Updated setup.py to use STIR 5.2 directly. No need for the custom ver…

…sion at the moment

setup.py

@@ -100,11 +100,13 @@ def install_stir(stir_dir, simset_dir, log_file):
     os.makedirs(install_dir)
     os.chdir(stir_dir)
     print("Cloning the SimSET input branch from STIR repo...")
-    icom = 'git clone --single-branch --branch simset_input https://github.com/txusser/STIR.git'
+    icom = 'wget https://github.com/UCL/STIR/archive/refs/tags/rel_5.2.0.zip'
+    rsystem(icom)
+    icom = 'unzip rel_5.2.0.zip'
     rsystem(icom)
 
     os.chdir(build_dir)
-    rsystem('cmake ../STIR/')
+    rsystem('cmake ../STIR-rel_5.2.0/')
 
     makefile = join(build_dir, 'CMakeCache.txt')
     newmakefile = join(stir_dir, 'build', 'new_CMakeCache.txt')
@@ -131,9 +133,9 @@ def install_stir(stir_dir, simset_dir, log_file):
     f_new.close()
 
     shutil.move(newmakefile, makefile)
-    rsystem('cmake ../STIR/')
+    rsystem('cmake ../STIR-rel_5.2.0/')
 
-    print('Building STIR....')
+    print('Building STIR with %s cores....' % cpu_count())
     icom = 'make -s -j%s & make install' % str(cpu_count())
     rsystem(icom)
 
@@ -266,7 +268,7 @@ def verify_test_simulation(simpet_dir):
 
 import simpet
 
-test = simpet.SimPET('Params_test.yml')
+test = simpet.wholebody_simulation('Params_test.yml')
 test.run()
 
 verify_test_simulation(simpet_dir)

setup.sh

@@ -1,15 +1,21 @@
-#! /usr/bin/bash
 
-export PATH=$PWD/include/fruitcake/bin:$PATH
-export LD_LIBRARY_PATH=$PWD/include/fruitcake/book/lib:$LD_LIBRARY_PATH
-export PATH=$PWD/include/format_converters:$PATH
 
 sudo apt update -y && sudo apt upgrade -y -q
 
-sudo apt install unzip libboost-dev libboost-all-dev libpcre3 libpcre3-dev libncurses-dev cmake swig -y -q
+sudo apt install gcc g++ make  cmake cmake-curses-gui libx11-dev libpng-dev tcsh -y -q
+
+sudo apt install python python-dev python-numpy ipython python-matplotlib mayavi2 -y -q
+
+sudo apt install mpi-default-dev mpi-default-bin libinsighttoolkit4-dev libtiff5-dev -y -q
+
+sudo apt install unzip libboost-dev libboost-all-dev libpcre3 libpcre3-dev libncurses-dev swig -y -q
 
 sudo apt install python3 python3-pip python3-ipython python3-numpy python3-scipy python3-nibabel python3-matplotlib python3-pandas -y -q
 
 pip3 install -U PyYAML nilearn nipype
 
+export PATH=$PWD/include/fruitcake/bin:$PATH
+export LD_LIBRARY_PATH=$PWD/include/fruitcake/book/lib:$LD_LIBRARY_PATH
+export PATH=$PWD/include/format_converters:$PATH
+
 python3 setup.py