From f31de8191d68b00e134fe6c419123cf363527a0e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vincent=20No=C3=ABl?= Date: Mon, 17 Jun 2024 12:19:58 -0300 Subject: [PATCH 1/3] Fibre and Cell settings are now part of the custom data, allowing different types of cells and fibres --- addons/PhysiMeSS/PhysiMeSS.cpp | 2 +- addons/PhysiMeSS/PhysiMeSS_cell.cpp | 12 +-- addons/PhysiMeSS/PhysiMeSS_fibre.cpp | 24 +++--- .../mymodel_fibremaze.xml | 61 +++++++------- .../Cell_Fibre_Mechanics/mymodel_hinge.xml | 65 ++++++++------- .../Cell_Fibre_Mechanics/mymodel_pushing.xml | 60 +++++++------- .../Cell_Fibre_Mechanics/mymodel_rotating.xml | 52 ++++++------ .../mymodel_extended_fibre_crosslink_test.xml | 66 +++++++-------- .../mymodel_simple_fibre_crosslink_test.xml | 81 ++++++++++--------- .../mymodel_fibre_degradation.xml | 58 +++++++------ .../mymodel_matrix_degradation.xml | 66 +++++++-------- .../mymodel_initialisation.xml | 62 +++++++------- .../mymodel_initialisation_maze.xml | 71 ++++++++-------- .../mymodel_neighbours.xml | 65 +++++++-------- .../physimess/config/PhysiCell_settings.xml | 35 ++++---- .../physimess/custom_modules/custom.cpp | 21 ++--- .../physimess/custom_modules/custom.h | 3 +- 17 files changed, 392 insertions(+), 412 deletions(-) diff --git a/addons/PhysiMeSS/PhysiMeSS.cpp b/addons/PhysiMeSS/PhysiMeSS.cpp index 79034b0a5..da010c21d 100644 --- a/addons/PhysiMeSS/PhysiMeSS.cpp +++ b/addons/PhysiMeSS/PhysiMeSS.cpp @@ -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 diff --git a/addons/PhysiMeSS/PhysiMeSS_cell.cpp b/addons/PhysiMeSS/PhysiMeSS_cell.cpp index 0eb9714e4..70a67b124 100644 --- a/addons/PhysiMeSS/PhysiMeSS_cell.cpp +++ b/addons/PhysiMeSS/PhysiMeSS_cell.cpp @@ -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); @@ -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;; @@ -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; diff --git a/addons/PhysiMeSS/PhysiMeSS_fibre.cpp b/addons/PhysiMeSS/PhysiMeSS_fibre.cpp index cf2aced0b..8f341f812 100644 --- a/addons/PhysiMeSS/PhysiMeSS_fibre.cpp +++ b/addons/PhysiMeSS/PhysiMeSS_fibre.cpp @@ -49,15 +49,15 @@ std::vector* 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; @@ -65,10 +65,12 @@ PhysiMeSS_Fibre::PhysiMeSS_Fibre() 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); } @@ -135,7 +137,7 @@ void PhysiMeSS_Fibre::check_out_of_bounds(std::vector& 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; @@ -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; @@ -227,7 +229,7 @@ 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 old_orientation(3, 0.0); for (int i = 0; i < 2; i++) { old_orientation[i] = state.orientation[i]; @@ -235,7 +237,7 @@ 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; @@ -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 fibre_centre_to_crosslink(3, 0.0); for (int i = 0; i < 2; i++) { @@ -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; diff --git a/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_fibremaze.xml