Refactored code and optimized inputs

Params_template.yml

@@ -5,28 +5,28 @@ sim_type: "SimSET"        # SimSET, STIR or GATE (only SimSET working)
 # Run parameters
 do_simulation: 1          # Set to 0 to reconstruction previous simulation
 do_reconstruction: 1      # Set to 0 to generate adq data only
-divisions: 8              # Number os subprocesses for parallel simulation
+divisions: 6              # Number os subprocesses for parallel simulation
 
 
 # PET system
-scanner: "Vereos" # Scanner Model (Vereos, Siemens_mCT, Discovery_ST, Discovery_STE, GE_Advance)
-model_type: "simple_pet" # SimSET Model (simple_pet, cylindrical)
+scanner: "Discovery_ST" # Scanner Model (Vereos, Siemens_mCT, Discovery_ST, Discovery_STE, GE_Advance)
+model_type: "cylindrical" # SimSET Model (simple_pet, cylindrical)
 
 
 # Input and output directories
-patient_dirname: "example_input_dir"   # Name of the directory in Data where phantoms are located
-output_dir: "example_output_dir"       # Name of the Results Dir
+patient_dirname: "test_brain_FDG"   # Name of the directory in Data where phantoms are located
+output_dir: "test_brain"       # Name of the Results Dir
 
 
 # Variables needed for single simulation
-act_map: "example_act.hdr"    # Activity map name 
-att_map: "example_att.hdr"    # Attenuation map name
-center_slice:  153      # The slice number to be placed on the center of the scanner. If 0, automatically, the middle slice will be used
+act_map: "S1_actMap.nii"    # Activity map name
+att_map: "S1_attMap.nii"    # Attenuation map name
+center_slice: 153      # The slice number to be placed on the center of the scanner. If 0, automatically, the middle slice will be used
 
 
 # Variables needed for whole_body simulation
-z_min: 75               # Only for wholebody simulations (start of the acquisition, slice)
-z_max: 316              # Only for wholebody simulations (end of the acquisition, slice). 
+z_min: 283               # Only for wholebody simulations (start of the acquisition, slice)
+z_max: 584              # Only for wholebody simulations (end of the acquisition, slice).
 # We calculate the number of beeds based on (z_max - z_min) and the scanner FOV.
 
 

Params_test.yml

@@ -21,7 +21,7 @@ output_dir: "Test"            # Name of the Results Dir
 # Variables needed for single simulation
 act_map: "act.hdr"
 att_map: "att.hdr"
-center_slice:  7      # The slice number to be placed on the center of the scanner. If 0, automatically, the half of the slices will be calculated and used
+center_slice: 7      # The slice number to be placed on the center of the scanner. If 0, automatically, the half of the slices will be calculated and used
 
 
 # Variables needed for whole_body simulation

config.yml

@@ -1,8 +1,8 @@
 # Directories to the necesary binaries
-dir_stir:  "/home/jesus/simpet/include/STIR/install"
-dir_simset:  "/home/jesus/simpet/include/SimSET/2.9.2"
-matlab_mcr_path:  "/media/usuario3/HDD/SPM_standalone/MCR/v713"
-spm_path:  "/media/usuario3/HDD/SPM_standalone/spm12"
+dir_stir: "/mnt/c/Users/jesus/Work/repos/simpet/include/STIR/install"
+dir_simset: "/mnt/c/Users/jesus/Work/repos/simpet/include/SimSET"
+matlab_mcr_path: "/media/usuario3/HDD/SPM_standalone/MCR/v713"
+spm_path: "/media/usuario3/HDD/SPM_standalone/spm12"
 dir_data_path: ""
 dir_results_path: ""
 
@@ -14,7 +14,7 @@ stratification: "true"
 forced_detection: "true"
 forced_non_absortion: "true"
 acceptance_angle: 90.0
-positron_range:  "true"
+positron_range: "true"
 non_colinearity: "true"
 minimum_energy: 350.0
 weight_window_ratio: 1.0

setup.py

@@ -3,9 +3,9 @@
 Don't run this script if you think all the needed dependencies are already fulfilled.
 """
 import os
-from os.path import join, basename, exists
 import shutil
 from multiprocessing import cpu_count
+from os.path import join, exists
 
 
 def rsystem(command):
@@ -44,7 +44,6 @@ def install_simset(simset_dir, log_file):
 
     os.chdir(simset_dir)
 
-
     makefile = join(simset_dir, 'make.files', 'simset.make')
     newmakefile = join(simset_dir, 'make.files', 'simset.make.new')
 
@@ -216,15 +215,15 @@ def verify_test_simulation(simpet_dir):
     import numpy as np
 
     results_dir = join(simpet_dir, 'Results', 'Test', 'SimSET_Sim_Discovery_ST', 'division_0')
-    
+
     checks = ['trues.hdr', 'scatter.hdr', 'randoms.hdr']
 
     for i in checks:
         file_ = join(results_dir, i)
         if exists(file_):
             img_d = nib.load(file_).get_fdata()
             counts = np.sum(img_d)
-            print("Counts in %s: %s" % (i,counts))
+            print("Counts in %s: %s" % (i, counts))
 
         else:
             raise Exception('Failed to build %s' % i)
@@ -239,6 +238,7 @@ def verify_test_simulation(simpet_dir):
         else:
             raise Exception('Failed to reconstruct %s' % i)
 
+
 # Setup run lines
 simpet_dir = os.getcwd()
 log_file = join(simpet_dir, 'log_setup.txt')
@@ -250,7 +250,6 @@ def verify_test_simulation(simpet_dir):
     os.makedirs(dest_dir)
 os.chdir(dest_dir)
 
-
 simset_dir = join(dest_dir, "SimSET")
 install_simset(simset_dir, log_file)
 verify_simset_install(simset_dir)
@@ -273,5 +272,5 @@ def verify_test_simulation(simpet_dir):
 
 verify_test_simulation(simpet_dir)
 
-print("\nNice! It seems that we are good to go. Consider adding the lines in simpet_paths.sh to your .bashrc. Enjoy SimPET!.")
-
+print(
+    "\nNice! It seems that we are good to go. Consider adding the lines in simpet_paths.sh to your .bashrc. Enjoy SimPET!.")