cellset.h
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#ifndef STIM_CELLSET_H
#define STIM_CELLSET_H
#include <stim/math/vec3.h>
#include <vector>
#include <list>
#include <unordered_map>
#include <fstream>
namespace stim{
class cellset{
private:
static const char delim = ' ';
protected:
std::vector<double*> cells; //vector storing field data for each cell
std::unordered_map<std::string, size_t> fields; //unordered map storing field->index information for each field
size_t ip[3]; //hard code to position indices (for speed)
void init(){
}
/// Initialize fields for a standard cell set containing three points and a radius
void init_p3(){
fields.insert(std::pair<std::string, size_t>("x", 0));
ip[0] = 0;
fields.insert(std::pair<std::string, size_t>("y", 1));
ip[1] = 1;
fields.insert(std::pair<std::string, size_t>("z", 2));
ip[2] = 2;
}
void init_p3r(){
init_p3();
fields.insert(std::pair<std::string, size_t>("radius", 3));
ip[3] = 3;
}
public:
/// Constructor - create an empty cell set
cellset(){
init();
}
/// Constructor - load a cellset from a file
cellset(std::string filename){
init(); //initialize an empty cellset
load(filename); //load the cellset from an existing file
}
/// Loads a cellset from a file
void load(std::string filename){
std::ifstream infile(filename);
std::string header; //allocate space for the file header
std::getline(infile, header); //get the file header
// break the header into fields
std::stringstream ss(header); //create a string stream
std::string field; //store a single field name
size_t i = 0; //current field index
while (std::getline(ss, field, delim)) { //split the header into individual fields
std::pair<std::string, size_t> p(field, i); //create a pair associating the header name with the index
fields.insert(p); //insert the pair into the fields map
i++; //increment the data index
}
size_t nfields = fields.size(); //store the number of fields for each cell
//load each cell and all associated fields
std::string cell_line; //string holds all information for a cell
std::list<std::string> cell_list; //list will be temporary storage for the cell fields
while(std::getline(infile, cell_line)){ //for each cell entry
cell_list.push_back(cell_line); //push the cell entry into the list
}
//convert the list into actual data
size_t ncells = cell_list.size(); //count the number of cells
cells.resize(ncells); //allocate enough space in the array to store all cells
for(size_t c = 0; c < ncells; c++){ //for each cell entry in the list
cells[c] = (double*) malloc(sizeof(double) * nfields); //allocate enough space for each field
std::stringstream fss(cell_list.front()); //turn the string representing the cell list into a stringstream
for(size_t f = 0; f < nfields; f++){ //for each field
fss>>cells[c][f]; //load the field
}
cell_list.pop_front(); //pop the read string off of the front of the list
}
infile.close(); //close the input file
ip[0] = fields["x"]; //hard code the position indices for speed
ip[1] = fields["y"]; // this assumes all cells have positions
ip[2] = fields["z"];
}
/// Return the value a specified field for a cell
/// @param c is the cell index
/// @param f is the field
double value(size_t c, std::string f){
size_t idx = fields[f];
return cells[c][idx];
}
/// returns an ID used to look up a field
bool exists(std::string f){
std::unordered_map<std::string, size_t>::iterator iter = fields.find(f);
if(iter == fields.end()) return false;
else return true;
}
/// Return the position of cell [i]
stim::vec3<double> p(size_t i){
stim::vec3<double> pos(cells[i][ip[0]], cells[i][ip[1]], cells[i][ip[2]]);
return pos;
}
/// Return the number of cells in the set
size_t size(){
return cells.size();
}
/// Return the maximum value of a field in this cell set
double max(std::string field){
size_t idx = fields[field]; //get the field index
size_t ncells = cells.size(); //get the total number of cells
double maxval, val; //stores the current and maximum values
for(size_t c = 0; c < ncells; c++){ //for each cell
val = cells[c][idx]; //get the field value for this cell
if(c == 0) maxval = val; //if this is the first cell, just assign the maximum
else if(val > maxval) maxval = val; // otherwise text for the size of val and assign it as appropriate
}
return maxval;
}
/// Return the maximum value of a field in this cell set
double min(std::string field){
size_t idx = fields[field]; //get the field index
size_t ncells = cells.size(); //get the total number of cells
double minval, val; //stores the current and maximum values
for(size_t c = 0; c < ncells; c++){ //for each cell
val = cells[c][idx]; //get the field value for this cell
if(c == 0) minval = val; //if this is the first cell, just assign the maximum
else if(val < minval) minval = val; // otherwise text for the size of val and assign it as appropriate
}
return minval;
}
/// adds a cell to the cell set
void add(double x, double y, double z, double r = 0){
if(cells.size() == 0){ //if the cell set is empty
if(r == 0) //if the radius is zero
init_p3(); //initialize without a radius
else
init_p3r(); //otherwise initialize with a radius
}
size_t nf = fields.size(); //get the number of fields
size_t bytes = sizeof(double) * nf; //get the size of a cell field
double* newcell = (double*) malloc(bytes); //allocate memory for the new cell
memset(newcell, 0, bytes); //initialize all fields to zero
newcell[ip[0]] = x;
newcell[ip[1]] = y;
newcell[ip[2]] = z;
if(r != 0){ //if the user specifies a radius
size_t ir = fields["radius"]; //get the index for the radius field
newcell[ir] = r; //add the radius to the field
}
cells.push_back(newcell); //push the new memory entry into the cell array
}
void save(std::string filename){
size_t ncells = cells.size(); // get the number of cells
std::ofstream file(filename); //open a file to store the cell's coordinates
if (file.is_open()) {
file << "x y z radius\n"; //write the file header
for (size_t c=0; c < ncells; c++){ //for each cell
if (cells[c][ip[3]] != NULL) //check if for the current cell, radius has been assigned
file << cells[c][ip[0]] << delim << cells[c][ip[1]] << delim << cells[c][ip[2]] << delim << cells[c][ip[3]] << '\n' ;
else //check if for the current cell, radius has not been assigned, set radius to zero
file << cells[c][ip[0]] << delim << cells[c][ip[1]] << delim << cells[c][ip[2]] << delim << 0 << '\n' ;
}
}
file.close();
}
}; //end class cellset
}; //end namespace stim
#endif