 
  </para>
 </listitem>
 <listitem>
  <para>
  associated <emphasis>E/Gamma reconstucted object</emphasis>. 
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="SNP">
 <title id="SNP.title">7.2.6 Simulated Neutral Particles in Calorimeter,
  Neutral Truth (SNP)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="EmTauROI">
 <title id="EmTauROI.title">7.2.7 Regions Of Interest (EmTauROI)</title>
 
 <para>
 Regions of interest are &Delta;&phi;&times;&Delta;&eta; 
 regions of solid angle defined by the trigger system. 
 They may be viewed in the &phi;/&eta; 
 (<xref endterm="VP.title" linkend="VP"></xref>) projection and the 
 Lego Plot (<xref endterm="LegoPlot.title" linkend="LegoPlot"></xref>). 
 </para>
 
 <para>
 The color of each ROI is defined by the <emphasis>color function</emphasis> 
 which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all ROI's, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each ROI being given the color of its 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>index</emphasis>: in the range 0 to numROI-1. 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="JetROI">
 <title id="JetROI.title">7.2.8 Jet Region of Interest (JetROI)</title>
 
 <para>
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="LVL1TriggerTower">
 <title id="LVL1TriggerTower.title">7.2.9 Level-1 Calorimeter Trigger Input Data:
  E/Gamma, tau/had (LVL1TriggerTower)</title>
 
 <para>
 The data of reduced granularity used inside the Level-1 Calorimeter Trigger
 system can be displayed in the 
 Lego Plot (<xref endterm="LegoPlot.title" linkend="LegoPlot"></xref>). 
 The switch
 "View" allows to select "LVL1TriggerTower" and "LVL1JetElement". The first
 set is used inside the E/Gamma and tau/had trigger, the second is the jet and
 energysum trigger. The granularity displayed matched the real system.
 </para>
 
 <para>
 The color of each Trigger data is defined by the <emphasis>color 
 function</emphasis> which can only be <emphasis>constant</emphasis>, and the 
 <emphasis>constant</emphasis> color is used for all Trigger data.
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="LVL1JetElement">
 <title id="LVL1JetElement.title">7.2.10 Level-1 Calorimeter Trigger Input Data:
  jet, ET-Miss/ET-Sum (LVL1JetElement)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Calorimeter">
 <title id="Calorimeter.title">7.2.11 Calorimeter Attributes</title>
 
 <para>
 <emphasis>Available Projections</emphasis>
 </para>
 
 <para>
 In Atlantis, the calorimeters 
 (LAr (<xref endterm="LAr.title" linkend="LAr"></xref>), 
 TILE (<xref endterm="TILE.title" linkend="TILE"></xref>), 
 HEC (<xref endterm="HEC.title" linkend="HEC"></xref>), 
 FCAL (<xref endterm="FCAL.title" linkend="FCAL"></xref>)) 
 can be seen in the following projections:
 
 <table frame="topbot" pgwide="0">
 <title>Projections and calorimeters</title>
 <tgroup cols="2">
 <colspec colnum="1" colname="colone" colwidth="130" align="left"></colspec>
 <colspec colnum="2" colname="coltwo" colwidth="300" align="left"></colspec>
 <thead>
  <row rowsep="1">
   <entry>Projection</entry>
   <entry>Calorimeter</entry>
  </row>
 </thead>
 <tbody>
  <row rowsep="1">
   <entry><emphasis>Y/X
    (<xref endterm="YX.title" linkend="YX"></xref>)</emphasis>
    </entry>
   <entry>LAr barrel, TILE barrel and extended barrel</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>&rho;/Z
    (<xref endterm="RZ.title" linkend="RZ"></xref>)</emphasis></entry>
   <entry>LAr barrel and endcap, TILE, HEC and FCAL</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>&phi;/&rho;
    (<xref endterm="FR.title" linkend="FR"></xref>)</emphasis>
   </entry>
   <entry>LAr barrel, TILE barrel and extended barrel</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>&phi;/Z
    (<xref endterm="FZ.title" linkend="FZ"></xref>)</emphasis>
   </entry>
   <entry>LAr endcap and HEC</entry>
  </row>
  <row rowsep="1">
   <entry><emphasis>&phi;/&eta;
    (<xref endterm="VP.title" linkend="VP"></xref>)</emphasis>
   </entry>
   <entry>LAr, TILE, HEC, FCAL</entry></row>
 </tbody>
 </tgroup>
 </table> 
 </para>
 
 <para>
 <emphasis>Cells</emphasis>
 </para>
 
 <para>
 To display only the calorimeter histograms without the calorimeter cells 
 the cells must be switched off via the <emphasis>Cells</emphasis> parameter. 
 </para>
 
 <para>
 <emphasis>Energy Representation</emphasis>
 </para>
 
 <para>
 The energy deposited in a calorimeter cell is represented by a polygon 
 whose area is proportional to the energy in that cell. The process of 
 generating such a polygon is: 
 
 <itemizedlist>
 <listitem>
  <para>
  Calculate the real shape of the cell. 
  </para>
 </listitem>
 <listitem>
  <para>
  Get the centroid of the cell. 
  </para>
 </listitem>
 <listitem>
  <para>
  Scale the cell with respect to the centroid according to the 
  energy density in the cell. 
  </para>
 </listitem>
 </itemizedlist>
 
 The scaling according to energy density (calibration) can be done in 
 different ways according to the <emphasis>Energy Calibration</emphasis> 
 parameter: 
 
 <itemizedlist>
 <listitem>
  <para>
  Overall calibration - a single calibration for all the
  calorimeters. 
  Allows to compare energy deposition in different calorimeters. 
  </para>
 </listitem>
 <listitem>
  <para>
  By Energy Type calibration - two independent calibrations for 
  electromagnetic and hadronic energies. 
  </para>
 </listitem>
 <listitem>
  <para>
  By calorimeter calibration - a separate calibration for each
  calorimeter. 
  </para>
 </listitem>
 </itemizedlist>
 
