Merge branch 'develop' into v2.2-rc1

.gitignore

@@ -50,6 +50,9 @@ log
 .cproject
 .project
 
+#ignore build type file
+.buildtype
+
 #ignore dot files
 *.dot
 

.travis.yml

@@ -5,18 +5,24 @@ services:
 script:
 - docker build -t jeffersonlab/remoll .
 - for suite in load validate overlap ; do
-    docker run -t jeffersonlab/remoll "scripts/tests/test_geometries.sh ${suite}" ;
+    docker run --rm -t jeffersonlab/remoll scripts/tests/test_geometries.sh ${suite} ;
   done
-- for suite in unit commit release ; do
-    docker run -t jeffersonlab/remoll "scripts/tests/test_macros.sh ${suite}" || exit 1 ;
-    docker start $(docker ps -l -q) ;
-    docker exec $(docker ps -l -q) scripts/tests/targz_macros.sh ${suite} ;
+- for suite in unit ; do
+    docker run --rm -t jeffersonlab/remoll scripts/tests/test_macros.sh ${suite} ;
+  done
+- for suite in commit release ; do
+    docker run -t jeffersonlab/remoll sh -c "
+      scripts/tests/test_macros.sh ${suite} &&
+      scripts/tests/targz_macros.sh ${suite} &&
+      scripts/tests/watermark.sh rootfiles/tests/${suite}/analysis
+    " || exit 1 ;
     docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.${suite}.log.tar.gz" . ;
     docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.${suite}.root.tar.gz" . ;
     docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.${suite}.analysis.log.tar.gz" . ;
     docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.${suite}.analysis.pdf.tar.gz" . ;
     docker cp $(docker ps -l -q):"/jlab/remoll/remolltest.${suite}.analysis.root.tar.gz" . ;
-    docker stop $(docker ps -l -q) ;
+    docker cp $(docker ps -l -q):"/jlab/remoll/rootfiles_tests_${suite}_analysis.pdf" . ;
+    docker rm $(docker ps -l -q) ;
   done
 
 after_success:
@@ -38,13 +44,15 @@ deploy:
   - remolltest.commit.log.tar.gz
   - remolltest.commit.root.tar.gz
   - remolltest.commit.analysis.log.tar.gz
-  - remolltest.commit.analysis.png.tar.gz
+  - remolltest.commit.analysis.pdf.tar.gz
   - remolltest.commit.analysis.root.tar.gz
+  - rootfiles_tests_release_analysis.pdf
   - remolltest.release.log.tar.gz
   - remolltest.release.root.tar.gz
   - remolltest.release.analysis.log.tar.gz
   - remolltest.release.analysis.pdf.tar.gz
   - remolltest.release.analysis.root.tar.gz
+  - rootfiles_tests_release_analysis.pdf
   skip_cleanup: true
   on:
     repo: JeffersonLab/remoll

CMakeLists.txt

@@ -236,6 +236,18 @@ foreach(file ${exefiles})
   )
 endforeach()
 
+#
+# custom targets
+#
+add_custom_target(create-manual
+  COMMAND ./remoll -g ${PROJECT_SOURCE_DIR}/geometry/mollerMother.gdml ${PROJECT_SOURCE_DIR}/macros/manual.mac | awk '/Command directory path/,/Graphics systems deleted/' > manual.txt
+  BYPRODUCTS manual.txt
+  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+  DEPENDS remoll)
+add_custom_target(check-manual
+  COMMAND diff ${PROJECT_SOURCE_DIR}/manual.txt manual.txt || true
+  WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+  DEPENDS create-manual)
 