b/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_fibremaze.xml index d1b08c970..c678f72e6 100644 --- a/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_fibremaze.xml +++ b/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_fibremaze.xml @@ -169,7 +169,20 @@ - 1.0 + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + + 0.0 + 1.0 + 0.0 + + 0.6 + 0.1 + 1.0 @@ -261,9 +274,15 @@ - 1.0 - - + 1.0 + 60.0 + 0.0 + 2.0 + 0.0 + 1.57 + 0.0 + + @@ -353,8 +372,13 @@ - 1.0 - + 1.0 + 60.0 + 0.0 + 2.0 + 0.0 + 1.57 + 0.0 @@ -461,31 +485,8 @@ 0 0 - 2000 - true - 60.0 - 0.0 - 2.0 - 0.0 - 1.57 - 0.0 - - false - 0.01 - false - 10.0 - 0.05 - 10.0 false - - false - 1.0 - false - - 0.6 - 0.1 - 1.0 - + \ No newline at end of file diff --git a/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_hinge.xml b/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_hinge.xml index 35ef69c10..9a2bb90ff 100644 --- a/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_hinge.xml +++ b/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_hinge.xml @@ -163,7 +163,20 @@ - 1.0 + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + + 0.0 + 1.0 + 1.0 + + 0.6 + 0.1 + 1.0 @@ -255,9 +268,15 @@ - 1.0 - - + 1.0 + 60.0 + 0.0 + 2.0 + 0.0 + 1.57 + 0.0 + + @@ -347,11 +366,18 @@ - 1.0 - - + 1.0 + 60.0 + 0.0 + 2.0 + 0.0 + 1.57 + 0.0 - + + + + @@ -455,31 +481,8 @@ 0 0 - 2000 - true - 60.0 - 0.0 - 2.0 - 0.0 - 1.57 - 0.0 - - false - 0.01 - false - 10.0 - 0.05 - 10.0 false - - false - 1.0 - true - - 0.6 - 0.1 - 1.0 \ No newline at end of file diff --git a/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_pushing.xml b/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_pushing.xml index c8c28fa12..35f03a44b 100644 --- a/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_pushing.xml +++ b/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_pushing.xml @@ -165,9 +165,22 @@ - 1.0 - - + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + + 1.0 + 1.0 + 0.0 + + 0.6 + 0.1 + 1.0 + + @@ -258,7 +271,15 @@ - 1.0 + + 1.0 + 40.0 + 0.0 + 2.0 + 0.0 + 1.57 + 0.0 + @@ -365,34 +386,13 @@ - 0 - - 1 - 1000 - - true - 40.0 - 0.0 - 2.0 - 0.0 - 1.57 - 0.0 - - false - 0.01 - false - 10.0 - 0.05 - 10.0 - false + 0 - true - 1.0 - false + 1 + 1000 + false - 0.6 - 0.1 - 1.0 + \ No newline at end of file diff --git a/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_rotating.xml b/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_rotating.xml index e8fd8ac3d..00a114827 100644 --- a/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_rotating.xml +++ b/sample_projects/physimess/config/Cell_Fibre_Mechanics/mymodel_rotating.xml @@ -165,7 +165,19 @@ - 1.0 + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + 0.0 + 1.0 + 1.0 + 0.6 + 0.1 + 1.0 + @@ -258,11 +270,17 @@ - 1.0 - - + 1.0 + 40.0 + 0.0 + 2.0 + 0.0 + 1.57 + 0.0 + + - + @@ -369,30 +387,8 @@ 1 1000 - - true - 40.0 - 0.0 - 2.0 - 0.0 - 1.57 - 0.0 - - false - 0.01 - false - 10.0 - 0.05 - 10.0 false - - false - 1.0 - true - - 0.6 - 0.1 - 1.0 + \ No newline at end of file diff --git