 Additionally, the user can change the default calibration by switching on 
 the <emphasis>E/S</emphasis> parameter and specifying for each calorimeter 
 independently 
 a different value of energy density than that automatically calculated by 
 the program. The value of energy density calculated automatically corresponds 
 to that which would completely fill the geometrical area of the cell with 
 the highest density. 
 </para>
 
 <para>
 <emphasis>Overlapping Cells</emphasis>
 </para>
 
 <para>
 In some projections the cells of the same calorimeter may be overlaid on 
 top of each other. In this case the user has two options in displaying 
 them according to the <emphasis>Energy Mode</emphasis> parameter: 
 
 <itemizedlist>
 <listitem>
  <para>
  Display the energy <emphasis>Sum</emphasis> - the energy
  displayed is the sum of that in all the overlapping cells. 
  </para>
 </listitem>
 <listitem>
  <para>
  Display the energy <emphasis>Maximum</emphasis> - the maximum
  energy cell of all the overlapping cells is calculated and displayed. 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>Coloring Schemes</emphasis>
 </para>
 
 <para>
 The scaled-by-energy-density cells can be colored in different ways 
 according to the <emphasis>Color Function</emphasis> parameter: 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Constant</emphasis> - a single color is used, which
  is given by the <emphasis>Constant</emphasis> parameter. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Sub Detector</emphasis> - the cells are colored by
  the sub detector in which they are. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Cluster</emphasis> - coloring by energy cluster
  which comes with data. 
  If the cell does not belong to any cluster it is colored using the color 
  defined by <emphasis>Unconnected</emphasis> parameter. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Sampling</emphasis> - coloring by the
  sampling(layer) in which the cell is. 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Jet</emphasis> - coloring by the jet to which the
  cell is associated. 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 <emphasis>Cell Frames and Geometry</emphasis>
 </para>
 
 <para>
 Each cell may have a frame which is drawn on the boundary of the cells 
 polygon. The color and the width of this frame can be given by setting 
 the <emphasis>Frame</emphasis> and <emphasis>Frame Width</emphasis> 
 parameters. Whether the frame is drawn or not is controlled by the state of 
 the <emphasis>Frame</emphasis> parameter.
 </para>
 
 <para>
 In some cases it may be useful to see not only the scaled cells but also 
 the initial (real) cells. This can be obtained by switching on the 
 <emphasis>Cell Geometry</emphasis> parameter. The background color used to 
 draw the cell geometry is given by the value of the same parameter. 
 </para>
 
 <para>
 <emphasis>Histograms</emphasis>
 </para>
 
 <para>
 Another possibility to represent the energy deposition in the calorimeters 
 is by Histograms. Where appropriate the energy deposition is summed over 
 layers and depth. A histogram can be obtained by switching on the 
 <emphasis>Histogram</emphasis> parameter. The histogram can get different 
 colors according to the value of the <emphasis>Histogram</emphasis> parameter. 
 They can also have a frame with a color given by the 
 <emphasis>Histo Frame</emphasis> parameter.
 </para>
 
 <para>
 The energy is represented as the length of the histogram tower. 
 The energy to length mapping can be customized by changing the value of 
 <emphasis>Histo Scale</emphasis> parameter.
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="MuonDet">
 <title id="MuonDet.title">7.3 Muon Detector (MuonDet)</title>
 
 <para>
 Control of the attributes of data from the muon system, namely:
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Track</emphasis>
  (<xref endterm="MuonTrack.title" linkend="MuonTrack"></xref>)
  : Reconstructed Track Collections
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Segment</emphasis>
  (<xref endterm="MuonSegment.title" linkend="MuonSegment"></xref>)
  : Segments of Muon Tracks
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>MDT</emphasis> (<xref endterm="MDT.title" linkend="MDT"></xref>)
  : Monitored Drift Tubes
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>CSC</emphasis> (<xref endterm="CSC.title" linkend="CSC"></xref>)
  : Cathode Strip Chambers
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>RPC</emphasis> (<xref endterm="RPC.title" linkend="RPC"></xref>)
  : Resistive Plate Chambers
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TGC</emphasis> (<xref endterm="TGC.title" linkend="TGC"></xref>)
  : Thin Gap Chambers
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>SMTr</emphasis> (<xref endterm="SMTr.title" linkend="SMTr"></xref>)
  : Simulated Muon tracks
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>MuonROI</emphasis>
  (<xref endterm="MuonROI.title" linkend="MuonROI"></xref>)
  : Muon Region of Interest
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="MDT">
 <title id="MDT.title">7.3.1 Monitored Drift Tubes (MDT)</title>
 
 <para>
 The MDT's provide precision tracking of muons, bending in the toroidal 
 magnetic field, over a cylindrical region of 11m in radius and 23 m in 
 half-length. Each MDT is a straw with a diameter of 3 cm and a length in 
 the range from 70 to 630 cm. The drift radius within each straw is measured 
 with a precision of &thkap;80&micro;m. The straws are grouped in modules 
 which are rectangular in the barrel region and trapezoidal in the endcap 
 regions. The modules are arranged in three radial stations in the barrel 
 and three axial stations in the endcaps, and 16 sectors in azimuth. 
 Within each module the straws are arranged in two groups of multi-layers, 
 with four straws in each multi-layer in the inner station and three straws 
 in each multi-layer in the middle and outer stations. 
 </para>
 
 <para>
 <emphasis>Viewing MDT Data</emphasis>
 </para>
 
 <para>
 Within each sector, straws are aligned perpendicular to the radial line 
 joining the nominal origin to the center of that sector. 
 The data from the MDT straws are best viewed in the X'/Z projection 
 (<xref endterm="XZ.title" linkend="XZ"></xref>) by 
 selecting the azimuthal angle of its corresponding sector by switching on 
 the <emphasis>MDT Sector</emphasis> mode and selecting the appropriate sector 
 number. 
 Sector number 0 is at 3 o'clock and the sector numbers increase in a 
 counter-clockwise direction. The selected sector is shown on the top half 
 of the picture and the geometrically opposite sector is shown on the 
 bottom half. The MDT hits are normally viewed as circles but they can be 
 drawn as lines by selecting the appropriate <emphasis>mode</emphasis>. 
 In the X'/Z projection 
 (<xref endterm="XZ.title" linkend="XZ"></xref>) the 
 MDT hits may be compared directly to the tracks measured in the muon system. 
 </para>
 
