View source for JAPAN Doc Portal

Documentation for new Prex/Crex analysis is curated here

== Important Resources ==
*[[Analyzer_Meeting|Analyzer Meeting list]]
*[[Github_Guide|Contributing on Github]]
*[[CODA_Running_Quickstart|CODA Running Quickstart]]
*[[JLab_Computing|JLab Scientific Computing Guide]]

==Resources==
* [[Media:Counting_House_TipsTricks-Jun2017.pdf|Brad's Counting House computer guide]]
* [[Media:Computing_tools-tricks-Jun2019.pdf|Brad's scientific computing/ifarm guide]]
* Source code: [https://github.com/JeffersonLab/japan JAPAN Github]
* [[Github_Guide|Guide to using Github]]
* List of cut bits in Japan source code: [https://github.com/JeffersonLab/japan/blob/develop/Analysis/include/QwTypes.h#L165 here]

==Using JAPAN on adaq cluster==
In the apar account, execute "gojapan" to setup the environment variables and change to the "official" copy of JAPAN (~apar/PREX/japan).

Some typical calls to the analyzer:
* ''./build/qwparity --config prexCH.conf --detectors prexCH_detectors_no_hel.map -r 1107''<br />This does the analysis for parity_CH mode data files (run 1107 in this particular case), where the helicity patterns are treated as always being quartets with polarities "+ - - +".
* ''./build/qwparity --config prex.conf -r 1036''<br />This analyzes the parity_ALL mode data files, using the injector helicity data to build quartets.  The current default analysis mode is in quartets, if the DAQ is changed to octets or other patterns, we will need to update the injector helicity configuration used by the analyzer.
* ''./build/qwparity --config prexinj.conf -r ####''<br />This analyzes the parity_INJ mode data files.  The current default analysis mode is in quartets, if the DAQ is changed to octets or other patterns, we will need to update the injector helicity configuration used by the analyzer.

== Example install of Japan on ifarm - not in apar@adaq3 or even for main DAQ data ==

To analyze any CODA DAQ .dat file with [https://github.com/jeffersonlab/japan JAPAN], do the following
 source /site/12gev_phys/softenv.csh 2.3
 cd /directory/to/store/japan/
 git clone https://github.com/JeffersonLab/japan
 cd japan
 git checkout tedf-test-stand
 source setup_japan.tcsh
 mkdir build; cd build; cmake ..; make; cd ..
 ./build/qwparity --config tedf_testing.conf -r [number]
** The config file (contained within the Parity/prminput folder) should contain all of the necessary information for JAPAN to decode the data
** Care must be taken to ensure that the maps correspond to what configuration the DAQ channels were in during the data collection for that run
** Run numbers can be used automatically to do this, but the user must define the map files appropriately so it works
** It is important to turn off the beam current normalization for channel readouts
* The raw .dat data files should be copied over network ([[JLab_Computing#Transferring_Huge_Files|see guide]]) into a folder you have read and write privileges on (in the ifarm perhaps, especially in /volatile or /scratch directories, [[JLab_Computing|see guide]])
** These resultant root files will only be accessible to you, so if you need to share then consider just using the standard arap@adaq3:~/PREX/japan install, and if there are features you need to add to that instance of the analyzer then use the [https://github.com/JeffersonLab/japan/tree/develop Github repo].
* The ROOT output should go into your (setup_japan.tcsh initialized environment variable location) ${QW_ROOTFILES}, for analysis done on the corresponding .dat file in ${QW_DATA}
* After analyzing your run, be sure to look at the JAPAN outputs and read the Error Summary list
** Any number above 0 indicates that an event has failed some check and the data was not saved to the ROOTfile (or it was, but has an error code assigned to it)
** See [https://github.com/JeffersonLab/japan/blob/4d495cb831d3cb10e58a822522d08390e7412602/Analysis/include/QwTypes.h#L163 the source code for a catalog of error codes]

==Compilation==
The code as is compiles fine on ifarm machines (1401 or 1402). For local installation you need to have:
* mysql++ 
* root with minuit2 library
* boost libraries

Verified compilation with:
 -- The C compiler identification is GNU 4.8.5
 -- The CXX compiler identification is GNU 4.8.5
 -- Check for working C compiler: /bin/cc
 -- Check for working C compiler: /bin/cc -- works
 -- Detecting C compiler ABI info
 -- Detecting C compiler ABI info - done
 -- Detecting C compile features
 -- Detecting C compile features - done
 -- Check for working CXX compiler: /bin/c++
 -- Check for working CXX compiler: /bin/c++ -- works
 -- Detecting CXX compiler ABI info
 -- Detecting CXX compiler ABI info - done
 -- Detecting CXX compile features
 -- Detecting CXX compile features - done
 -- System name Linux
 -- Found ROOT 6.12/04 in /home/ciprian/root/root6/root/build
 -- Boost version: 1.53.0
 -- Found the following Boost libraries:
 --   program_options
 --   filesystem
 --   system
 --   regex
 No QwAnalysis dictionaries needed for ROOT 6.12/04.
 -- Configuring done
 -- Generating done
 -- Build files have been written to: /home/ciprian/prex/japan/build

== Minimal Working Configuration Files ==
For more detailed information on JAPAN configurations [[Japan_options_and_maps|see here]].

