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Merge pull request #250 from drbergman/feature-check-duplicates
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Throw error if duplicate substrate or parameter
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@MathCancer
MathCancer authored Aug 16, 2024
2 parents e2ddf2a + 8f19f0b commit b1b9314
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Showing 3 changed files with 46 additions and 216 deletions.
136 changes: 7 additions & 129 deletions BioFVM/BioFVM_microenvironment.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -475,146 +475,24 @@ void Microenvironment::add_density( void )
{
// fix in PhysiCell preview November 2017
// default_microenvironment_options.use_oxygen_as_first_field = false;

// update 1, 0
zero.push_back( 0.0 );
one.push_back( 1.0 );

// update units
density_names.push_back( "unnamed" );
density_units.push_back( "none" );

// update coefficients
diffusion_coefficients.push_back( 0.0 );
decay_rates.push_back( 0.0 );

// update sources and such
for( unsigned int i=0; i < temporary_density_vectors1.size() ; i++ )
{
temporary_density_vectors1[i].push_back( 0.0 );
temporary_density_vectors2[i].push_back( 0.0 );
}

// resize the gradient data structures
for( unsigned int k=0 ; k < mesh.voxels.size() ; k++ )
{
gradient_vectors[k].resize( number_of_densities() );
for( unsigned int i=0 ; i < number_of_densities() ; i++ )
{
(gradient_vectors[k])[i].resize( 3, 0.0 );
}
}

gradient_vector_computed.resize( mesh.voxels.size() , false );

one_half = one;
one_half *= 0.5;

one_third = one;
one_third /= 3.0;

dirichlet_value_vectors.assign( mesh.voxels.size(), one );
dirichlet_activation_vector.push_back( true );
dirichlet_activation_vectors.assign( mesh.voxels.size(), dirichlet_activation_vector );

// Fixes in PhysiCell preview November 2017
default_microenvironment_options.Dirichlet_condition_vector.push_back( 1.0 ); // = one;
default_microenvironment_options.Dirichlet_activation_vector.push_back( false );

default_microenvironment_options.initial_condition_vector.push_back( 1.0 );

default_microenvironment_options.Dirichlet_all.push_back( true );
// default_microenvironment_options.Dirichlet_interior.push_back( true );
default_microenvironment_options.Dirichlet_xmin.push_back( false );
default_microenvironment_options.Dirichlet_xmax.push_back( false );
default_microenvironment_options.Dirichlet_ymin.push_back( false );
default_microenvironment_options.Dirichlet_ymax.push_back( false );
default_microenvironment_options.Dirichlet_zmin.push_back( false );
default_microenvironment_options.Dirichlet_zmax.push_back( false );

default_microenvironment_options.Dirichlet_xmin_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_xmax_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_ymin_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_ymax_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_zmin_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_zmax_values.push_back( 1.0 );

return;
return add_density( "unnamed" , "none" );
}

void Microenvironment::add_density( std::string name , std::string units )
{
// fix in PhysiCell preview November 2017
// default_microenvironment_options.use_oxygen_as_first_field = false;

// update 1, 0
zero.push_back( 0.0 );
one.push_back( 1.0 );

// update units
density_names.push_back( name );
density_units.push_back( units );

// update coefficients
diffusion_coefficients.push_back( 0.0 );
decay_rates.push_back( 0.0 );

// update sources and such
for( unsigned int i=0; i < temporary_density_vectors1.size() ; i++ )
{
temporary_density_vectors1[i].push_back( 0.0 );
temporary_density_vectors2[i].push_back( 0.0 );
}

