diff -u -r1.2 -r1.3
--- make_setup_script.sh	7 Jun 2010 16:56:08 -0000	1.2
+++ make_setup_script.sh	8 Jun 2010 21:43:01 -0000	1.3
@@ -15,6 +15,13 @@

 
 echo -e \
 "#!/bin/bash

-export PANDORAPFA=$PANDORAPFA
-export LCIO=$LCIO
-export LD_LIBRARY_PATH=${PANDORAPFA}/lib:${LCIO}/lib:${PWD}/lib:\$LD_LIBRARY_PATH" > mysetup.sh

+export PANDORAPFA=$PANDORAPFA" > mysetup.sh
+
+if [ -n "$PANDORA_RELEASE" ]; then
+    echo "PANDORA_RELEASE=$PANDORA_RELEASE"
+    echo "export PANDORA_RELEASE=$PANDORA_RELEASE" >> mysetup.sh
+fi
+
+echo -e \
+"export LCIO=$LCIO
+export LD_LIBRARY_PATH=${PANDORAPFA}/lib:${LCIO}/lib:${PWD}/lib:\$LD_LIBRARY_PATH" >> mysetup.sh

diff -u -r1.12 -r1.13
--- Makefile	11 Mar 2010 22:19:13 -0000	1.12
+++ Makefile	8 Jun 2010 21:43:01 -0000	1.13
@@ -1,4 +1,4 @@

-# $Id: Makefile,v 1.12 2010/03/11 22:19:13 jeremy Exp $

+# $Id: Makefile,v 1.13 2010/06/08 21:43:01 jeremy Exp $

 
 #
 # Makefile for the slicPandora project.  It requires that 

@@ -50,8 +50,19 @@

 TESTS=$(basename $(notdir $(TESTSRCS)))
 
 # compiler flags

+#CXXFLAGS=-v -Wall -g $(INCLUDES)

 CXXFLAGS=-Wall -g $(INCLUDES)
 

+# Compile for release version.
+ifdef PANDORA_RELEASE
+CXXFLAGS+="-DPANDORA_RELEASE="$(PANDORA_RELEASE)
+endif
+
+# Debug output for PFO creation.
+ifdef PFOPROCESSOR_DEBUG
+CXXFLAGS+="-DPFOPROCESSOR_DEBUG=1"
+endif
+

 # Create library and tests.
 all: libs tests
 

@@ -96,4 +107,4 @@

 
 # Clean up the object files and build directories.
 clean:

-	@rm -rf $(OBJS) $(PWD)/lib $(PWD)/bin

\ No newline at end of file

+	@rm -rf $(OBJS) $(PWD)/lib $(PWD)/bin

diff -N PandoraSettingsRelease.xml
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ PandoraSettingsRelease.xml	8 Jun 2010 21:43:02 -0000	1.1
@@ -0,0 +1,85 @@

