io.cpp

//Add <nowarn/> to the root of init files to disable warnings about missing agent properties
void readInitialStates(char* inputpath, xmachine_memory_keratinocyte_list* h_keratinocytes, int* h_xmachine_memory_keratinocyte_count)
{

  //These values aren't used
	int temp = 0;
	int* itno = &temp;
	
	/* Initialise variables */
    agent_maximum.x = 0;
    agent_maximum.y = 0;
    agent_maximum.z = 0;
    agent_minimum.x = 0;
    agent_minimum.y = 0;
    agent_minimum.z = 0;

	
	//set all keratinocyte values to 0
	//If this is not done then it will cause errors in emu mode where undefined memory is not 0
	for (int k=0; k<xmachine_memory_keratinocyte_MAX; k++)
	{	
		h_keratinocytes->id[k] = 0;
		h_keratinocytes->type[k] = 0;
		h_keratinocytes->x[k] = 0;
		h_keratinocytes->y[k] = 0;
		h_keratinocytes->z[k] = 0;
		h_keratinocytes->force_x[k] = 0;
		h_keratinocytes->force_y[k] = 0;
		h_keratinocytes->force_z[k] = 0;
		h_keratinocytes->num_xy_bonds[k] = 0;
		h_keratinocytes->num_z_bonds[k] = 0;
		h_keratinocytes->num_stem_bonds[k] = 0;
		h_keratinocytes->cycle[k] = 0;
		h_keratinocytes->diff_noise_factor[k] = 0;
		h_keratinocytes->dead_ticks[k] = 0;
		h_keratinocytes->contact_inhibited_ticks[k] = 0;
		h_keratinocytes->motility[k] = 0;
		h_keratinocytes->dir[k] = 0;
		h_keratinocytes->movement[k] = 0;
	}
	

  /* Open file for parsing */
	rapidxml::xml_document<> doc;    // character type defaults to char
	std::ifstream file(inputpath);
	if (!file.is_open())
	{
		printf("ERROR: Could not open initialisation file %s\n", inputpath);
		exit(0);
	}
	std::stringstream buffer;
	buffer << file.rdbuf();
	std::string content(buffer.str());
	doc.parse<0>(&content[0]);
  
  //Allocate buffers for array properties
  

  
  //Allocate nodes
  rapidxml::xml_node<> *root_node = doc.first_node("states");
  rapidxml::xml_node<> *xagent_node = root_node->first_node("xagent");
  rapidxml::xml_node<> *env_node = root_node->first_node("environment");
  rapidxml::xml_node<> *name_node=0, *t_node=0;
  bool noWarn = doc.first_node("nowarn")!=0;
  
  //Set itno
  t_node = root_node->first_node("itno");
  if(t_node)
    (*itno) = atoi(t_node->value());
  
  //Iterate all xagent nodes
  while (xagent_node)
  {
    //Extract name of xagent
    name_node = xagent_node->first_node("name");
    
    //Check: Name node missing
    if(!name_node){
      printf("ERROR: Agent node missing name property.\n");
      exit(0);
    }
    if (strcmp(name_node->value(), "keratinocyte") == 0)
    {
      //Check: Too many agents
      if (*h_xmachine_memory_keratinocyte_count > xmachine_memory_keratinocyte_MAX){
        printf("ERROR: MAX Buffer size (%i) for agent keratinocyte exceeded whilst reading data\n", xmachine_memory_keratinocyte_MAX);
        exit(0);
      }
      //Extract the agent properties
      t_node = xagent_node->first_node("id");
      if(t_node){
        h_keratinocytes->id[*h_xmachine_memory_keratinocyte_count] = (int) atoi(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'id' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("type");
      if(t_node){
        h_keratinocytes->type[*h_xmachine_memory_keratinocyte_count] = (int) atoi(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'type' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("x");
      if(t_node){
        h_keratinocytes->x[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'x' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("y");
      if(t_node){
        h_keratinocytes->y[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'y' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("z");
      if(t_node){
        h_keratinocytes->z[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'z' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("force_x");
      if(t_node){
        h_keratinocytes->force_x[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'force_x' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("force_y");
      if(t_node){
        h_keratinocytes->force_y[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'force_y' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("force_z");
      if(t_node){
        h_keratinocytes->force_z[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'force_z' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("num_xy_bonds");
      if(t_node){
        h_keratinocytes->num_xy_bonds[*h_xmachine_memory_keratinocyte_count] = (int) atoi(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'num_xy_bonds' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("num_z_bonds");
      if(t_node){
        h_keratinocytes->num_z_bonds[*h_xmachine_memory_keratinocyte_count] = (int) atoi(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'num_z_bonds' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("num_stem_bonds");
      if(t_node){
        h_keratinocytes->num_stem_bonds[*h_xmachine_memory_keratinocyte_count] = (int) atoi(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'num_stem_bonds' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("cycle");
      if(t_node){
        h_keratinocytes->cycle[*h_xmachine_memory_keratinocyte_count] = (int) atoi(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'cycle' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("diff_noise_factor");
      if(t_node){
        h_keratinocytes->diff_noise_factor[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'diff_noise_factor' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("dead_ticks");
      if(t_node){
        h_keratinocytes->dead_ticks[*h_xmachine_memory_keratinocyte_count] = (int) atoi(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'dead_ticks' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("contact_inhibited_ticks");
      if(t_node){
        h_keratinocytes->contact_inhibited_ticks[*h_xmachine_memory_keratinocyte_count] = (int) atoi(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'contact_inhibited_ticks' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("motility");
      if(t_node){
        h_keratinocytes->motility[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'motility' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("dir");
      if(t_node){
        h_keratinocytes->dir[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'dir' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      
      t_node = xagent_node->first_node("movement");
      if(t_node){
        h_keratinocytes->movement[*h_xmachine_memory_keratinocyte_count] = (float) atof(t_node->value());
      }else if(!noWarn){printf("WARNING: Agent keratinocyte[%d] is missing property 'movement' in init file, 0 used.\n",(*h_xmachine_memory_keratinocyte_count));}
      

