update SDF

CMakeLists.txt

@@ -35,7 +35,7 @@ FIND_PACKAGE(Python
 set (LIBDIR     lib)
 set (INCLUDEDIR include)
 set (BINDIR     bin)
-set (PYPATH     ${LIBDIR}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR})
+set (PYPATH     ${LIBDIR}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages)
 message( "PYPATH=${PYPATH}" )
 
 set (DOCDIR share/doc)

Modules/Diffractors/CrystFELPhotonDiffractor/CMakeLists.txt

@@ -18,7 +18,9 @@ MESSAGE("HDF5_VERSION= ${HDF5_VERSION}")
 MESSAGE("HDF5_LIBRARY_DIRS= ${HDF5_LIBRARY_DIRS}")
 
 FIND_PACKAGE (GSL REQUIRED)
-
+find_package(ZLIB)
+include_directories(${ZLIB_INCLUDE_DIRS})
+# TARGET_LINK_LIBRARIES( ${ZLIB_LIBRARIES})
 # This macro invokes the HDF5 compiler wrapper, it parses the output and
 # extracts the path where library are stored.
 # Usage:
@@ -103,6 +105,7 @@ ExternalProject_Add( crystfel
 )
 
 # Install needed crystfel binaries, scripts and doc material.
+ExternalProject_Get_Property(crystfel BINARY_DIR)
 ExternalProject_Get_Property(crystfel SOURCE_DIR)
 ExternalProject_Get_Property(crystfel BINARY_DIR)
 #

Modules/Others/sdf/CMakeLists.txt

@@ -2,7 +2,8 @@ INCLUDE(ExternalProject)
 
 ExternalProject_Add(
 sdf
-GIT_REPOSITORY https://github.com/PaNOSC-ViNYL/SDF.git
+GIT_REPOSITORY https://cfsa-pmw.warwick.ac.uk/SDF/SDF.git
+GIT_TAG 642be14ccae3bc7db53995f3fa8ea831bbbd3c6a
 GIT_SUBMODULES C utilities
-CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
+CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${PYPATH}
 )

README.md

@@ -3,8 +3,8 @@ SimEx
 
 Software platform for **Sim**ulation of advanced photon **Ex**periments.
 
-[![Build Status](https://travis-ci.org/PaNOSC-ViNYL/SimEx.svg?branch=master)](https://travis-ci.org/PaNOSC-ViNYL/SimEx)
-[![Build Status](https://travis-ci.org/PaNOSC-ViNYL/SimEx.svg?branch=develop)](https://travis-ci.org/PaNOSC-ViNYL/SimEx)
+[![Build Status master](https://travis-ci.org/PaNOSC-ViNYL/SimEx.svg?branch=master)](https://travis-ci.org/github/panosc-vinyl/simex/branches)
+[![Build Status develop](https://travis-ci.org/PaNOSC-ViNYL/SimEx.svg?branch=develop)](https://travis-ci.org/github/panosc-vinyl/simex/branches)
 
 
 ## Purpose of SimEx

Sources/python/SimEx/Analysis/DiffractionAnalysis.py

@@ -719,11 +719,13 @@ def photonStatistics(stack):
 
 
     print("*************************")
+    print ("Photon number statistics per pattern"
     print("avg = %6.5e" % (avg_photons))
     print("std = %6.5e" % (rms_photons))
-    print("avg_mean = %6.5e" % (avg_mean))
-    print("avg_max = %6.5e" % (avg_max))
-    print("avg_min = %6.5e" % (avg_min))
+    print ("Photon number statistics per pixel"
+    print("avg_mean_pixel = %6.5e" % (avg_mean))
+    print("avg_max_pixel = %6.5e" % (avg_max))
+    print("avg_min_pixel = %6.5e" % (avg_min))
     print("*************************")
 
 