 <para>
 In the &rho;/Z projection 
 (<xref endterm="RZ.title" linkend="RZ"></xref>) the 
 MDT data are represented in an approximate way, essentially the 
 X'/Z projection of all 
 16 MDT sectors are drawn superimposed, with 8 in the top half of the 
 picture and 8 in the bottom. In this way one can easily see the data 
 from all 16 sectors in the same picture. However &rho; is only approximated 
 for these MDT hits which can therefore only be approximately compared to 
 tracks measured in the muon system which are still drawn with their true 
 &rho;. 
 </para>
 
 <para>
 <emphasis>Graphical Representation</emphasis>
 </para>
 
 <para>
 The color of each hit is defined by the <emphasis>color function</emphasis> 
 which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all hits, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each hit being given the color of its associated 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>simulated track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and <emphasis>shared</emphasis> hits can
  be selected, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>reconstructed track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and <emphasis>shared</emphasis> hits can
  be selected, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>subdetector</emphasis> (Endcap-,Barrel,Endcap+). 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="CSC">
 <title id="CSC.title">7.3.2 Cathode Strip Chambers (CSC)</title>
 
 <para>
 The CSC's are used to provide precision coordinates in the extreme 
 endcap regions (&eta;&gt;1.9) where MDT's 
 (<xref endterm="MDT.title" linkend="MDT"></xref>) can't be used. 
 They are multiwire proportional chambers with cathode strip readout. 
 The precision coordinaate is obtained by measuring the charge induced 
 on a segmented cathode by the avalanche produced on an anode wire. 
 The cathode strips for the precision measurement are oriented orthogonal 
 to the anode wires. High precision is obtained by charge interpolation 
 between neighbouring strips on the segmented cathode. The anode wire pitch 
 is 2.54 mm and the cathode readout pitch is 5.08 mm. The precision 
 coordinate is measured from a cluster of neighbouring strips with a 
 resolution of around 60 &micro;m.  A second orthogonal coordinate is 
 measured with less precision from cathode strips oriented parallel to 
 the anode wires (this coordinaate is not yet available in Atlantis). 
 The resolution of the precision coordinaate measurement is sensitive to 
 the Lorentz angle and the chambers are therefore oriented so that high 
 momentum tracks originating from the interaction enter at normal incidence. 
 CSC's are arranged in two layers of modules each of which provides 
 four coordinate measurements. 
 </para>
 
 <para>
 <emphasis>Viewing CSC strips and clusters</emphasis>
 </para>
 
 <para>
 The precision cathode strips are aligned parallel to the MDT 
 (<xref endterm="MDT.title" linkend="MDT"></xref>) straws and may 
 be best viewed together with them in the X'/Z 
 (<xref endterm="XZ.title" linkend="XZ"></xref>) and &rho;/Z 
 projections (<xref endterm="RZ.title" linkend="RZ"></xref>).  
 The user may select <emphasis>data</emphasis> from the strips, the clusters 
 formed from the strips or both. The strips are represented as a histogram of 
 the measured charge. The clusters are respresented by a line corresponding 
 to the one standard deviation uncertainty on the position measurement. 
 </para>
 
 <para>
 <emphasis>Graphical Representation</emphasis>
 </para>
 
 <para>
 The color of each strip is defined by the <emphasis>strip</emphasis> color. 
 </para>
 
 <para>
 The color of each cluster is defined by the 
 <emphasis>color function</emphasis> which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all hits, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each hit being given the color of its associated 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>simulated track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and <emphasis>shared</emphasis> hits can
  be selected, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>reconstructed track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and <emphasis>shared</emphasis> hits can
  be selected, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>subdetector</emphasis> (Endcap-,Endcap+). 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="RPC">
 <title id="RPC.title">7.3.3 Resistive Plate Chambers (RPC)</title>
 
 <para>
 The RPC's are mainly used to provide a muon trigger but they also 
 provide a second coordinate measurement orthogonal to those from the MDT's 
 (<xref endterm="MDT.title" linkend="MDT"></xref>). The RPC's are 
 present only in the barrel region, in the endcap regions the same role 
 is performed by the TGC's (<xref endterm="TGC.title" linkend="TGC"></xref>). 
 Each RPC module 
 consists of two rectangular chambers. Each of these chambers are read 
 out by an orthogonal series of pick-up strips. The &eta;-strips are 
 parallel to the MDT straws and the &phi;-strips are orthogonal to the 
 MDT straws. The strip pitch varies between 3 and 4 cm. Two RPC modules 
 are arranged on the inner and outer faces of each MDT module in the middle 
 station and a third is positioned on either the inner or outer face of 
 each MDT module in the outer station. 
 </para>
 
 <para>
 <emphasis>Viewing RPC strips</emphasis>
 </para>
 
 <para>
 The &eta;-strips are aligned parallel to the MDT 
 (<xref endterm="MDT.title" linkend="MDT"></xref>) 
 straws and may be best viewed together with them in the X'/Z 
 (<xref endterm="XZ.title" linkend="XZ"></xref>) and &rho;/Z 
 projections (<xref endterm="RZ.title" linkend="RZ"></xref>). 
 The &phi;-strips may be best viewed in the Y/X 
 (<xref endterm="YX.title" linkend="YX"></xref>) and &phi;/&rho; 
 (<xref endterm="FR.title" linkend="FR"></xref>) projections. 
 </para>
 
 <para>
 <emphasis>R3D: RPC space points</emphasis>
 </para>
 
 <para>
 From pairs of orthogonal strips belonging to the same RPC chamber a 
 small 3D box may be formed. These R3D hits, which are currently constructed 
 internally in Atlantis from the RPC strips, may be viewed in any projection. 
 The formation of these R3D hits from there corresponding strips is best 
 visualised in the RPC <emphasis>View</emphasis>'s of the &phi;/Z projection 
 (<xref endterm="FZ.title" linkend="FZ"></xref>). 
 </para>
 
