Anthony Barbier | a3adb3a | 2017-09-13 16:03:39 +0100 | [diff] [blame^] | 1 | /* |
| 2 | Copyright 2017 Leon Merten Lohse |
| 3 | |
| 4 | Permission is hereby granted, free of charge, to any person obtaining a copy |
| 5 | of this software and associated documentation files (the "Software"), to deal |
| 6 | in the Software without restriction, including without limitation the rights |
| 7 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
| 8 | copies of the Software, and to permit persons to whom the Software is |
| 9 | furnished to do so, subject to the following conditions: |
| 10 | |
| 11 | The above copyright notice and this permission notice shall be included in |
| 12 | all copies or substantial portions of the Software. |
| 13 | |
| 14 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
| 15 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
| 16 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
| 17 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
| 18 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
| 19 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE |
| 20 | SOFTWARE. |
| 21 | */ |
| 22 | |
| 23 | #include <complex> |
| 24 | #include <fstream> |
| 25 | #include <string> |
| 26 | #include <sstream> |
| 27 | #include <cstdint> |
| 28 | #include <vector> |
| 29 | #include <endian.h> |
| 30 | #include <typeinfo> |
| 31 | #include <typeindex> |
| 32 | #include <stdexcept> |
| 33 | #include <algorithm> |
| 34 | #include <map> |
| 35 | #include <regex> |
| 36 | |
| 37 | namespace npy { |
| 38 | namespace { |
| 39 | /** Convert integer and float values to string. Reference: support/ToolchainSupport.h |
| 40 | * |
| 41 | * @note This function implements the same behaviour as to_string. The |
| 42 | * latter is missing in some Android toolchains. |
| 43 | * |
| 44 | * @param[in] value Value to be converted to string. |
| 45 | * |
| 46 | * @return String representation of @p value. |
| 47 | */ |
| 48 | template <typename T, typename std::enable_if<std::is_arithmetic<typename std::decay<T>::type>::value, int>::type = 0> |
| 49 | inline std::string to_string(T && value) |
| 50 | { |
| 51 | std::stringstream stream; |
| 52 | stream << std::forward<T>(value); |
| 53 | return stream.str(); |
| 54 | } |
| 55 | } |
| 56 | |
| 57 | const char magic_string[] = "\x93NUMPY"; |
| 58 | const size_t magic_string_length = 6; |
| 59 | |
| 60 | const unsigned char little_endian_char = '<'; |
| 61 | const unsigned char big_endian_char = '>'; |
| 62 | const unsigned char no_endian_char = '|'; |
| 63 | |
| 64 | // check if host is little endian |
| 65 | inline bool isle(void) { |
| 66 | unsigned int i = 1; |
| 67 | char *c = (char*)&i; |
| 68 | if (*c) |
| 69 | return true; |
| 70 | else |
| 71 | return false; |
| 72 | } |
| 73 | |
| 74 | inline void write_magic(std::ostream& ostream, unsigned char v_major=1, unsigned char v_minor=0) { |
| 75 | ostream.write(magic_string, magic_string_length); |
| 76 | ostream.put(v_major); |
| 77 | ostream.put(v_minor); |
| 78 | } |
| 79 | |
| 80 | inline void read_magic(std::istream& istream, unsigned char *v_major, unsigned char *v_minor) { |
| 81 | char *buf = new char[magic_string_length+2]; |
| 82 | istream.read(buf, magic_string_length+2); |
| 83 | |
| 84 | if(!istream) { |
| 85 | throw std::runtime_error("io error: failed reading file"); |
| 86 | } |
| 87 | |
| 88 | for (size_t i=0; i < magic_string_length; i++) { |
| 89 | if(buf[i] != magic_string[i]) { |
| 90 | throw std::runtime_error("this file do not have a valid npy format."); |
| 91 | } |
| 92 | } |
