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Merge pull request #291 from sysbio-curie/physimess_1.0.1
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PhysiMeSS 1.0.1
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@MathCancer
MathCancer authored Sep 10, 2024
2 parents a3cc8dc + c260aa0 commit b4bf258
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Showing 43 changed files with 9,866 additions and 9,886 deletions.
2 changes: 1 addition & 1 deletion addons/PhysiMeSS/PhysiMeSS.cpp
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Expand Up @@ -22,7 +22,7 @@ void remove_physimess_out_of_bounds_fibres()
void physimess_update_cell_velocity( Cell* pCell, Phenotype& phenotype, double dt)
{

double movement_threshold = PhysiCell::parameters.doubles("fibre_stuck_threshold");
double movement_threshold = pCell->custom_data["fibre_stuck_threshold"];
if (!isFibre(pCell) && phenotype.motility.is_motile) {

// Here I changed this, because here we don't have access to the old position, and I didn't want to track the old position
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4 changes: 2 additions & 2 deletions addons/PhysiMeSS/PhysiMeSS.h
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Expand Up @@ -10,7 +10,7 @@

using namespace PhysiCell;

static std::string PhysiMeSS_Version = "1.0.0";
static std::string PhysiMeSS_Version = "1.0.1";

void remove_physimess_out_of_bounds_fibres();

Expand All @@ -20,4 +20,4 @@ void physimess_update_cell_velocity( Cell* pCell, Phenotype& phenotype, double d
void fibre_agent_SVG(std::ofstream& os, PhysiCell::Cell* pCell, double z_slice, std::vector<std::string> (*cell_coloring_function)(Cell*), double X_lower, double Y_lower);
void fibre_agent_legend(std::ofstream& os, Cell_Definition* cell_definition, double& cursor_x, double& cursor_y, std::vector<std::string> (*cell_coloring_function)(Cell*), double temp_cell_radius);

#endif
#endif
12 changes: 6 additions & 6 deletions addons/PhysiMeSS/PhysiMeSS_cell.cpp
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Expand Up @@ -95,10 +95,10 @@ void PhysiMeSS_Cell::add_potentials_from_fibre(PhysiMeSS_Fibre* pFibre)
double xip = pow(xi, p_exponent);
double xiq = pow((1 - xi * xi), q_exponent);

fibre_adhesion = PhysiCell::parameters.doubles("vel_adhesion") * xip *
(1 - cell_velocity / PhysiCell::parameters.doubles("cell_velocity_max"));
fibre_adhesion = this->custom_data["vel_adhesion"] * xip *
(1 - cell_velocity / this->custom_data["cell_velocity_max"]);

fibre_repulsion = PhysiCell::parameters.doubles("vel_contact") * xiq;
fibre_repulsion = this->custom_data["vel_contact"] * xiq;

axpy(&(velocity), fibre_adhesion, pFibre->state.orientation);
naxpy(&(velocity), fibre_repulsion, previous_velocity);
Expand All @@ -119,8 +119,8 @@ void PhysiMeSS_Cell::degrade_fibre(PhysiMeSS_Fibre* pFibre)
distance = std::max(sqrt(distance), 0.00001);

// Fibre degradation by cell - switched on by flag fibre_degradation
double stuck_threshold = PhysiCell::parameters.doubles("fibre_stuck_time");
if (PhysiCell::parameters.bools("fibre_degradation") && stuck_counter >= stuck_threshold) {
double stuck_threshold = this->custom_data["fibre_stuck_time"];
if (this->custom_data["fibre_degradation"] > 0.5 && stuck_counter >= stuck_threshold) {
// if (stuck_counter >= stuck_threshold){
// std::cout << "Cell " << ID << " is stuck at time " << PhysiCell::PhysiCell_globals.current_time
// << " near fibre " << pFibre->ID << std::endl;;
Expand All @@ -129,7 +129,7 @@ void PhysiMeSS_Cell::degrade_fibre(PhysiMeSS_Fibre* pFibre)
double dotproduct = dot_product(displacement, phenotype.motility.motility_vector);
if (dotproduct >= 0) {
double rand_degradation = PhysiCell::UniformRandom();
double prob_degradation = PhysiCell::parameters.doubles("fibre_degradation_rate");
double prob_degradation = this->custom_data["fibre_degradation_rate"];
if (rand_degradation <= prob_degradation) {
//std::cout << " --------> fibre " << (*other_agent).ID << " is flagged for degradation " << std::endl;
// (*other_agent).parameters.degradation_flag = true;
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24 changes: 13 additions & 11 deletions addons/PhysiMeSS/PhysiMeSS_fibre.cpp
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Expand Up @@ -49,26 +49,28 @@ std::vector<PhysiCell::Cell_Definition*>* getFibreCellDefinitions() {

