text: //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>
  #include<stdexcept>
  #include <regex>
  
  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];
              uint32_t size = *(uint32_t*) &local_header[18]; // using index 18 instead of 22 enables support for compressed data
              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;
  }
  
  
  
  