 <para>
 <emphasis>Graphical Representation</emphasis>
 </para>
 
 <para>
 The color of each hit is defined by the <emphasis>color function</emphasis> 
 which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all hits, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each hit being given the color of its associated 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>simulated track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and <emphasis>shared</emphasis> hits can
  be selected, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>reconstructed track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and <emphasis>shared</emphasis> hits can
  be selected, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or each hit may be given a color which indicates whether it is part 
 of an R3D space point 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>is3D</emphasis>. 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="TGC">
 <title id="TGC.title">7.3.4 Thin Gap Chambers (TGC)</title>
 
 <para>
 The TGC's are present only in the endcap regions, in the barrel 
 region the same role is performed by the 
 RPC's (<xref endterm="RPC.title" linkend="RPC"></xref>). 
 The TGC's are mainly used to provide a muon trigger but they also 
 provide a second coordinate measurement orthogonal to those from the 
 MDT's (<xref endterm="MDT.title" linkend="MDT"></xref>). 
 TGC modules are constructed from either doublets or triplets of chambers. 
 There is a doublet module in the inner station which is used only to 
 provide the second coordinate measurement. There are two doublet modules 
 and one triplet module in the middle station which are used to provide 
 both the trigger and second coordinate measurement. Each chamber consists 
 of orthogonal sets of anode wires and cathode readout strips. 
 The anode wires are parallel to the MDT straws and the cathode strips are 
 orthogonal to both the MDT straws and the beam axis. The anode wires are 
 read out in groups leading to an effective pitch between 0.7 and 3.6 cm. 
 The cathode strip pitch is ?.? cm. 
 </para>
 
 <para>
 <emphasis>Viewing TGC strips and wires</emphasis>
 </para>
 
 <para>
 The anode wires are aligned parallel to the MDT 
 (<xref endterm="MDT.title" linkend="MDT"></xref>) 
 straws and may be best viewed together with them in the X'/Z 
 (<xref endterm="XZ.title" linkend="XZ"></xref>) and &rho;/Z 
 (<xref endterm="RZ.title" linkend="RZ"></xref>) projections.  
 The cathode strips may be best viewed in the &phi;/Z 
 (<xref endterm="FZ.title" linkend="FZ"></xref>) projection. 
 </para>
 
 <para>
 <emphasis>T3D: TGC space points</emphasis>
 </para>
 
 <para>
 From pairs of orthogonal strips and wires belonging to the same TGC 
 chamber a small 3D box may be formed. These T3D hits, which are currently 
 constructed internally in Atlantis from the TGC data, may be viewed in 
 any projection. The formation of these T3D hits from their corresponding 
 strips and wires is best visualised in the TGC <emphasis>View</emphasis>'s of 
 the Y/X projection (<xref endterm="YX.title" linkend="YX"></xref>). 
 </para>
 
 <para>
 <emphasis>Graphical Representation</emphasis>
 </para>
 
 <para>
 The color of each hit is defined by the <emphasis>color function</emphasis> 
 which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all hits, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each hit being given the color of its associated 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>simulated track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and <emphasis>shared</emphasis> hits can
  be selected, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>reconstructed track</emphasis>, the colors of
  <emphasis>unconnected</emphasis> and <emphasis>shared</emphasis> hits can
  be selected, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>subdetector</emphasis> (Endcap-,Endcap+), 
  </para>
 </listitem>
 </itemizedlist> 
 
 or each hit may be given a color which indicates whether it is 
 part of an T3D space point 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>is3D</emphasis>. 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="SMTr">
 <title id="SMTr.title">7.3.5 Simulated Muon Tracks (SMTr)</title>
 
 <para>
 Simulated muon tracks from the Monte Carlo truth information. The paths 
 of these tracks may pass through material and regions of non-uniform 
 magnetic fields. They are stored a three dimensional polyline, with a 
 high density of points in the region of active MDT 
 (<xref endterm="MDT.title" linkend="MDT"></xref>), RPC 
 (<xref endterm="RPC.title" linkend="RPC"></xref>) and TGC detectors 
 (<xref endterm="TGC.title" linkend="TGC"></xref>), 
 and a lower density of points elsewhere. 
 </para>
 
 <para>
 The color of each simulated track is defined by the 
 <emphasis>color function</emphasis> which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all tracks, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each track being given the color of its 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>index</emphasis>: in the range 0 to numSMTr-1, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>identifier</emphasis>. 
  </para>
 </listitem>
 </itemizedlist> 
 
 Track images are easier recognised if tracks get a black 
 <emphasis>frame</emphasis> with a small <emphasis>frame width</emphasis>, 
 especially in the V-plot if calorimeters are displayed as well. 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="MuonSegment">
 <title id="MuonSegment.title">7.3.6 Segments of Muon Tracks (Segment)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="MuonTrack">
 <title id="MuonTrack.title">7.3.7 Reconstructed Muon Tracks (Track)</title>
 
 <para>
 Muon tracks reconstructed by the MOORE package. The paths of these tracks 
 may pass through material and regions of non-uniform magnetic fields. 
 They are stored as a three dimensional polyline, with a high density of 
 points in the region of active MDT 
 (<xref endterm="MDT.title" linkend="MDT"></xref>), RPC 
 (<xref endterm="RPC.title" linkend="RPC"></xref>) and TGC 
 detectors (<xref endterm="TGC.title" linkend="TGC"></xref>), 
 and a lower density of points elsewhere. 
 </para>
 
 <para>
 The color of each reconstructed track is defined by the 
 <emphasis>color function</emphasis> which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all tracks, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each track being given the color of its 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>index</emphasis>: in the range 0 to numMTr-1, 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>identifier</emphasis>. 
  </para>
 </listitem>
 </itemizedlist> 
 
 Track images are easier recognised if tracks get a black 
 <emphasis>frame</emphasis> with a small <emphasis>frame width</emphasis>, 
 especially in the V-plot if calorimeters are displayed as well. 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="MuonROI">
 <title id="MuonROI.title">7.3.8 Muon Region of Interest (MuonROI)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="AOD">
 <title id="AOD.title">7.4 Analysis Object Data (AOD)</title>
 
