cnpy.cpp

Go to the documentation of this file.

//Copyright (C) 2011  Carl Rogers
//Released under MIT License
//license available in LICENSE file, or at http://www.opensource.org/licenses/mit-license.php
 
#include <complex>
#include <cstdlib>
#include <algorithm>
#include <cstring>
#include <iomanip>
#include <stdint.h>
#include <stdexcept>
#include <regex>
 
#include <cnpy/cnpy.h>
 
char cnpy::BigEndianTest() {
    int x = 1;
    return (((char *) &x)[0]) ? '<' : '>';
}
 
char cnpy::map_type(const std::type_info &t) {
    if (t == typeid(float)) return 'f';
    if (t == typeid(double)) return 'f';
    if (t == typeid(long double)) return 'f';
 
    if (t == typeid(int)) return 'i';
    if (t == typeid(char)) return 'i';
    if (t == typeid(short)) return 'i';
    if (t == typeid(long)) return 'i';
    if (t == typeid(long long)) return 'i';
 
    if (t == typeid(unsigned char)) return 'u';
    if (t == typeid(unsigned short)) return 'u';
    if (t == typeid(unsigned long)) return 'u';
    if (t == typeid(unsigned long long)) return 'u';
    if (t == typeid(unsigned int)) return 'u';
 
    if (t == typeid(bool)) return 'b';
 
    if (t == typeid(std::complex < float > )) return 'c';
    if (t == typeid(std::complex < double > )) return 'c';
    if (t == typeid(std::complex < long double > )) return 'c';
 
    else return '?';
}
 
template<>
std::vector<char> &cnpy::operator+=(std::vector<char> &lhs, const std::string rhs) {
    lhs.insert(lhs.end(), rhs.begin(), rhs.end());
    return lhs;
}
 
template<>
std::vector<char> &cnpy::operator+=(std::vector<char> &lhs, const char *rhs) {
    //write in little endian
    size_t len = strlen(rhs);
    lhs.reserve(len);
    for (size_t byte = 0; byte < len; byte++) {
        lhs.push_back(rhs[byte]);
    }
    return lhs;
}
 
void
cnpy::parse_npy_header(unsigned char *buffer, size_t &word_size, std::vector <size_t> &shape, bool &fortran_order) {
    //std::string magic_string(buffer,6);
    uint8_t major_version = *reinterpret_cast<uint8_t *>(buffer + 6);
    uint8_t minor_version = *reinterpret_cast<uint8_t *>(buffer + 7);
    uint16_t header_len = *reinterpret_cast<uint16_t *>(buffer + 8);
    std::string header(reinterpret_cast<char *>(buffer + 9), header_len);
 
    size_t loc1, loc2;
 
    //fortran order
    loc1 = header.find("fortran_order") + 16;
    fortran_order = (header.substr(loc1, 4) == "True" ? true : false);
 
    //shape
    loc1 = header.find("(");
    loc2 = header.find(")");
 
    std::regex num_regex("[0-9][0-9]*");
    std::smatch sm;
    shape.clear();
 
    std::string str_shape = header.substr(loc1 + 1, loc2 - loc1 - 1);
    while (std::regex_search(str_shape, sm, num_regex)) {
        shape.push_back(std::stoi(sm[0].str()));
        str_shape = sm.suffix().str();
    }
 
    //endian, word size, data type
    //byte order code | stands for not applicable. 
    //not sure when this applies except for byte array
    loc1 = header.find("descr") + 9;
    bool littleEndian = (header[loc1] == '<' || header[loc1] == '|' ? true : false);
    assert(littleEndian);
 
    //char type = header[loc1+1];
    //assert(type == map_type(T));
 
    std::string str_ws = header.substr(loc1 + 2);
    loc2 = str_ws.find("'");
    word_size = atoi(str_ws.substr(0, loc2).c_str());
}
 
void cnpy::parse_npy_header(FILE *fp, size_t &word_size, std::vector <size_t> &shape, bool &fortran_order) {
    char buffer[256];
    size_t res = fread(buffer, sizeof(char), 11, fp);
    if (res != 11)
        throw std::runtime_error("parse_npy_header: failed fread");
    std::string header = fgets(buffer, 256, fp);
    assert(header[header.size() - 1] == '\n');
 
    size_t loc1, loc2;
 
    //fortran order
    loc1 = header.find("fortran_order");
    if (loc1 == std::string::npos)
        throw std::runtime_error("parse_npy_header: failed to find header keyword: 'fortran_order'");
    loc1 += 16;
    fortran_order = (header.substr(loc1, 4) == "True" ? true : false);
 