+<!-- Pandora settings xml file -->
+<pandora>
+
+    <IsMonitoringEnabled> true </IsMonitoringEnabled>
+    <MipNCellsForNearbyHit> 2 </MipNCellsForNearbyHit>
+    <IsolationDensityWeightCutECal> 0.1 </IsolationDensityWeightCutECal>
+    <IsolationDensityWeightCutHCal> 0.1 </IsolationDensityWeightCutHCal>
+    <ShouldUseSimpleIsolationScheme> false </ShouldUseSimpleIsolationScheme>
+    <IsolationCutDistanceECal> 25. </IsolationCutDistanceECal>
+    <IsolationCutDistanceHCal> 200. </IsolationCutDistanceHCal>
+    <IsolationMaxNearbyHits> 2 </IsolationMaxNearbyHits>
+
+    <!-- Select the tracks to use for clustering -->
+    <algorithm type = "TrackSelection"></algorithm>
+
+    <!-- Primary clustering algorithm runs Clustering algorithm -->
+    <algorithm type = "PrimaryClustering">
+        <algorithm type = "Clustering" description = "ClusterFormation" instance = "mainClustering"/>
+
+        <!-- Topological associations, to be run after clustering -->
+        <algorithm type = "TopologicalAssociation" description = "ClusterAssociation" instance = "mainTopologicalAssoc">
+            <associationAlgorithms>
+                <algorithm type = "LoopingTracks"/>
+                <algorithm type = "BrokenTracks"/>
+                <algorithm type = "ShowerMipMerging"/>
+                <algorithm type = "ShowerMipMerging2"/>
+                <algorithm type = "BackscatteredTracks"/>
+                <algorithm type = "BackscatteredTracks2"/>
+                <algorithm type = "ShowerMipMerging3"/>
+                <algorithm type = "ShowerMipMerging4"/>
+                <algorithm type = "ProximityBasedMerging">
+                    <algorithm type = "TrackClusterAssociation"/>
+                </algorithm>
+                <algorithm type = "ConeBasedMerging">
+                    <algorithm type = "TrackClusterAssociation"/>
+                </algorithm>
+                <algorithm type = "SoftClusterMerging">
+                    <algorithm type = "TrackClusterAssociation"/>
+                    <ShouldUsePhotonClusters> false </ShouldUsePhotonClusters>
+                    <PhotonClusterListName> photonClusters </PhotonClusterListName>
+                </algorithm>
+                <algorithm type = "IsolatedHitMerging">
+                    <ShouldUsePhotonClusters> false </ShouldUsePhotonClusters>
+                    <PhotonClusterListName> photonClusters </PhotonClusterListName>
+                </algorithm>
+            </associationAlgorithms>
+        </algorithm>
+        <ClusterListName> PrimaryClusterList </ClusterListName>
+    </algorithm>
+
+    <!-- Photon recovery -->
+    <algorithm type = "PhotonRecovery">
+        <algorithm type = "TrackClusterAssociation"/>
+    </algorithm>
+
+    <algorithm type = "ClusterPreparation" description = "ClusterPreparation">
+        <CandidateListNames>PrimaryClusterList</CandidateListNames>
+    </algorithm>
+
+    <algorithm type = "TrackPreparation" description = "TrackPreparation">
+        <trackClusterAssociationAlgorithms>
+            <algorithm type = "TrackClusterAssociation"/>
+            <algorithm type = "LoopingTrackAssociation"/>
+            <algorithm type = "TrackRecovery"/>
+            <algorithm type = "TrackRecoveryHelix"/>
+            <algorithm type = "TrackRecoveryInteractions"/>
+        </trackClusterAssociationAlgorithms>
+    </algorithm>
+
+    <algorithm type = "FragmentRemoval" description = "FragmentRemoval">
+        <fragmentRemovalAlgorithms>
+            <algorithm type = "MainFragmentRemoval"/>
+            <algorithm type = "NeutralFragmentRemoval"/>
+        </fragmentRemovalAlgorithms>
+    </algorithm>
+    
+    <algorithm type = "PfoCreation" description = "PfoCreation">
+    </algorithm>
+
+    <algorithm type = "ForceSplitTrackAssociations"/>
+
+    <!-- Final particle id for particle flow objects -->
+    <algorithm type = "FinalParticleId"/>
+
+</pandora>

diff -u -r1.7 -r1.8
--- CalorimeterHitProcessor.cpp	19 May 2010 22:25:41 -0000	1.7
+++ CalorimeterHitProcessor.cpp	8 Jun 2010 21:43:02 -0000	1.8
@@ -1,4 +1,4 @@

-// $Id: CalorimeterHitProcessor.cpp,v 1.7 2010/05/19 22:25:41 jeremy Exp $

+// $Id: CalorimeterHitProcessor.cpp,v 1.8 2010/06/08 21:43:02 jeremy Exp $

 
 #include "CalorimeterHitProcessor.h"
 

@@ -22,7 +22,7 @@

 
 void CalorimeterHitProcessor::processEvent(EVENT::LCEvent* event)
 {

-    //std::cout << "CalorimeterHitProcessor::processEvent" << std::endl;

+    m_totalEHits = 0.;

 
     const pandora::Pandora& pandora = getJobManager()->getPandora();
     DetectorGeometry* geom = getJobManager()->getDetectorGeometry();

@@ -60,7 +60,9 @@

         std::cout << "-----------------------------------------------------" << std::endl;
 #endif
     }

-    

+
+    std::cout << "totalEHits: " << m_totalEHits << std::endl;    
+    m_totalEHits = 0;

 }
 
 PandoraApi::CaloHit::Parameters CalorimeterHitProcessor::makeCaloHitParameters(

@@ -68,6 +70,9 @@

     DetectorGeometry::ExtraSubDetectorParameters* xsubdet,
     CalorimeterHit* hit)
 {

