(r16) TbUT < LHCb

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---+!!  TbUT analysis software

This page provides information about the TbUT package. The software is a part of the  [[https://lbtwiki.cern.ch/bin/view/VELO/Tpx3TestbeamSoftware][Kepler project]]. The main aim of this software is to perform whole processing of the testbeam data using [[http://lhcb-comp.web.cern.ch/lhcb-comp/Frameworks/Gaudi/][Gaudi framework]]. 
%TOC%

---+  Contact persons
Adam Dendek  [[mailto:adendek@cern.ch][Mail]]

---+  Setup

Follow these steps to setup TbUT in your working directory

   * Setup project and get source code from LHCb's SVN repository 
   <pre>
lb-dev Kepler v3r0
cd ./KeplerDev_v3r0
svn co http://svn.cern.ch/guest/lhcb/Kepler/trunk/Tb
 </pre> 

   * Compile the source code
 <pre>
make -j20
make install
 </pre> 

   * Mount EOS
   <pre>
eosmount ~/eos
   </pre>

   * Prepare the running environment
   <pre>
./run bash
   </pre>


---+  Running the TbUT software
The TbUT software can be run in two modes, *Pedestal* and *Run*. The description below contains instructions on how to run TbUT in *standalone mode* (no other Kepler stuff). 
You should also look at the [[SoftwareEnvTools][Tools for the LHCb Software Environment TWiki page]] for a better understanding how to run Gaudi-like application. 
---++ Pedestal mode -- computing the pedestals
   * The aim of the pedestal training is to calculate the pedestals values, which will then be used in Run mode in order to subtract the pedestal from the raw data during execution of the Pedestal Subtraction algorithm.
   * In this mode only 2 algorithms are executed : =Raw Data Reader= and =Pedestal Subtractor= for more detailed description of this algorithms look to the [[#Developers_section][developers section]].
   * Preparation of the options. You just need to modify the file ( =Tb/TbUT/options/TbUTPedestal.py= ):
      | *option name* | *brief description* |
      | app.inputData | String, contains path to the input data (*you have to set this, see NOTE below*) |
      | app.isAType| Boolean, choose if sensor is type A (true) or D (false) |
      | app.eventMax | Integer, number of event to process |
      | app.app.pedestaOutputData | String, contains path to the output file (contains pedestal values in a flat list).  |

   * NOTE: The input files are located on EOS. Currently, you either need to copy files from EOS to a local directory (you will run out of space fast) or you can mount eos temporarily
      * To mount EOS: 
      <pre> eosmount ~/eos </pre> 
      If you do this, please add <pre>eosumount ~/eos</pre> to your ~/.logout file. 
      * July 2015 testbeam files for board D9, for example, are located here: =eos/lhcb/testbeam/ut/OfficialData/July2015/BoardD9/RawData/*.dat=

   * Run the TbUT in *Pedestal mode*:
    <pre>
   cd Tb/TbUT
   gaudirun.py options/TbUTPedestal.py
    </pre> 
   * After the execution of the application, the output file contains pedestal values, one number per channel is output. The name of the file is specified in the options file ( line =app.pedestalOutputData= )

---++ Run mode
   * In run mode the TbUT performs the whole processing of testbeam data.
   * In this mode all processing algorithms are executed.
      | *algorithm* | *brief description* |
      | Raw Data Reader | Reads raw data from the DUT (Mamba board output) and saves the output into the TES |
      | Pedestal Subtractor | Gets raw data from the TES, removes the calculated pedestals from the Pedestal mode run, and stores the output into theTES |
      | Common Mode Subtractor (CMS) | Gets data after Pedestal Subtraction; removes the common mode noise, a single value per 32 Beetle channels (mean value of ADC); save the output into the TES |
      | Cluster Creator | Gets data after CMS, create clusters and saves it information in the TES |

   Beyond the listed algorithms, a set of corresponding monitoring algorithms has been implemented. The detailed descriptions of processing and monitoring algorithms see [[#Developers_section][developers section]].  