 <para>
 Control the attributes of analysis object data, namely
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>BJet</emphasis> (<xref endterm="BJet.title" linkend="BJet"></xref>)
  : B-tagged Jet
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Electron</emphasis>
  (<xref endterm="Electron.title" linkend="Electron"></xref>)
  : Electron
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Muon</emphasis>
  (<xref endterm="Muon.title" linkend="Muon"></xref>)
  : Muon
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Photon</emphasis>
  (<xref endterm="Photon.title" linkend="Photon"></xref>)
  : Photon
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>TauJet</emphasis>
  (<xref endterm="TauJet.title" linkend="TauJet"></xref>)
  : Tau
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Comp.Part.</emphasis>
  (<xref endterm="CompPart.title" linkend="CompPart"></xref>)
  : Composite Particle
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 All AOD data is taken from the AOD Collections. It may be viewed in 
 &phi;/&eta; projection 
 (<xref endterm="VP.title" linkend="VP"></xref>) and Lego Plot 
 (<xref endterm="LegoPlot.title" linkend="LegoPlot"></xref>). 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>&phi;/&eta; projection</emphasis>
  : AOD objects are displayed in circles, with size
  of the circle scales with Pt or ET. A cross ('x') in the
  center of the circle marks the object's position in &phi; and &eta;.
  Detailed information of the objects can be obtained by Pick
  (<xref endterm="Pick.title" linkend="Pick"></xref>) on the circles.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Lego Plot</emphasis>
  : Electron, Muon and Photon are displayed as towers, and the others
  are displayed in circles on the &phi;&eta; plane, with the center
  of the circle marks the object's position in &phi; and &eta;.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 The color of each AOD data is set based on a same principle. Using BJet as an
 example. The color of each b-tagged jet is defined by the 
 <emphasis>color function</emphasis> which may be either
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all b-tagged jets,
  </para>
 </listitem>
 </itemizedlist>
 
 or it may vary with each b-tagged jet being given the color of its
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>index</emphasis>: in the range 0 to numBJet-1.
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="BJet">
 <title id="BJet.title">7.4.1 B-tagged Jet (BJet)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Electron">
 <title id="Electron.title">7.4.2 Electron (Electron)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Muon">
 <title id="Muon.title">7.4.3 Muon (Muon)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Photon">
 <title id="Photon.title">7.4.4 Photon (Photon)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 
 <sect2 id="TauJet">
 <title id="TauJet.title">7.4.5 Tau (TauJet)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="CompPart">
 <title id="CompPart.title">7.4.6 Composite Particle (CompPart)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="ATLAS">
 <title id="ATLAS.title">7.5 Whole Detector (ATLAS)</title>
 
 <para>
 Control the attributes of data from the whole detector, namely
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>Jet</emphasis> (<xref endterm="Jet.title" linkend="Jet"></xref>)
  : Jet Collections
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>ETMis</emphasis>
  (<xref endterm="ETMis.title" linkend="ETMis"></xref>)
  : Missing ET Collections
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>Detector</emphasis>
  (<xref endterm="Det.title" linkend="Det"></xref>)
  : Constant Colors of Detector
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Jet">
 <title id="Jet.title">7.5.1 Jet Collections (Jet)</title>
 
 <para>
 Jets are formed from energy deposits in the cells of the calorimeters. 
 Jets may currently only be viewed in the &phi;/&eta; projection 
 (<xref endterm="VP.title" linkend="VP"></xref>), 
 where they are represented by a circle centred on the jet direction with an 
 area proportional to the jet energy. 
 </para>
 
 <para>
 The color of each jet is defined by the <emphasis>color function</emphasis> 
 which may be either 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>constant</emphasis>, in which case the
  <emphasis>constant</emphasis> color is used for all jets, 
  </para>
 </listitem>
 </itemizedlist> 
 
 or it may vary with each jet being given the color of its 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>index</emphasis>: in the range 0 to numJet-1. 
  </para>
 </listitem>
 </itemizedlist> 
 </para>
 
 <para>
 More information about colors in Atlantis is given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref>.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="ETMis">
 <title id="ETMis.title">7.5.2 Missing ET Collections (ETMis)</title>
 
 <para>
 To be filled!
 </para>
 
 </sect2>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 
 <sect1 id="Det">
 <title id="Det.title">7.6 Detector Colors (Det)</title>
 
 <para>
 This section lists detector elements and their color attributes. 
 Toggle switches are used to display/hide elements and choice menus are used 
 to select colors. The options are: 
 
 <itemizedlist>
 <listitem>
  <para>
  Pixel color
  </para>
 </listitem>
 <listitem>
  <para>
  SCT color
  </para>
 </listitem>
 <listitem>
  <para>
  TRT color
  </para>
 </listitem>
 <listitem>
  <para>
  Solenoid color
  </para>
 </listitem>
 <listitem>
  <para>
  LAr calorimeter color
  </para>
 </listitem>
 <listitem>
  <para>
  Tile calorimeter color
  </para>
 </listitem>
 <listitem>
  <para>
  RPC color
  </para>
 </listitem>
 <listitem>
  <para>
  TGC color
  </para>
 </listitem>
 <listitem>
  <para>
  MDT color
  </para>
 </listitem>
 <listitem>
  <para>
  CSC color
  </para>
 </listitem>
 <listitem>
  <para>
  Background color
  </para>
 </listitem>
 <listitem>
  <para>
  InDet geometry detail
  </para>
 </listitem>
 <listitem>
  <para>
  Calorimetry cell structure
  </para>
 </listitem>
 <listitem>
  <para>
  Show detectors
  </para>
 </listitem>
 <listitem>
  <para>
  Show detectors outline
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <para>
 More information about detector colors and element display are given in 
 <xref endterm="ColorUse.title" linkend="ColorUse"></xref> and 
 <xref endterm="Attributes.title" linkend="Attributes"></xref>. 
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="GenInfo">
 <title id="GenInfo.title">7.7 General Information</title>
 