 #----------------------------------------------------------------------------
 # Copy all scripts to the build directory, i.e. the directory in which we
@@ -307,6 +319,23 @@ install(FILES
      ${REMOLL_MAP_DIR}/blockyHybrid_rm_3.0.txt
      ${REMOLL_MAP_DIR}/blockyUpstream_rm_1.1.txt
      DESTINATION ${CMAKE_INSTALL_DATADIR}/remoll)
+if(ADDITIONAL_FIELDS)
+  message(STATUS "Ensuring additional fields are available")
+  file(DOWNLOAD
+     ${REMOLL_DOWNLOADS}/upstreamSymmetric_sensR_0.1.txt
+     ${REMOLL_MAP_DIR}/upstreamSymmetric_sensR_0.1.txt
+     EXPECTED_MD5 849d9dc5abab0842fc13fef7f4918648)
+  file(DOWNLOAD
+     ${REMOLL_DOWNLOADS}/hybridSymmetric_sensR_0.1.txt
+     ${REMOLL_MAP_DIR}/hybridSymmetric_sensR_0.1.txt
+     EXPECTED_MD5 78fad2ffa5b5ae129df11bdf0ce25333)
+  install(FILES
+     ${REMOLL_MAP_DIR}/upstreamSymmetric_sensR_0.0.txt
+     ${REMOLL_MAP_DIR}/hybridSymmetric_sensR_0.0.txt
+     DESTINATION ${CMAKE_INSTALL_DATADIR}/remoll)
+else()
+  message(STATUS "Download additional fields with '-DADDITIONAL_FIELDS=ON'.")
+endif()
 
 
 #----------------------------------------------------------------------------

Dockerfile

@@ -1,5 +1,10 @@
 FROM jeffersonlab/jlabce:2.3
 
+# Install libgcj and pdftk
+RUN wget https://copr.fedorainfracloud.org/coprs/robert/gcj/repo/epel-7/robert-gcj-epel-7.repo -P /etc/yum.repos.d && \
+    wget https://copr.fedorainfracloud.org/coprs/robert/pdftk/repo/epel-7/robert-pdftk-epel-7.repo -P /etc/yum.repos.d && \
+    yum install -y pdftk ghostscript
+
 ENV JLAB_VERSION=2.3
 ENV JLAB_ROOT=/jlab
 ENV JLAB_SOFTWARE=/jlab/2.3/Linux_CentOS7.2.1511-x86_64-gcc4.8.5
@@ -17,14 +22,15 @@ RUN source $JLAB_ROOT/$JLAB_VERSION/ce/jlab.sh && \
     make -j$(nproc) && \
     make install
 
-# Create entry point bash script
-RUN echo '#!/bin/bash'                                >  /usr/local/bin/entrypoint.sh && \
-    echo 'unset OSRELEASE'                            >> /usr/local/bin/entrypoint.sh && \
-    echo 'source $JLAB_ROOT/$JLAB_VERSION/ce/jlab.sh' >> /usr/local/bin/entrypoint.sh && \
-    echo 'export PATH=${REMOLL}/bin:${PATH}'          >> /usr/local/bin/entrypoint.sh && \
-    echo 'export REMOLL=${REMOLL}'                    >> /usr/local/bin/entrypoint.sh && \
-    echo 'cd $REMOLL && exec $*'                      >> /usr/local/bin/entrypoint.sh && \
-    chmod +x /usr/local/bin/entrypoint.sh
+# Create environment point bash script
+RUN echo '#!/bin/bash'                                >  /entrypoint.sh && \
+    echo 'unset OSRELEASE'                            >> /entrypoint.sh && \
+    echo 'source $JLAB_ROOT/$JLAB_VERSION/ce/jlab.sh' >> /entrypoint.sh && \
+    echo 'export PATH=${REMOLL}/bin:${PATH}'          >> /entrypoint.sh && \
+    echo 'export REMOLL=${REMOLL}'                    >> /entrypoint.sh && \
+    echo 'cd $REMOLL && exec "$@"'                    >> /entrypoint.sh && \
+    chmod +x /entrypoint.sh
 
-ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
+ENTRYPOINT ["/entrypoint.sh"]
 
