Merge pull request #203 from drbergman/feature-probability-dists-for-…

…initial-cell-behavior

Setting initial behaviors from config-defined distributions

modules/PhysiCell_geometry.cpp

@@ -336,6 +336,321 @@ bool load_cells_from_pugixml( pugi::xml_node root )
 bool load_cells_from_pugixml( void )
 { return load_cells_from_pugixml( physicell_config_root ); }
 
+
+void set_parameters_from_distributions( const pugi::xml_node root )
+{
+	// find the start of cell definitions 
+	pugi::xml_node node = root.child( "cell_definitions" ); 
+
+	// find the first cell definition 
+	node = node.child( "cell_definition" ); 
+
+	std::string celltype;
+	Cell_Definition *pCD;
+	while (node)
+	{
+		pugi::xml_node node_ipd = node.child("initial_parameter_distributions");
+		if (node_ipd && (node_ipd.attribute("enabled").empty() || node_ipd.attribute("enabled").as_bool()))
+		{
+			celltype = node.attribute("name").as_string();
+			pCD = find_cell_definition(celltype);
+			set_distributed_parameters(node_ipd, pCD);
+		}
+		node = node.next_sibling("cell_definition");
+	}
+	return;
+}
+
+void set_distributed_parameters(const pugi::xml_node node_ipd, Cell_Definition *pCD)
+{
+	pugi::xml_node node_dist = node_ipd.child("distribution");
+	while (node_dist)
+	{
+		if (node_dist.attribute("enabled").empty() || node_dist.attribute("enabled").as_bool()) // if enabled attribute is missing or true, set the distribution (I put this here rather than in the function because the logic is clearer this way without negations)
+		{
+			set_distributed_parameter(node_dist, pCD);
+		}
+		node_dist = node_dist.next_sibling("distribution");
+	}
+	return;
+}
+
+void set_distributed_parameter(pugi::xml_node node_dist, Cell_Definition *pCD)
+{
+	static std::vector<std::string> supported_distributions = {"Uniform","LogUniform","Normal","LogNormal","Log10Normal"};
+	std::string type = node_dist.attribute("type").as_string();
+	std::string behavior = xml_get_string_value(node_dist, "behavior");
+	if (!is_in(type, supported_distributions))
+	{
+		std::cout << "ERROR: Only supporting these distributions:" << std::endl
+				  << "\t\t" << supported_distributions << std::endl
+				  << "\tBut " << behavior << " for " << pCD->name << " using " << type << "." << std::endl;
+		exit(-1);
+	}
+
+	if (!strcmpi(behavior,"volume") && find_behavior_index(behavior) == -1)
+	{
+		std::cout << "ERROR: Initial parameter distributions can only be set for volume and cell behaviors." << std::endl
+				  << "\t" << behavior << " is not among these." << std::endl;
+		exit(-1);
+	}
+	set_distributed_parameter(pCD, behavior, type, node_dist);
+	return;
+}
+
+bool is_in(const std::string x, const std::vector<std::string> A)
+{
+	// checks if x is in A
+	for (unsigned int i = 0; i < A.size(); i++)
+	{
+		if (strcmpi(x, A[i]))
+		{ return true; }
+	}
+	return false;
+}
+
+void set_distributed_parameter(Cell_Definition *pCD, std::string behavior, std::string type, pugi::xml_node node_dist)
+{
+	double base_value;
+	if (strcmpi(behavior, "volume"))
+	{
+		base_value = pCD->phenotype.volume.total;
+	}
+	else
+	{
+		base_value = get_single_base_behavior(pCD, behavior);
+	}
+	bool check_base = node_dist.attribute("check_base").empty() || node_dist.attribute("check_base").as_bool(); // if check_base not provided, default to true
+	if (strcmpi(type,"uniform"))
+	{
+		double min = xml_get_double_value(node_dist, "min");
+		double max = xml_get_double_value(node_dist, "max");
+		if (check_base && (base_value < min || base_value > max))
+		{
+			std::cout << "ERROR: The base value for " << behavior << " in " << pCD->name << " is " << base_value << std::endl
+					  << "\tThis value is outside the range of the uniform distribution." << std::endl
+					  << "\tmin = " << min << ", max = " << max << "." << std::endl
+					  << "\tIf you want to allow the base value to be outside the range, set check_base to false." << std::endl;
+			exit(-1);
+		}
+		double dv = max - min;
+		if (dv < 0)
+		{
+			std::cout << "ERROR: The min and max values for " << behavior << " in " << pCD->name << " do not satisfy min <= max." << std::endl