return result;
}

PhysiMeSS_Fibre::PhysiMeSS_Fibre()
{
// std::cout << "PhysiMeSS_Fibre constructor,";
fibres_crosslinkers.clear();
fibres_crosslink_point.clear();

mLength = PhysiCell::NormalRandom(PhysiCell::parameters.doubles("fibre_length"), PhysiCell::parameters.doubles("length_normdist_sd")) / 2.0;
mRadius = PhysiCell::parameters.doubles("fibre_radius");
// mLength = PhysiCell::NormalRandom(PhysiCell::parameters.doubles("fibre_length"), PhysiCell::parameters.doubles("length_normdist_sd")) / 2.0;
// mRadius = PhysiCell::parameters.doubles("fibre_radius");
// std::cout << "mLength = " << mLength;
X_crosslink_count = 0;
fail_count = 0;
}

void PhysiMeSS_Fibre::assign_fibre_orientation()
{
mLength = PhysiCell::NormalRandom(this->custom_data["fibre_length"], this->custom_data["length_normdist_sd"]) / 2.0;
mRadius = this->custom_data["fibre_radius"];
this->assign_orientation();
if (default_microenvironment_options.simulate_2D) {
if (PhysiCell::parameters.bools("anisotropic_fibres")){
double theta = PhysiCell::NormalRandom(PhysiCell::parameters.doubles("fibre_angle"),PhysiCell::parameters.doubles("angle_normdist_sd"));
if (this->custom_data["anisotropic_fibres"] > 0.5){
double theta = PhysiCell::NormalRandom(this->custom_data["fibre_angle"], this->custom_data["angle_normdist_sd"]);
this->state.orientation[0] = cos(theta);
this->state.orientation[1] = sin(theta);
}
Expand Down Expand Up @@ -135,7 +137,7 @@ void PhysiMeSS_Fibre::check_out_of_bounds(std::vector<double>& position)
break after 10 failures
It needs re-writing at some stage to handle the 3D case properly */

if (PhysiCell::parameters.bools("anisotropic_fibres")) {
if (this->custom_data["anisotropic_fibres"]) {
if (xs < Xmin || xe > Xmax || xe < Xmin || xs > Xmax ||
ys < Ymin || ye > Ymax || ye < Ymin || ys > Ymax) {
fail_count = 10;
Expand Down Expand Up @@ -205,7 +207,7 @@ void PhysiMeSS_Fibre::add_potentials_from_cell(PhysiMeSS_Cell* cell)
// cell-fibre pushing only if fibre no crosslinks
if (X_crosslink_count == 0) {
//fibre pushing turned on
if (PhysiCell::parameters.bools("fibre_pushing")) {
if (cell->custom_data["fibre_pushing"] > 0.5) {
// as per PhysiCell
static double simple_pressure_scale = 0.027288820670331;
// temp_r = 1 - distance/R;
Expand All @@ -227,15 +229,15 @@ void PhysiMeSS_Fibre::add_potentials_from_cell(PhysiMeSS_Cell* cell)
}

