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cnpy.cpp
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//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"cnpy.h"
#include<complex>
#include<cstdlib>
#include<algorithm>
#include<cstring>
#include<iomanip>
#include<stdint.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);
int 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::string str_shape = header.substr(loc1+1,loc2-loc1-1);
size_t ndims;
if(str_shape[str_shape.size()-1] == ',') ndims = 1;
else ndims = std::count(str_shape.begin(),str_shape.end(),',')+1;
shape.resize(ndims);
for(size_t i = 0;i < ndims;i++) {
loc1 = str_shape.find(",");
shape[i] = atoi(str_shape.substr(0,loc1).c_str());
str_shape = str_shape.substr(loc1+1);
}
//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');
int loc1, loc2;
//fortran order
loc1 = header.find("fortran_order");
if (loc1 < 0)
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 < 0 || loc2 < 0)
throw std::runtime_error("parse_npy_header: failed to find header keyword: '(' or ')'");
std::string str_shape = header.substr(loc1+1,loc2-loc1-1);
size_t ndims;
if(str_shape[str_shape.size()-1] == ',') ndims = 1;
else ndims = std::count(str_shape.begin(),str_shape.end(),',')+1;
shape.resize(ndims);
for(size_t i = 0;i < ndims;i++) {
loc1 = str_shape.find(",");
shape[i] = atoi(str_shape.substr(0,loc1).c_str());
str_shape = str_shape.substr(loc1+1);
}
//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 < 0)
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) {
printf("npz_load: Error! Unable to open file %s!\n",fname.c_str());
abort();
}
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
size_t size = *(uint32_t*) &local_header[22];
fseek(fp,size,SEEK_CUR);
}
}
fclose(fp);
printf("npz_load: Error! Variable name %s not found in %s!\n",varname.c_str(),fname.c_str());
abort();
}
cnpy::NpyArray cnpy::npy_load(std::string fname) {
FILE* fp = fopen(fname.c_str(), "rb");
if(!fp) {
printf("npy_load: Error! Unable to open file %s!\n",fname.c_str());
abort();
}
NpyArray arr = load_the_npy_file(fp);
fclose(fp);
return arr;
}