| 93 | |
| 94 | *v_major = buf[magic_string_length]; |
| 95 | *v_minor = buf[magic_string_length+1]; |
| 96 | delete[] buf; |
| 97 | } |
| 98 | |
| 99 | |
| 100 | |
| 101 | inline std::string get_typestring(const std::type_info& t) { |
| 102 | std::string endianness; |
| 103 | std::string no_endianness(no_endian_char, 1); |
| 104 | // little endian or big endian? |
| 105 | if (isle()) |
| 106 | endianness = little_endian_char; |
| 107 | else |
| 108 | endianness = big_endian_char; |
| 109 | |
| 110 | std::map<std::type_index, std::string> map; |
| 111 | |
| 112 | map[std::type_index(typeid(float))] = endianness + "f" + to_string(sizeof(float)); |
| 113 | map[std::type_index(typeid(double))] = endianness + "f" + to_string(sizeof(double)); |
| 114 | map[std::type_index(typeid(long double))] = endianness + "f" + to_string(sizeof(long double)); |
| 115 | |
| 116 | map[std::type_index(typeid(char))] = no_endianness + "i" + to_string(sizeof(char)); |
| 117 | map[std::type_index(typeid(short))] = endianness + "i" + to_string(sizeof(short)); |
| 118 | map[std::type_index(typeid(int))] = endianness + "i" + to_string(sizeof(int)); |
| 119 | map[std::type_index(typeid(long))] = endianness + "i" + to_string(sizeof(long)); |
| 120 | map[std::type_index(typeid(long long))] = endianness + "i" + to_string(sizeof(long long)); |
| 121 | |
| 122 | map[std::type_index(typeid(unsigned char))] = no_endianness + "u" + to_string(sizeof(unsigned char)); |
| 123 | map[std::type_index(typeid(unsigned short))] = endianness + "u" + to_string(sizeof(unsigned short)); |
| 124 | map[std::type_index(typeid(unsigned int))] = endianness + "u" + to_string(sizeof(unsigned int)); |
| 125 | map[std::type_index(typeid(unsigned long))] = endianness + "u" + to_string(sizeof(unsigned long)); |
| 126 | map[std::type_index(typeid(unsigned long long))] = endianness + "u" + to_string(sizeof(unsigned long long)); |
| 127 | |
| 128 | map[std::type_index(typeid(std::complex<float>))] = endianness + "c" + to_string(sizeof(std::complex<float>)); |
| 129 | map[std::type_index(typeid(std::complex<double>))] = endianness + "c" + to_string(sizeof(std::complex<double>)); |
| 130 | map[std::type_index(typeid(std::complex<long double>))] = endianness + "c" + to_string(sizeof(std::complex<long double>)); |
| 131 | |
| 132 | if (map.count(std::type_index(t)) > 0) |
| 133 | return map[std::type_index(t)]; |
| 134 | else |
| 135 | throw std::runtime_error("unsupported data type"); |
| 136 | } |
| 137 | |
| 138 | inline void parse_typestring( std::string typestring){ |
| 139 | std::regex re ("'([<>|])([ifuc])(\\d+)'"); |
| 140 | std::smatch sm; |
| 141 | |
| 142 | std::regex_match(typestring, sm, re ); |
| 143 | |
| 144 | if ( sm.size() != 4 ) { |
| 145 | throw std::runtime_error("invalid typestring"); |
| 146 | } |
| 147 | } |
| 148 | |
| 149 | inline std::string unwrap_s(std::string s, char delim_front, char delim_back) { |
| 150 | if ((s.back() == delim_back) && (s.front() == delim_front)) |
| 151 | return s.substr(1, s.length()-2); |
| 152 | else |
| 153 | throw std::runtime_error("unable to unwrap"); |
| 154 | } |
| 155 | |
| 156 | inline std::string get_value_from_map(std::string mapstr) { |
| 157 | size_t sep_pos = mapstr.find_first_of(":"); |
| 158 | if (sep_pos == std::string::npos) |
| 159 | return ""; |
| 160 | |
| 161 | return mapstr.substr(sep_pos+1); |
| 162 | } |
| 163 | |
| 164 | inline void pop_char(std::string& s, char c) { |
| 165 | if (s.back() == c) |
| 166 | s.pop_back(); |
| 167 | } |
| 168 | |