// fibre rotation turned on (2D)
if (PhysiCell::parameters.bools("fibre_rotation")) {
if (cell->custom_data["fibre_rotation"] > 0.5) {
std::vector<double> old_orientation(3, 0.0);
for (int i = 0; i < 2; i++) {
old_orientation[i] = state.orientation[i];
}

double moment_arm_magnitude = sqrt(
point_of_impact[0] * point_of_impact[0] + point_of_impact[1] * point_of_impact[1]);
double impulse = PhysiCell::parameters.doubles("fibre_sticky")*(*cell).phenotype.motility.migration_speed * moment_arm_magnitude;
double impulse = cell->custom_data["fibre_sticky"]*(*cell).phenotype.motility.migration_speed * moment_arm_magnitude;
double fibre_length = 2 * mLength;
double angular_velocity = impulse / (0.5 * fibre_length * fibre_length);
double angle = angular_velocity;
Expand All @@ -246,7 +248,7 @@ void PhysiMeSS_Fibre::add_potentials_from_cell(PhysiMeSS_Cell* cell)
}

// fibre rotation around other fibre (2D only and fibres intersect at a single point)
if (PhysiCell::parameters.bools("fibre_rotation") && X_crosslink_count == 1) {
if (cell->custom_data["fibre_rotation"] > 0.5 && X_crosslink_count == 1) {
double distance_fibre_centre_to_crosslink = 0.0;
std::vector<double> fibre_centre_to_crosslink(3, 0.0);
for (int i = 0; i < 2; i++) {
Expand All @@ -261,7 +263,7 @@ void PhysiMeSS_Fibre::add_potentials_from_cell(PhysiMeSS_Cell* cell)
}
double moment_arm_magnitude = sqrt(
point_of_impact[0] * point_of_impact[0] + point_of_impact[1] * point_of_impact[1]);
double impulse = PhysiCell::parameters.doubles("fibre_sticky")*(*cell).phenotype.motility.migration_speed * moment_arm_magnitude;
double impulse = cell->custom_data["fibre_sticky"]*(*cell).phenotype.motility.migration_speed * moment_arm_magnitude;
double fibre_length = 2 * mLength;
double angular_velocity = impulse / (0.5 * fibre_length * fibre_length);
double angle = angular_velocity;
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61 changes: 31 additions & 30 deletions sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_fibremaze.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,20 @@

</phenotype>
<custom_data>
<sample>1.0</sample>
<fibre_degradation units="none" description="flag for fibre degradation">0.0</fibre_degradation>
<fibre_degradation_rate units="1/min" description="fibre degradation rate">0.01</fibre_degradation_rate>
<fibre_custom_degradation units="none" description="flag for having degradation depends on pressure">0.0</fibre_custom_degradation>
<fibre_stuck_time units="1/min" description="time before stuck cell can degrade fibre">10.0</fibre_stuck_time>
<fibre_stuck_threshold units="none" description="movement threshold to declare a cell stuck">0.05</fibre_stuck_threshold>
<fibre_pressure_threshold units="1/min" description="time before stuck cell can degrade fibre">10.0</fibre_pressure_threshold>

<fibre_pushing units="none" description="flag for fibre pushing">0.0</fibre_pushing>
<fibre_sticky units="none" description="measure of how easy it is to move a fibre">1.0</fibre_sticky>
<fibre_rotation units="none" description="flag for fibre rotation">0.0</fibre_rotation>

<vel_adhesion units="" description="cell velocity parallel to fibre">0.6</vel_adhesion>
<vel_contact units="" description="cell velocity orthogonal to fibre">0.1</vel_contact>
<cell_velocity_max units="" description="max cell velocity">1.0</cell_velocity_max>
</custom_data>
</cell_definition>

Expand Down Expand Up @@ -261,9 +274,15 @@

</phenotype>
<custom_data>
<sample>1.0</sample>
</custom_data>
</cell_definition>
<anisotropic_fibres units="none" description="flag for whether we want anisotropic fibres">1.0</anisotropic_fibres>
<fibre_length units="microns" description="length of fibres">60.0</fibre_length>
<length_normdist_sd units="microns" description="standard deviation of fibre length">0.0</length_normdist_sd>
<fibre_radius units="microns" description="radius of fibres">2.0</fibre_radius>
<radius_normdist_sd units="microns" description="standard deviation of fibre radius">0.0</radius_normdist_sd>
<fibre_angle units="radians" description="angle of fibre orientation">1.57</fibre_angle>
<angle_normdist_sd units="radians" description="standard deviation of fibre orientation angle">0.0</angle_normdist_sd>
</custom_data>
</cell_definition>