+					  << "\tmin = " << min << ", max = " << max << std::endl;
+			exit(-1);
+		}
+		for (unsigned int i = 0; i < (*all_cells).size(); i++)
+		{
+			if ((*all_cells)[i]->type_name != pCD->name)
+			{
+				continue;
+			}
+			double val = min + dv * UniformRandom();
+			set_distributed_parameter((*all_cells)[i], behavior, val);
+		}
+	}
+	else if (strcmpi(type,"loguniform"))
+	{
+		double min = xml_get_double_value(node_dist, "min");
+		if (min <= 0)
+		{
+			std::cout << "ERROR: The log uniform distirbution must be defined on a positive interval." << std::endl
+					  << "\tThe min value for " << behavior << " in " << pCD->name << " is " << min << std::endl
+					  << "\tSet the min and max as the bounds on the value you want, not the bounds on the exponent." << std::endl
+					  << "\tFor example, if you want a value between 0.1 and 10, set min=0.1 and max=10, not min=-1 and max=1." << std::endl;
+			exit(-1);
+		}
+		double max = xml_get_double_value(node_dist, "max");
+		if (check_base && (base_value < min || base_value > max))
+		{
+			std::cout << "ERROR: The base value for " << behavior << " in " << pCD->name << " is " << base_value << std::endl
+					  << "\tThis value is outside the range of the loguniform distribution." << std::endl
+					  << "\tmin = " << min << ", max = " << max << "." << std::endl
+					  << "\tIf you want to allow the base value to be outside the range, set check_base to false." << std::endl;
+			exit(-1);
+		}
+		min = log(min);
+		max = log(max);
+		double dv = max - min;
+		if (dv < 0)
+		{
+			std::cout << "ERROR: The min and max values for " << behavior << " in " << pCD->name << " do not satisfy min <= max." << std::endl
+					  << "\tmin = " << min << ", max = " << max << std::endl;
+			exit(-1);
+		}
+		for (unsigned int i = 0; i < (*all_cells).size(); i++)
+		{
+			if ((*all_cells)[i]->type_name != pCD->name)
+			{
+				continue;
+			}
+			double val = exp(min + dv * UniformRandom());
+			set_distributed_parameter((*all_cells)[i], behavior, val);
+		}
+	}
+	else if (strcmpi(type,"normal"))
+	{
+		double mu = xml_get_double_value(node_dist, "mu");
+		double sigma = xml_get_double_value(node_dist, "sigma");
+		double lb = -9e99;
+		double ub = 9e99;
+		if (node_dist.child("lower_bound"))
+		{ lb = xml_get_double_value(node_dist, "lower_bound"); }
+		if (node_dist.child("upper_bound"))
+		{ ub = xml_get_double_value(node_dist, "upper_bound"); }
+		if (lb > ub)
+		{
+			std::cout << "ERROR: The lower and upper bounds for " << behavior << " in " << pCD->name << " do not satisfy lb <= ub." << std::endl
+					  << "\tlb = " << lb << ", ub = " << ub << std::endl;
+			exit(-1);
+		}
+		if (check_base && (base_value < lb || base_value > ub))
+		{
+			std::cout << "ERROR: The base value for " << behavior << " in " << pCD->name << " is " << base_value << std::endl
+					  << "\tThis value is outside the range of the truncated normal distribution." << std::endl
+					  << "\tExpecting values between " << lb << " and " << ub << "." << std::endl
+					  << "\tIf you want to allow the base value to be outside the range, set check_base to false." << std::endl;
+			exit(-1);
+		}
+		print_drawing_expectations(mu, sigma, lb, ub, (*all_cells).size());
+		for (unsigned int i = 0; i < (*all_cells).size(); i++)
+		{
+			if ((*all_cells)[i]->type_name != pCD->name)
+			{
+				continue;
+			}
+			double val=lb;
+			while (val<=lb || val>=ub)
+			{ val = NormalRandom(mu, sigma); }
+			set_distributed_parameter((*all_cells)[i], behavior, val);
+		}
+	}
+	else if (strcmpi(type,"lognormal"))
+	{
+		double mu = xml_get_double_value(node_dist, "mu");
+		double sigma = xml_get_double_value(node_dist, "sigma");
+		double lb = 0;
+		double ub = 9e99;
+		get_log_normal_bounds(node_dist, behavior, pCD, lb, ub, base_value, check_base);
+		print_drawing_expectations(mu, sigma, log(lb), log(ub), (*all_cells).size());
+		for (unsigned int i = 0; i < (*all_cells).size(); i++)
+		{
+			if ((*all_cells)[i]->type_name != pCD->name)
+			{
+				continue;
+			}
+			double val=lb;
+			while (val<=lb || val>=ub)
+			{ val = exp(NormalRandom(mu, sigma)); }
+			set_distributed_parameter((*all_cells)[i], behavior, val);