| 169 | inline void ParseHeader(std::string header, std::string& descr, bool *fortran_order, std::vector<unsigned long>& shape) { |
| 170 | /* |
| 171 | The first 6 bytes are a magic string: exactly "x93NUMPY". |
| 172 | |
| 173 | The next 1 byte is an unsigned byte: the major version number of the file format, e.g. x01. |
| 174 | |
| 175 | The next 1 byte is an unsigned byte: the minor version number of the file format, e.g. x00. Note: the version of the file format is not tied to the version of the numpy package. |
| 176 | |
| 177 | The next 2 bytes form a little-endian unsigned short int: the length of the header data HEADER_LEN. |
| 178 | |
| 179 | The next HEADER_LEN bytes form the header data describing the array's format. It is an ASCII string which contains a Python literal expression of a dictionary. It is terminated by a newline ('n') and padded with spaces ('x20') to make the total length of the magic string + 4 + HEADER_LEN be evenly divisible by 16 for alignment purposes. |
| 180 | |
| 181 | The dictionary contains three keys: |
| 182 | |
| 183 | "descr" : dtype.descr |
| 184 | An object that can be passed as an argument to the numpy.dtype() constructor to create the array's dtype. |
| 185 | "fortran_order" : bool |
| 186 | Whether the array data is Fortran-contiguous or not. Since Fortran-contiguous arrays are a common form of non-C-contiguity, we allow them to be written directly to disk for efficiency. |
| 187 | "shape" : tuple of int |
| 188 | The shape of the array. |
| 189 | For repeatability and readability, this dictionary is formatted using pprint.pformat() so the keys are in alphabetic order. |
| 190 | */ |
| 191 | |
| 192 | // remove trailing newline |
| 193 | if (header.back() != '\n') |
| 194 | throw std::runtime_error("invalid header"); |
| 195 | header.pop_back(); |
| 196 | |
| 197 | // remove all whitespaces |
| 198 | header.erase(std::remove(header.begin(), header.end(), ' '), header.end()); |
| 199 | |
| 200 | // unwrap dictionary |
| 201 | header = unwrap_s(header, '{', '}'); |
| 202 | |
| 203 | // find the positions of the 3 dictionary keys |
| 204 | size_t keypos_descr = header.find("'descr'"); |
| 205 | size_t keypos_fortran = header.find("'fortran_order'"); |
| 206 | size_t keypos_shape = header.find("'shape'"); |
| 207 | |
| 208 | // make sure all the keys are present |
| 209 | if (keypos_descr == std::string::npos) |
| 210 | throw std::runtime_error("missing 'descr' key"); |
| 211 | if (keypos_fortran == std::string::npos) |
| 212 | throw std::runtime_error("missing 'fortran_order' key"); |
| 213 | if (keypos_shape == std::string::npos) |
| 214 | throw std::runtime_error("missing 'shape' key"); |
| 215 | |
| 216 | // make sure the keys are in order |
| 217 | if (keypos_descr >= keypos_fortran || keypos_fortran >= keypos_shape) |
| 218 | throw std::runtime_error("header keys in wrong order"); |
| 219 | |
| 220 | // get the 3 key-value pairs |
| 221 | std::string keyvalue_descr; |
| 222 | keyvalue_descr = header.substr(keypos_descr, keypos_fortran - keypos_descr); |
| 223 | pop_char(keyvalue_descr, ','); |
| 224 | |
| 225 | std::string keyvalue_fortran; |
| 226 | keyvalue_fortran = header.substr(keypos_fortran, keypos_shape - keypos_fortran); |
| 227 | pop_char(keyvalue_fortran, ','); |
| 228 | |
| 229 | std::string keyvalue_shape; |
| 230 | keyvalue_shape = header.substr(keypos_shape, std::string::npos); |
| 231 | pop_char(keyvalue_shape, ','); |
| 232 | |
| 233 | // get the values (right side of `:') |
| 234 | std::string descr_s = get_value_from_map(keyvalue_descr); |
| 235 | std::string fortran_s = get_value_from_map(keyvalue_fortran); |