 <para>
 This section contains general information about system wide parameters:
 
 <itemizedlist>
 <listitem>
  <para>
  <xref endterm="ColorUse.title" linkend="ColorUse"></xref>
  </para>
 </listitem>
 <listitem>
  <para>
  <xref endterm="Attributes.title" linkend="Attributes"></xref>
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="ColorUse">
 <title id="ColorUse.title">7.7.1 About the Use of Colors</title>
 
 <para>
 The Atlantis projections (except the &phi;/&eta; projection) 
 are chosen in such a way that detector volumes do not overlap. Therefore, 
 one can replace transparent wire frame images by filled areas surrounded 
 by frames, which are easier to perceive intuitively. The fill colors of 
 the various detectors and of the background may be modified. 
 </para>
 
 <para>
 <emphasis>N.B.:</emphasis>
 </para>
 
 <para>
 Small points, lines or cells are better distinguished from background with 
 high intensity contrast. The intensity I of colors can be very roughly 
 estimated, by: 
 </para>
 
 <para>
 I = 4&times;I<subscript>green</subscript> +
  2&times;I<subscript>red</subscript> 
  + b&times;I<subscript>blue</subscript> &nbsp;&nbsp; with b between 0.5 and 1. 
 </para>
 
 <para>
 <emphasis>N.B.:</emphasis>
 </para>
 
 <para>
 Blue or magenta backgrounds change colors of very small objects: 
 yellow to white, green to cyan and red to magenta. 
 </para>
 
 <para>
 When <emphasis>printing</emphasis> on normal quality color printers it is 
 advisable to 
 avoid muted colors for areas onto which small objects are drawn. Therefore 
 printed files have their own color set, which takes this into account. 
 Print colors may therefore be different from display colors. 
 </para>
 
 <para>
 <emphasis>N.B.:</emphasis>
 </para>
 
 <para>
 The background color of the &phi;/&eta; projection 
 (<xref endterm="VP.title" linkend="VP"></xref>) 
 is controlled by the projection and may be modified there.
 </para>
 
 </sect2>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect2 id="Attributes">
 <title id="Attributes.title">7.7.2 Graphics Attributes of Hits</title>
 
 <para>
 In general point-like hit data are displayed as <emphasis>symbols</emphasis> 
 which may be chosen from 
 
 <itemizedlist>
 <listitem>
  <para>
  <emphasis>filled square</emphasis> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>horizontal line</emphasis> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>vertical line</emphasis> 
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>plus</emphasis> 
  </para>
 </listitem>
 </itemizedlist> 
 
 and drawn with a size determined by the <emphasis>symbol size</emphasis>. 
 </para>
 
 <para>
 Tracks and non-point-like hit data are displayed as lines with a selectable 
 <emphasis>line width</emphasis>. For non-point-like hit data (e.g. TRT) under 
 certain 
 zooming conditions it is possible for the two ends of the line representing 
 each hit to be separated by very small distances, i.e., less than one pixel 
 on the screen. In such cases hit data may not be visible if drawn as lines. 
 To avoid this situation a <emphasis>MinSize</emphasis> may be specified such 
 that if all 
 the lines from a given detector have a length in screen coordinates (pixels) 
 smaller than <emphasis>MinSize</emphasis> then the data from this detector 
 are drawn as 
 symbols (squares by default) with a size <emphasis>MinSize</emphasis>. 
 Furthermore the user 
 may force non-point-like hit data to be drawn as symbol with size 
 <emphasis>MinSize</emphasis> using <emphasis>Force Symbols</emphasis>. 
 </para>
 
 <para>
 For noise hits, where noise hits are those which are not connected to 
 simulated or reconstructed tracks (and in the case of S3D hits are ungrouped 
 by the filter), either a special <emphasis>noise</emphasis> symbol with a 
 special <emphasis>noise size</emphasis> or a special 
 <emphasis>noise width</emphasis> can be selected. 
 By default unconnected or ungrouped hits are white and not easy to 
 distinguish from yellow hits. It is easier to distinguish noise and 
 yellow hits when a different symbol for noise hits is set. 
 </para>
 
 <para>
 To better distinguish hits from tracks of the same color or from a colored 
 background, they may get a <emphasis>frame</emphasis>, where the color can be 
 selected, with a <emphasis>frame width</emphasis> which can be modified.
 </para>
 
 </sect2>
 
 </sect1>
 
 </chapter>
 
 <!--=======================================================================-->
 <chapter id="Athena">
 <title id="Athena.title">Interactive Athena</title>
 
 <para>
 <ulink url="http://atlas.web.cern.ch/Atlas/GROUPS/SOFTWARE/OO/architecture/">
 Athena</ulink> can be accessed interactively from Atlantis via 
 the Interactive Athena dialog window.  This window is popped up by selecting 
 the <emphasis>File&rarr;Interactive Athena</emphasis> menu option of the 
 Control Window.
 </para>
 
 <para>
 By means of this dialog the user is able to steer the Athena framework 
 directly from the Atlantis display. The other necessary component is the 
 Python script <emphasis>InteractiveServer.py</emphasis>, that is started on 
 the Athena interactive prompt. 
 </para>
 
 <para>
 It is possible to perform various actions from the Atlantis dialog window as 
 if the commands were typed on the Athena interactive prompt directly, e.g. 
 changing/querying the values of the job options, executing the methods of 
 Athena algtools/algorithms, directing Athena to process the next event by 
 calling <emphasis>theApp.nextEvent()</emphasis> and eventually getting the 
 XML event data. 
 </para>
 
 <para>
 <emphasis>InteractiveServer.py</emphasis> is a Python script that is used to 
 interface the 
 Atlantis Interactive Athena dialog and the Athena interactive Python prompt 
 (when Athena is started by <emphasis>athena -i [job_option_file]</emphasis>). 
 Once the 
 script is started, the created server receives requests from the Atlantis 
 user, processes these requests and sends the results back to Atlantis. 
 </para>
 