// resize the gradient data structures,
for( unsigned int k=0 ; k < mesh.voxels.size() ; k++ )
{
gradient_vectors[k].resize( number_of_densities() );
for( unsigned int i=0 ; i < number_of_densities() ; i++ )
{
(gradient_vectors[k])[i].resize( 3, 0.0 );
}
}
gradient_vector_computed.resize( mesh.voxels.size() , false );

one_half = one;
one_half *= 0.5;

one_third = one;
one_third /= 3.0;

dirichlet_value_vectors.assign( mesh.voxels.size(), one );
dirichlet_activation_vector.push_back( false );
dirichlet_activation_vectors.assign( mesh.voxels.size(), dirichlet_activation_vector );

// fix in PhysiCell preview November 2017
default_microenvironment_options.Dirichlet_condition_vector.push_back( 1.0 ); // = one;
default_microenvironment_options.Dirichlet_activation_vector.push_back( false ); // assign( number_of_densities(), false );

default_microenvironment_options.Dirichlet_all.push_back( false );
default_microenvironment_options.Dirichlet_xmin.push_back( false );
default_microenvironment_options.Dirichlet_xmax.push_back( false );
default_microenvironment_options.Dirichlet_ymin.push_back( false );
default_microenvironment_options.Dirichlet_ymax.push_back( false );
default_microenvironment_options.Dirichlet_zmin.push_back( false );
default_microenvironment_options.Dirichlet_zmax.push_back( false );

default_microenvironment_options.Dirichlet_xmin_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_xmax_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_ymin_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_ymax_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_zmin_values.push_back( 1.0 );
default_microenvironment_options.Dirichlet_zmax_values.push_back( 1.0 );

default_microenvironment_options.initial_condition_vector.push_back( 1.0 );

return;
return add_density( name , units , 0.0 , 0.0 );
}

void Microenvironment::add_density( std::string name , std::string units, double diffusion_constant, double decay_rate )
{
// fix in PhysiCell preview November 2017
// default_microenvironment_options.use_oxygen_as_first_field = false;
if ( find_density_index( name ) != -1 )
{
std::cout << "ERROR: density named " << name << " already exists. You probably want your substrates all have unique names!" << std::endl;
exit(-1);
}

// update 1, 0
zero.push_back( 0.0 );
Expand Down
120 changes: 36 additions & 84 deletions modules/PhysiCell_settings.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -470,72 +470,24 @@ Parameters<T>::Parameters()
template <class T>
void Parameters<T>::add_parameter( std::string my_name )
{
Parameter<T>* pNew;
pNew = new Parameter<T> ;
pNew->name = my_name ;

int n = parameters.size();

parameters.push_back( *pNew );

name_to_index_map[ my_name ] = n;
return;
// this function is not currently (2024-06-03) called in the code, so these defaults largely do not matter; very unlikely others are directly calling this function, let alone this implementation
T my_value = T(); // for {int, double, bool, string} this will be {0, 0.0, false, ""} (this would technically change the behavior for strings since it is hardcoded above to default to "none", but nobody should rely on the default value of a string being "none")
return add_parameter( my_name , my_value );
}

template <class T>
void Parameters<T>::add_parameter( std::string my_name , T my_value )
{
Parameter<T>* pNew;
pNew = new Parameter<T> ;
pNew->name = my_name ;
pNew->value = my_value;

int n = parameters.size();

parameters.push_back( *pNew );

name_to_index_map[ my_name ] = n;
return;
}
/*
template <class T>
void Parameters<T>::add_parameter( std::string my_name , T my_value )
{
Parameter<T>* pNew;
pNew = new Parameter<T> ;
pNew->name = my_name ;
pNew->value = my_value;
int n = parameters.size();
parameters.push_back( *pNew );
name_to_index_map[ my_name ] = n;
return;
// this function is not currently (2024-06-03) called in the code, so these defaults largely do not matter; very unlikely others are directly calling this function, let alone this implementation
std::string my_units = "dimensionless"; // technically this would change the behavior for strings since it is hardcoded above to default to "none", but nobody should be using units on strings; also, if the xml does not have units, then "dimensionless" is used even for strings
return add_parameter( my_name , my_value , my_units );
}
*/

template <class T>
void Parameters<T>::add_parameter( std::string my_name , T my_value , std::string my_units )
{
Parameter<T>* pNew;
pNew = new Parameter<T> ;
pNew->name = my_name ;
pNew->value = my_value;
pNew->units = my_units;

int n = parameters.size();

parameters.push_back( *pNew );

name_to_index_map[ my_name ] = n;
return;
}
assert_not_exists(my_name);

