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This tutorial will show you how to process SLIC output files with the Pandora PFA New package, currently the best performing PFA algorithm, in order Particle Flow Algorithm to produce Particle Flow Objects (PFOs) (also called ReconstructedParticles) for analysis. It covers . PFOs are represented by the ReconstructedParticle class in the LCIO event data format.

These instructions cover building and installing a slic-specific frontend called slicPandora and all its dependencies. Then it will go through the steps will be shown for processing slic the output using LCSim in order to prepare it for Pandora. Finally, it shows how to run slicPandora using there are instructions for running these events in slicPandora. There is also a note on how to generate brief section on generating a Pandora detector XML files file from compact descriptions.

Setup

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a compact detector description, the XML format used by lcsim to represent detector and geometry information.

Building SlicPandora

Preliminary Setup

A Linux or Unix platform is assumed and the bash shell is used for all command-line instructions. The actual setup procedures have been tested on Redhat Enterprise Linux 5.5 (Tikanga).

The cmake tool must be installed for building several of the packages.

You will need the standard GNU tools installed, e.g. Make, gcc/g++, etc.

The cvs and svn command-line tools are also required for obtaining project source codes.

The cmake tool must be installed, as it is used to build most of the dependencies.

Dependencies

The slicPandora package currently has the following dependencies.

Installing Packages

LCIO

Checkout the LCIO project from cvs.

cd /workdir
cvs -d :pserver:anonymous@cvs.freehep.org:/cvs/lcd co lcio

Building this project requires the CMake tool, the installation of which is not covered here. It additionally requires command-line GNU Make.

cd lcio
cmake .
make

The cvs head or last release tag should both work.

Set the LCIO environment variable.

export LCIO=`pwd`

This variable will be used by subsequent packages to locate LCIO and make a setup script.

CMakeModules

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There are build instructions below that show all the steps necessary to build these packages.

Build Instructions

These commands can be executed to produce a working slicPandora.

Start by making a directory where Pandora and its dependencies will be installed.

This is just an example. Any directory with enough space will do.

mkdir /work/pandora_build
cd /work/pandora_build

The following commands should then be executed in order from this working directory to make the slicPandora binary. You should execute each new package build from your working dir.

ilcutil

svn co httpshttp://svnsrv.desy.de/public/ilctools/CMakeModulesilcutil/trunk/ CMakeModules

Make an environment variable that will be referenced later.

cd CMakeModules
export CMAKE_MODULE_PATH=`pwd`

This package does not need to be compiled. It just provides some CMake macros.

PandoraPFANew

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 ilcutil
cd ilcutil
mkdir build
cd build
cmake ..
make install
cd ..
export ILCUTIL_DIR=`pwd`

Pandora

svn co httpshttp://svnsrv.desy.de/public/PandoraPFANew/PandoraPFANew/trunk PandoraPFANew

Now we need to build another package before configuring Pandora.

PandoraMonitoring

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cd PandoraPFANew
mkdir build
cd build
cmake -DILCUTIL_DIR=$ILCUTIL_DIR -DCMAKE_SKIP_RPATH=1 ..
make install
cd ..
export PandoraPFANew_DIR=`pwd`

LCIO

svn co httpssvn://svnsrvsvn.desyfreehep.deorg/publiclcio/PandoraPFANew/PandoraMonitoring/trunk PandoraMonitoring

Now configure the build using cmake.

tags/v02-01-01 lcio
cd lcio
mkdir build
cd build
cmake -DROOTDINSTALL_HOME=/path/to/rootDOC=OFF -DCMAKEDBUILD_MODULE32BIT_PATH=$CMAKE_MODULE_PATHCOMPATIBLE=OFF -DPandoraPFANewDCMAKE_SKIP_HOME=/path/to/pandoraRPATH=1 .

Set the environment variable.

.
make install
cd ..
export PANDORAMONITORINGLCIO_DIR=`pwd`

Technically, the monitoring package is optional, though it is quite useful for event and detector visualization.

PandoraPFANew Continued

Since Pandora has minimal external dependencies, it is straightforward to build. Only the CMakeModules must be located for the build and PandoraMonitoring, and the latter is optional.

cd PandoraPFANew
cmake -DCMAKE_MODULE_PATH=$CMAKE_MODULE_PATH -DPandoraMonitoring_Home=/path/to/PandoraMonitoring .
make

If monitoring is not being used, this CMake command can be used instead.

cmake -DCMAKE_MODULE_PATH=$CMAKE_MODULE_PATH .