    //shape
    loc1 = header.find("(");
    loc2 = header.find(")");
    if (loc1 == std::string::npos || loc2 == std::string::npos)
        throw std::runtime_error("parse_npy_header: failed to find header keyword: '(' or ')'");
 
    std::regex num_regex("[0-9][0-9]*");
    std::smatch sm;
    shape.clear();
 
    std::string str_shape = header.substr(loc1 + 1, loc2 - loc1 - 1);
    while (std::regex_search(str_shape, sm, num_regex)) {
        shape.push_back(std::stoi(sm[0].str()));
        str_shape = sm.suffix().str();
    }
 
    //endian, word size, data type
    //byte order code | stands for not applicable. 
    //not sure when this applies except for byte array
    loc1 = header.find("descr");
    if (loc1 == std::string::npos)
        throw std::runtime_error("parse_npy_header: failed to find header keyword: 'descr'");
    loc1 += 9;
    bool littleEndian = (header[loc1] == '<' || header[loc1] == '|' ? true : false);
    assert(littleEndian);
 
    //char type = header[loc1+1];
    //assert(type == map_type(T));
 
    std::string str_ws = header.substr(loc1 + 2);
    loc2 = str_ws.find("'");
    word_size = atoi(str_ws.substr(0, loc2).c_str());
}
 
void cnpy::parse_zip_footer(FILE *fp, uint16_t &nrecs, size_t &global_header_size, size_t &global_header_offset) {
    std::vector<char> footer(22);
    fseek(fp, -22, SEEK_END);
    size_t res = fread(&footer[0], sizeof(char), 22, fp);
    if (res != 22)
        throw std::runtime_error("parse_zip_footer: failed fread");
 
    uint16_t disk_no, disk_start, nrecs_on_disk, comment_len;
    disk_no = *(uint16_t * ) & footer[4];
    disk_start = *(uint16_t * ) & footer[6];
    nrecs_on_disk = *(uint16_t * ) & footer[8];
    nrecs = *(uint16_t * ) & footer[10];
    global_header_size = *(uint32_t * ) & footer[12];
    global_header_offset = *(uint32_t * ) & footer[16];
    comment_len = *(uint16_t * ) & footer[20];
 
    assert(disk_no == 0);
    assert(disk_start == 0);
    assert(nrecs_on_disk == nrecs);
    assert(comment_len == 0);
}
 
cnpy::NpyArray load_the_npy_file(FILE *fp) {
    std::vector <size_t> shape;
    size_t word_size;
    bool fortran_order;
    cnpy::parse_npy_header(fp, word_size, shape, fortran_order);
 
    cnpy::NpyArray arr(shape, word_size, fortran_order);
    size_t nread = fread(arr.data<char>(), 1, arr.num_bytes(), fp);
    if (nread != arr.num_bytes())
        throw std::runtime_error("load_the_npy_file: failed fread");
    return arr;
}
 
cnpy::NpyArray load_the_npz_array(FILE *fp, uint32_t compr_bytes, uint32_t uncompr_bytes) {
 
    std::vector<unsigned char> buffer_compr(compr_bytes);
    std::vector<unsigned char> buffer_uncompr(uncompr_bytes);
    size_t nread = fread(&buffer_compr[0], 1, compr_bytes, fp);
    if (nread != compr_bytes)
        throw std::runtime_error("load_the_npy_file: failed fread");
 
    int err;
    z_stream d_stream;
 
    d_stream.zalloc = Z_NULL;
    d_stream.zfree = Z_NULL;
    d_stream.opaque = Z_NULL;
    d_stream.avail_in = 0;
    d_stream.next_in = Z_NULL;
    err = inflateInit2(&d_stream, -MAX_WBITS);
 
    d_stream.avail_in = compr_bytes;
    d_stream.next_in = &buffer_compr[0];
    d_stream.avail_out = uncompr_bytes;
    d_stream.next_out = &buffer_uncompr[0];
 
    err = inflate(&d_stream, Z_FINISH);
    err = inflateEnd(&d_stream);
 
    std::vector <size_t> shape;
    size_t word_size;
    bool fortran_order;
    cnpy::parse_npy_header(&buffer_uncompr[0], word_size, shape, fortran_order);
 
    cnpy::NpyArray array(shape, word_size, fortran_order);
 
    size_t offset = uncompr_bytes - array.num_bytes();
    memcpy(array.data<unsigned char>(), &buffer_uncompr[0] + offset, array.num_bytes());
 
    return array;
}
 
cnpy::npz_t cnpy::npz_load(std::string fname) {
    FILE *fp = fopen(fname.c_str(), "rb");
 
    if (!fp) {
        throw std::runtime_error("npz_load: Error! Unable to open file " + fname + "!");
    }
 
    cnpy::npz_t arrays;
 
    while (1) {
        std::vector<char> local_header(30);
        size_t headerres = fread(&local_header[0], sizeof(char), 30, fp);
        if (headerres != 30)
            throw std::runtime_error("npz_load: failed fread");
 