/*
template <class T>
void Parameters<T>::add_parameter( std::string my_name , T my_value , std::string my_units )
{
Parameter<T>* pNew;
pNew = new Parameter<T> ;
pNew->name = my_name ;
Expand All @@ -549,17 +501,28 @@ void Parameters<T>::add_parameter( std::string my_name , T my_value , std::strin
name_to_index_map[ my_name ] = n;
return;
}
*/

template <class T>
void Parameters<T>::add_parameter( Parameter<T> param )
{
assert_not_exists(param.name);

int n = parameters.size();
parameters.push_back( param);
name_to_index_map[ param.name ] = n;
return;
}

template <class T>
void Parameters<T>::assert_not_exists( std::string search_name )
{
if( find_index( search_name ) == -1 )
{ return; }

std::cout << "ERROR: Parameter " << search_name << " already exists. Make sure all parameters (of a given type) have unique names." << std::endl;
exit(-1);
}

std::ostream& operator<<( std::ostream& os , const User_Parameters up )
{
os << "Bool parameters:: " << std::endl << up.bools << std::endl;
Expand All @@ -583,44 +546,33 @@ void User_Parameters::read_from_pugixml( pugi::xml_node parent_node )
{ units = "dimensionless"; }

std::string type = node1.attribute( "type" ).value();

bool done = false ;
if( type == "bool" && done == false )

if (type == "bool")
{
bool value = xml_get_my_bool_value( node1 );
bools.add_parameter( name , value, units );
done = true;
bool value = xml_get_my_bool_value(node1);
bools.add_parameter(name, value, units);
}

if( type == "int" && done == false )
else if (type == "int")
{
int value = xml_get_my_int_value( node1 );
ints.add_parameter( name , value, units );
done = true;
int value = xml_get_my_int_value(node1);
ints.add_parameter(name, value, units);
}

if( type == "double" && done == false )
else if (type == "double")
{
double value = xml_get_my_double_value( node1 );
doubles.add_parameter( name , value, units );
done = true;
double value = xml_get_my_double_value(node1);
doubles.add_parameter(name, value, units);
}

if( done == false && type == "string" )
else if (type == "string")
{
std::string value = xml_get_my_string_value( node1 );
strings.add_parameter( name, value , units );
done = true;
std::string value = xml_get_my_string_value(node1);
strings.add_parameter(name, value, units);
}

/* default if no type specified: */
if( done == false )
else // default if no type specified
{
double value = xml_get_my_double_value( node1 );
doubles.add_parameter( name , value, units );
done = true;
double value = xml_get_my_double_value(node1);
doubles.add_parameter(name, value, units);
}

node1 = node1.next_sibling();
i++;
}
Expand Down
6 changes: 3 additions & 3 deletions modules/PhysiCell_settings.h
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Original file line number Diff line number Diff line change
Expand Up @@ -186,9 +186,7 @@ class Parameters

void add_parameter( std::string my_name );
void add_parameter( std::string my_name , T my_value );
// void add_parameter( std::string my_name , T my_value );
void add_parameter( std::string my_name , T my_value , std::string my_units );
// void add_parameter( std::string my_name , T my_value , std::string my_units );

void add_parameter( Parameter<T> param );

Expand All @@ -202,7 +200,9 @@ class Parameters
Parameter<T>& operator[]( int i );
Parameter<T>& operator[]( std::string str );

int size( void ) const;
int size( void ) const;

void assert_not_exists(std::string search_name);
};

class User_Parameters
Expand Down

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