+    // Create a new, empty CaloHit Parameters.
+    PandoraApi::CaloHit::Parameters params;
+

     // Get the IDDecoder.
     IDDecoder* decoder = xsubdet->m_decoder;
 

@@ -79,48 +84,82 @@

 
     // Get the layer parameters for this layer.
     PandoraApi::GeometryParameters::LayerParametersList* layerList = &(subdet->m_layerParametersList);

+    int nlayers = layerList->size();
+
+#if PANDORA_RELEASE >= 1
+    // Set isInOuterSamplingLayer if hit is in the last 2 layers.
+    if (layer >= nlayers - 3)
+    {
+        params.m_isInOuterSamplingLayer = true;
+    }
+    else
+    {
+        params.m_isInOuterSamplingLayer = false;
+    }
+#endif
+

     PandoraApi::GeometryParameters::LayerParameters layerParams = (*layerList)[layer];
     DetectorGeometry::ExtraLayerParameters xlayerParams = xsubdet->m_extraLayerParams[layer];
 

+    // Mip Energy.

     float mipEnergy = xsubdet->m_mipEnergy.Get();
 

+    // Sampling fractions.

     float samplingFraction = xlayerParams.m_samplingFraction.Get();
     float emSamplingFraction = xlayerParams.m_emSamplingFraction.Get();
     float hadSamplingFraction = xlayerParams.m_hadSamplingFraction.Get();
 

-    // Recover raw energy to apply EM and HAD sampling fractions.
-    float rawEnergy = hit->getEnergy() * samplingFraction;

+    // Recover the raw energy with reverse calculation.
+    // Should work for both digital and analog because sampling fraction 
+    // is applied in SimCalorimeterHitProcessor for both places.
+    float rawEnergy = hit->getEnergy() * samplingFraction;        

 
     // Get the module number.
     int module = decoder->getFieldValue("module", cellId);
 

-    // Create a new, empty CaloHit Parameters.
-    PandoraApi::CaloHit::Parameters params;
-

     // Get the hit position.

-    const float* pos(hit->getPosition());
-
-    //
-    // Setup a CaloHit::Parameters object for this CalorimeterHit.
-    //

+    const float* pos(hit->getPosition());   

 
     // Position in mm.
     params.m_positionVector = pandora::CartesianVector(pos[0], pos[1], pos[2]);
 

-    // Hit energy in GeV.
-    params.m_inputEnergy = hit->getEnergy(); 

+    // Digital calorimeter setting.
+    params.m_isDigital = xsubdet->m_isDigital; 

-    // EM energy in GeV.
-    params.m_electromagneticEnergy = rawEnergy / emSamplingFraction;

+    // For digital hits, divide 1 by the sampling fraction.
+    if (params.m_isDigital.Get() == true)
+    {
+        // Hit energy in GeV.  
+        params.m_inputEnergy = 1. / samplingFraction;

-    // HAD energy in GeV.
-    params.m_hadronicEnergy = rawEnergy / hadSamplingFraction;

+        // EM energy in GeV.
+        params.m_electromagneticEnergy = 1. / emSamplingFraction;
+        
+        // HAD energy in GeV.
+        params.m_hadronicEnergy = 1. / hadSamplingFraction;
+        
+        // MIP equivalent energy.
+        params.m_mipEquivalentEnergy = 1. / mipEnergy; 
+    }
+    // For analog hits, divide the raw energy by the sampling fraction.
+    else
+    {
+        // Hit energy in GeV.  Sampling fraction applied in SimCalorimeterHitProcessor.
+        params.m_inputEnergy = hit->getEnergy();        

-    // MIP equivalent energy.
-    params.m_mipEquivalentEnergy = rawEnergy / mipEnergy; 

+        // EM energy in GeV.
+        params.m_electromagneticEnergy = rawEnergy / emSamplingFraction;
+        
+        // HAD energy in GeV.
+        params.m_hadronicEnergy = rawEnergy / hadSamplingFraction;
+        
+        // MIP equivalent energy.
+        params.m_mipEquivalentEnergy = rawEnergy / mipEnergy; 
+    }

-    // Digital calorimeter setting.
-    params.m_isDigital = xsubdet->m_isDigital; 