 <para>
 The CVS location of the script is 
 <emphasis>offline/graphics/AtlantisJava/share/InteractiveServer.py</emphasis>. 
 In the Athena environment it can be obtained by 
 <emphasis>get_files InteractiveServer.py</emphasis> as well. 
 </para>
 
 <para>
 Establishing the communication between Atlantis and Athena is described in 
 <xref endterm="AthenaSetup.title" linkend="AthenaSetup"></xref>. 
 </para>
 
 <para>
 Using the Athena vertex fitter from Atlantis is described in 
 <xref endterm="AthenaVF.title" linkend="AthenaVF"></xref>.
 </para>
 
 <para>
 <emphasis>N.B.</emphasis>: If the user opts for some reason not to use the 
 Athena algtools 
 and still be able to start <emphasis>InteractiveServer.py</emphasis>, it's 
 possible to 
 create the server without initialising the algtools. Before starting the 
 script on the Python prompt by <emphasis>execfile 
 ("InteractiveServer.py")</emphasis> it 
 is necessary to make the following assignment: 
 </para>
 
 <para>
 <emphasis>argumentInteractiveServer = "NO_ALGTOOLS"</emphasis> 
 </para>
 
 <para>
 It is not then possible to obtain the XML event 
 data (JiveXML algtool) or run the vertexing in Athena. 
 </para>
 
 <para>
 <emphasis>N.B.</emphasis>: If due to network security restrictions the 
 connection between 
 Atlantis and the <emphasis>InteractiveServer.py</emphasis> on the Athena 
 prompt can't be 
 established directly, an SSH tunnel can be created throught which both 
 parties should be able to connect.
 </para>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="AthenaSetup">
 <title id="AthenaSetup.title">8.1 Setting up Atlantis &harr;
  Interactive Athena communication</title>
 
 <para>
 <itemizedlist>
 <listitem>
  <para>
  Atlantis has been started (most likely on the local machine)
  </para>
 </listitem>
 <listitem>
  <para>
  Athena environment is set up (most likely run remotely)
  </para>
 </listitem>
 <listitem>
  <para>
  Getting <emphasis>InteractiveServer.py</emphasis> to the run
  directory: <emphasis>get_files InteractiveServer.py</emphasis>
  (or copy from CVS)
  </para>
 </listitem>
 <listitem>
  <para>
  Starting Athena in the interactive mode:
  <emphasis>athena -i myTopOptions.py</emphasis>
  </para>
 </listitem>
 <listitem>
  <para>
  Type command: <emphasis>theApp.initialize()</emphasis>
  (it could also go at the bottom of the top options file)
  </para>
 </listitem>
 <listitem>
  <para>
  Start server by <emphasis>execfile
  ("InteractiveServer.py")</emphasis> after which the 
  interactive prompt is taken over by the script. 
  </para>
 </listitem>
 <listitem>
  <para>
  Provided that everything went well (no error messages were
  printed), algtools were initialised and the server was bound to the port,
  copy and paste this information into the Atlantis dialog:
  <itemizedlist>
  <listitem>
   <para>
   <emphasis>server name</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>server port</emphasis>
   </para>
  </listitem>
  <listitem>
   <para>
   <emphasis>key</emphasis>
   </para>
  </listitem>
  </itemizedlist>
  Key is a randomly generated string and is a protection against user's Athena 
  session being driven by another user who happens to put into his Atlantis 
  dialog window the name of the remote machine and the port that someone else 
  is using.
  </para>
 </listitem>
 <listitem>
  <para>
  Provided that there are no network security issues disabling
  direct communication, the user can now type the Athena commands in Atlantis,
  steer Athena and demand the actual XML event data or run the Athena vertex
  fitter from Atlantis.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>theApp.nextEvent()</emphasis> should be the first
  command to execute in order to be able to obtain some XML event data.
  </para>
 </listitem>
 <listitem>
  <para>
  Pressing Ctrl-c shuts down
  <emphasis>InteractiveServer.py</emphasis> and the 
  interactive prompt is given back to the user.
  </para>
 </listitem>
 <listitem>
  <para>
  <emphasis>myTopOptions.py</emphasis>
  (bottom of the file)
  </para>
  <para>
  doJiveXML = True
  </para>
  <para>
  include ("RecExCommon/RecExCommon_topOptions.py")
  </para>
  <para>
  include ("PyAnalysisCore/InitPyAnalysisCore.py")
  </para>
  <para>
  include ("InteractiveTools/jobOptionsBase.py")
  </para>
  <para>
  ToolSvc.EventData2XML.DataTypes += ["Vertex"]
  </para>
  <para>
  ToolSvc.EventData2XML.xKalmanTracks = "Tracks"
  </para>
  <para>
  # vertexing algorithms
  </para>
  <para>
  # ToolSvc.VxWrapperTool.VxToolName = "Trk::FastVertexFitter"
  </para>
  <para>
  ToolSvc.VxWrapperTool.VxToolName = "Trk::FullVertexFitter"
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect1>
 
 <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -->
 <sect1 id="AthenaVF">
 <title id="AthenaVF.title">8.2 Calling the Athena vertex fitter from
  Atlantis</title>
 