Tests/python/unittest/SimExTest/Calculators/TNSAIonMatterInteractorTest.py

@@ -48,7 +48,7 @@ def testConstructor(self):
         self.assertIsInstance(interact, AbstractIonInteractor)
 
     def testRun(self):
-        input_file = TestUtilities.generateTestFilePath('00101.sdf')
+        input_file = TestUtilities.generateTestFilePath('0010.sdf')
         mysource = TNSAIonMatterInteractor(parameters=self.params,
                                            input_path=input_file,
                                            output_path='Data/NeutronData.h5')

environment.yml

@@ -21,8 +21,8 @@
 
 name: simex
 channels:
-  - defaults
   - conda-forge
+  - ondateam
 dependencies:
   - Cython
   - cmake>=3.12.1
@@ -46,6 +46,7 @@ dependencies:
   - openpmd-api
   - python>=3.5
   - nomkl
+  - cfelpyutils
   - pip
   - pip:
     - xraydb

install.sh

@@ -8,6 +8,7 @@ usage: $0 MODE
 	MODE includes:
 	conda-env: create conda simex virtual environment
 	conda: install SimEx in current conda environment 
+	conda-develop: install SimEx in current conda environment with DEVELOPER_MODE=ON
 	maxwell
 	develop
 EOF
@@ -55,13 +56,31 @@ then
 	PYLIB=${PYVERSION%.*}
 	DEVELOPER_MODE=ON
 	XCSIT=OFF
+    export ZLIB_ROOT=$CONDA_PREFIX
 	export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
-	#export PYTHONPATH=$CONDA_PREFIX/lib/$PYLIB:$CONDA_PREFIX/lib/$PYLIB/site-packages:$PYTHONPATH
-	#echo "PYTHONPATH="$PYTHONPATH
+	# THIRD_PARTY_ROOT=/gpfs/exfel/data/group/spb-sfx/spb_simulation/simex
+	# export PYTHONPATH=$CONDA_PREFIX/lib/$PYLIB:$CONDA_PREFIX/lib/$PYLIB/site-packages:$PYTHONPATH
+	# echo "PYTHONPATH="$PYTHONPATH
+fi
+
+elif [ $MODE = "conda-develop" ]
+then
+	echo $MODE
+	CONDA_BIN=`which conda`
+	CONDA_BIN=${CONDA_BIN%/*}
+	source ${CONDA_BIN%/*}/etc/profile.d/conda.sh
+	INSTALL_PREFIX=$CONDA_PREFIX
+	PYVERSION=`python -V | tr  '[:upper:]' '[:lower:]' | tr -d ' '`
+	PYLIB=${PYVERSION%.*}
+	DEVELOPER_MODE=ON
+	XCSIT=OFF
+    export ZLIB_ROOT=$CONDA_PREFIX
+	export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
+	# THIRD_PARTY_ROOT=/gpfs/exfel/data/group/spb-sfx/spb_simulation/simex
+	# export PYTHONPATH=$CONDA_PREFIX/lib/$PYLIB:$CONDA_PREFIX/lib/$PYLIB/site-packages:$PYTHONPATH
+	# echo "PYTHONPATH="$PYTHONPATH
 fi
 
-XCSIT=ON
-THIRD_PARTY_ROOT=/gpfs/exfel/data/group/spb-sfx/spb_simulation/simex
 
 # Check for existing build directory, remove if found
 if [ -d build ]
@@ -109,15 +128,20 @@ cmake -DSRW_OPTIMIZED=ON \
       -DBOOST_ROOT=$BOOST_ROOT \
       ..
 # Build the project.
-make -j32
+make  -j32
 
 # Install the project.
 make install
 
+# Back to root dir.
 cd ..
 
-# Revert
-git checkout -- CMakeLists.txt
+# make and make install should be exec'ed not in this script (crystfel fails to compile).
+if [ $MODE = "conda" ] || [ $MODE = "conda-env " ]
+then
+    echo "In case of error in compiling crystfel, rerun make in the build dir."
+fi
+
 if [ $MODE = "develop" ]; then
 	echo "Please run 'source build/simex_vars.sh' before developing"
 fi

requirements.txt

@@ -11,6 +11,7 @@ openpmd-api
 periodictable>=1.4.1
 pint
 py3nvml
+cfelpyutils
 pyFAI<=0.16
 pyfftw
 scipy==1.3.1