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Merge pull request #167 from sysbio-curie/addon/physimess
PhysiMeSS addon and sample project
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,254 @@ | ||
| #include "PhysiMeSS.h" | ||
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| #include <algorithm> | ||
| #include <iterator> | ||
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| static double last_update_time = -mechanics_dt; | ||
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| void remove_physimess_out_of_bounds_fibres() | ||
| { | ||
| for (auto* cell : *all_cells) { | ||
| if (isFibre(cell) && static_cast<PhysiMeSS_Fibre*>(cell)->fail_count >= 10) | ||
| { | ||
| // std::cout << "I failed to place " << cell->type_name << " " | ||
| // << cell->ID << " in the domain - I am deleting agent " | ||
| // << std::endl; | ||
| delete_cell(cell); | ||
| } | ||
| } | ||
| } | ||
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| void physimess_update_cell_velocity( Cell* pCell, Phenotype& phenotype, double dt) | ||
| { | ||
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| double movement_threshold = PhysiCell::parameters.doubles("fibre_stuck_threshold"); | ||
| if (!isFibre(pCell) && phenotype.motility.is_motile) { | ||
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| // 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 | ||
| // So I'm using the previous velocity, which is not exactly the same (because of Adams-Bashforth), but is a good proxy | ||
| // if (dist(pCell->old_position, pCell->position) < movement_threshold) { | ||
| if (norm(pCell->get_previous_velocity())*mechanics_dt < movement_threshold) { | ||
| static_cast<PhysiMeSS_Cell*>(pCell)->stuck_counter++; | ||
| } else { | ||
| static_cast<PhysiMeSS_Cell*>(pCell)->stuck_counter = 0; | ||
| } | ||
| } | ||
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| if( pCell->functions.add_cell_basement_membrane_interactions ) | ||
| { | ||
| pCell->functions.add_cell_basement_membrane_interactions(pCell, phenotype,dt); | ||
| } | ||
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| pCell->state.simple_pressure = 0.0; | ||
| pCell->state.neighbors.clear(); // new 1.8.0 | ||
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| if (!isFibre(pCell)) { | ||
| //First check the neighbors in my current voxel | ||
| for (auto* neighbor: pCell->get_container()->agent_grid[pCell->get_current_mechanics_voxel_index()]) | ||
| { | ||
| if (!isFibre(neighbor)) { | ||
| pCell->add_potentials(neighbor); | ||
| } | ||
| } | ||
| for (auto neighbor_voxel_index: pCell->get_container()->underlying_mesh.moore_connected_voxel_indices[pCell->get_current_mechanics_voxel_index()]) | ||
| { | ||
| if(!is_neighbor_voxel(pCell, pCell->get_container()->underlying_mesh.voxels[pCell->get_current_mechanics_voxel_index()].center, pCell->get_container()->underlying_mesh.voxels[neighbor_voxel_index].center, neighbor_voxel_index)) | ||
| continue; | ||
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| for (auto* neighbor: pCell->get_container()->agent_grid[neighbor_voxel_index]) | ||
| { | ||
| if (!isFibre(neighbor)) { | ||
| pCell->add_potentials(neighbor); | ||
| } | ||
| } | ||
| } | ||
| } else { | ||
| // Count crosslinks | ||
| static_cast<PhysiMeSS_Fibre*>(pCell)->X_crosslink_count = 0; | ||
| if (static_cast<PhysiMeSS_Fibre*>(pCell)->fibres_crosslinkers.size() > 0){ | ||
| static_cast<PhysiMeSS_Fibre*>(pCell)->X_crosslink_count = static_cast<PhysiMeSS_Fibre*>(pCell)->fibres_crosslinkers.size(); | ||
| } | ||
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| } | ||
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| // std::cout << " AGENT " << pCell->type_name << " " << pCell->ID << " has " ; | ||
| //add potentials between pCell and its neighbors | ||
| for (auto* neighbor : static_cast<PhysiMeSS_Agent*>(pCell)->physimess_neighbors) | ||
| { | ||
| // std::cout << neighbor->type_name << " " << neighbor->ID << " " ; | ||
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| // if( this->ID == other_agent->ID ) | ||
| if( pCell != neighbor ) | ||
| { | ||
| if (!isFibre(pCell) && !isFibre(neighbor)) { | ||
| //Already done above | ||
| continue; | ||
| } else | ||
| if (!isFibre(pCell) && isFibre(neighbor)) { | ||
