Laboratoire RDP » Biophysics Team » Vascular Networks in Growing Leaves

#include <iostream>

#include <string.h>

#include <stdlib.h>

#include <stdio.h>

#include <time.h>

#include "step.h"

#include "constants.h"

#include <math.h>

#include <fstream>

#include "minimize_BFGS.h"

#include <omp.h>

#include <dirent.h>

#include "save_data.h"

#include "save_data_2.h"

#include <cmath>

#include "compute_lengths.h"

#include "optimize_width.h"

using namespace std;

int main(){

/// initialization of the seed for the random number generator

srand(time(NULL));

/// parallelizing over the 3 loops

#pragma omp parallel for collapse(3) schedule(dynamic,1)

for (int index_growth=0;index_growth<=4;index_growth+=1){ // law for growth of the veins

for (int index_stress=11;index_stress<=20;index_stress+=1){ // level of applied stress

for (int index_tissue=1;index_tissue<=57;index_tissue+=1){ // index of the tissue

//growth=2;

growth=index_growth;

growth_threshold=6;//10.;

//growth_threshold=1.+12.*(double)index_growth/20.;

//growth_threshold=0.6*(1.+12.*(double)index_growth/20.);

stress_x=0.;

/// the folder in which the data are saved

char folder[32]; strcpy(folder,"optimized_2/");

/// in this folder, the folder corresponding to each growth mode

char growth_char[32]; //sprintf(growth_char,"%d/",index_growth);

if (growth==0){ strcpy(growth_char,"linear/");}

if (growth==1){ strcpy(growth_char,"saturated/");}

if (growth==2){ strcpy(growth_char,"threshold/");}

if (growth==3){ strcpy(growth_char,"quadratic/");}

if (growth==4){ strcpy(growth_char,"max/");}

/// in this folder, the folder corresponding to the external stress level, then the beginning of the name of the file which corresponds to the index of the initial condition

char indices[8]; sprintf(indices,"%i/%i_",index_stress,index_tissue);

/// the total path to the file which will be saved

char file_name[256]; strcpy(file_name,"results/"); strcat(file_name,folder); strcat(file_name,growth_char); strcat(file_name,indices);

/// extraction of the intial data from Yohai

int vertex_number, edge_number, cell_number;

double * width; width=(double*)calloc(1,sizeof(double));

double * height; height=(double*)calloc(1,sizeof(double));

char file_name_init[256];

sprintf(file_name_init,"/home/jjulien/Documents/Programmation/Leaf/Init/%i.toy",index_tissue);

ifstream file;

file.open(file_name_init);

file >> width[0];

file >> height[0];

file >> vertex_number;

file >> edge_number;

file >> cell_number;

double * vertices; vertices=(double*)calloc(2*vertex_number,sizeof(double));

double * lengths; lengths=(double*)calloc(edge_number,sizeof(double)); /* lengths of the walls */

double * rest_lengths; rest_lengths=(double*)calloc(edge_number,sizeof(double)); /* targets of the walls */

double * edges_width; edges_width=(double*)calloc(edge_number,sizeof(double));

int * edges_cells; edges_cells=(int*)calloc(2*edge_number,sizeof(int));

int * edges_vertices; edges_vertices=(int*)calloc(2*edge_number,sizeof(double));

int * periodizer; periodizer=(int*)calloc(4*edge_number,sizeof(double));

int count=0;

while (count<(2*vertex_number)){

    file >> vertices[count];

    count++;

}

count=0;

while (count<edge_number){

    file >> edges_cells[2*count];

    file >> edges_cells[2*count+1];

    file >> edges_vertices[2*count];

    file >> periodizer[4*count];

    file >> periodizer[4*count+1];

    file >> edges_vertices[2*count+1];

    file >> periodizer[4*count+2];

    file >> periodizer[4*count+3];

    file >> rest_lengths[count];

    file >> edges_width[count];

    count++;

}

/// extraction of the initial data over

/// optimization of the width of the veins in order to get an homogeneous stress, then saving of the tissue

optimize_width(vertex_number, vertices, edge_number, edges_vertices, lengths, rest_lengths, edges_width, periodizer, width, height);

compute_lengths(vertices, edges_vertices, edge_number, lengths, periodizer, width[0], height[0]);

sigma=sqrt(30.*width[0]*height[0]/(pi*cell_number));

{FILE *f=NULL;  char file_name_2[256]; strcpy(file_name_2,file_name); strcat(file_name_2,"optimized.sce");

f=fopen(file_name_2,"w+");

save_data(f, vertex_number, vertices, edge_number, edges_vertices, lengths, rest_lengths, edges_width, edges_cells, periodizer, width[0], height[0], cell_number);

fclose(f);} // width optimized

/// noise in the width of the veins in order to get the non-affinity index consistent with the experimental data

for (int i=0; i<edge_number; i++){ edges_width[i]*=1.+0.4*(2.*(double)rand()/(double)RAND_MAX-1.);}

//{

//    double mean_width=0.;

//    for (int i=0; i<edge_number; i++){ mean_width+=edges_width[i];}

//    mean_width/=edge_number;

//    growth_threshold/=mean_width;

//}

/// application of the external stretching, then saving of the tissue

stress_x=(double)index_stress/10.;

minimize_BFGS(vertex_number, vertices, edge_number, edges_vertices, lengths, rest_lengths, edges_width, periodizer, width, height);

compute_lengths(vertices, edges_vertices, edge_number, lengths, periodizer, width[0], height[0]); //for (int i=0; i<edge_number;i++){printf("%f \n",(lengths[i]/*-rest_lengths[i]*/)/(rest_lengths[i]));}

sigma=sqrt(30.*width[0]*height[0]/(pi*cell_number));

{FILE *f=NULL;  char file_name_2[256]; strcpy(file_name_2,file_name); strcat(file_name_2,"before.sce");

f=fopen(file_name_2,"w+");

save_data(f, vertex_number, vertices, edge_number, edges_vertices, lengths, rest_lengths, edges_width, edges_cells, periodizer, width[0], height[0], cell_number);

fclose(f);} // tissue stretched

/// growth until the tissue double its size

int iteration=0.; double max_area=2.*width[0]*height[0];

while ((width[0]*height[0])<max_area){

    step(vertices, vertex_number, edge_number, edges_vertices, lengths, rest_lengths, edges_width, periodizer, width, height);

    compute_lengths(vertices, edges_vertices, edge_number, lengths, periodizer, width[0], height[0]);

    iteration++; printf("%d %d %d\n",index_stress,index_tissue, iteration);

} // end of growth

/// saving of the tissue

minimize_BFGS(vertex_number, vertices, edge_number, edges_vertices, lengths, rest_lengths, edges_width, periodizer, width, height);

compute_lengths(vertices, edges_vertices, edge_number, lengths, periodizer, width[0], height[0]);

sigma=sqrt(30.*width[0]*height[0]/(pi*cell_number));

{FILE *f=NULL;  char file_name_2[256]; strcpy(file_name_2,file_name); strcat(file_name_2,"after.sce");

f=fopen(file_name_2,"w+");

save_data_2(f, vertex_number, vertices, edge_number, edges_vertices, lengths, rest_lengths, edges_width, edges_cells, periodizer, width[0], height[0], cell_number);

fclose(f);} /// tissue saved

/// free the memory

free(vertices); free(edges_vertices); free(lengths); free(rest_lengths); free(edges_width); free(edges_cells); free(periodizer); free(width); free(height);

}}}

return 0;

}