a/sample_projects/physimess/config/Fibre_Crosslinks/mymodel_extended_fibre_crosslink_test.xml b/sample_projects/physimess/config/Fibre_Crosslinks/mymodel_extended_fibre_crosslink_test.xml index fe0ad3f62..ba3d17974 100644 --- a/sample_projects/physimess/config/Fibre_Crosslinks/mymodel_extended_fibre_crosslink_test.xml +++ b/sample_projects/physimess/config/Fibre_Crosslinks/mymodel_extended_fibre_crosslink_test.xml @@ -177,9 +177,22 @@ - 1.0 - - + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + + 0.0 + 1.0 + 0.0 + + 0.6 + 0.1 + 1.0 + + @@ -275,9 +288,16 @@ - 1.0 - - + 0.0 + 40.0 + 0.0 + 2.0 + 0.0 + 0.2 + 0.0 + + + @@ -387,34 +407,10 @@ - 0 - - 1 - 10000 - - false - 40.0 - 0.0 - 2.0 - 0.0 - 0.2 - 0.0 - - false - 0.01 - false - 10.0 - 0.05 - 10.0 - false - - false - 1.0 - false - - 0.6 - 0.1 - 1.0 - + 0 + 1 + 10000 + false + \ No newline at end of file diff --git a/sample_projects/physimess/config/Fibre_Crosslinks/mymodel_simple_fibre_crosslink_test.xml b/sample_projects/physimess/config/Fibre_Crosslinks/mymodel_simple_fibre_crosslink_test.xml index 75df8c2eb..f485995b2 100644 --- a/sample_projects/physimess/config/Fibre_Crosslinks/mymodel_simple_fibre_crosslink_test.xml +++ b/sample_projects/physimess/config/Fibre_Crosslinks/mymodel_simple_fibre_crosslink_test.xml @@ -162,9 +162,22 @@ - 1.0 - - + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + + 0.0 + 1.0 + 0.0 + + 0.6 + 0.1 + 1.0 + + @@ -254,11 +267,17 @@ - 1.0 - - + 0.0 + 75.0 + 0.0 + 2.0 + 0.0 + 0.2 + 0.0 + + - + @@ -346,11 +365,17 @@ - 1.0 - - + 0.0 + 75.0 + 0.0 + 2.0 + 0.0 + 0.2 + 0.0 + + - + @@ -360,34 +385,10 @@ - 0 - - 1 - 500 - - false - 75.0 - 0.0 - 2.0 - 0.0 - 0.2 - 0.0 - - false - 0.01 - false - 10.0 - 0.05 - 10.0 - false - - false - 1.0 - false - - 0.6 - 0.1 - 1.0 - + 0 + 1 + 500 + false + diff --git a/sample_projects/physimess/config/Fibre_Degradation/mymodel_fibre_degradation.xml b/sample_projects/physimess/config/Fibre_Degradation/mymodel_fibre_degradation.xml index b9e704b81..785b62717 100644 --- a/sample_projects/physimess/config/Fibre_Degradation/mymodel_fibre_degradation.xml +++ b/sample_projects/physimess/config/Fibre_Degradation/mymodel_fibre_degradation.xml @@ -163,7 +163,21 @@ - 1.0 + + 1.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + + 0.0 + 1.0 + 0.0 + + 0.6 + 0.1 + 1.0 @@ -255,7 +269,14 @@ - 1.0 + 0.0 + 40.0 + 0.0 + 2.0 + 0.0 + 0.0 + 0.0 + @@ -361,33 +382,10 @@ - 0 - 1 - - 1000 - false - 40.0 - 0.0 - 2.0 - 0.0 - 0.0 - 0.0 - - true - 0.01 - false - 10.0 - 0.05 - 10.0 - false - - false - 1.0 - false - - 0.6 - 0.1 - 1.0 - + 0 + 1 + 1000 + false + \ No newline at end of file diff --git a/sample_projects/physimess/config/Fibre_Degradation/mymodel_matrix_degradation.xml b/sample_projects/physimess/config/Fibre_Degradation/mymodel_matrix_degradation.xml index 6b9cc00ec..435cf404d 100644 --- a/sample_projects/physimess/config/Fibre_Degradation/mymodel_matrix_degradation.xml +++ b/sample_projects/physimess/config/Fibre_Degradation/mymodel_matrix_degradation.xml @@ -164,9 +164,20 @@ - 1.0 - - + 1.0 + 0.001 + 1.0 + 10000.0 + 0.05 + 10.0 + 0.0 + 1.0 + 0.0 + 0.6 + 0.1 + 1.0 + + @@ -256,11 +267,18 @@ - 1.0 - - + 0.0 + 40.0 + 0.0 + 2.0 + 0.0 + 0.0 + 0.0 + + + - + @@ -270,34 +288,10 @@ - 0 - 1 - - 1000 - false - 40.0 - 0.0 - 2.0 - 0.0 - 0.0 - 0.0 - - - true - 0.001 - true - 10000.0 - 0.05 - 10.0 - - false - 1.0 - false - - 0.6 - 0.1 - 1.0 - true - + 0 + 1 + 1000 + true + \ No newline at end of file diff --git a/sample_projects/physimess/config/Fibre_Initialisation/mymodel_initialisation.xml b/sample_projects/physimess/config/Fibre_Initialisation/mymodel_initialisation.xml index f03ca8ec9..b31e82b39 100644 --- a/sample_projects/physimess/config/Fibre_Initialisation/mymodel_initialisation.xml +++ b/sample_projects/physimess/config/Fibre_Initialisation/mymodel_initialisation.xml @@ -163,9 +163,20 @@ - 1.0 - - + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + 0.0 + 1.0 + 0.0 + 0.6 + 0.1 + 1.0 + + @@ -255,9 +266,15 @@ - 1.0 - - + 0.0 + 75.0 + 0.0 + 2.0 + 0.0 + 0.0 + 0.0 + + @@ -361,33 +378,10 @@ - 0 - 0 - - 2000 - false - 75.0 - 0.0 - 2.0 - 0.0 - 0.0 - 0.0 - - false - 0.01 - false - 10.0 - 0.05 - 10.0 - false - - false - 1.0 - false - - 0.6 - 0.1 - 1.0 - + 0 + 0 + 2000 + false + \ No newline at end of file diff --git a/sample_projects/physimess/config/Fibre_Initialisation/mymodel_initialisation_maze.xml b/sample_projects/physimess/config/Fibre_Initialisation/mymodel_initialisation_maze.xml index 820cc9919..153e35392 100644 --- a/sample_projects/physimess/config/Fibre_Initialisation/mymodel_initialisation_maze.xml +++ b/sample_projects/physimess/config/Fibre_Initialisation/mymodel_initialisation_maze.xml @@ -163,9 +163,20 @@ - 1.0 - - + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + 0.0 + 1.0 + 0.0 + 0.6 + 0.1 + 1.0 + + @@ -255,9 +266,15 @@ - 1.0 - - + 0.0 + 40.0 + 0.0 + 2.0 + 0.0 + 0.0 + 0.0 + + @@ -347,7 +364,14 @@ - 1.0 + 0.0 + 40.0 + 0.0 + 2.0 + 0.0 + 0.0 + 0.0 + @@ -361,33 +385,10 @@ - 0 - 0 - - 2000 - false - 40.0 - 0.0 - 2.0 - 0.0 - 0.0 - 0.0 - - false - 0.01 - false - 10.0 - 0.05 - 10.0 - false - - false - 1.0 - false - - 0.6 - 0.1 - 1.0 - + 0 + 0 + 2000 + false + \ No newline at end of file diff --git a/sample_projects/physimess/config/Neighbours_in_voxels/mymodel_neighbours.xml b/sample_projects/physimess/config/Neighbours_in_voxels/mymodel_neighbours.xml index 8ecd379cd..d29e7e193 100644 --- a/sample_projects/physimess/config/Neighbours_in_voxels/mymodel_neighbours.xml +++ b/sample_projects/physimess/config/Neighbours_in_voxels/mymodel_neighbours.xml @@ -177,9 +177,20 @@ - 1.0 - - + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 10.0 + 0.0 + 1.0 + 0.0 + 0.6 + 0.1 + 1.0 + + @@ -275,11 +286,17 @@ - 1.0 - - + 1.0 + 250.0 + 0.0 + 2.0 + 0.0 + 0.0 + 0.0 + + - + @@ -289,34 +306,10 @@ - 0 - - 1 - 10000 - - true - 250.0 - 0.0 - 2.0 - 0.0 - 0.0 - 0.0 - - false - 0.01 - false - 10.0 - 0.05 - 10.0 - false - - false - 1.0 - false - - 0.6 - 0.1 - 1.0 - + 0 + 1 + 10000 + false + \ No newline at end of file diff --git a/sample_projects/physimess/config/PhysiCell_settings.xml