| 236 | std::string shape_s = get_value_from_map(keyvalue_shape); |
| 237 | |
| 238 | parse_typestring(descr_s); |
| 239 | descr = unwrap_s(descr_s, '\'', '\''); |
| 240 | |
| 241 | // convert literal Python bool to C++ bool |
| 242 | if (fortran_s == "True") |
| 243 | *fortran_order = true; |
| 244 | else if (fortran_s == "False") |
| 245 | *fortran_order = false; |
| 246 | else |
| 247 | throw std::runtime_error("invalid fortran_order value"); |
| 248 | |
| 249 | // parse the shape Python tuple ( x, y, z,) |
| 250 | |
| 251 | // first clear the vector |
| 252 | shape.clear(); |
| 253 | shape_s = unwrap_s(shape_s, '(', ')'); |
| 254 | |
| 255 | // a tokenizer would be nice... |
| 256 | size_t pos = 0; |
| 257 | size_t pos_next; |
| 258 | for(;;) { |
| 259 | pos_next = shape_s.find_first_of(',', pos); |
| 260 | std::string dim_s; |
| 261 | if (pos_next != std::string::npos) |
| 262 | dim_s = shape_s.substr(pos, pos_next - pos); |
| 263 | else |
| 264 | dim_s = shape_s.substr(pos); |
| 265 | pop_char(dim_s, ','); |
| 266 | if (dim_s.length() == 0) { |
| 267 | if (pos_next != std::string::npos) |
| 268 | throw std::runtime_error("invalid shape"); |
| 269 | }else{ |
| 270 | std::stringstream ss; |
| 271 | ss << dim_s; |
| 272 | unsigned long tmp; |
| 273 | ss >> tmp; |
| 274 | shape.push_back(tmp); |
| 275 | } |
| 276 | if (pos_next != std::string::npos) |
| 277 | pos = ++pos_next; |
| 278 | else |
| 279 | break; |
| 280 | } |
| 281 | } |
| 282 | |
| 283 | inline void WriteHeader(std::ostream& out, const std::string& descr, bool fortran_order, unsigned int n_dims, const unsigned long shape[]) |
| 284 | { |
| 285 | std::ostringstream ss_header; |
| 286 | std::string s_fortran_order; |
| 287 | if (fortran_order) |
| 288 | s_fortran_order = "True"; |
| 289 | else |
| 290 | s_fortran_order = "False"; |
| 291 | |
| 292 | std::ostringstream ss_shape; |
| 293 | ss_shape << "("; |
| 294 | for (unsigned int n=0; n < n_dims; n++){ |
| 295 | ss_shape << shape[n] << ", "; |
| 296 | } |
| 297 | ss_shape << ")"; |
| 298 | |
| 299 | ss_header << "{'descr': '" << descr << "', 'fortran_order': " << s_fortran_order << ", 'shape': " << ss_shape.str() << " }"; |
| 300 | |
| 301 | size_t header_len_pre = ss_header.str().length() + 1; |
| 302 | size_t metadata_len = magic_string_length + 2 + 2 + header_len_pre; |
| 303 | |
| 304 | unsigned char version[2] = {1, 0}; |
| 305 | if (metadata_len >= 255*255) { |
| 306 | metadata_len = magic_string_length + 2 + 4 + header_len_pre; |
| 307 | version[0] = 2; |
| 308 | version[1] = 0; |
| 309 | } |
| 310 | size_t padding_len = 16 - metadata_len % 16; |
| 311 | std::string padding (padding_len, ' '); |
| 312 | ss_header << padding; |
| 313 | ss_header << '\n'; |
| 314 | |
| 315 | std::string header = ss_header.str(); |
| 316 | |
| 317 | // write magic |
| 318 | write_magic(out, version[0], version[1]); |
| 319 | |
| 320 | // write header length |
| 321 | if (version[0] == 1 && version[1] == 0) { |
| 322 | uint16_t header_len_le16 = htole16(header.length()); |
| 323 | out.write(reinterpret_cast<char *>(&header_len_le16), 2); |
| 324 | }else{ |
| 325 | uint32_t header_len_le32 = htole32(header.length()); |
| 326 | out.write(reinterpret_cast<char *>(&header_len_le32), 4); |
| 327 | } |
| 328 | |
| 329 | out << header; |
| 330 | } |
| 331 | |
| 332 | template<typename Scalar> |
| 333 | void SaveArrayAsNumpy( const std::string& filename, bool fortran_order, unsigned int n_dims, const unsigned long shape[], const std::vector<Scalar>& data) |
| 334 | { |
| 335 | std::string typestring = get_typestring(typeid(Scalar)); |