| static_cast<PhysiMeSS_Cell*>(pCell)->add_potentials_from_fibre(static_cast<PhysiMeSS_Fibre*>(neighbor)); | ||
| } else if (isFibre(pCell) && !isFibre(neighbor)) { | ||
| static_cast<PhysiMeSS_Fibre*>(pCell)->add_potentials_from_cell(static_cast<PhysiMeSS_Cell*>(neighbor)); | ||
| } else if (isFibre(pCell) && isFibre(neighbor)) { | ||
| static_cast<PhysiMeSS_Fibre*>(pCell)->add_potentials_from_fibre(static_cast<PhysiMeSS_Fibre*>(neighbor)); | ||
| } else { | ||
| // std::cout << " WARNING: interaction between errant cell-types has been called : " << pCell->type_name << ", " << neighbor->type_name << std::endl; | ||
| return; | ||
| } | ||
| } | ||
| } | ||
| // std::cout << std::endl; | ||
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| if (!isFibre(pCell)) { | ||
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| PhysiMeSS_Cell* ppCell = static_cast<PhysiMeSS_Cell*>(pCell); | ||
| int stuck_threshold = 10; | ||
| int unstuck_threshold = 1; | ||
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| if (ppCell->stuck_counter == stuck_threshold){ | ||
| // std::cout << "!HELP! cell " << pCell->ID << " gets stuck at time " | ||
| // << PhysiCell_globals.current_time << std::endl; | ||
| ppCell->stuck_counter = 0; | ||
| ppCell->unstuck_counter = 1; | ||
| } | ||
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| if (1 <= ppCell->unstuck_counter && ppCell->unstuck_counter < unstuck_threshold+1) { | ||
| /*std::cout << " getting unstuck at time " | ||
| << PhysiCell_globals.current_time << std::endl;*/ | ||
| ppCell->unstuck_counter++; | ||
| ppCell->force_update_motility_vector(dt); | ||
| ppCell->velocity += phenotype.motility.motility_vector; | ||
| } | ||
| else { | ||
| pCell->update_motility_vector(dt); | ||
| pCell->velocity += phenotype.motility.motility_vector; | ||
| } | ||
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| if(ppCell->unstuck_counter == unstuck_threshold+1){ | ||
| ppCell->unstuck_counter = 0; | ||
| } | ||
| } | ||
| return; | ||
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| } | ||
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| void physimess_mechanics( double dt ) | ||
| { | ||
| static double dt_tolerance = 0.001 * dt; | ||
| if(fabs(((PhysiCell_globals.current_time - last_update_time)) - dt) < dt_tolerance) | ||
| { | ||
| last_update_time = PhysiCell_globals.current_time; | ||
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| #pragma omp parallel for | ||
| for( int i=0; i < (*all_cells).size(); i++ ) | ||
| { | ||
| Cell* pC = (*all_cells)[i]; | ||
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| static_cast<PhysiMeSS_Agent*>(pC)->physimess_voxels.clear(); | ||
| if( !pC->is_out_of_domain ) | ||
| { | ||
| static_cast<PhysiMeSS_Agent*>(pC)->register_fibre_voxels(); | ||
| } | ||
| } | ||
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| #pragma omp parallel for | ||
| for( int i=0; i < (*all_cells).size(); i++ ) | ||
| { | ||
| Cell* pC = (*all_cells)[i]; | ||
| static_cast<PhysiMeSS_Agent*>(pC)->physimess_neighbors.clear(); | ||
| if (isFibre(pC)) { | ||
| static_cast<PhysiMeSS_Fibre*>(pC)->fibres_crosslinkers.clear(); | ||
| } | ||
| if( !pC->is_out_of_domain ) | ||
| { | ||
| static_cast<PhysiMeSS_Agent*>(pC)->find_agent_neighbors(); | ||
| } | ||
| } | ||
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| #pragma omp parallel for | ||
| for( int i=0; i < (*all_cells).size(); i++ ) | ||
| { | ||
| Cell* pC = (*all_cells)[i]; | ||
| if( !pC->is_out_of_domain ) | ||
| { | ||
| static_cast<PhysiMeSS_Agent*>(pC)->deregister_fibre_voxels(); | ||
| } | ||
| } | ||
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| // determine and add crosslinks | ||
| #pragma omp parallel for | ||
| for( int i=0; i < (*all_cells).size(); i++ ) | ||
| { | ||
| Cell* pC = (*all_cells)[i]; | ||
| if (isFibre(pC)) { | ||
| static_cast<PhysiMeSS_Fibre*>(pC)->add_crosslinks(); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| void fibre_agent_SVG(std::ofstream& os, PhysiCell::Cell* pC, double z_slice, std::vector<std::string> (*cell_coloring_function)(Cell*), double X_lower, double Y_lower) { | ||
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| // place a rod if it's a fibre (note fibre already renamed here) | ||
| if (isFibre(pC) ){ | ||