+    // DEBUG
+    m_totalEHits += params.m_inputEnergy.Get();
+    // END DEBUG

 
     // Layer number.
     params.m_layer = layer;

diff -u -r1.13 -r1.14
--- DetectorGeometry.cpp	7 Jun 2010 22:43:22 -0000	1.13
+++ DetectorGeometry.cpp	8 Jun 2010 21:43:02 -0000	1.14
@@ -27,8 +27,6 @@

 
 void DetectorGeometry::loadFromFile(std::string filename)
 {

-    //std::cout << "DetectorGeometry::loadFromFile()" << std::endl;
-

     // Load doc and check if valid.
     TiXmlDocument doc(filename.c_str());
     if (!doc.LoadFile())

@@ -54,13 +52,15 @@

         PandoraApi::GeometryParameters::SubDetectorParameters* subdet = 
             getSubDetectorFromType(subdetType);
 

-        ExtraSubDetectorParameters extras;
-
-        if (subdet == 0)

+        // Check if subdetector type is known and skip if not.
+        if (0 == subdet)

         {

-            std::cerr << "FATAL ERROR: Could not find subdetector with type " << subdetType << ".  Exiting!"  << std::endl;
-            exit(1);
-        }            

+            std::cerr << "WARNING: Ignoring unknown subdetType " << subdetType << "." << std::endl;
+            continue;
+        }
+
+        // Extra parameters defined by the GeomConverter format.
+        ExtraSubDetectorParameters extras;

 
         // Numerical parameters which are attributes on calorimeter.
         float innerR, innerZ, innerPhi;

@@ -99,6 +99,13 @@

         subdet->m_outerPhiCoordinate = outerPhi;
         subdet->m_outerSymmetryOrder = outerSym;
 

+        // Inner and outer symmetry are different.
+        if (innerSym != outerSym)
+        {
+            std::cerr << "Inner and outer symmetry are different.  Don't know how to handle this case!" << std::endl;
+            exit(1);
+        }
+

         // Number of layers.
         TiXmlElement* layers = (TiXmlElement*) calElem->FirstChild("layers");
         layers->QueryIntAttribute("nlayers", &nlayers);

@@ -191,21 +198,13 @@

 
         // Make an IDDecoder for this calorimeter.
         IDDecoder* decoder = new IDDecoder(fields);

+        extras.m_decoder = decoder;

 
         // Set extra subdetector parameters.

-        extras.m_decoder = decoder;

         extras.m_inputHitType = getHitType(subdetType);
         extras.m_inputDetectorRegion = getDetectorRegion(subdetType);
         extras.m_mipEnergy = mipEnergy;

-
-        
-
-        if (innerSym != outerSym)
-        {
-            std::cerr << "Inner and outer symmetry are different.  Don't know how to handle this case!" << std::endl;
-            exit(1);
-        }
-

+       

         // Calculate the subdetector normal vectors for a barrel region.
         if (extras.m_inputDetectorRegion.Get() == pandora::BARREL)
         {

@@ -321,12 +320,20 @@

     {
         return &(geom.m_hCalEndCapParameters);
     }

+#if PANDORA_RELEASE >= 1
+    else if ( strcmp( subdetType, "MUON_BARREL" ) == 0 )
+    {
+        return &(geom.m_muonBarrelParameters);
+    }
+    else if ( strcmp( subdetType, "MUON_ENDCAP" ) == 0 )
+    {
+        return &(geom.m_muonEndCapParameters);
+    }
+#endif

     else
     {

-        runtime_error("Unknown subdetector type.");

+        return 0;

     }

-    // Next line removes compilation warning.  Code should never get here!
-    return 0;

 }
 
 void DetectorGeometry::printOut(const char* subdetType, PandoraApi::GeometryParameters::SubDetectorParameters* subdet)

@@ -379,7 +386,13 @@

     else if (calType == "HAD_BARREL" || calType == "HAD_ENDCAP")
     {
             return pandora::HCAL;

+    } 
+#if PANDORA_RELEASE >= 1
+    else if (calType == "MUON_BARREL" || calType == "MUON_ENDCAP")
+    {
+        return pandora::MUON;

     }

+#endif

     else
     {
         std::cout << "Unknown CalorimeterType <" << calType << ">." << std::endl;

@@ -388,11 +401,11 @@

 
 inline pandora::InputDetectorRegion DetectorGeometry::getDetectorRegion(const std::string& calType) const
 {

-    if (calType == "EM_BARREL" || calType == "HAD_BARREL")