+		}
+	}
+	else if (strcmpi(type,"log10normal"))
+	{
+		static double log10_ = log(10.0);
+		double mu = xml_get_double_value(node_dist, "mu");
+		double sigma = xml_get_double_value(node_dist, "sigma");
+		double lb = -9e99;
+		double ub = 9e99;
+		get_log_normal_bounds(node_dist, behavior, pCD, lb, ub, base_value, check_base);
+		print_drawing_expectations(mu, sigma, log(lb), log(ub), (*all_cells).size());
+		for (unsigned int i = 0; i < (*all_cells).size(); i++)
+		{
+			if ((*all_cells)[i]->type_name != pCD->name)
+			{
+				continue;
+			}
+			double val=lb;
+			while (val<=lb || val>=ub)
+			{ val = exp(log10_ * NormalRandom(mu, sigma)); }
+			set_distributed_parameter((*all_cells)[i], behavior, val);
+		}
+	}
+	return;
+}
+
+void get_log_normal_bounds(pugi::xml_node node_dist, std::string behavior, Cell_Definition *pCD, double &lb, double &ub, double base_value, bool check_base)
+{
+	if (node_dist.child("lower_bound"))
+	{
+		lb = xml_get_double_value(node_dist, "lower_bound");
+		if (lb < 0)
+		{
+			std::cout << "ERROR: The lower bound for a lognormal/log10normal distribution only matters if it is non-negative." << std::endl
+					  << "\tThe lower bound for " << behavior << " in " << pCD->name << " is " << lb << "." << std::endl
+					  << "\tThe lower bound is for the actual assigned value while the mean and standard deviation are for the log/log10 of the value." << std::endl
+					  << "\tSince this seems to imply (understandable!) confusion about the lognormal/log10normal distribution, I'm going to exit." << std::endl;
+			exit(-1);
+		}
+	}
+	if (node_dist.child("upper_bound"))
+	{
+		ub = xml_get_double_value(node_dist, "upper_bound");
+	}
+	if (lb > ub)
+	{
+		std::cout << "ERROR: The lower and upper bounds for " << behavior << " in " << pCD->name << " do not satisfy lb <= ub." << std::endl
+				  << "\tlb = " << lb << ", ub = " << ub << std::endl;
+		exit(-1);
+	}
+	if (check_base && (base_value < lb || base_value > ub))
+	{
+		std::cout << "ERROR: The base value for " << behavior << " in " << pCD->name << " is " << base_value << std::endl
+				  << "\tThis value is outside the range of the lognormal/log10normal distribution." << std::endl
+				  << "\tExpecting values between " << lb << " and " << ub << "." << std::endl
+				  << "\tIf you want to allow the base value to be outside the range, set check_base to false." << std::endl;
+		exit(-1);
+	}
+}
+
+void print_drawing_expectations(double mu, double sigma, double lb, double ub, int n)
+{
+	// calculate the z-scores for lb and ub
+    double z_lb = (lb - mu) / sigma;
+    double z_ub = (ub - mu) / sigma;
+
+    // calculate the probabilities for lb and ub
+    double p_lb = 0.5 * (1 + std::erf(z_lb / std::sqrt(2)));
+    double p_ub = 0.5 * (1 + std::erf(z_ub / std::sqrt(2)));
+
+    // the probability of finding a value between lb and ub is the difference between the probabilities for ub and lb
+    double success_probability = p_ub - p_lb;
+	double num_expected = n / success_probability;
+
+	std::cout << "Drawing up to " << n << " values from a normal distribution with mu=" << mu << " and sigma=" << sigma << std::endl
+			  << "\tExpecting values between " << lb << " and " << ub << std::endl
+			  << "\tIt will take about " << num_expected << " draws to get " << n << " values in the range." << std::endl
+			  << "\tIf one draw takes 1 microsecond, this will take about " << num_expected * 1e-6 / 60 << " minutes." << std::endl;
+}
+
+void set_distributed_parameter(Cell* pCell, std::string behavior, double val)
+{
+	if (strcmpi(behavior, "volume"))
+	{
+		pCell->set_total_volume(val);
+	}
+	else
+	{
+		set_single_behavior(pCell, behavior, val);
+	}
+}
+
+bool strcmpi(std::string x, std::string y)
+{
+	// case-Insensitive compare strings
+	for (auto& a : x) {
+        a = tolower(a);
+    }
+	for (auto& a : y) {
+        a = tolower(a);
+    }
+	return x==y;
+}
+
+void set_parameters_from_distributions( void )
+{ return set_parameters_from_distributions( physicell_config_root ); }
+
 std::vector<std::string> split_csv_labels( std::string labels_line )
 {
 	std::vector< std::string > label_tokens; 

