/*M/////////////////////////////////////////////////////////////////////////////////////// // // IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING. // // By downloading, copying, installing or using the software you agree to this license. // If you do not agree to this license, do not download, install, // copy or use the software. // // // License Agreement // For Open Source Computer Vision Library // // Copyright (C) 2013, OpenCV Foundation, all rights reserved. // Third party copyrights are property of their respective owners. // // Redistribution and use in source and binary forms, with or without modification, // are permitted provided that the following conditions are met: // // * Redistribution's of source code must retain the above copyright notice, // this list of conditions and the following disclaimer. // // * Redistribution's in binary form must reproduce the above copyright notice, // this list of conditions and the following disclaimer in the documentation // and/or other materials provided with the distribution. // // * The name of the copyright holders may not be used to endorse or promote products // derived from this software without specific prior written permission. // // This software is provided by the copyright holders and contributors "as is" and // any express or implied warranties, including, but not limited to, the implied // warranties of merchantability and fitness for a particular purpose are disclaimed. // In no event shall the Intel Corporation or contributors be liable for any direct, // indirect, incidental, special, exemplary, or consequential damages // (including, but not limited to, procurement of substitute goods or services; // loss of use, data, or profits; or business interruption) however caused // and on any theory of liability, whether in contract, strict liability, // or tort (including negligence or otherwise) arising in any way out of // the use of this software, even if advised of the possibility of such damage. // //M*/ //Copyright (C) 2011 Carl Rogers //Released under MIT License //license available in LICENSE file, or at http://www.opensource.org/licenses/mit-license.php #ifndef LIBCNPY_H_ #define LIBCNPY_H_ #include #include #include #include #include #include #include #include #include #if defined(HAVE_ZLIB) && HAVE_ZLIB #include #endif #ifndef NDEBUG #define cnpy_assert(expression) assert(expression) #else #define cnpy_assert(expression) ((void)(expression)) #endif namespace cnpy { struct NpyArray { char* data; std::vector shape; unsigned int word_size; bool fortran_order; void destruct() {delete[] data;} }; struct npz_t : public std::map { void destruct() { npz_t::iterator it = this->begin(); for(; it != this->end(); ++it) (*it).second.destruct(); } }; char BigEndianTest(); char map_type(const std::type_info& t); template std::vector create_npy_header(const T* data, const unsigned int* shape, const unsigned int ndims); void parse_npy_header(FILE* fp,unsigned int& word_size, unsigned int*& shape, unsigned int& ndims, bool& fortran_order); void parse_zip_footer(FILE* fp, unsigned short& nrecs, unsigned int& global_header_size, unsigned int& global_header_offset); npz_t npz_load(std::string fname); NpyArray npz_load(std::string fname, std::string varname); NpyArray npy_load(std::string fname); template std::vector& operator+=(std::vector& lhs, const T rhs) { //write in little endian for(char byte = 0; (size_t)byte < sizeof(T); byte++) { char val = *((char*)&rhs+byte); lhs.push_back(val); } return lhs; } template<> std::vector& operator+=(std::vector& lhs, const std::string rhs); template<> std::vector& operator+=(std::vector& lhs, const char* rhs); template std::string tostring(T i, int = 0, char = ' ') { std::stringstream s; s << i; return s.str(); } template void npy_save(std::string fname, const T* data, const unsigned int* shape, const unsigned int ndims, std::string mode = "w") { FILE* fp = NULL; if(mode == "a") fp = fopen(fname.c_str(),"r+b"); if(fp) { //file exists. we need to append to it. read the header, modify the array size unsigned int word_size, tmp_dims; unsigned int* tmp_shape = 0; bool fortran_order; parse_npy_header(fp,word_size,tmp_shape,tmp_dims,fortran_order); cnpy_assert(!fortran_order); if(word_size != sizeof(T)) { std::cout<<"libnpy error: "< header = create_npy_header(data,tmp_shape,ndims); fwrite(&header[0],sizeof(char),header.size(),fp); fseek(fp,0,SEEK_END); delete[] tmp_shape; } else { fp = fopen(fname.c_str(),"wb"); std::vector header = create_npy_header(data,shape,ndims); fwrite(&header[0],sizeof(char),header.size(),fp); } unsigned int nels = 1; for(unsigned i = 0;i < ndims;i++) nels *= shape[i]; fwrite(data,sizeof(T),nels,fp); fclose(fp); } template void npz_save(std::string zipname, std::string fname, const T* data, const unsigned int* shape, const unsigned int ndims, std::string mode = "w") { //first, append a .npy to the fname fname += ".npy"; //now, on with the show FILE* fp = NULL; unsigned short nrecs = 0; unsigned int global_header_offset = 0; std::vector global_header; if(mode == "a") fp = fopen(zipname.c_str(),"r+b"); if(fp) { //zip file exists. we need to add a new npy file to it. //first read the footer. this gives us the offset and size of the global header //then read and store the global header. //below, we will write the the new data at the start of the global header then append the global header and footer below it unsigned int global_header_size; parse_zip_footer(fp,nrecs,global_header_size,global_header_offset); fseek(fp,global_header_offset,SEEK_SET); global_header.resize(global_header_size); size_t res = fread(&global_header[0],sizeof(char),global_header_size,fp); if(res != global_header_size){ throw std::runtime_error("npz_save: header read error while adding to existing zip"); } fseek(fp,global_header_offset,SEEK_SET); } else { fp = fopen(zipname.c_str(),"wb"); } std::vector npy_header = create_npy_header(data,shape,ndims); unsigned long nels = 1; for (unsigned m=0; m local_header; local_header += "PK"; //first part of sig local_header += (unsigned short) 0x0403; //second part of sig local_header += (unsigned short) 20; //min version to extract local_header += (unsigned short) 0; //general purpose bit flag local_header += (unsigned short) 0; //compression method local_header += (unsigned short) 0; //file last mod time local_header += (unsigned short) 0; //file last mod date local_header += (unsigned int) crc; //crc local_header += (unsigned int) nbytes; //compressed size local_header += (unsigned int) nbytes; //uncompressed size local_header += (unsigned short) fname.size(); //fname length local_header += (unsigned short) 0; //extra field length local_header += fname; //build global header global_header += "PK"; //first part of sig global_header += (unsigned short) 0x0201; //second part of sig global_header += (unsigned short) 20; //version made by global_header.insert(global_header.end(),local_header.begin()+4,local_header.begin()+30); global_header += (unsigned short) 0; //file comment length global_header += (unsigned short) 0; //disk number where file starts global_header += (unsigned short) 0; //internal file attributes global_header += (unsigned int) 0; //external file attributes global_header += (unsigned int) global_header_offset; //relative offset of local file header, since it begins where the global header used to begin global_header += fname; //build footer std::vector footer; footer += "PK"; //first part of sig footer += (unsigned short) 0x0605; //second part of sig footer += (unsigned short) 0; //number of this disk footer += (unsigned short) 0; //disk where footer starts footer += (unsigned short) (nrecs+1); //number of records on this disk footer += (unsigned short) (nrecs+1); //total number of records footer += (unsigned int) global_header.size(); //nbytes of global headers footer += (unsigned int) (global_header_offset + nbytes + local_header.size()); //offset of start of global headers, since global header now starts after newly written array footer += (unsigned short) 0; //zip file comment length //write everything fwrite(&local_header[0],sizeof(char),local_header.size(),fp); fwrite(&npy_header[0],sizeof(char),npy_header.size(),fp); fwrite(data,sizeof(T),nels,fp); fwrite(&global_header[0],sizeof(char),global_header.size(),fp); fwrite(&footer[0],sizeof(char),footer.size(),fp); fclose(fp); } template std::vector create_npy_header(const T*, const unsigned int* shape, const unsigned int ndims) { std::vector dict; dict += "{'descr': '"; dict += BigEndianTest(); dict += map_type(typeid(T)); dict += tostring(sizeof(T)); dict += "', 'fortran_order': False, 'shape': ("; dict += tostring(shape[0]); for(unsigned i = 1;i < ndims;i++) { dict += ", "; dict += tostring(shape[i]); } if(ndims == 1) dict += ","; dict += "), }"; //pad with spaces so that preamble+dict is modulo 16 bytes. preamble is 10 bytes. dict needs to end with \n int remainder = 16 - (10 + dict.size()) % 16; dict.insert(dict.end(),remainder,' '); dict.back() = '\n'; std::vector header; header += (unsigned char) 0x93; header += "NUMPY"; header += (char) 0x01; //major version of numpy format header += (char) 0x00; //minor version of numpy format header += (unsigned short) dict.size(); header.insert(header.end(),dict.begin(),dict.end()); return header; } } #endif