b/sample_projects/physimess/config/PhysiCell_settings.xml index f2b54c3de..9f7549eee 100644 --- a/sample_projects/physimess/config/PhysiCell_settings.xml +++ b/sample_projects/physimess/config/PhysiCell_settings.xml @@ -219,7 +219,17 @@ - 1.0 + 0.0 + 0.01 + 0.0 + 10.0 + 0.05 + 0.0 + 1.0 + 0.0 + 0.6 + 0.1 + 1.0 @@ -360,6 +370,12 @@ 1.0 + 0.0 + 75.0 + 0.0 + 2.0 + 0.0 + 0.0 @@ -516,23 +532,6 @@ 0 0 2000 - false - 75.0 - 0.0 - 2.0 - 0.0 - 0.0 - false - 0.01 - false - 10.0 - 0.05 - false - 1.0 - false - 0.6 - 0.1 - 1.0 true diff --git a/sample_projects/physimess/custom_modules/custom.cpp b/sample_projects/physimess/custom_modules/custom.cpp index 0f5a7d4d3..6fc97a914 100644 --- a/sample_projects/physimess/custom_modules/custom.cpp +++ b/sample_projects/physimess/custom_modules/custom.cpp @@ -87,10 +87,7 @@ void create_cell_types( void ) initialize_default_cell_definition(); cell_defaults.phenotype.secretion.sync_to_microenvironment( µenvironment ); - if (PhysiCell::parameters.bools("fibre_custom_degradation")) - cell_defaults.functions.instantiate_cell = instantiate_physimess_cell_custom_degrade; - else - cell_defaults.functions.instantiate_cell = instantiate_physimess_cell; + cell_defaults.functions.instantiate_cell = instantiate_physimess_cell; cell_defaults.functions.volume_update_function = standard_volume_update_function; cell_defaults.functions.update_velocity = physimess_update_cell_velocity; @@ -141,7 +138,13 @@ void create_cell_types( void ) pCD->functions.plot_agent_legend = fibre_agent_legend; } - + + for (auto* pCD: cell_definitions_by_index){ + if (!isFibre(pCD) && pCD->custom_data.find_variable_index("fibre_custom_degradation") > 0){ + if (pCD->custom_data["fibre_custom_degradation"] > 0.5) + pCD->functions.instantiate_cell = instantiate_physimess_cell_custom_degrade; + } + } /* This builds the map of cell definitions and summarizes the setup. */ @@ -314,9 +317,9 @@ void PhysiMeSS_Cell_Custom_Degrade::degrade_fibre(PhysiMeSS_Fibre* pFibre) // Fibre degradation by cell - switched on by flag fibre_degradation - double stuck_threshold = PhysiCell::parameters.doubles("fibre_stuck_time"); - double pressure_threshold = PhysiCell::parameters.doubles("fibre_pressure_threshold"); - if (PhysiCell::parameters.bools("fibre_degradation") && (stuck_counter >= stuck_threshold + double stuck_threshold = this->custom_data["fibre_stuck_time"]; + double pressure_threshold = this->custom_data["fibre_pressure_threshold"]; + if (this->custom_data["fibre_degradation"] > 0.5 && (stuck_counter >= stuck_threshold || state.simple_pressure > pressure_threshold)) { // if (stuck_counter >= stuck_threshold){ // std::cout << "Cell " << ID << " is stuck at time " << PhysiCell::PhysiCell_globals.current_time @@ -330,7 +333,7 @@ void PhysiMeSS_Cell_Custom_Degrade::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 (state.simple_pressure > pressure_threshold){ prob_degradation *= state.simple_pressure; } diff --git a/sample_projects/physimess/custom_modules/custom.h b/sample_projects/physimess/custom_modules/custom.h index