modules/PhysiCell_geometry.h

@@ -96,7 +96,20 @@ void load_cells_mat( std::string filename );
 void load_cells_physicell( std::string filename ); 
 
 bool load_cells_from_pugixml( pugi::xml_node root ); 
-bool load_cells_from_pugixml( void ); // load cells based on default config XML root 
+bool load_cells_from_pugixml( void ); // load cells based on default config XML root
+
+void set_parameters_from_distributions( const pugi::xml_node root );
+void set_parameters_from_distributions(void);
+void set_distributed_parameters(pugi::xml_node node, Cell_Definition *pCD);
+void set_distributed_parameter(pugi::xml_node node_dist, Cell_Definition *pCD);
+void set_distributed_parameter(Cell_Definition *pCD, std::string behavior, std::string type, pugi::xml_node node_dist);
+
+void get_log_normal_bounds(pugi::xml_node node_dist, std::string behavior, Cell_Definition *pCD, double &lb, double &ub, double base_value, bool check_base);
+void set_distributed_parameter(Cell* pCell, std::string behavior, double val);
+void print_drawing_expectations(double mu, double sigma, double lb, double ub, int n);
+
+bool is_in(std::string x, std::vector<std::string> A);
+bool strcmpi(std::string x, std::string y);
 
 //	
 // 2D functions 

sample_projects/template/config/PhysiCell_settings.xml

@@ -319,6 +319,21 @@
 			<custom_data>  
 				<sample units="dimensionless" conserved="false">1.0</sample>
 			</custom_data>
+
+			<initial_parameter_distributions enabled="false">
+				<distribution enabled="false" type="Log10Normal" check_base="true">
+					<behavior>Volume</behavior> 
+					<mu>4</mu>
+					<sigma>2</sigma>
+					<upper_bound>100000</upper_bound>
+				</distribution>
+				<distribution enabled="false" type="LogUniform" check_base="true">
+					<behavior>apoptosis</behavior>
+					<min>1e-6</min>
+					<max>1e-2</max>
+				</distribution>
+			</initial_parameter_distributions>
+
 		</cell_definition>
 	</cell_definitions>
 

sample_projects/template/custom_modules/custom.cpp

@@ -192,7 +192,8 @@ void setup_tissue( void )
 	std::cout << std::endl; 
 
 	// load cells from your CSV file (if enabled)
-	load_cells_from_pugixml(); 	
+	load_cells_from_pugixml();
+	set_parameters_from_distributions();
 
 	return; 
 }