| 336 | |
| 337 | std::ofstream stream( filename, std::ofstream::binary); |
| 338 | if(!stream) { |
| 339 | throw std::runtime_error("io error: failed to open a file."); |
| 340 | } |
| 341 | WriteHeader(stream, typestring, fortran_order, n_dims, shape); |
| 342 | |
| 343 | size_t size = 1; |
| 344 | for (unsigned int i=0; i<n_dims; ++i) |
| 345 | size *= shape[i]; |
| 346 | stream.write(reinterpret_cast<const char*>(&data[0]), sizeof(Scalar) * size); |
| 347 | } |
| 348 | |
| 349 | inline std::string read_header_1_0(std::istream& istream) { |
| 350 | // read header length and convert from little endian |
| 351 | uint16_t header_length_raw; |
| 352 | char *header_ptr = reinterpret_cast<char *>(&header_length_raw); |
| 353 | istream.read(header_ptr, 2); |
| 354 | uint16_t header_length = le16toh(header_length_raw); |
| 355 | |
| 356 | if((magic_string_length + 2 + 2 + header_length) % 16 != 0) { |
| 357 | // display warning |
| 358 | } |
| 359 | |
| 360 | char *buf = new char[header_length]; |
| 361 | istream.read(buf, header_length); |
| 362 | std::string header (buf, header_length); |
| 363 | delete[] buf; |
| 364 | |
| 365 | return header; |
| 366 | } |
| 367 | |
| 368 | inline std::string read_header_2_0(std::istream& istream) { |
| 369 | // read header length and convert from little endian |
| 370 | uint32_t header_length_raw; |
| 371 | char *header_ptr = reinterpret_cast<char *>(&header_length_raw); |
| 372 | istream.read(header_ptr, 4); |
| 373 | uint32_t header_length = le32toh(header_length_raw); |
| 374 | |
| 375 | if((magic_string_length + 2 + 4 + header_length) % 16 != 0) { |
| 376 | // display warning |
| 377 | } |
| 378 | |
| 379 | char *buf = new char[header_length]; |
| 380 | istream.read(buf, header_length); |
| 381 | std::string header (buf, header_length); |
| 382 | delete[] buf; |
| 383 | |
| 384 | return header; |
| 385 | } |
| 386 | |
| 387 | template<typename Scalar> |
| 388 | void LoadArrayFromNumpy(const std::string& filename, std::vector<unsigned long>& shape, std::vector<Scalar>& data) |
| 389 | { |
| 390 | std::ifstream stream(filename, std::ifstream::binary); |
| 391 | if(!stream) { |
| 392 | throw std::runtime_error("io error: failed to open a file."); |
| 393 | } |
| 394 | // check magic bytes an version number |
| 395 | unsigned char v_major, v_minor; |
| 396 | read_magic(stream, &v_major, &v_minor); |
| 397 | |
| 398 | std::string header; |
| 399 | |
| 400 | if(v_major == 1 && v_minor == 0){ |
| 401 | header = read_header_1_0(stream); |
| 402 | }else if(v_major == 2 && v_minor == 0) { |
| 403 | header = read_header_2_0(stream); |
| 404 | }else{ |
| 405 | throw std::runtime_error("unsupported file format version"); |
| 406 | } |
| 407 | |
| 408 | // parse header |
| 409 | bool fortran_order; |
| 410 | std::string typestr; |
| 411 | |
| 412 | ParseHeader(header, typestr, &fortran_order, shape); |
| 413 | |
| 414 | // check if the typestring matches the given one |
| 415 | std::string expect_typestr = get_typestring(typeid(Scalar)); |
| 416 | if (typestr != expect_typestr) { |
| 417 | throw std::runtime_error("formatting error: typestrings not matching"); |
| 418 | } |
| 419 | |
| 420 | // compute the data size based on the shape |
| 421 | size_t total_size = 1; |
| 422 | for(size_t i=0; i<shape.size(); ++i) { |
| 423 | total_size *= shape[i]; |
| 424 | } |
| 425 | data.resize(total_size); |
| 426 | |
| 427 | // read the data |
| 428 | stream.read(reinterpret_cast<char*>(&data[0]), sizeof(Scalar)*total_size); |
| 429 | } |
| 430 | |
| 431 | } // namespace npy |