356 lines
9.7 KiB
C++
356 lines
9.7 KiB
C++
/*
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* Pre-processor to generate signed distance function from segmented data
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* segmented data should be stored in a raw binary file as 1-byte integer (type char)
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* will output distance functions for phases
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <math.h>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include "common/Array.h"
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#include "common/Domain.h"
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int main(int argc, char **argv)
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{
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int rank=0;
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/* bool MULTINPUT=false;
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int NWP,SOLID,rank_offset;
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SOLID=atoi(argv[1]);
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NWP=atoi(argv[2]);
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if (rank==0){
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printf("Solid Label: %i \n",SOLID);
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printf("NWP Label: %i \n",NWP);
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}
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if (argc > 3){
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rank_offset = atoi(argv[3]);
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}
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else{
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MULTINPUT=true;
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rank_offset=0;
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}
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*/
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string filename;
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if (argc > 1)
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filename=argv[1];
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else{
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ERROR("lbpm_serial_decomp: no in put database provided \n");
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}
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int rank_offset=0;
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//.......................................................................
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// Reading the domain information file
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//.......................................................................
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int64_t i,j,k,n;
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int64_t xStart,yStart,zStart;
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int checkerSize;
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int inlet_count_x, inlet_count_y, inlet_count_z;
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int outlet_count_x, outlet_count_y, outlet_count_z;
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// char fluidValue,solidValue;
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xStart=yStart=zStart=0;
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inlet_count_x = 0;
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inlet_count_y = 0;
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inlet_count_z = 0;
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outlet_count_x = 0;
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outlet_count_y = 0;
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outlet_count_z = 0;
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checkerSize = 32;
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// read the input database
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auto db = std::make_shared<Database>( filename );
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auto domain_db = db->getDatabase( "Domain" );
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// Read domain parameters
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auto Filename = domain_db->getScalar<std::string>( "Filename" );
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//auto L = domain_db->getVector<double>( "L" );
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auto size = domain_db->getVector<int>( "n" );
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auto SIZE = domain_db->getVector<int>( "N" );
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auto nproc = domain_db->getVector<int>( "nproc" );
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if (domain_db->keyExists( "offset" )){
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auto offset = domain_db->getVector<int>( "offset" );
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xStart = offset[0];
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yStart = offset[1];
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zStart = offset[2];
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}
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if (domain_db->keyExists( "InletLayers" )){
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auto InletCount = domain_db->getVector<int>( "InletLayers" );
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inlet_count_x = InletCount[0];
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inlet_count_y = InletCount[1];
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inlet_count_z = InletCount[2];
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}
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if (domain_db->keyExists( "OutletLayers" )){
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auto OutletCount = domain_db->getVector<int>( "OutletLayers" );
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outlet_count_x = OutletCount[0];
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outlet_count_y = OutletCount[1];
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outlet_count_z = OutletCount[2];
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}
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if (domain_db->keyExists( "checkerSize" )){
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checkerSize = domain_db->getScalar<int>( "checkerSize" );
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}
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else {
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checkerSize = SIZE[0];
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}
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auto ReadValues = domain_db->getVector<int>( "ReadValues" );
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auto WriteValues = domain_db->getVector<int>( "WriteValues" );
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auto ReadType = domain_db->getScalar<std::string>( "ReadType" );
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if (ReadType == "8bit"){
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}
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else if (ReadType == "16bit"){
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}
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else{
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printf("INPUT ERROR: Valid ReadType are 8bit, 16bit \n");
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ReadType = "8bit";
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}
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int nx = size[0];
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int ny = size[1];
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int nz = size[2];
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int nprocx = nproc[0];
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int nprocy = nproc[1];
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int nprocz = nproc[2];
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long int Nx = SIZE[0];
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long int Ny = SIZE[1];
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long int Nz = SIZE[2];
