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support for SWC input format

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This commit is contained in:
James McClure 2022-05-16 11:17:47 -04:00
parent 0e65364954
commit c4a97c0589
1 changed files with 10 additions and 6 deletions
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16
common/Domain.cpp
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@ -42,6 +42,7 @@ static inline void fgetl(char *str, int num, FILE *stream) {
void Domain::read_swc(const std::string &Filename) { void Domain::read_swc(const std::string &Filename) {
//...... READ IN SWC FILE................................... //...... READ IN SWC FILE...................................
int count = 0;
int number_of_lines = 0; int number_of_lines = 0;
if (rank() == 0){ if (rank() == 0){
cout << "Reading SWC file..." << endl; cout << "Reading SWC file..." << endl;
@ -52,9 +53,11 @@ void Domain::read_swc(const std::string &Filename) {
++number_of_lines; ++number_of_lines;
number_of_lines -= 1; number_of_lines -= 1;
} }
std::cout << "Number of lines in SWC file: " << number_of_lines; std::cout << "Number of lines in SWC file: " << number_of_lines << endl;
} }
Comm.bcast(number_of_lines,0); count = Comm.sumReduce(number_of_lines); // nonzero only for rank=0
number_of_lines = count;
printf("***rank=%i , number of lines = %i\n",rank(),number_of_lines);
// set up structures to read // set up structures to read
double *List_cx = new double [number_of_lines]; double *List_cx = new double [number_of_lines];
@ -73,7 +76,7 @@ void Domain::read_swc(const std::string &Filename) {
fgetl(line, 100, fid); fgetl(line, 100, fid);
//........read the spheres.................. //........read the spheres..................
// We will read until a blank like or end-of-file is reached // We will read until a blank like or end-of-file is reached
int count = 0; count = 0;
while (!feof(fid) && fgets(line, 100, fid) != NULL) { while (!feof(fid) && fgets(line, 100, fid) != NULL) {
char *line2 = line; char *line2 = line;
List_index[count] = int(strtod(line2, &line2)); List_index[count] = int(strtod(line2, &line2));
@ -104,6 +107,7 @@ void Domain::read_swc(const std::string &Filename) {
start_x = rank_info.ix*(Nx-2)*voxel_length; start_x = rank_info.ix*(Nx-2)*voxel_length;
start_y = rank_info.jy*(Ny-2)*voxel_length; start_y = rank_info.jy*(Ny-2)*voxel_length;
start_z = rank_info.kz*(Nz-2)*voxel_length; start_z = rank_info.kz*(Nz-2)*voxel_length;
printf(" rank = %i: %f %f %f \n",rank(),start_x,start_y,start_z);
finish_x = (rank_info.ix+1)*(Nx-2)*voxel_length; finish_x = (rank_info.ix+1)*(Nx-2)*voxel_length;
finish_y = (rank_info.jy+1)*(Ny-2)*voxel_length; finish_y = (rank_info.jy+1)*(Ny-2)*voxel_length;
finish_z = (rank_info.kz+1)*(Nz-2)*voxel_length; finish_z = (rank_info.kz+1)*(Nz-2)*voxel_length;
@ -125,7 +129,7 @@ void Domain::read_swc(const std::string &Filename) {
int cy = int((List_cy[idx] - start_y)/voxel_length) + 1; int cy = int((List_cy[idx] - start_y)/voxel_length) + 1;
int cz = int((List_cz[idx] - start_z)/voxel_length) + 1; int cz = int((List_cz[idx] - start_z)/voxel_length) + 1;
if (rank()==0) printf("%i %i %i %i %i\n",label,cx,cy,cz,radius_in_voxels); if (rank()==1) printf("%i %i %i %i %i\n",label,cx,cy,cz,radius_in_voxels);
/* get the little box to loop over*/ /* get the little box to loop over*/
int start_idx = int((List_cx[idx] - List_rad[idx] - start_x)/voxel_length) + 1; int start_idx = int((List_cx[idx] - List_rad[idx] - start_x)/voxel_length) + 1;
@ -148,8 +152,8 @@ void Domain::read_swc(const std::string &Filename) {
if (finish_idy > Ny-1 ) finish_idy = Ny; if (finish_idy > Ny-1 ) finish_idy = Ny;
if (finish_idz > Nz-1 ) finish_idz = Nz; if (finish_idz > Nz-1 ) finish_idz = Nz;
if (rank()==0) printf( "start: %i, %i, %i \n",start_idx,start_idy,start_idz); if (rank()==1) printf( "start: %i, %i, %i \n",start_idx,start_idy,start_idz);
if (rank()==0) printf( "finish: %i, %i, %i \n",finish_idx,finish_idy,finish_idz); if (rank()==1) printf( "finish: %i, %i, %i \n",finish_idx,finish_idy,finish_idz);
for (int k = start_idz; k<finish_idz; k++){ for (int k = start_idz; k<finish_idz; k++){
for (int j = start_idy; j<finish_idy; j++){ for (int j = start_idy; j<finish_idy; j++){