+    if (calType == "EM_BARREL" || calType == "HAD_BARREL" || calType == "MUON_BARREL")

     {
         return pandora::BARREL;
     }

-    else if (calType == "EM_ENDCAP" || calType == "HAD_ENDCAP")

+    else if (calType == "EM_ENDCAP" || calType == "HAD_ENDCAP" || calType == "MUON_ENDCAP")

     {
         return pandora::ENDCAP;
     }

diff -u -r1.2 -r1.3
--- PfoConstructionAlgorithm.cpp	10 Mar 2010 20:16:14 -0000	1.2
+++ PfoConstructionAlgorithm.cpp	8 Jun 2010 21:43:02 -0000	1.3
@@ -4,6 +4,9 @@

  *  @brief  Implementation of the pfo construction algorithm class.
  * 
  *  $Log: PfoConstructionAlgorithm.cpp,v $

+ *  Revision 1.3  2010/06/08 21:43:02  jeremy
+ *  make compatible with Pandora release1 (set PANDORA_RELEASE macro to enable); add basic code for digital calorimetry
+ *

  *  Revision 1.2  2010/03/10 20:16:14  jeremy
  *  updates to compile against PandoraPFANew svn trunk; update example setup script; a few small changes to JobManagerTest
  *

@@ -12,7 +15,9 @@

  *
  */
 

-#include "Algorithms/PfoConstructionAlgorithm.h"

+#include "PfoConstructionAlgorithm.h"
+
+#include "Api/PandoraApi.h"

 
 using namespace pandora;
 

diff -u -r1.13 -r1.14
--- SimCalorimeterHitProcessor.cpp	7 Jun 2010 22:59:48 -0000	1.13
+++ SimCalorimeterHitProcessor.cpp	8 Jun 2010 21:43:02 -0000	1.14
@@ -117,10 +117,10 @@

             long long cellId = ((long long)cellId1)<<32 | cellId0;
 
             // Decode the layer number from the id.

-            int layer = decoder->getFieldValue("layer", cellId);

+            int layer = decoder->getFieldValue("layer", cellId);            

 
             // Get the layer parameters for this layer.

-            PandoraApi::GeometryParameters::LayerParameters layerParams = (*layerList)[layer];

+            PandoraApi::GeometryParameters::LayerParameters layerParams = (*layerList)[layer];                        

 
             // Get the extra layer parameters for this layer (sampling).
             DetectorGeometry::ExtraLayerParameters xlayerParams = xsubdet.m_extraLayerParams[layer];

diff -u -r1.3 -r1.4
--- CalorimeterHitProcessor.h	11 Mar 2010 22:18:44 -0000	1.3
+++ CalorimeterHitProcessor.h	8 Jun 2010 21:43:02 -0000	1.4
@@ -65,6 +65,11 @@

      * Print the given CalHit::Parameters to cout.
      */
     void printCaloHitParameters(const PandoraApi::CaloHit::Parameters&);

+
+private:
+
+    float m_totalEHits;
+

 };
 
 #endif

diff -u -r1.2 -r1.3
--- PfoConstructionAlgorithm.h	9 Mar 2010 20:13:42 -0000	1.2
+++ PfoConstructionAlgorithm.h	8 Jun 2010 21:43:02 -0000	1.3
@@ -1,10 +1,13 @@

-// $Id: PfoConstructionAlgorithm.h,v 1.2 2010/03/09 20:13:42 jeremy Exp $

+// $Id: PfoConstructionAlgorithm.h,v 1.3 2010/06/08 21:43:02 jeremy Exp $

 /**
  *  @file   PandoraPFANew/include/Algorithms/PfoConstructionAlgorithm.h
  * 
  *  @brief  Header file for the pfo construction algorithm class.
  * 
  *  $Log: PfoConstructionAlgorithm.h,v $

+ *  Revision 1.3  2010/06/08 21:43:02  jeremy
+ *  make compatible with Pandora release1 (set PANDORA_RELEASE macro to enable); add basic code for digital calorimetry
+ *

  *  Revision 1.2  2010/03/09 20:13:42  jeremy
  *  checkpoint
  *

@@ -17,6 +20,8 @@

 
 #include "Algorithms/Algorithm.h"
 

+//#include "Algorithms/PfoConstruction/PfoCreationAlgorithm.h"
+

 /**
  *  @brief  PfoConstructionAlgorithm class
  */