   * Preparation of the options. You just need to modify the file ( =Tb/TbUT/options/TbUTRun.py= ):
      | *option name* | *brief description* |
      | app.inputData | type of  string, contains path to the input data |
      | app.isAType| type of  Boolean, choose if sensor is type A (true) or D (false) |
      | app..sensorType| type of  String, choose if sensor is  P-type ("PType") or N-type ("NType") or both - calibration run ("Both") |
      | app.eventMax | type of integer, number of event to process |
      | app.pedestalInputData | type of  string, contains path to pedestal file (created during execution TbUT in Pedestal mode)  |
      | app.eventNumberDisplay | type of  integer, informs how many event snapshots will be saved (see section [[#Exemplary_outputs][exemplary outputs]]  )  |


   * Running TbUT in *Run mode*:
    <pre>
cd Tb/TbUT
gaudirun.py options/TbUTRun.py
    </pre> 

---++ DUT and Telescope analysis

   * These steps require runnign with a ROOT version 5, so it is helpful to type the following before running the combination of DUT and telescope data:
<pre>
LbLogin -c x86_64-slc6-gcc48-opt
SetupProject LHCb v36r2
</pre>
This ensures the proper root version will be used
   * After computing pedestal and CMS, the data from the DUT can be combined with the information from the telescope. Once in the Tb/TbUT directory, the script for appending the DUT data with the telescope data can be run by doing the following:

<pre>
cd scripts/AddTrigTracks
make
./combDUTwithTrack -i ~/inputDUT_Tuple.root -t ~/eos/lhcb/testbeam/ut/TelescopeData/July2016/RootFiles/RunXXXX/Output/Kepler-tuple.root -n ~/inputDUT_noise.root -o outputFile.root
</pre>
where inputDUT_Tuple.root is the file resulting from the the run mode, inputDUT_noise.root is the file containing the noise information (nominally the same as inputDUT_Tuple.root but without the 'Tuple' appendage), ~/Kepler-tuple.root is the data from the telescope, and outputFile.root is the desired output file name.

---+  Known issues
   * The TbUT cannot read eos files. *workaround:  copy analyzed file into your work directory or use eosmount as shown above. 
   * TbUT (run mode) need to be executed *twice* to correct calculate noise and extract clusters. 
   * The tools should inherit from GaudTool class.
   * The unit test have to be implemented
 
---+  Developers section
---++ General overview
Every  TbUT component class is a member of =TbUT= namespace. 
---+++ Algorithms
The TbUT is a Gaudi based application. The application is separated into two sets of Gaudi algorithms. First group is responsible for processing the testbeam data. This algorithms inherit from *GaudiAlgorithm* class.
The names of it contains string =Algorithm= for instance[[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTRawDataReaderAlgorithm.cpp][TbUTRawDataReaderAlgorithm]] . 

*To understand TbUT source code, the algorithm classes should be treated as a starting point !*
 
The second group was designed to prepare monitoring plots. This classes inherit from base called [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTDataMonitorAlgorithm.h][TbUTDataMonitorAlgorithm]] (  see also  [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTDataMonitorAlgorithm.cpp][ implementation ]]). 
According to the file name convention it's names have to contains string  =DataMonitorAlgorithm= in their's file names. E.g.  [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTPedestalSubtractorDataMonitorAlgorithm.cpp][TbUTPedestalSubtractorDataMonitorAlgorithm]] .
 
---+++ Tools
That kind of classes are responsible of performing the data modification. Each of this inherit from virtual interface called  [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTIProcessingEngine.h][IProcessingEngine]], therefore they have to implement =processEvent= method. 

---+++ Tool's Factories
This kind of classes are responsible for dynamic, depend of options, creation of proper version of tools. This classes based on [[https://en.wikipedia.org/wiki/Factory_method_pattern][Factory design pattern]] (see also the [[https://www.youtube.com/watch?v=N8_wwa90tzM&list=PL6A29DA14366FF6C3&index=13][beautiful explanation]] why is is so useful).  See for example [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTRawDataFactory.h][Raw Data Reader Factory]] and it [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTRawDataFactory.cpp][implementation]]

---+++ Other types
   * *Data structures* (inherits from  =GaudiKernel/DataObject= ) are used to be manipulated via the tools and be stored in TES. The TbUT package contains  [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTRawData.h][Raw Data]] and [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTCluster.h][Clusters]] .  
   * *Additional data structures*. Can be distinguished [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTNoise.cpp][noise]] and [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTPedestal.cpp][pedestals]]. Their are used as a auxiliary structures by the tools. 
   * *Additional services*. Used for manipulation of the *additional data structures*. See for instance  [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTNoiseCalculator.h][Noise Calculator]]. Each of this services has own interface ( e.g. Noise calculator are based on [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTINoiseCalculator.h][INoiseCalculator]]).  
 