To get a minimal working version of a Japan config file you need to do the following steps in order
 git clone git@github.com:JeffersonLab/japan (https://github.com/JeffersonLab/japan)
 cd japan
 mkdir build
 cd build
 cmake ../
 make
 cd ../Parity/prminput
* The engine needs to know where to look for CODA files and where to put ROOT files, this can be done either with environment variables or command line options
 setenv QW_DATA [path to CODA data files]
 setenv QW_ROOTFILES [path to where you want to store output files]
* or included when populating the [config_name].conf with the following options (a conf file stands in place of a long string of command line options, and Japan default assumes that a qwparity.conf file exists and fails if it is not overwritten with --config [config_name].conf instead).
 vim [config_name].conf
* fill the CODA and ROOT file options
 data = /path/to/coda/files
 rootfiles = /path/to/root/output/files
* The engine will search for a default data file name "QwRun_#.log" and so you should overwrite the prefix and data extension with the following .conf options
 codafile-stem = [CODA file stem (prex_ALL_)]
 codafile-ext = [extension (dat)]
* The engine will search for a default map file for the detector names and channel map in "detectors.map" and should be overwritten with
 detectors = [map name (prex_detectors.map)]
* Because the ROCs for the Parity DAQ are < 31 we need to add a flag (either in a separate conf file or by itself)
 add-config = prexbankflag.conf
** Where prexbankflag.conf contains 
 allow-low-subbank-ids = yes
* The engine will automatically give the Rootfile prefix as "Qweak_#.trees.root" and can be overwritten with 
 rootfile-stem = [stem (prexALL_)]
* To use the analyzer on the command line now you will need to pass your config file and the run number (or else it will use runnumber 0)
 ./build/qwparity --conf [config name.conf] -r [run number]
With all of these in place the analyzer will behave in a user defined and consistent way.

== Basic level map files ==
The basic map file should contain at least one subsystem array, with at least a channel map and a set of event cuts
 [QwBlindDetectorArray]
 name     = MainDets
 map      = prex_maindet.map
 param    = prex_maindet_pedestal.map
 eventcut = prex_maindet_eventcuts.map
Where event cuts file should at least contain the following line:
 EVENTCUTS = 3
and additional lines are used to give global level event cuts for various subsystem array elements.
The basics of the subsystem array map are to decode the CODA data file and should look like this
 ROC=25
 Bank=0x5
 vqwk_buffer_offset=1
 sample_size=16564
 !means we are in a commented out line
 !Hardware name, module number, channel number, channel object type, channel name  blinding status
 VQWK, 0, 0,  IntegrationPMT,  usl           not_blindable
 VQWK, 0, 1,  IntegrationPMT,  dsl           not_blindable

The options for possible subsystem arrays include:
* QwBeamLine
* QwHelicity
* QwDetectorArray
* QwBlindDetectorArray
* QwScaler
And any one of them can be called multiple times with unique map files for each instance.

If no helicity subsystem is defined then Japan will default to use quartet pattern with a non-random simple alternating pattern.

An example of a working non-PREX setup that uses the same CRL and Japan analysis is the [https://github.com/JeffersonLab/japan/tree/tedf-test-stand/Parity/prminput TEDf test stand analysis] (which is somewhat stale, but works nonetheless on a different data set and channel maps).

For more information on optional options and map features see [[Japan options and maps]]

== Recently Asked Questions ==
'''Shift Taker How To'''
* [[Online_analysis|Online Analysis How To]]

'''How to establish pedestals for a channel'''
* For beam-off pedestals 
** Plot values like "cav4bx.hw_sum_raw/cav4bx.num_samples" during a known period of beam off, and find the mean.
** Then you will add lines to the prexCH_beamline_pedestal.***.map for your channels
** In each line, the channel name is first, then the pedestal, then the gain

'''I need to do cuts on non-zero ErrorFlags while working on evt tree. Do I need to do the same thing while working on mul tree too or the mul tree itself makes cuts on non-zero ErrorFlag?'''
* You would also need to do the cuts in the mul tree

'''When I applied ErrorFlag==0 cut, I am left with only a few entries out of the run. Is there something wrong or it is normal.'''
* For a high-beam-off run, it is likely normal
** Take a look at "yield_bcm_an_ds10" with and without the cut
** You'll see how many events have non-zero beam current

'''ErrorFlag ==0 events are those with non-zero beam current, right?'''
* prexCH_beamline_eventcuts.map contains the condition of ErrorFlag
* At the moment the ErrorFlag is set by the one "global" cut (a line marked with a "g" in the event cuts file) and that is on bcm_an_ds3
** Its value must be above 1 uA and below 1e6 uA, and there is an eye-balled stability cut as well

'''How do I use the HV GUI, especially for SAM running?'''
* See the following page and associated links: [[SAMs_HV_Settings|SAMs HV Settings]]

== Expert Notes ==

* [[Japan_options_and_maps|JAPAN Options and Maps]]
* [[JAPAN/Data Handler]] - Describes the functionality of the data handler classes.

[[Category:Analyzer]]