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PhysiBoSS 2.2.3 update #217

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merged 9 commits into from
Jun 3, 2024
Merged

PhysiBoSS 2.2.3 update #217

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3695482
Updated setup_libmaboss.py. Now in the addons/PhysiBoSS folder, out o…
vincent-noel Feb 5, 2024
9f4432f
introduced steepness, a new parameter that the user can define in the…
marcorusc Jul 31, 2023
fc4589b
Added error checking in PhysiBoSS for BND/CFG files existence and acc…
vincent-noel Feb 7, 2024
71385fb
Printing steepness value in display
vincent-noel Feb 26, 2024
9e9999d
Mapping rules now have a flag to define if they work during death
vincent-noel Feb 26, 2024
58f59b8
Added MaBoSS license in the licenses folder
vincent-noel Nov 16, 2023
6867d21
Added PhysiBoSS URL and DOI in maboss_intracellular.h
vincent-noel Nov 16, 2023
585c723
Improved PhysiBoSS citation in CITATION.TXT
vincent-noel Nov 16, 2023
98cc80e
Bumped PhysiBoSS version to 2.2.3
vincent-noel Mar 4, 2024
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Mapping rules now have a flag to define if they work during death
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@vincent-noel
vincent-noel committed Mar 4, 2024
commit 9e9999d1d6560e314e77fdde15441bbb83035725
49 changes: 30 additions & 19 deletions addons/PhysiBoSS/src/maboss_intracellular.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -69,32 +69,38 @@ void MaBoSSIntracellular::update_inputs(PhysiCell::Cell* cell, PhysiCell::Phenot
int i=0;
for (auto& input: listOfInputs)
{
if (input.second.isNode()) {
maboss.set_node_value(
input.first,
input.second.updateNode(maboss.get_node_value(input.second.intracellular_name), signals[i])
);
} else if (input.second.isParameter()) {
maboss.set_parameter_value(
input.first,
input.second.updateParameter(signals[i])
);
if (cell->phenotype.death.dead == false || input.second.use_for_dead == true) {

if (input.second.isNode()) {
maboss.set_node_value(
input.first,
input.second.updateNode(maboss.get_node_value(input.second.intracellular_name), signals[i])
);
} else if (input.second.isParameter()) {
maboss.set_parameter_value(
input.first,
input.second.updateParameter(signals[i])
);
}
}
i++;
}
}

void MaBoSSIntracellular::update_outputs(PhysiCell::Cell* cell, PhysiCell::Phenotype& phenotype, double dt)
{
std::vector<double> signals = std::vector<double>(listOfOutputs.size(), 0.0);

int i=0;

for (auto& output: listOfOutputs)
{
signals[i] = output.second.update(maboss.get_node_value(output.second.intracellular_name));
if (cell->phenotype.death.dead == false || output.second.use_for_dead == true) {
PhysiCell::set_single_behavior(
cell, indicesOfOutputs[i],
output.second.update(maboss.get_node_value(output.second.intracellular_name))
);
}
i++;
}
PhysiCell::set_selected_behaviors(cell, indicesOfOutputs, signals);
}


Expand Down Expand Up @@ -366,7 +372,8 @@ void MaBoSSIntracellular::initialize_intracellular_from_pugixml(pugi::xml_node&
node_input.attribute( "physicell_name" ).value(),
intracellular_name,
(settings && settings.child( "scaling" ) ? PhysiCell::xml_get_my_double_value( settings.child( "scaling" )) : 1.0),
(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0)
(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0),
(settings && settings.child( "use_for_dead" ) ? PhysiCell::xml_get_my_bool_value( settings.child( "use_for_dead" )) : false)
);

// This construct is a trick to avoid making inputs and outputs constructible and assignable, or using c++17 insert_or_assign
Expand All @@ -382,7 +389,8 @@ void MaBoSSIntracellular::initialize_intracellular_from_pugixml(pugi::xml_node&
PhysiCell::xml_get_my_string_value(settings.child("action")),
PhysiCell::xml_get_my_double_value(settings.child("threshold")),
(settings && settings.child( "inact_threshold" ) ? PhysiCell::xml_get_my_double_value( settings.child( "inact_threshold" )) : PhysiCell::xml_get_my_double_value(settings.child("threshold"))),
(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0)
(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0),
(settings && settings.child( "use_for_dead" ) ? PhysiCell::xml_get_my_bool_value( settings.child( "use_for_dead" )) : false)
);