---+++ TbUT high level architecture

   <th width="40%"> <img width="600" align="middle" alt="TbUT high Level architecture" src="%ATTACHURLPATH%/TbUT_Architecture.png" />

---++ Description of the algorithms

---+++ Raw Data Reader

This algorithm is designed to read raw data from specific input file. Currently TbUT can work with files produced by Alibava and Mamba DAQs. The heart of this algorithm is tool inherit from interface [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTIDataReader.h][IDataReader]]. This tool acts [[https://en.wikipedia.org/wiki/Facade_pattern][fascade]] for specific DAQ reader. 

The execution of Raw Data Reader can be modified using options:

 | *option name* | *brief description* |
      | InputDataType | type of string, choose one of DAQs data format (Mamba or Alibava)  |
      | inputData | type of string, path to the input data. |
      | standalone | type of  boolean, if is true the run is executed with Kepler (haven't been tested yet)  |

---+++ Pedestal Subtractor 
The pedestal subtraction algorithm has two phases. In first, optional one, the pedestal values are calculated.  This phase is also called training. During the second one the determined pedestal values are subtracted from the raw ADC data.
From technical point of view the [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTPedestalSubtractorAlgorithm.cpp][Pedestal Subtractor Algorithm]] calls two types of tools. One of them calculates or retrieves pedestals values( this classes inherit from [[https://svnweb.cern.ch/trac/lhcb/browser/Kepler/trunk/Tb/TbUT/src/TbUTIPedestalFollowing.h][I pedestal following]] ) and the second one remove pedestals values from the raw data. See data flow. 

  <img width="400"  src="%ATTACHURLPATH%/Pedestal_Subtrator.png" alt="Pedestal_Subtrator.png"  /></verbatim>

The execution of Pedestal Subtractor Algorithm can be modified using options:

 | *option name* | *brief description* |
      | FollowingOption | type of string, choose type of execution (training  or run)  |
      | treningEntry | type of integer, number of training entry |
      | ChannelMaskInputLocation | type of string, location of the channel mask |
      | PedestalInputFile | type of string, path to the location where previously calculated pedestals are stored |
      | PedestalOutputFile | type of string, path to the location where calculated pedestal have to be stored  |
      | standalone | type of  boolean, if is true the run is executed with Kepler (haven't been tested yet)  |

---++++ Pedestal following
From the mathematical point of view the calculation of the pedestal can be described as a running average. In every training event then pedestal sum is updated. This update takes into account the previous value of the pedestal sum and the current ADC count. The pedestal sum is calculated for each channel separately. To be more precisely, the pedestal sum, %$p_i(n)$%, for channel %$n$% and event %$i$% can be expressed as follows:

%$P_{i}^{sum}(n+1)=P^{sum}_{i}(n) + \frac{\Delta_{i}(n+1)}{N}$%

Where the %$\Delta_{i}(n+1)$% is a event to pedestal correction. This correction is expressed as:

%$\Delta_{i}(n+1)=ADC_{i}(n+1)-P^{sum}_{i}(n)$%

To increase the suitability of the pedestal the limit for correction is applied. If the condition:
%$ \left| \Delta_{i}(n+1) \right| \leq 15  $%
is not fulfilled the correction value is set to 15.

To determinate the pedestal values the pedestal sum should be normalized, so:
%$p_{i}=\frac{P^{sum}_{i}}{N}$%

---++++ Pedestal removing algorithm
The second phase of the pedestal subtraction algorithm is subtraction determined pedestal values from the raw data. This procedure can be expressed as fallows:

%$ADC_{i}=ADC^{RAW}_{i}-p_{i}$%

where: %$ADC_{i}$% is signal value after pedestal subtraction for event %$i$%, %$ADC^{RAW}_{i}$% is a raw data and the %$p_{i}$% is the pedestal value. Each of this quantities are in the unit of ADC counts. 


---+  Additional scripts
   All scripts are stored in =TbUT/scripts= directory. (Not yet committed)  
   * *Noise monitor* This script takes as an input noise file. The exemplary output: 

 <th width="40%"> <img width="400" alt="Thresholds" src="%ATTACHURLPATH%/Thresholds.png" />

-- Main.AdamMateuszDendek - 2015-08-03
Attachments
Topic attachments
I	Attachment	History	Action	Size	Date	Who	Comment
png	Pedestal_Subtrator.png	r1	manage	53.7 K	2015-08-26 - 19:21	AdamMateuszDendek	Pedestal Subtractor Data Flow
png	TbUT_Architecture.png	r1	manage	103.6 K	2015-08-26 - 18:26	AdamMateuszDendek	TbUT high level architecture
png	Thresholds.png	r1	manage	27.8 K	2015-08-26 - 13:59	AdamMateuszDendek
Topic revision: r16 - 2016-05-03 - ChristopherBetancourt1
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