Set the environment variable.

cd PandoraPFANew
export PandoraPFANew_HOME=`pwd`

This will be referenced in the build of the next package.

If the release compiles successfully, you're now ready to setup the project that interfaces SLIC to Pandora.

slicPandora

Checkout the slicPandora project from cvs.

slicPandora

cvs -d :pserver:anonymous@cvs.freehep.org:/cvs/lcd co slicPandora
cd slicPandora
export SLICPANDORA_DIR=`pwd`
mkdir build
cd build
cmake -DILCUTIL_DIR=$ILCUTIL_DIR -DLCIO_DIR=$LCIO_DIR -DPandoraPFANew_DIR=$PandoraPFANew_DIR -DCMAKE_SKIP_RPATH=1 ..
make install

If this step completes successfully without compilation or link errors, you should see a binary at slicPandora/bin/PandoraFrontend. You are basically done building slicPandora.

Pandora Settings (optional)

You should also check out the project that contains example config files for Pandora.

svn co http://svnsrv.desy.de/public/PandoraPFANew/Settings/trunk PandoraSettings

LCDetectors (optional)

There are some slicPandora geometry xml files here. (This is a rather big cvs module so might take some time to checkout.)

cd /workdir
cvs -d :pserver:anonymous@cvs.freehep.org:/cvs/lcd co LCDetectors

For example, see LCDetectors/detectors/sidloi3/sidloi3_pandora.xml and its compact detector description.

Setting the LD_LIBRARY_PATH

The shared library locations need to be specified in the LD_LIBRARY_PATH for slicPandora

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to run. The variable needs to be defined as follows, based on environment settings from the build.

export LD_LIBRARY_PATH=$SLICPANDORA_DIR/lib:$LCIO_DIR/lib:$PandoraPFANew_DIR/lib

If these variables are not set in the environment, then using the full, explicit path to the library directories will work fine.

Checking the Build

Now you should be able to run this command to load slicPandora.The following should generate a setup script called mysetup.sh for setting up your runtime and compilation environment later.

./make_setup_script.sh

This setup script looks for the following environment variables to determine your Pandora setup.

If ROOTSYS and PANDORAMONITORING are not defined in the environment, then visualization will be disabled.

Source the new setup script that was generated.

. mysetup.sh

Now build the slicPandora project.

make

The slicPandora project should now be built successfully, if its dependencies are present and setup correctly. If compilation or linking errors occur, then check that LCIO and Pandora were both installed successfully and that the setup script is pointing to the correct locations of these packages. If monitoring has been enabled, check that ROOT and PandoraMonitoring are configured and built successfully and that their environment variables are set.

slicPandora/bin/PandoraFrontend

The help message should show for slicPandora. If there are errors about missing libraries, set the LD_LIBRARY_PATH variable accordingly.

PandoraFrontend

The PandoraFrontend binary provides a simple frontend to slicPandora. It uses GNU style command line switches for user input.

The following table explains the function of each of these switches.

The geometry file is in an XML format. It can be created from a compact detector description using GeomConverter with the option "-o pandora". You are required to provide some additional parameters related to sampling fractions (see LCDetectors/detectors/sidloi3 for example).

The Pandora settings XML file contains settings to configure the Pandora PFA algorithm. Example configuration files can be found in the Pandora Settings SVN project (see building instructions above) (see PandoraSettings/PandoraSettingsBasic.xml).

The LCIO input events should contain collections of LCIO CalorimeterHits named according to their subdetectors, plus a collection of LCIO Track objects called "Tracks." There also needs to be a collection called "TrackStates" containing momentum measurements at various points along the Track (see below for details of generating these files).

The LCIO output file will contain the contents of the input file plus the PFO collections created by Pandora, as well as some intermediate collections of hit objects. This file is generated by slicPandora.

The number of events to run should be a positive integer. If slicPandora runs out of events, it will print and warning but should not crash.

The number of events to skip should be a positive integer. These events are read in and discarded before event processing begins.

Here is a contrived example using all input parameters.

./bin/PandoraFrontend -g myGeometry.xml -c PandoraSettings.xml -i inputEvents.slcio -l myCollections.xml -o myOutput.slcio -r 1000 -s 10

These are example arguments only. Actual usage will require files in the correct input data formats, namely the geometry XML, the Pandora settings file, and the XML specifying which LCIO input collections to use, if different from the defaults.

