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add current cycle phase index to signals #381

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add current cycle phase index to signals #381

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6097a2f
add (spring) attachment and cycle phase signals
drbergman Jun 24, 2025
e52e73b
add current cycle phase index to signals
drbergman Aug 19, 2025
0845a55
Merge branch 'feature-cycle-phase-index-as-signal' into more-signals
drbergman Aug 22, 2025
26c2a4d
fix bug
drbergman Aug 25, 2025
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62 changes: 59 additions & 3 deletions core/PhysiCell_signal_behavior.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -141,14 +141,21 @@ void setup_signal_behavior_dictionaries( void )

map_index++;
}


// current cycle phase index
signal_to_int["current cycle phase"] = map_index;
int_to_signal[map_index] = "current cycle phase";
// synonyms
signal_to_int["current cycle phase index"] = map_index;
signal_to_int["cycle phase"] = map_index;
signal_to_int["cycle phase index"] = map_index;

// mechanical pressure
// int map_index = m;
map_index++;
signal_to_int[ "pressure"] = map_index;
int_to_signal[map_index] = "pressure";

// total volume

map_index++;
signal_to_int[ "volume"] = map_index;
int_to_signal[map_index] = "volume";
Expand Down Expand Up @@ -207,6 +214,16 @@ void setup_signal_behavior_dictionaries( void )
int_to_signal[map_index] = "contact with basement membrane";
// synonym
signal_to_int["contact with BM"] = map_index;

// number of attachments
map_index++;
signal_to_int["number of attachments"] = map_index;
int_to_signal[map_index] = "number of attachments";

// number of spring attachments
map_index++;
signal_to_int["number of spring attachments"] = map_index;
int_to_signal[map_index] = "number of spring attachments";

// damage state

Expand Down Expand Up @@ -795,6 +812,10 @@ std::vector<double> get_signals( Cell* pCell )
for( int i=0; i < m ; i++ )
{ signals[start_substrate_grad_ind+i] = norm( pCell->nearest_gradient(i) ); }

// current cycle phase
static int cycle_phase_ind = find_signal_index( "cycle phase" );
signals[cycle_phase_ind] = pCell->phenotype.cycle.data.current_phase_index;

// mechanical pressure
static int pressure_ind = find_signal_index( "pressure");
signals[pressure_ind] = pCell->state.simple_pressure;
Expand Down Expand Up @@ -857,6 +878,14 @@ std::vector<double> get_signals( Cell* pCell )
static int BM_contact_ind = find_signal_index( "contact with basement membrane");
signals[BM_contact_ind] = (int) pCell->state.contact_with_basement_membrane;

// number of attachments
static int num_attachments_ind = find_signal_index( "number of attachments");
signals[num_attachments_ind] = pCell->state.attached_cells.size();

// number of spring attachments
static int num_spring_attachments_ind = find_signal_index( "number of spring attachments");
signals[num_spring_attachments_ind] = pCell->state.spring_attachments.size();

// damage
static int damage_ind = find_signal_index( "damage");
signals[damage_ind] = pCell->phenotype.cell_integrity.damage;
Expand Down Expand Up @@ -1044,6 +1073,15 @@ double get_single_signal( Cell* pCell, int index )
return out;
}

// current cycle phase
static int cycle_phase_ind = find_signal_index( "cycle phase" );
if( index == cycle_phase_ind )
{
out = pCell->phenotype.cycle.data.current_phase_index;
out /= signal_scales[index];
return out;
}

// mechanical pressure
static int pressure_ind = find_signal_index( "pressure" );
if( index == pressure_ind )
Expand Down Expand Up @@ -1153,6 +1191,24 @@ double get_single_signal( Cell* pCell, int index )
return out;
}

// number of attachments
static int num_attachments_ind = find_signal_index( "number of attachments");
if( index == num_attachments_ind )
{
out = pCell->state.attached_cells.size();
out /= signal_scales[index];
return out;
}

// number of spring attachments
static int num_spring_attachments_ind = find_signal_index( "number of spring attachments");
if( index == num_spring_attachments_ind )
{
out = pCell->state.spring_attachments.size();
out /= signal_scales[index];
return out;
}

// damage
static int damage_ind = find_signal_index( "damage");
if( index == damage_ind )
Expand Down
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