<cell_definition name="fibre_horizontal" ID="2">
<phenotype>
Expand Down Expand Up @@ -353,8 +372,13 @@

</phenotype>
<custom_data>
<sample>1.0</sample>
</custom_data>
<anisotropic_fibres units="none" description="flag for whether we want anisotropic fibres">1.0</anisotropic_fibres>
<fibre_length units="microns" description="length of fibres">60.0</fibre_length>
<length_normdist_sd units="microns" description="standard deviation of fibre length">0.0</length_normdist_sd>
<fibre_radius units="microns" description="radius of fibres">2.0</fibre_radius>
<radius_normdist_sd units="microns" description="standard deviation of fibre radius">0.0</radius_normdist_sd>
<fibre_angle units="radians" description="angle of fibre orientation">1.57</fibre_angle>
<angle_normdist_sd units="radians" description="standard deviation of fibre orientation angle">0.0</angle_normdist_sd> </custom_data>
</cell_definition>

<cell_definition name="attractant" ID="3">
Expand Down Expand Up @@ -461,31 +485,8 @@
<user_parameters>
<random_seed type="int" units="dimensionless" description="">0</random_seed>
<number_of_cells type="int" units="none" description="initial number of cells (for each cell type)">0</number_of_cells>

<number_of_fibres type="int" units="none" description="initial number of fibres (for each fibre type)">2000</number_of_fibres>
<anisotropic_fibres type="bool" units="none" description="flag for whether we want anisotropic fibres">true</anisotropic_fibres>
<fibre_length type="double" units="microns" description="length of fibres">60.0</fibre_length>
<length_normdist_sd type="double" units="microns" description="standard deviation of fibre length">0.0</length_normdist_sd>
<fibre_radius type="double" units="microns" description="radius of fibres">2.0</fibre_radius>
<radius_normdist_sd type="double" units="microns" description="standard deviation of fibre radius">0.0</radius_normdist_sd>
<fibre_angle type="double" units="radians" description="angle of fibre orientation">1.57</fibre_angle>
<angle_normdist_sd type="double" units="radians" description="standard deviation of fibre orientation angle">0.0</angle_normdist_sd>

<fibre_degradation type="bool" units="none" description="flag for fibre degradation">false</fibre_degradation>
<fibre_degradation_rate type="double" units="1/min" description="fibre degradation rate">0.01</fibre_degradation_rate>
<fibre_custom_degradation type="bool" units="none" description="flag for having degradation depends on pressure">false</fibre_custom_degradation>
<fibre_stuck_time type="double" units="1/min" description="time before stuck cell can degrade fibre">10.0</fibre_stuck_time>
<fibre_stuck_threshold type="double" units="none" description="movement threshold to declare a cell stuck">0.05</fibre_stuck_threshold>
<fibre_pressure_threshold type="double" units="1/min" description="time before stuck cell can degrade fibre">10.0</fibre_pressure_threshold>
<color_cells_by_pressure type="bool" units="" description="flag for coloring cells by pressure">false</color_cells_by_pressure>

<fibre_pushing type="bool" units="none" description="flag for fibre pushing">false</fibre_pushing>
<fibre_sticky type="double" units="none" description="measure of how easy it is to move a fibre">1.0</fibre_sticky>
<fibre_rotation type="bool" units="none" description="flag for fibre rotation">false</fibre_rotation>

<vel_adhesion type="double" units="" description="cell velocity parallel to fibre">0.6</vel_adhesion>
<vel_contact type="double" units="" description="cell velocity orthogonal to fibre">0.1</vel_contact>
<cell_velocity_max type="double" units="" description="max cell velocity">1.0</cell_velocity_max>
</user_parameters>
</user_parameters>

</PhysiCell_settings>
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