auto const res = listOfInputs.insert(std::pair<std::string, MaBoSSInput>(intracellular_name, input));
Expand All @@ -404,7 +412,8 @@ void MaBoSSIntracellular::initialize_intracellular_from_pugixml(pugi::xml_node&
PhysiCell::xml_get_my_double_value(settings.child("value")),
(settings && settings.child( "base_value" ) ? PhysiCell::xml_get_my_double_value( settings.child( "base_value" )) : PhysiCell::xml_get_my_double_value(settings.child("value"))),
(settings && settings.child( "smoothing" ) ? PhysiCell::xml_get_my_int_value( settings.child( "smoothing" )) : 0),
(settings && settings.child( "steepness" ) ? PhysiCell::xml_get_my_int_value( settings.child( "steepness" )) : 10)
(settings && settings.child( "steepness" ) ? PhysiCell::xml_get_my_int_value( settings.child( "steepness" )) : 10),
(settings && settings.child( "use_for_dead" ) ? PhysiCell::xml_get_my_bool_value( settings.child( "use_for_dead" )) : false)
);

auto const res = listOfOutputs.insert(std::pair<std::string, MaBoSSOutput>(physicell_name, output));
Expand Down Expand Up @@ -443,14 +452,16 @@ void MaBoSSIntracellular::display(std::ostream& os)
os << "\t\t " << listOfInputs.size() << " input mapping defined" << std::endl;
for (const auto& input : listOfInputs)
os << "\t\t\t" << input.second.physicell_name << " = " << input.first
<< "(" << input.second.threshold << ", " << input.second.inact_threshold << ", " << input.second.smoothing << ")"
<< "(" << input.second.threshold << ", " << input.second.inact_threshold
<< ", " << input.second.smoothing << ", " << input.second.use_for_dead << ")"
<< std::endl;

os << "\t\t " << listOfOutputs.size() << " output mapping defined" << std::endl;
for (const auto& output : listOfOutputs)
os << "\t\t\t" << output.first << " = " << output.second.intracellular_name
<< "(" << output.second.value << ", " << output.second.base_value
<< ", " << output.second.smoothing << ", " << output.second.steepness << ")"
<< ", " << output.second.smoothing << ", " << output.second.steepness
<< ", " << output.second.use_for_dead << ")"
<< std::endl;

os << "\t\t global inheritance = " << inherit_state << std::endl;
Expand Down
10 changes: 4 additions & 6 deletions addons/PhysiBoSS/src/maboss_intracellular.h
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Original file line number Diff line number Diff line change
Expand Up @@ -68,12 +68,10 @@ class MaBoSSIntracellular : public PhysiCell::Intracellular {
}

void update(PhysiCell::Cell * cell, PhysiCell::Phenotype& phenotype, double dt) {
if (!cell->phenotype.death.dead) {
this->update_inputs(cell, phenotype, dt);
this->maboss.run_simulation();
this->update_outputs(cell, phenotype, dt);
this->next_physiboss_run += this->maboss.get_time_to_update();
}
this->update_inputs(cell, phenotype, dt);
this->maboss.run_simulation();
this->update_outputs(cell, phenotype, dt);
this->next_physiboss_run += this->maboss.get_time_to_update();
}

bool need_update() {
Expand Down
11 changes: 7 additions & 4 deletions addons/PhysiBoSS/src/utils.h
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Original file line number Diff line number Diff line change
Expand Up @@ -17,12 +17,14 @@ class MaBoSSInput
double scaling;
int smoothing;
double smoothed_value;
MaBoSSInput(std::string physicell_name, std::string intracellular_name, std::string action, double threshold, double inact_threshold, int smoothing) : physicell_name(physicell_name), intracellular_name(intracellular_name), action(action), threshold(threshold), inact_threshold(inact_threshold), smoothing(smoothing) {
bool use_for_dead;

MaBoSSInput(std::string physicell_name, std::string intracellular_name, std::string action, double threshold, double inact_threshold, int smoothing, bool use_for_dead) : physicell_name(physicell_name), intracellular_name(intracellular_name), action(action), threshold(threshold), inact_threshold(inact_threshold), smoothing(smoothing), use_for_dead(use_for_dead){
type = NODE;
smoothed_value = 0;
}

MaBoSSInput(std::string physicell_name, std::string intracellular_parameter, double scaling, int smoothing) : physicell_name(physicell_name), intracellular_parameter(intracellular_parameter), scaling(scaling), smoothing(smoothing) {
MaBoSSInput(std::string physicell_name, std::string intracellular_parameter, double scaling, int smoothing, bool use_for_dead) : physicell_name(physicell_name), intracellular_parameter(intracellular_parameter), scaling(scaling), smoothing(smoothing), use_for_dead(use_for_dead) {
type = PARAMETER;
smoothed_value = 0;
}
Expand Down Expand Up @@ -84,13 +86,14 @@ class MaBoSSOutput
double probability;
bool initialized = false;
int steepness;
bool use_for_dead;

MaBoSSOutput(std::string physicell_name, std::string intracellular_name,
std::string action, double value, double base_value,
int smoothing, int steepness)
int smoothing, int steepness, bool use_for_dead)
: physicell_name(physicell_name), intracellular_name(intracellular_name),
action(action), value(value), base_value(base_value),
smoothing(smoothing), steepness(steepness) {
smoothing(smoothing), steepness(steepness), use_for_dead(use_for_dead) {
probability = 0.5;
}

Expand Down