115 lines
4.0 KiB
C++
115 lines
4.0 KiB
C++
#include "common/ReadMicroCT.h"
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#include "common/Utilities.h"
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#include "zlib.h"
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#include <cstring>
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// Read a file into memory
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std::vector<char> readFile(const std::string &filename) {
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auto fid = fopen(filename.c_str(), "rb");
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INSIST(fid, "File does not exist: " + filename);
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fseek(fid, 0, SEEK_END);
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size_t bytes = ftell(fid);
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fseek(fid, 0, SEEK_SET);
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std::vector<char> data(bytes);
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size_t bytes2 = fread(data.data(), 1, bytes, fid);
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ASSERT(bytes == bytes2);
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fclose(fid);
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return data;
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}
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// Decompress a gzip buffer
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std::vector<char> gunzip(const std::vector<char> &in) {
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z_stream stream;
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std::vector<char> out(1000000);
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stream.next_in = (Bytef *)in.data();
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stream.avail_in = in.size();
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stream.total_in = 0;
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stream.zalloc = Z_NULL;
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stream.zfree = Z_NULL;
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stream.opaque = Z_NULL;
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stream.next_out = (Bytef *)out.data();
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stream.avail_out = out.size();
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stream.total_out = 0;
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ASSERT(inflateInit2(&stream, 16 + MAX_WBITS) == Z_OK);
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bool finished = inflate(&stream, Z_SYNC_FLUSH) == Z_STREAM_END;
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while (!finished && stream.msg == Z_NULL) {
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out.resize(2 * out.size());
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stream.next_out = (Bytef *)&out[stream.total_out];
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stream.avail_out = out.size() - stream.total_out;
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finished = inflate(&stream, Z_SYNC_FLUSH) == Z_STREAM_END;
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}
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ASSERT(stream.msg == Z_NULL);
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out.resize(stream.total_out);
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inflateEnd(&stream);
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return out;
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}
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// Read the compressed micro CT data
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Array<uint8_t> readMicroCT(const std::string &filename) {
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auto in = readFile(filename);
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auto out = gunzip(in);
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ASSERT(out.size() == 1024 * 1024 * 1024);
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Array<uint8_t> data(1024, 1024, 1024);
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memcpy(data.data(), out.data(), data.length());
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return data;
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}
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// Read the compressed micro CT data and distribute
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Array<uint8_t> readMicroCT(const Database &domain, const Utilities::MPI &comm) {
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// Get the local problem info
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auto n = domain.getVector<int>("n");
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int rank = comm.getRank();
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auto nproc = domain.getVector<int>("nproc");
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RankInfoStruct rankInfo(rank, nproc[0], nproc[1], nproc[2]);
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// Determine the largest file number to get
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int Nfx = (n[0] * rankInfo.nx + 1023) / 1024;
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int Nfy = (n[1] * rankInfo.ny + 1023) / 1024;
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int Nfz = (n[2] * rankInfo.nz + 1023) / 1024;
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// Load one of the files if rank < largest file
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Array<uint8_t> data;
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RankInfoStruct srcRankInfo(rank, Nfx, Nfy, Nfz);
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if (srcRankInfo.ix >= 0) {
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auto filename = domain.getScalar<std::string>("Filename");
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char tmp[100];
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if (filename.find("0x_0y_0z.gbd.gz") != std::string::npos) {
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sprintf(tmp, "%ix_%iy_%iz.gbd.gz", srcRankInfo.ix, srcRankInfo.jy,
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srcRankInfo.kz);
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filename = filename.replace(filename.find("0x_0y_0z.gbd.gz"), 15,
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std::string(tmp));
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} else if (filename.find("x0_y0_z0.gbd.gz") != std::string::npos) {
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sprintf(tmp, "x%i_y%i_z%i.gbd.gz", srcRankInfo.ix, srcRankInfo.jy,
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srcRankInfo.kz);
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filename = filename.replace(filename.find("x0_y0_z0.gbd.gz"), 15,
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std::string(tmp));
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} else {
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ERROR("Invalid name for first file");
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}
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data = readMicroCT(filename);
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}
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// Redistribute the data
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data = redistribute(srcRankInfo, data, rankInfo, {n[0], n[1], n[2]}, comm);
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// Relabel the data
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auto ReadValues = domain.getVector<int>("ReadValues");
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auto WriteValues = domain.getVector<int>("WriteValues");
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ASSERT(ReadValues.size() == WriteValues.size());
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int readMaxValue = 0;
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for (auto v : ReadValues)
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readMaxValue = std::max(data.max() + 1, v);
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std::vector<int> map(readMaxValue + 1, -1);
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for (size_t i = 0; i < ReadValues.size(); i++)
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map[ReadValues[i]] = WriteValues[i];
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for (size_t i = 0; i < data.length(); i++) {
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int t = data(i);
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ASSERT(t >= 0 && t <= readMaxValue);
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data(i) = map[t];
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}
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return data;
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}
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