 <para>
 <itemizedlist>
 <listitem>
  <para>
  It is necessary to carry out the procedure described in
  <xref endterm="AthenaSetup.title" linkend="AthenaSetup"></xref>
  The actual vertexing algorithm type is chosen in myTopOptions.py.
  The picture below shows the vertexing process.
  </para>
 </listitem>
 <listitem>
  <para>
  Tracks whose IDs are to be sent to the Athena vertex fitter
  have to be selected with the "rubberband" Atlantis interaction.
  After doing so, a pop-up menu appears on the canvas where the user selects
  <emphasis>New List</emphasis>, into which these tracks are put.
  </para>
 </listitem>
 <listitem>
  <para>
  The most recent list is now highlighted in the Atlantis List
  manager dialog window. 
  </para>
  <para>
  If only <emphasis>Track</emphasis> tracks were put into the list (and no
  other objects such as hits or tracks of other types), an item
  <emphasis>Vertex in Athena</emphasis> appears in the context menu after
  right-clicking on the list item in the List manager.
  </para>
  <para>
  Only with <emphasis>Track</emphasis> tracks one can call the Athena vertex
  fitter.  The Atlantis internal vertex fitter can be called upon
  <emphasis>Track</emphasis> tracks and <emphasis>iPatTrack</emphasis> tracks.
  </para>
 </listitem>
 <listitem>
  <para>
  Given that proper information was filled in the Atlantis
  Interactive Athena dialog and the connection to
  <emphasis>InteractiveServer.py</emphasis> could be established, the
  <emphasis>Track</emphasis> tracks IDs were sent to Athena and the fitter
  called. This can be observed in the window where Athena is started from.
  </para>
  <para>
  In order to find out whether or not the listed tracks come from a common 
  vertex, the user has to hit the <emphasis>Get Event</emphasis> button and
  search for a new item of the <emphasis>RecVertex</emphasis> datatype (see
  event summary in the output window in the bottom part of the GUI or
  <emphasis>File &rarr; Event Properties</emphasis>) once updated event data
  arrive. If the vertex was found and the <emphasis>RecVertex</emphasis>
  datatype is switched on (Data tabpane, InDet) a newly calculated vertex will
  be displayed for instance in the XY projection as an ellipse. The tracks
  which form this vertex will be shortened to the centre of that ellipse
  (in XY). 
  </para>
 </listitem>
 <listitem>
  <para>
  The picture below demonstrates the aforementioned procedure. 
  </para>
  <para>
  <figure float="0">
   <title>Vertexing process</title>
   <mediaobject id="vertexingProcess">
    <imageobject>
     <imagedata fileref="vertexing.png" format="png" scale="100">
     </imagedata>
    </imageobject>
    <caption><para>
    </para></caption>
   </mediaobject>
  </figure>
  </para>
 </listitem>
 </itemizedlist>
 </para>
 
 </sect1>
 
 </chapter>
 
 <!--=======================================================================-->
 <glossary id="atlantisglossary">
 <title>Glossary</title>
 
 <glossentry>
 <glossterm>Atlantis Canvas</glossterm>
 <glossdef>
  <para>
  The name of the Display Window or Canvas. See <emphasis>Canvas</emphasis>.
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Atlantis GUI</glossterm>
 <glossdef>
  <para>
  The name of the Control Window.  See <emphasis>Control Window</emphasis>.
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Canvas</glossterm>
 <glossdef>
  <para>
  Or Display Window. The permanent window used by Atlantis to show pictures. 
  The Canvas contains one or more <emphasis>canvas pads</emphasis> in which
  the pictures are shown.
  </para>
  <para>
  (See <xref linkend="Canvas"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Canvas Control (Control Window)</glossterm>
 <glossdef>
  <para>
  For selection and control of <emphasis>canvas pads</emphasis>.
  </para>
  <para>
  (See <xref linkend="WindowControl"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Canvas Pad</glossterm>
 <glossdef>
  <para>
  A part of the <emphasis>Canvas</emphasis> that shows a picture of a specific
  event with specific cuts, transformations and interactions applied. 
  </para>
  <para>
  (See <xref linkend="Window"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Central Point</glossterm>
 <glossdef>
  <para>
  Used by the ZMR interaction for zooming and rotation in a canvas window.
  </para>
  <para>
  (See <xref linkend="CentralPoint"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Control Window</glossterm>
 <glossdef>
  <para>
  Permanent window named "Atlantis GUI".  
  The window used by Atlantis for control and management. 
  It contains <emphasis>Menu</emphasis>, <emphasis>Canvas Control</emphasis>,
  <emphasis>Interaction Control</emphasis>, 
  <emphasis>Parameter Control</emphasis> and
  <emphasis>Output Display</emphasis> parts.
  </para>
  <para>
  (See <xref linkend="ControlWindow"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Display Window</glossterm>
 <glossdef>
  <para>
  Or Canvas. See <emphasis>Canvas</emphasis>.
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Interaction Control (Control Window)</glossterm>
 <glossdef>
  <para>
  To select and control <emphasis>interactions</emphasis>.
  </para>
  <para>
  (See <xref linkend="InteractionControl"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Interactions</glossterm>
 <glossdef>
  <para>
  The real work! Zoom, move, rotate, select, special transformations, etc.
  </para>
  <para>
  (See <xref linkend="Interactions"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Menu (Control Window)</glossterm>
 <glossdef>
  <para>
  To select and print events, to set personal preferences, to get help
  and to reset Atlantis.
  </para>
  <para>
  (See <xref linkend="Menu"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Modifier Key</glossterm>
 <glossdef>
  <para>
  Combinations of a keyboard key and a mouse key, that are used to
  generate pop-up menus or to perform interactions.
  </para>
  <para>
  (See <xref linkend="MouseModifierKeys"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Output Display (Control Window)</glossterm>
 <glossdef>
  <para>
  Output area to display information about various topics, e.g. track 
  information, pick information, cuts summary.
  </para>
  <para>
  (See <xref linkend="OutputDisplay"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Pad, Canvas</glossterm>
 <glossdef>
  <para>
  See <emphasis>Canvas Pad</emphasis>.
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Parameter Control (Control Window)</glossterm>
 <glossdef>
  <para>
  To view and modify Atlantis parameters.
  </para>
  <para>
  (See <xref linkend="ParametersControl"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Window, Control</glossterm>
 <glossdef>
  <para>
  See <emphasis>Control Window</emphasis>.
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>Window, Display</glossterm>
 <glossdef>
  <para>
  Or Canvas. See <emphasis>Canvas</emphasis>.
  </para>
 </glossdef>
 </glossentry>
 
 <glossentry>
 <glossterm>ZMR</glossterm>
 <glossdef>
  <para>
  Interaction to zoom, move and/or rotate a picture in a 
  <emphasis>canvas pad</emphasis>.
  </para>
  <para>
  (See <xref linkend="ZMR"></xref>)
  </para>
 </glossdef>
 </glossentry>
 
 </glossary>
 
 <!--=======================================================================-->
 </book>