Using GeomConverter to Output the Pandora Geometry Format

The GeomConverter package can convert from compact detector descriptions to various output formats, including one for input to slicPandora.

For example, to generate the Pandora settings for the sidloi3 detector.

cvs -d :pserver:anonymous@co LCDetectors
cd LCDetectors/detectors/sidloi3
java -jar ~/.m2/repository/org/lcsim/GeomConverter/1.13-SNAPSHOT/GeomConverter-1.13-SNAPSHOT-bin.jar -o pandora compact.xml sidloi3_pandora.xml

This will create the file sidloi3_pandora.xml that can be used as input to slicPandora.

FIXME: Need to document the conditions used to set sampling fractions.

Running Events in SlicPandora

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Steps

The essential steps to generating slicPandora events with SlicPandora are as follows.

1) Use SLIC to generate an LCIO simulation datafile.
2) Add tracks to the event by running a tracking package such as LCSim's SeedTracker.
3) Add the TrackState collections so slicPandora knows the Track momenta. (can be combined with #2 into one LCSim job)
4) Run slicPandora SlicPandora with the LCSim output, a Pandora XML geometry generated by GeomConverter, and a Pandora settings XML file.

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<lcsim xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
        xs:noNamespaceSchemaLocation="http://www.lcsim.org/schemas/lcsim/1.0/lcsim.xsd">
    <inputFiles>
        <file>./pi_Theta90_10GeV-0-1000_SLIC-v2r8p3_geant4-v9r3p1_QGSP_BERT_sidloi3.slcio</file>
    </inputFiles>
    <control>
        <numberOfEvents>1000</numberOfEvents>
        <verbose>true</verbose>
        <printSystemProperties>false</printSystemProperties>
    </control>
    <execute>
        <driver name="EventMarkerDriver"/>
        <driver name="CalInfoDriver"/>
        <driver name="MainTrackingDriver"/>
        <driver name="TrackStateDriver"/>
        <driver name="Writer"/>
    </execute>
    <drivers>
        <driver name="CalInfoDriver"   
                type="org.lcsim.recon.util.CalInfoDriver"/>
        <driver name="MainTrackingDriver"
                type="org.lcsim.recon.tracking.seedtracker.trackingdrivers.sidloi2.MainTrackingDriver"/>
        <driver name="EventMarkerDriver" 
                type="org.lcsim.job.EventMarkerDriver">
            <eventInterval>10</eventInterval>
        </driver>
        <driver name="TrackStateDriver"
                type="org.lcsim.recon.tracking.seedtracker.SeedTrackerTrackStateDriver"/>
        <driver name="Writer"
                type="org.lcsim.util.loop.LCIODriver">
            <outputFilePath>./pi_Theta90_10GeV-0-1000_SLIC-v2r8p3_geant4-v9r3p1_QGSP_BERT_sidloi3_lcsimTracking.slcio</outputFilePath>
        </driver>
    </drivers>
</lcsim>

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<driver name="CalInfoDriver"   
        type="org.lcsim.recon.util.CalInfoDriver"/>
<driver name="TrackStateDriver"
        type="org.lcsim.recon.tracking.seedtracker.SeedTrackerTrackStateDriver"/>

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Now that tracks and track states have been added to the events, we are ready to use Pandora itself.

PandoraFrontend

The PandoraFrontend binary provides a simple frontend to slicPandora.

The syntax of this command is the following.

./bin/PandoraFrontend geometry.xml pandoraSettings.xml inputEvents.slcio reconOutput.slcio [nevents]

The nevents command is optional, but all other arguments are required and must be supplied in order.

For example, to repeat the results of the JobManagerTest using PandoraFrontend, execute this command.

./bin/PandoraFrontend ./examples/sidloi3_pandora.xml ./examples/PandoraSettingsRelease.xml ./input.slcio ./pandoraRecon.slcio 2

The above command requires that the input events were generated in the sidloi3 detector and that a symlink has been setup pointing from "input.slcio" to your input event file.

Using GeomConverter to Output the Pandora Geometry Format

The GeomConverter package can convert from compact detector descriptions to various output formats, including one for input to slicPandora. (Installation of GeomConverter is not covered here.)

Use this command from your GeomConverter root directory to generate a Pandora geometry file from a compact detector description.

java -jar ./target/GeomConverter-1.10-SNAPSHOT-bin.jar -o pandora ./myCompactDetector.xml ./myPandoraGeom.xml

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Links

• PandoraPFANew FAQ
• Pandora SVN Repository