Check for random_seed in user_pars before setting

To allow users to make use of the new <options><randomseed> element wholly from within studio, and to allow parameters.ints("random_seed") to override this behavior, we must allow users to delete the random_seed user_par and then not have that throw an error when running create_cell_types() in the standard custom.cpp. If/when we insist on the random_seed being in its new home, then we can delete these SeedRandom calls entirely. We could add a warning if random_seed is found as a user_parameter that this old syntax is no longer supported. PhysiCell 2.0.0 thing.
Danariki99 · Jun 7, 2024 · 9c49dea · 9c49dea
1 parent e4a8511
commit 9c49dea
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Showing 23 changed files with 90 additions and 23 deletions.
diff --git a/modules/PhysiCell_settings.cpp b/modules/PhysiCell_settings.cpp
@@ -259,9 +259,10 @@ void PhysiCell_Settings::read_from_pugixml( void )
 		}
 
 		pugi::xml_node random_seed_node = xml_find_node(node_options, "random_seed");
-		std::string random_seed = "";
+		std::string random_seed = ""; // default is system clock, even if this element is not present
 		if (random_seed_node)
 		{ random_seed = xml_get_my_string_value(random_seed_node); }
+
 		if (random_seed == "" || random_seed == "random" || random_seed == "system_clock")
 		{
 			std::cout << "Using system clock for random seed" << std::endl;

diff --git a/sample_projects/biorobots/custom_modules/custom.cpp b/sample_projects/biorobots/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/cancer_biorobots/custom_modules/custom.cpp b/sample_projects/cancer_biorobots/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/celltypes3/custom_modules/custom.cpp b/sample_projects/celltypes3/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/heterogeneity/custom_modules/custom.cpp b/sample_projects/heterogeneity/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/interactions/custom_modules/custom.cpp b/sample_projects/interactions/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/mechano/custom_modules/custom.cpp b/sample_projects/mechano/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/physimess/custom_modules/custom.cpp b/sample_projects/physimess/custom_modules/custom.cpp
@@ -72,7 +72,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/pred_prey_farmer/custom_modules/custom.cpp b/sample_projects/pred_prey_farmer/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/rules_sample/custom_modules/custom.cpp b/sample_projects/rules_sample/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/template/custom_modules/custom.cpp b/sample_projects/template/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/virus_macrophage/custom_modules/custom.cpp b/sample_projects/virus_macrophage/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects/worm/custom_modules/custom.cpp b/sample_projects/worm/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects_intracellular/boolean/cancer_invasion/custom_modules/custom.cpp b/sample_projects_intracellular/boolean/cancer_invasion/custom_modules/custom.cpp
@@ -73,7 +73,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/custom_modules/custom.cpp b/sample_projects_intracellular/boolean/physiboss_cell_lines/custom_modules/custom.cpp
@@ -76,7 +76,10 @@ std::vector<bool> nodes;
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects_intracellular/boolean/template_BM/custom_modules/custom.cpp b/sample_projects_intracellular/boolean/template_BM/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects_intracellular/boolean/tutorial/custom_modules/custom.cpp b/sample_projects_intracellular/boolean/tutorial/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects_intracellular/fba/cancer_metabolism/custom_modules/cancer_metabolism.cpp b/sample_projects_intracellular/fba/cancer_metabolism/custom_modules/cancer_metabolism.cpp
@@ -72,7 +72,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/sample_projects_intracellular/ode/ode_energy/custom_modules/custom.cpp b/sample_projects_intracellular/ode/ode_energy/custom_modules/custom.cpp
@@ -78,7 +78,10 @@ extern "C" rrc::RRHandle createRRInstance();
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/unit_tests/custom_DCs_2substrates/custom_modules/custom.cpp b/unit_tests/custom_DCs_2substrates/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/unit_tests/custom_DCs_2substrates/custom_modules/custom_v1.cpp b/unit_tests/custom_DCs_2substrates/custom_modules/custom_v1.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/unit_tests/custom_DCs_2substrates/custom_modules/custom_v2.cpp b/unit_tests/custom_DCs_2substrates/custom_modules/custom_v2.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you 

diff --git a/unit_tests/custom_voxel_values/custom_modules/custom.cpp b/unit_tests/custom_voxel_values/custom_modules/custom.cpp
@@ -70,7 +70,10 @@
 void create_cell_types( void )
 {
 	// set the random seed 
-	SeedRandom( parameters.ints("random_seed") );  
+	if (parameters.ints.find_index("random_seed") != -1)
+	{
+		SeedRandom(parameters.ints("random_seed"));
+	}
 
 	/* 
 	   Put any modifications to default cell definition here if you