+CMD ["build/remoll","-h"]

analysis/hyperon/hyperon_pion_rates.C

@@ -0,0 +1,36 @@
+// Run using (for example):
+//   build/reroot -l -q 'analysis/hyperon/hyperon_pion_rates.C("hyperon_lambda_2M.root")'
+
+void hyperon_pion_rates(const TString& files)
+{
+  TChain* T = new TChain("T");
+  T->Add(files);
+
+  std::vector<remollEventParticle_t>* parts = 0;
+  std::vector<remollGenericDetectorHit_t>* hits = 0;
+
+  T->SetBranchAddress("hit", &hits);
+  T->SetBranchAddress("part", &parts);
+
+  TH1F h_hit_r("h_hit_r","Pion hit radius at the main detector plane",20,0,2000);
+
+  // Loop over events
+  for (size_t iev = 0; iev < T->GetEntries(); iev++) {
+    T->GetEntry(iev);
+
+    // Store hits on main detector
+    for (size_t ihit = 0; ihit < hits->size(); ihit++) {
+      remollGenericDetectorHit_t hit = hits->at(ihit);
+      if (hit.det == 28 && hit.pid == -211) {
+        h_hit_r.Fill(hit.r);
+      }
+    }
+    for (size_t ipart = 0; ipart < parts->size(); ipart++) {
+      remollEventParticle_t part = parts->at(ipart);
+    }
+  }
+
+  TCanvas c;
+  h_hit_r.Draw();
+  c.SaveAs("images/hyperon_pion_rates_hit_r.png");
+}

cmake/modules/BuildType.cmake

@@ -1,7 +1,10 @@
 # Set a default build type if none was specified
 set(DEFAULT_CMAKE_BUILD_TYPE "Release")
 if (EXISTS "${CMAKE_SOURCE_DIR}/.git")
-  set(DEFAULT_CMAKE_BUILD_TYPE "Debug")
+  set(DEFAULT_CMAKE_BUILD_TYPE "RelWithDebInfo")
+endif()
+if (EXISTS "${CMAKE_SOURCE_DIR}/.buildtype")
+  file(STRINGS "${CMAKE_SOURCE_DIR}/.buildtype" DEFAULT_CMAKE_BUILD_TYPE)
 endif()
 if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
   message(STATUS "Setting build type to '${DEFAULT_CMAKE_BUILD_TYPE}' as none was specified.")

generators/aniol/.gitignore

@@ -1,6 +1,6 @@
 a.out
 hyperon-gen
 hyperon_decay
+lambda_decay
 
-hyperon_outp.dat
-hyperon_particle_decays.dat
+*.dat

generators/aniol/Makefile

@@ -2,14 +2,14 @@ CC=g++
 CFLAGS=
 LIBS=-lm
 
-EXES=hyperon_decay hyperon-gen
+EXES=hyperon_decay hyperon-gen lambda_decay
 
 all: $(EXES)
 
-%.o: %.c
+%.o: %.c %.h
 	$(CC) -c -o $@ $< $(CFLAGS)
 
-%: %.o
+%: %.o %.h
 	$(CC) -o $@ $^ $(CFLAGS) $(LIBS)
 
 .PHONY: clean

generators/aniol/README.md

@@ -1,12 +1,16 @@
 Note: this directory and included files are obtained from Konrad Aniol's personal page at:
   https://userweb.jlab.org/~aniol/moller/scripts/readme.dat
+
 They represent the code as of 19-Jun-2013 (accessed 16-Jul-2018).
+
+Since the order of output of these codes is strongly correlated with physical parameters
+(in particular position in target), it makes sense to shuffle the data before using it.
 ---
 
 In order to create the code which produces the lambda distribution file (x,y,v,px,py,pz,weight) simply
 compile 
 ```
-g++ hyperon-gen.cpp
+g++ -o hyperon-gen hyperon-gen.cpp
 ```
 
 There is an input file used by hyperon-gen.cpp called hyperon-gen.h. You can set the parameters used in the code here.
@@ -32,7 +36,7 @@ edit lambda_decay.cpp to set the electron helicity, h. This is found in the foll
 ```
 
 ```
-g++ lambda_decay.cpp
+g++ -o lambda_decay lambda_decay.cpp
 ```
 
 The include file, hyperon_decay.h must be adjusted to indicate the desired decay products.