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printf("Input media: %s\n",Filename.c_str());
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printf("Relabeling %lu values\n",ReadValues.size());
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for (size_t idx=0; idx<ReadValues.size(); idx++){
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int oldvalue=ReadValues[idx];
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int newvalue=WriteValues[idx];
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printf("oldvalue=%d, newvalue =%d \n",oldvalue,newvalue);
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}
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int nprocs=nprocx*nprocy*nprocz;
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char *SegData = NULL;
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// Rank=0 reads the entire segmented data and distributes to worker processes
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if (rank==0){
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printf("Dimensions of segmented image: %ld x %ld x %ld \n",Nx,Ny,Nz);
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int64_t SIZE = Nx*Ny*Nz;
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SegData = new char[SIZE];
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if (ReadType == "8bit"){
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printf("Reading 8-bit input data \n");
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FILE *SEGDAT = fopen(Filename.c_str(),"rb");
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if (SEGDAT==NULL) ERROR("Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(SegData,1,SIZE,SEGDAT);
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if (ReadSeg != size_t(SIZE)) printf("lbpm_segmented_decomp: Error reading segmented data (rank=%i)\n",rank);
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fclose(SEGDAT);
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}
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else if (ReadType == "16bit"){
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printf("Reading 16-bit input data \n");
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short int *InputData;
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InputData = new short int[SIZE];
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FILE *SEGDAT = fopen(Filename.c_str(),"rb");
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if (SEGDAT==NULL) ERROR("Error reading segmented data");
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size_t ReadSeg;
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ReadSeg=fread(InputData,2,SIZE,SEGDAT);
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if (ReadSeg != size_t(SIZE)) printf("lbpm_segmented_decomp: Error reading segmented data (rank=%i)\n",rank);
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fclose(SEGDAT);
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for (int n=0; n<SIZE; n++){
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SegData[n] = char(InputData[n]);
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}
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}
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printf("Read segmented data from %s \n",Filename.c_str());
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}
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// relabel the data
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std::vector<long int> LabelCount(ReadValues.size(),0);
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for (int k = 0; k<Nz; k++){
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for (int j = 0; j<Ny; j++){
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for (int i = 0; i<Nx; i++){
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n = k*Nx*Ny+j*Nx+i;
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//char locval = loc_id[n];
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char locval = SegData[n];
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for (size_t idx=0; idx<ReadValues.size(); idx++){
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signed char oldvalue=ReadValues[idx];
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signed char newvalue=WriteValues[idx];
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if (locval == oldvalue){
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SegData[n] = newvalue;
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LabelCount[idx]++;
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idx = ReadValues.size();
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}
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}
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}
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}
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}
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if (rank==0){
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for (size_t idx=0; idx<ReadValues.size(); idx++){
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long int label=ReadValues[idx];
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long int count=LabelCount[idx];
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printf("Label=%ld, Count=%ld \n",label,count);
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}
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}
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if (inlet_count_x > 0){
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// use checkerboard pattern
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printf("Checkerboard pattern at x inlet for %i layers \n",inlet_count_x);
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for (int k = 0; k<Nz; k++){
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for (int j = 0; j<Ny; j++){
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for (int i = xStart; i < xStart+inlet_count_x; i++){
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if ( (j/checkerSize + k/checkerSize)%2 == 0){
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// void checkers
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SegData[k*Nx*Ny+j*Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*Nx*Ny+j*Nx+i] = 0;
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}
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}
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}
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}
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}
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if (inlet_count_y > 0){
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printf("Checkerboard pattern at y inlet for %i layers \n",inlet_count_y);
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// use checkerboard pattern
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for (int k = 0; k<Nz; k++){
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for (int j = yStart; j < yStart+inlet_count_y; j++){
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for (int i = 0; i<Nx; i++){
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if ( (i/checkerSize + k/checkerSize)%2 == 0){
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// void checkers
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SegData[k*Nx*Ny+j*Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*Nx*Ny+j*Nx+i] = 0;
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}
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}
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}
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}
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}
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if (inlet_count_z > 0){
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printf("Checkerboard pattern at z inlet for %i layers \n",inlet_count_z);
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// use checkerboard pattern
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for (int k = zStart; k < zStart+inlet_count_z; k++){
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for (int j = 0; j<Ny; j++){
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for (int i = 0; i<Nx; i++){