e4dac7cfc..a17087254 100644 --- a/sample_projects/physimess/custom_modules/custom.h +++ b/sample_projects/physimess/custom_modules/custom.h @@ -100,5 +100,4 @@ class PhysiMeSS_Cell_Custom_Degrade : public PhysiMeSS_Cell { public: void degrade_fibre(PhysiMeSS_Fibre* pFibre); -}; -// void PhysiMeSS_Cell::other_degrade_fibre(PhysiMeSS_Fibre* pFibre); \ No newline at end of file +}; \ No newline at end of file From 95cea8d5d7633fc2f993e716e9fc08bc5ef7e0b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vincent=20No=C3=ABl?= Date: Tue, 9 Jul 2024 14:53:22 -0300 Subject: [PATCH 2/3] Bumped PhysiMeSS version to 1.0.1 --- addons/PhysiMeSS/PhysiMeSS.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/addons/PhysiMeSS/PhysiMeSS.h b/addons/PhysiMeSS/PhysiMeSS.h index de1911a17..005fdf4fd 100644 --- a/addons/PhysiMeSS/PhysiMeSS.h +++ b/addons/PhysiMeSS/PhysiMeSS.h @@ -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(); @@ -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 (*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 (*cell_coloring_function)(Cell*), double temp_cell_radius); -#endif \ No newline at end of file +#endif From c260aa073396b1b4f8c177a72ac62860e2c1a090 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vincent=20No=C3=ABl?= Date: Fri, 6 Sep 2024 16:09:24 -0300 Subject: [PATCH 3/3] Updated test case for physimess --- .../snapshot00000000.svg | 752 ++++++++--------- .../snapshot00000001.svg | 758 +++++++++--------- .../snapshot00000002.svg | 758 +++++++++--------- .../snapshot00000003.svg | 758 +++++++++--------- .../snapshot00000004.svg | 758 +++++++++--------- .../snapshot00000005.svg | 758 +++++++++--------- .../snapshot00000006.svg | 758 +++++++++--------- .../snapshot00000007.svg | 758 +++++++++--------- .../snapshot00000008.svg | 758 +++++++++--------- .../snapshot00000009.svg | 758 +++++++++--------- .../snapshot00000010.svg | 758 +++++++++--------- .../snapshot00000011.svg | 758 +++++++++--------- .../snapshot00000012.svg | 758 +++++++++--------- .../snapshot00000013.svg | 758 +++++++++--------- .../snapshot00000014.svg | 758 +++++++++--------- .../snapshot00000015.svg | 758 +++++++++--------- .../snapshot00000016.svg | 758 +++++++++--------- .../snapshot00000017.svg | 758 +++++++++--------- .../snapshot00000018.svg | 758 +++++++++--------- .../snapshot00000019.svg | 758 +++++++++--------- .../snapshot00000020.svg | 758 +++++++++--------- .../snapshot00000021.svg | 758 +++++++++--------- .../snapshot00000022.svg | 758 +++++++++--------- .../snapshot00000023.svg | 758 +++++++++--------- .../snapshot00000024.svg | 758 +++++++++--------- 25 files changed, 9472 insertions(+), 9472 deletions(-) diff --git a/tests/cases/output_physimess-sample/snapshot00000000.svg b/tests/cases/output_physimess-sample/snapshot00000000.svg index a8e1cda47..9c56e60f3 100644 --- a/tests/cases/output_physimess-sample/snapshot00000000.svg +++ b/tests/cases/output_physimess-sample/snapshot00000000.svg @@ -32,1129 +32,1129 @@ - 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