From 3a28d0595dbe963b562f63554ae61f9a757d61e7 Mon Sep 17 00:00:00 2001
From: jpmetzca <johnmetzcar@gmail.com>
Date: Tue, 4 Jun 2024 11:24:28 -0400
Subject: [PATCH] updated code to use the PhysiCell random number generator
 ONLY. previously, some functions used BioFVM random number generator.
 Hopefully I got them all. Also updated the gitignore.

---
 .gitignore                                   | 66 ++++++++++++++++++++
 config/leader_follower_model.xml             |  1 +
 custom_modules/AMIGOS-invasion_uncoupled.cpp |  2 +-
 custom_modules/fibrosis.cpp                  |  2 +-
 main-ecm.cpp                                 |  6 +-
 5 files changed, 72 insertions(+), 5 deletions(-)

diff --git a/.gitignore b/.gitignore
index 079ae21..19e4162 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,6 +22,72 @@ out*.txt
 final*.txt
 initial*.txt
 
+output/*.xml
+output/*.csv
+output/*.html
+output/*.txt
+!output/empty.txt
+output/detailed_rules.html
+output/detailed_rules.txt
+output/dictionaries.txt
+output/rules.html
+output/rules.txt
+
+fibrosis_test/*.xml
+fibrosis_test/*.csv
+fibrosis_test/*.html
+fibrosis_test/*.txt
+!fibrosis_test/empty.txt
+fibrosis_test/detailed_rules.html
+fibrosis_test/detailed_rules.txt
+fibrosis_test/dictionaries.txt
+fibrosis_test/rules.html
+fibrosis_test/rules.txt
+fibrosis_test/*.py
+fibrosis
+
+invasive_carcinoma_output/*.xml
+invasive_carcinoma_output/*.csv
+invasive_carcinoma_output/*.html
+invasive_carcinoma_output/*.txt
+!invasive_carcinoma_output/empty.txt
+invasive_carcinoma_output/detailed_rules.html
+invasive_carcinoma_output/detailed_rules.txt
+invasive_carcinoma_output/dictionaries.txt
+invasive_carcinoma_output/rules.html
+invasive_carcinoma_output/rules.txt
+invasive_carcinoma/*.py
+invasive_carcinoma
+
+leader_follower/*.xml
+leader_follower/*.csv
+leader_follower/*.html
+leader_follower/*.txt
+!leader_follower/empty.txt
+leader_follower/detailed_rules.html
+leader_follower/detailed_rules.txt
+leader_follower/dictionaries.txt
+leader_follower/rules.html
+leader_follower/rules.txt
+leader_follower/*.py
+
+simple_test0/
+simple_test1/
+simple_test2/PhysiCell_settings.xml
+simple_test2/cell_rules.csv
+simple_test2/detailed_rules.html
+simple_test2/detailed_rules.txt
+simple_test2/dictionaries.txt
+simple_test2/rules.html
+simple_test2/rules.txt
+simple_test2/simple_test2_random_1_D_circles.xml
+simple_test2/simple_test_movies_cells_only.py
+simple_test2/simple_test_stills_cells_and_environment_only.py
+simple_test3/
+simple_test4/
+
+stochastic_replicates/
+
 # Development
 *.xcworkspace
 .vscode*
diff --git a/config/leader_follower_model.xml b/config/leader_follower_model.xml
index 61723de..0451a63 100644
--- a/config/leader_follower_model.xml
+++ b/config/leader_follower_model.xml
@@ -415,5 +415,6 @@
         <march_unit_test_setup type="int" units="" description="Testing set up: 1 for cell march, 0 for typical simulation">0</march_unit_test_setup>
         <visual_guideline_pattern type="string" units="" description="Specifies pattern of line overlay: none, horizontal lines, vertical lines, or concentric circles">none</visual_guideline_pattern>
         <enable_ecm_outputs type="bool" units="" description="">true</enable_ecm_outputs>
+        <random_seed type="int" units="" description="">0</random_seed>
     </user_parameters>
 </PhysiCell_settings>
\ No newline at end of file
diff --git a/custom_modules/AMIGOS-invasion_uncoupled.cpp b/custom_modules/AMIGOS-invasion_uncoupled.cpp
index 42d7d82..b43b905 100755
--- a/custom_modules/AMIGOS-invasion_uncoupled.cpp
+++ b/custom_modules/AMIGOS-invasion_uncoupled.cpp
@@ -305,7 +305,7 @@ void setup_extracellular_matrix( void )
 		// For random 2-D initalization 
 		if(parameters.strings( "ECM_orientation_setup") == "random")
 		{
-			double theta = 6.2831853071795864769252867665590 * uniform_random(); 
+			double theta = 6.2831853071795864769252867665590 * UniformRandom(); 
 			ecm.ecm_voxels[n].ecm_fiber_alignment = {cos(theta), sin(theta), 0.0};
 		}
 		// for starburst initialization 
diff --git a/custom_modules/fibrosis.cpp b/custom_modules/fibrosis.cpp
index 3068688..80eb7a8 100755
--- a/custom_modules/fibrosis.cpp
+++ b/custom_modules/fibrosis.cpp
@@ -405,7 +405,7 @@ void alter_cell_uptake_secretion_saturation ( void )
 void setup_tissue( void )
 {	
 	// Setting seed so cells always start with same initial configuration
-	SeedRandom(0);
+	SeedRandom(parameters.ints("random_seed"));
 	static Cell_Definition* fibroblast = find_cell_definition("fibroblast");	
 	static Cell_Definition* dead_cell = find_cell_definition("dead cell");	
 	static Cell_Definition* macrophage = find_cell_definition("macrophage");
diff --git a/main-ecm.cpp b/main-ecm.cpp
index a02491e..e39eac3 100644
--- a/main-ecm.cpp
+++ b/main-ecm.cpp
@@ -153,9 +153,9 @@ int main( int argc, char* argv[] )
 	omp_set_num_threads(PhysiCell_settings.omp_num_threads);
 	
 	// PNRG setup 
-	SeedRandom(0);  //rwh do here, just once
-	// if( parameters.ints("unit_test_setup") == 1) 
-	// {SeedRandom(0);}
+	SeedRandom(parameters.ints("random_seed"));  //rwh do here, just once
+	if( parameters.ints("unit_test_setup") == 1) 
+		{SeedRandom(0);}
 
 	
 	// time setup