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add update_density and update_parameter function #298

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add update_density and update_parameter function #298

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5ac68be
add_parameter functions throw now an error if the parameter already e…
elmbeech Sep 21, 2024
876cc60
bigfix.
elmbeech Sep 21, 2024
47c3cc3
bigfix.
elmbeech Sep 21, 2024
252f029
Microenvironment::update_density and Parameters<T>::update_parameter …
elmbeech Sep 25, 2024
a0cc668
Microenvironment::update_density and Parameters<T>::update_parameter …
elmbeech Sep 25, 2024
58cd783
write update_density and update_parameter in a more concise way.
elmbeech Oct 2, 2024
df4e374
write update_density and update_parameter in a concise and speedy way.
elmbeech Oct 3, 2024
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137 changes: 83 additions & 54 deletions BioFVM/BioFVM_microenvironment.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -253,7 +253,7 @@ bool Microenvironment::get_substrate_dirichlet_activation( int substrate_index )
// TODO? fix confusing swapped usage of args
double Microenvironment::get_substrate_dirichlet_value( int substrate_index, int index )
{
return dirichlet_value_vectors[index][substrate_index];
return dirichlet_value_vectors[index][substrate_index];
}

// new functions for finer-grained control of Dirichlet conditions -- 1.7.0
Expand Down Expand Up @@ -487,76 +487,105 @@ void Microenvironment::add_density( std::string name , std::string units )

void Microenvironment::add_density( std::string name , std::string units, double diffusion_constant, double decay_rate )
{
// fix in PhysiCell preview November 2017
if ( find_density_index( name ) != -1 )
// fix in PhysiCell preview November 2017
// default_microenvironment_options.use_oxygen_as_first_field = false;

// check if density exist
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);
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 );

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

// update coefficients
diffusion_coefficients.push_back( diffusion_constant );
decay_rates.push_back( decay_rate );
// update sources and such
// update coefficients
diffusion_coefficients.push_back( diffusion_constant );
decay_rates.push_back( decay_rate );

// 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 );
temporary_density_vectors1[i].push_back( 0.0 );
temporary_density_vectors2[i].push_back( 0.0 );
}

// resize the gradient data structures
// resize the gradient data structures
for( unsigned int k=0 ; k < mesh.voxels.size() ; k++ )
{
gradient_vectors[k].resize( number_of_densities() );
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 );
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.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 );
one_half = one;
one_half *= 0.5;

return;
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.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;
}

int Microenvironment::assert_density_exists( std::string search_name )
{
int density_index = find_density_index( search_name );
if( density_index != -1 )
{ return density_index; }

std::cout << "Error: density named " << search_name << " does not exist. Cannot update density!" << std::endl;
exit(-1);
}

void Microenvironment::update_density( std::string name , std::string units )
{
int density_index = assert_density_exists( name );
density_units[ density_index ] = units;
return;
}

void Microenvironment::update_density( std::string name , std::string units, double diffusion_constant, double decay_rate )
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Can you use the above implementation of update_density to simplify this function and the codebase?

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@elmbeech elmbeech Oct 2, 2024 •
edited
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is this ok?

image

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yup

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i still think it is odd to have to implement a slower version because of code maintenance.
before we had to call the find_index function 1 time, now 3 or 4 times.
just to avoid storing the value in a variable?

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@elmbeech elmbeech Oct 3, 2024 •
edited
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this is the compromise i suggest between maintenance (as closed as it get to the existing add_parameter function) and speed.
i hope this is acceptable.

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and the same for the densities:

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i pushed these changes and hope they are ok and get merged.

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@elmbeech elmbeech Oct 12, 2024 •
edited
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@drbergman could you please confirm that the conflict / conversation / change you requested has resolved (as i think so ).
or let me know if otherwise?

i don't think it is appropriate when i click the resolved button.

thank you, Elmar

{
int density_index = assert_density_exists( name );
density_units[ density_index ] = units;
diffusion_coefficients[ density_index ] = diffusion_constant;
decay_rates[ density_index ] = decay_rate;
return;
}

int Microenvironment::find_density_index( std::string name )
Expand Down Expand Up @@ -1427,7 +1456,7 @@ void initialize_microenvironment( void )
}
*/

// April 2023: no longer necessary after flipping our approach and doing an "additive" instead of "subtractive" DCs handling. I.e., we assume DC activation is false by default; make true on-demand.
// April 2023: no longer necessary after flipping our approach and doing an "additive" instead of "subtractive" DCs handling. I.e., we assume DC activation is false by default; make true on-demand.

// // set the Dirichlet condition activation vector to match the microenvironment options
// for( int i=0 ; i < default_microenvironment_options.Dirichlet_activation_vector.size(); i++ )
Expand Down
21 changes: 13 additions & 8 deletions BioFVM/BioFVM_microenvironment.h
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Original file line number Diff line number Diff line change
Expand Up @@ -181,16 +181,21 @@ class Microenvironment
void resize_space( double x_start, double x_end, double y_start, double y_end, double z_start, double z_end , double dx_new , double dy_new , double dz_new );
void resize_space_uniform( double x_start, double x_end, double y_start, double y_end, double z_start, double z_end , double dx_new );

void resize_densities( int new_size );
void add_density( void );
void resize_densities( int new_size );

void add_density( void );
void add_density( std::string name , std::string units );
void add_density( std::string name , std::string units, double diffusion_constant, double decay_rate );
void add_density( std::string name , std::string units, double diffusion_constant, double decay_rate );

void set_density( int index , std::string name , std::string units );
void set_density( int index , std::string name , std::string units , double diffusion_constant , double decay_rate );
void update_density( std::string name , std::string units );
void update_density( std::string name , std::string units, double diffusion_constant, double decay_rate );

void set_density( int index , std::string name , std::string units );
void set_density( int index , std::string name , std::string units , double diffusion_constant , double decay_rate );

int find_density_index( std::string name );
int assert_density_exists( std::string search_name );

int find_density_index( std::string name );

int voxel_index( int i, int j, int k );
std::vector<unsigned int> cartesian_indices( int n );

Expand Down Expand Up @@ -254,7 +259,7 @@ class Microenvironment
void set_substrate_dirichlet_activation( int index, std::vector<bool>& new_value );
bool get_substrate_dirichlet_activation( int substrate_index, int index );

double get_substrate_dirichlet_value( int substrate_index, int index );
double get_substrate_dirichlet_value( int substrate_index, int index );

bool& is_dirichlet_node( int voxel_index );

Expand Down
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