Skip to content

update the if-query so that it spans all possible contact with cells cases. #411

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
elmbeech wants to merge 2 commits into
base: development
Choose a base branch
from
+6 −4
Open

update the if-query so that it spans all possible contact with cells cases. #411

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
2cfbc80
Update the if-query so that it spans all possible contact with cells …
elmbeech Feb 18, 2026
5eef794
add contact_with_built_in variable and change the code accordingly.
elmbeech Mar 21, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 6 additions & 4 deletions core/PhysiCell_signal_behavior.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,8 @@ std::map<std::string,int> behavior_to_int;
std::map<int,std::string> int_to_signal;
std::map<int,std::string> int_to_behavior;

int contact_with_built_in = 5; // live, dead, apoptotic, necrotic, other

void setup_signal_behavior_dictionaries( void )
{
extern std::unordered_map<std::string,int> cell_definition_indices_by_name;
Expand Down Expand Up @@ -804,7 +806,7 @@ std::vector<double> get_signals( Cell* pCell )
signals[volume_ind] = pCell->phenotype.volume.total;

// physical contact with cells (of each type)
// increment signals
// increment signals
int dead_cells = 0;
int apop_cells = 0;
int necro_cells = 0;
Expand Down Expand Up @@ -964,7 +966,7 @@ std::vector<double> get_cell_contact_signals( Cell* pCell )
// rescale
std::string search_for = "contact with " + cell_definitions_by_type[0]->name;
static int scaling_start_index = find_signal_index( search_for );
for( int i=0; i < n+2 ; i++ )
for( int i=0; i < n+contact_with_built_in; i++ )
{ output[i] /= signal_scales[scaling_start_index+i]; }

return output;
Expand All @@ -986,7 +988,7 @@ std::vector<double> get_selected_signals( Cell* pCell , std::vector<int> indices
for( int i=0; i < indices.size() ; i++ )
{
int ind = indices[i];
if( ind >= contact_start_index && ind < contact_start_index+n+2)
if( ind >= contact_start_index && ind < contact_start_index+n+contact_with_built_in )
{ signals[i] = contact_signals[ind-contact_start_index]; }
else
{ signals[i] = get_single_signal( pCell , ind ); }
Expand Down Expand Up @@ -1065,7 +1067,7 @@ double get_single_signal( Cell* pCell, int index )
// physical contact with cells (of each type)
// individual contact signals are a bit costly
static int contact_ind = find_signal_index( "contact with " + cell_definitions_by_type[0]->name );
if( contact_ind <= index && index < contact_ind + n+2 )
if( contact_ind <= index && index < contact_ind+n+contact_with_built_in )
{
std::vector<int> counts( n , 0 );
// process all neighbors
Expand Down
Loading