        //if we've reached the global header, stop reading
        if (local_header[2] != 0x03 || local_header[3] != 0x04) break;
 
        //read in the variable name
        uint16_t name_len = *(uint16_t * ) & local_header[26];
        std::string varname(name_len, ' ');
        size_t vname_res = fread(&varname[0], sizeof(char), name_len, fp);
        if (vname_res != name_len)
            throw std::runtime_error("npz_load: failed fread");
 
        //erase the lagging .npy        
        varname.erase(varname.end() - 4, varname.end());
 
        //read in the extra field
        uint16_t extra_field_len = *(uint16_t * ) & local_header[28];
        if (extra_field_len > 0) {
            std::vector<char> buff(extra_field_len);
            size_t efield_res = fread(&buff[0], sizeof(char), extra_field_len, fp);
            if (efield_res != extra_field_len)
                throw std::runtime_error("npz_load: failed fread");
        }
 
        uint16_t compr_method = *reinterpret_cast<uint16_t *>(&local_header[0] + 8);
        uint32_t compr_bytes = *reinterpret_cast<uint32_t *>(&local_header[0] + 18);
        uint32_t uncompr_bytes = *reinterpret_cast<uint32_t *>(&local_header[0] + 22);
 
        if (compr_method == 0) { arrays[varname] = load_the_npy_file(fp); }
        else { arrays[varname] = load_the_npz_array(fp, compr_bytes, uncompr_bytes); }
    }
 
    fclose(fp);
    return arrays;
}
 
cnpy::NpyArray cnpy::npz_load(std::string fname, std::string varname) {
    FILE *fp = fopen(fname.c_str(), "rb");
 
    if (!fp) throw std::runtime_error("npz_load: Unable to open file " + fname);
 
    while (1) {
        std::vector<char> local_header(30);
        size_t header_res = fread(&local_header[0], sizeof(char), 30, fp);
        if (header_res != 30)
            throw std::runtime_error("npz_load: failed fread");
 
        //if we've reached the global header, stop reading
        if (local_header[2] != 0x03 || local_header[3] != 0x04) break;
 
        //read in the variable name
        uint16_t name_len = *(uint16_t * ) & local_header[26];
        std::string vname(name_len, ' ');
        size_t vname_res = fread(&vname[0], sizeof(char), name_len, fp);
        if (vname_res != name_len)
            throw std::runtime_error("npz_load: failed fread");
        vname.erase(vname.end() - 4, vname.end()); //erase the lagging .npy
 
        //read in the extra field
        uint16_t extra_field_len = *(uint16_t * ) & local_header[28];
        fseek(fp, extra_field_len, SEEK_CUR); //skip past the extra field
 
        uint16_t compr_method = *reinterpret_cast<uint16_t *>(&local_header[0] + 8);
        uint32_t compr_bytes = *reinterpret_cast<uint32_t *>(&local_header[0] + 18);
        uint32_t uncompr_bytes = *reinterpret_cast<uint32_t *>(&local_header[0] + 22);
 
        if (vname == varname) {
            NpyArray array = (compr_method == 0) ? load_the_npy_file(fp) : load_the_npz_array(fp, compr_bytes,
                                                                                              uncompr_bytes);
            fclose(fp);
            return array;
        } else {
            //skip past the data
            uint32_t size = *(uint32_t * ) & local_header[22];
            fseek(fp, size, SEEK_CUR);
        }
    }
 
    fclose(fp);
 
    //if we get here, we haven't found the variable in the file
    throw std::runtime_error("npz_load: Variable name " + varname + " not found in " + fname);
}
 
cnpy::NpyArray cnpy::npy_load(std::string fname) {
 
    FILE *fp = fopen(fname.c_str(), "rb");
 
    if (!fp) throw std::runtime_error("npy_load: Unable to open file " + fname);
 
    NpyArray arr = load_the_npy_file(fp);
 
    fclose(fp);
    return arr;
}