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if ( (i/checkerSize+j/checkerSize)%2 == 0){
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// void checkers
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SegData[k*Nx*Ny+j*Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*Nx*Ny+j*Nx+i] = 0;
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}
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}
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}
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}
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}
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if (outlet_count_x > 0){
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// use checkerboard pattern
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printf("Checkerboard pattern at x outlet for %i layers \n",outlet_count_x);
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for (int k = 0; k<Nz; k++){
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for (int j = 0; j<Ny; j++){
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for (int i = xStart + nx*nprocx - outlet_count_x; i < xStart + nx*nprocx; i++){
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if ( (j/checkerSize + k/checkerSize)%2 == 0){
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// void checkers
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SegData[k*Nx*Ny+j*Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*Nx*Ny+j*Nx+i] = 0;
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}
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}
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}
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}
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}
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if (outlet_count_y > 0){
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printf("Checkerboard pattern at y outlet for %i layers \n",outlet_count_y);
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// use checkerboard pattern
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for (int k = 0; k<Nz; k++){
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for (int j = yStart + ny*nprocy - outlet_count_y; j < yStart + ny*nprocy; j++){
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for (int i = 0; i<Nx; i++){
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if ( (i/checkerSize + k/checkerSize)%2 == 0){
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// void checkers
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SegData[k*Nx*Ny+j*Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*Nx*Ny+j*Nx+i] = 0;
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}
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}
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}
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}
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}
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if (outlet_count_z > 0){
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printf("Checkerboard pattern at z outlet for %i layers \n",outlet_count_z);
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// use checkerboard pattern
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for (int k = zStart + nz*nprocz - outlet_count_z; k < zStart + nz*nprocz; k++){
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for (int j = 0; j<Ny; j++){
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for (int i = 0; i<Nx; i++){
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if ( (i/checkerSize+j/checkerSize)%2 == 0){
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// void checkers
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SegData[k*Nx*Ny+j*Nx+i] = 2;
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}
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else{
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// solid checkers
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SegData[k*Nx*Ny+j*Nx+i] = 0;
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}
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}
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}
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}
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}
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// number of sites to use for periodic boundary condition transition zone
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int64_t z_transition_size = (nprocz*nz - (Nz - zStart))/2;
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if (z_transition_size < 0) z_transition_size=0;
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char LocalRankFilename[40];
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char *loc_id;
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loc_id = new char [(nx+2)*(ny+2)*(nz+2)];
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// Set up the sub-domains
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if (rank==0){
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printf("Distributing subdomains across %i processors \n",nprocs);
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printf("Process grid: %i x %i x %i \n",nprocx,nprocy,nprocz);
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printf("Subdomain size: %i x %i x %i \n",nx,ny,nz);
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printf("Size of transition region: %ld \n", z_transition_size);
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for (int kp=0; kp<nprocz; kp++){
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for (int jp=0; jp<nprocy; jp++){
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for (int ip=0; ip<nprocx; ip++){
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// rank of the process that gets this subdomain
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int rnk = kp*nprocx*nprocy + jp*nprocx + ip;
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// Pack and send the subdomain for rnk
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for (k=0;k<nz+2;k++){
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for (j=0;j<ny+2;j++){
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for (i=0;i<nx+2;i++){
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int64_t x = xStart + ip*nx + i-1;
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int64_t y = yStart + jp*ny + j-1;
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// int64_t z = zStart + kp*nz + k-1;
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int64_t z = zStart + kp*nz + k-1 - z_transition_size;
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if (x<xStart) x=xStart;
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if (!(x<Nx)) x=Nx-1;
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if (y<yStart) y=yStart;
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if (!(y<Ny)) y=Ny-1;
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if (z<zStart) z=zStart;
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if (!(z<Nz)) z=Nz-1;
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int64_t nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
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int64_t nglobal = z*Nx*Ny+y*Nx+x;
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loc_id[nlocal] = SegData[nglobal];
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}
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}
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}
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// Write the data for this rank data
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sprintf(LocalRankFilename,"ID.%05i",rnk+rank_offset);
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FILE *ID = fopen(LocalRankFilename,"wb");
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fwrite(loc_id,1,(nx+2)*(ny+2)*(nz+2),ID);
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fclose(ID);
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}
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}
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}
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}
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}
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