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| PhysiMeSS_Fibre* pFibre = static_cast<PhysiMeSS_Fibre*>(pC); | ||
| int crosslinks = pFibre->X_crosslink_count; | ||
| if (crosslinks >= 3){ | ||
| // if fibre has cross-links different colour than if not | ||
| Write_SVG_line(os, (pC->position)[0] - (pFibre->mLength) * (pC->state.orientation)[0] - X_lower, | ||
| (pC->position)[1] - (pFibre->mLength) * (pC->state.orientation)[1] - Y_lower, | ||
| (pC->position)[0] + (pFibre->mLength) * (pC->state.orientation)[0] - X_lower, | ||
| (pC->position)[1] + (pFibre->mLength) * (pC->state.orientation)[1] - Y_lower, | ||
| 4.0, "darkblue"); | ||
| } | ||
| else if (crosslinks == 2){ | ||
| // if fibre has cross-links different colour than if not | ||
| Write_SVG_line(os, (pC->position)[0] - (pFibre->mLength) * (pC->state.orientation)[0] - X_lower, | ||
| (pC->position)[1] - (pFibre->mLength) * (pC->state.orientation)[1] - Y_lower, | ||
| (pC->position)[0] + (pFibre->mLength) * (pC->state.orientation)[0] - X_lower, | ||
| (pC->position)[1] + (pFibre->mLength) * (pC->state.orientation)[1] - Y_lower, | ||
| 4.0, "blue"); | ||
| } | ||
| else if (crosslinks == 1){ | ||
| // if fibre has cross-links different colour than if not | ||
| Write_SVG_line(os, (pC->position)[0] - (pFibre->mLength) * (pC->state.orientation)[0] - X_lower, | ||
| (pC->position)[1] - (pFibre->mLength) * (pC->state.orientation)[1] - Y_lower, | ||
| (pC->position)[0] + (pFibre->mLength) * (pC->state.orientation)[0] - X_lower, | ||
| (pC->position)[1] + (pFibre->mLength) * (pC->state.orientation)[1] - Y_lower, | ||
| 4.0, "steelblue"); | ||
| } | ||
| else { | ||
| Write_SVG_line(os, (pC->position)[0] - (pFibre->mLength) * (pC->state.orientation)[0] - X_lower, | ||
| (pC->position)[1] - (pFibre->mLength) * (pC->state.orientation)[1] - Y_lower, | ||
| (pC->position)[0] + (pFibre->mLength) * (pC->state.orientation)[0] - X_lower, | ||
| (pC->position)[1] + (pFibre->mLength) * (pC->state.orientation)[1] - Y_lower, | ||
| 4.0, "lightskyblue"); | ||
| } | ||
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| } | ||
| else{ | ||
| standard_agent_SVG(os, pC, z_slice, cell_coloring_function, X_lower, Y_lower); | ||
| } | ||
| } | ||
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| 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) { | ||
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| // switch to the cell type | ||
| Cell C; | ||
| C.convert_to_cell_definition( *cell_definition ); | ||
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| // get the colors using the current coloring function | ||
| std::vector<std::string> colors = cell_coloring_function(&C); | ||
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| // place the label | ||
| // place a rod if it's a fibre (note fibre not yet renamed) | ||
| if (isFibre(&C)) { | ||
| //Write_SVG_fibre(os, cursor_x, cursor_y , 0.5*temp_cell_radius , 1.0 , colors[1] , colors[0] ); | ||
| Write_SVG_line(os, cursor_x, cursor_y-20.0 , cursor_x , cursor_y+20.0 , 4.0 , "lightskyblue" ); | ||
| } | ||
| else { | ||
| standard_agent_legend(os, cell_definition, cursor_x, cursor_y, cell_coloring_function, temp_cell_radius); | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| #ifndef __PHYSIMESS__ | ||
| #define __PHYSIMESS__ | ||
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| #include "../../core/PhysiCell_cell.h" | ||
| #include "../../modules/PhysiCell_pathology.h" | ||
| #include "PhysiMeSS_cell.h" | ||
| #include "PhysiMeSS_fibre.h" | ||
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| #include <list> | ||
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| using namespace PhysiCell; | ||
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| static std::string PhysiMeSS_Version = "1.0.0"; | ||
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| void remove_physimess_out_of_bounds_fibres(); | ||
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| void physimess_mechanics( double dt ); | ||
| void physimess_update_cell_velocity( Cell* pCell, Phenotype& phenotype, double dt); | ||
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| 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); | ||
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| #endif |
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