      //Calculate agent min/max
      //Check maximum x value
      if(agent_maximum.x < h_keratinocytes->x[*h_xmachine_memory_keratinocyte_count])
          agent_maximum.x = (float)h_keratinocytes->x[*h_xmachine_memory_keratinocyte_count];
      //Check minimum x value
      if(agent_minimum.x > h_keratinocytes->x[*h_xmachine_memory_keratinocyte_count])
          agent_minimum.x = (float)h_keratinocytes->x[*h_xmachine_memory_keratinocyte_count];
      //Check maximum y value
      if(agent_maximum.y < h_keratinocytes->y[*h_xmachine_memory_keratinocyte_count])
          agent_maximum.y = (float)h_keratinocytes->y[*h_xmachine_memory_keratinocyte_count];
      //Check minimum y value
      if(agent_minimum.y > h_keratinocytes->y[*h_xmachine_memory_keratinocyte_count])
          agent_minimum.y = (float)h_keratinocytes->y[*h_xmachine_memory_keratinocyte_count];
      //Check maximum z value
      if(agent_maximum.z < h_keratinocytes->z[*h_xmachine_memory_keratinocyte_count])
          agent_maximum.z = (float)h_keratinocytes->z[*h_xmachine_memory_keratinocyte_count];
      //Check minimum z value
      if(agent_minimum.z > h_keratinocytes->z[*h_xmachine_memory_keratinocyte_count])
          agent_minimum.z = (float)h_keratinocytes->z[*h_xmachine_memory_keratinocyte_count];
      
      //Increment keratinocyte agent count
      (*h_xmachine_memory_keratinocyte_count)++;
    }
    
    //Find next xagent node
    xagent_node = xagent_node->next_sibling("xagent");
	}
  
  //Parse environment variables
  if(env_node)
  {
    
    t_node = env_node->first_node("calcium_level");
    if(t_node)
    {
      float t = (float)atof(t_node->value());
      set_calcium_level(&t);
    }
    
    t_node = env_node->first_node("CYCLE_LENGTH");
    if(t_node)
    {
      int t = (int)atoi(t_node->value());
      set_CYCLE_LENGTH(&t);
    }
    
    t_node = env_node->first_node("SUBSTRATE_FORCE");
    if(t_node)
    {
      float t = (float)atof(t_node->value());
      set_SUBSTRATE_FORCE(&t);
    }
    
    t_node = env_node->first_node("DOWNWARD_FORCE");
    if(t_node)
    {
      float t = (float)atof(t_node->value());
      set_DOWNWARD_FORCE(&t);
    }
    
    t_node = env_node->first_node("FORCE_MATRIX");
    if(t_node)
    {
      float t = (float)atof(t_node->value());
      set_FORCE_MATRIX(&t);
    }
    
    t_node = env_node->first_node("FORCE_REP");
    if(t_node)
    {
      float t = (float)atof(t_node->value());
      set_FORCE_REP(&t);
    }
    
    t_node = env_node->first_node("FORCE_DAMPENER");
    if(t_node)
    {
      float t = (float)atof(t_node->value());
      set_FORCE_DAMPENER(&t);
    }
    
    t_node = env_node->first_node("BASEMENT_MAX_Z");
    if(t_node)
    {
      int t = (int)atoi(t_node->value());
      set_BASEMENT_MAX_Z(&t);
    }
    
  }
}