| /* |
| Copyright 2017 Leon Merten Lohse |
| |
| Permission is hereby granted, free of charge, to any person obtaining a copy |
| of this software and associated documentation files (the "Software"), to deal |
| in the Software without restriction, including without limitation the rights |
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell |
| copies of the Software, and to permit persons to whom the Software is |
| furnished to do so, subject to the following conditions: |
| |
| The above copyright notice and this permission notice shall be included in |
| all copies or substantial portions of the Software. |
| |
| THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR |
| IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, |
| FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE |
| AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER |
| LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, |
| OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE |
| SOFTWARE. |
| */ |
| |
| #ifndef NPY_HPP_ |
| #define NPY_HPP_ |
| |
| #include <complex> |
| #include <fstream> |
| #include <string> |
| #include <iostream> |
| #include <sstream> |
| #include <cstdint> |
| #include <cstring> |
| #include <array> |
| #include <vector> |
| #include <stdexcept> |
| #include <algorithm> |
| #include <unordered_map> |
| #include <type_traits> |
| #include <typeinfo> |
| #include <typeindex> |
| #include <iterator> |
| #include <utility> |
| |
| |
| namespace npy { |
| |
| /* Compile-time test for byte order. |
| If your compiler does not define these per default, you may want to define |
| one of these constants manually. |
| Defaults to little endian order. */ |
| #if defined(__BYTE_ORDER) && __BYTE_ORDER == __BIG_ENDIAN || \ |
| defined(__BIG_ENDIAN__) || \ |
| defined(__ARMEB__) || \ |
| defined(__THUMBEB__) || \ |
| defined(__AARCH64EB__) || \ |
| defined(_MIBSEB) || defined(__MIBSEB) || defined(__MIBSEB__) |
| const bool big_endian = true; |
| #else |
| const bool big_endian = false; |
| #endif |
| |
| |
| const char magic_string[] = "\x93NUMPY"; |
| const size_t magic_string_length = 6; |
| |
| const char little_endian_char = '<'; |
| const char big_endian_char = '>'; |
| const char no_endian_char = '|'; |
| |
| constexpr std::array<char, 3> |
| endian_chars = {little_endian_char, big_endian_char, no_endian_char}; |
| constexpr std::array<char, 4> |
| numtype_chars = {'f', 'i', 'u', 'c'}; |
| |
| constexpr char host_endian_char = (big_endian ? |
| big_endian_char : |
| little_endian_char); |
| |
| /* npy array length */ |
| typedef unsigned long int ndarray_len_t; |
| |
| typedef std::pair<char, char> version_t; |
| |
| struct dtype_t { |
| const char byteorder; |
| const char kind; |
| const unsigned int itemsize; |
| |
| // TODO(llohse): implement as constexpr |
| inline std::string str() const { |
| const size_t max_buflen = 16; |
| char buf[max_buflen]; |
| std::snprintf(buf, max_buflen, "%c%c%u", byteorder, kind, itemsize); |
| return std::string(buf); |
| } |
| |
| inline std::tuple<const char, const char, const unsigned int> tie() const { |
| return std::tie(byteorder, kind, itemsize); |
| } |
| }; |
| |
| |
| struct header_t { |
| const dtype_t dtype; |
| const bool fortran_order; |
| const std::vector <ndarray_len_t> shape; |
| }; |
| |
| inline void write_magic(std::ostream &ostream, version_t version) { |
| ostream.write(magic_string, magic_string_length); |
| ostream.put(version.first); |
| ostream.put(version.second); |
| } |
| |
| inline version_t read_magic(std::istream &istream) { |
| char buf[magic_string_length + 2]; |
| istream.read(buf, magic_string_length + 2); |
| |
| if (!istream) { |
| throw std::runtime_error("io error: failed reading file"); |
| } |
| |
| if (0 != std::memcmp(buf, magic_string, magic_string_length)) |
| throw std::runtime_error("this file does not have a valid npy format."); |
| |
| version_t version; |
| version.first = buf[magic_string_length]; |
| version.second = buf[magic_string_length + 1]; |
| |
| return version; |
| } |
| |
| const std::unordered_map<std::type_index, dtype_t> dtype_map = { |
| {std::type_index(typeid(float)), {host_endian_char, 'f', sizeof(float)}}, |
| {std::type_index(typeid(double)), {host_endian_char, 'f', sizeof(double)}}, |
| {std::type_index(typeid(long double)), {host_endian_char, 'f', sizeof(long double)}}, |
| {std::type_index(typeid(char)), {no_endian_char, 'i', sizeof(char)}}, |
| {std::type_index(typeid(signed char)), {no_endian_char, 'i', sizeof(signed char)}}, |
| {std::type_index(typeid(short)), {host_endian_char, 'i', sizeof(short)}}, |
| {std::type_index(typeid(int)), {host_endian_char, 'i', sizeof(int)}}, |
| {std::type_index(typeid(long)), {host_endian_char, 'i', sizeof(long)}}, |
| {std::type_index(typeid(long long)), {host_endian_char, 'i', sizeof(long long)}}, |
| {std::type_index(typeid(unsigned char)), {no_endian_char, 'u', sizeof(unsigned char)}}, |
| {std::type_index(typeid(unsigned short)), {host_endian_char, 'u', sizeof(unsigned short)}}, |
| {std::type_index(typeid(unsigned int)), {host_endian_char, 'u', sizeof(unsigned int)}}, |
| {std::type_index(typeid(unsigned long)), {host_endian_char, 'u', sizeof(unsigned long)}}, |
| {std::type_index(typeid(unsigned long long)), {host_endian_char, 'u', sizeof(unsigned long long)}}, |
| {std::type_index(typeid(std::complex<float>)), {host_endian_char, 'c', sizeof(std::complex<float>)}}, |
| {std::type_index(typeid(std::complex<double>)), {host_endian_char, 'c', sizeof(std::complex<double>)}}, |
| {std::type_index(typeid(std::complex<long double>)), {host_endian_char, 'c', sizeof(std::complex<long double>)}} |
| }; |
| |
| |
| // helpers |
| inline bool is_digits(const std::string &str) { |
| return std::all_of(str.begin(), str.end(), ::isdigit); |
| } |
| |
| template<typename T, size_t N> |
| inline bool in_array(T val, const std::array <T, N> &arr) { |
| return std::find(std::begin(arr), std::end(arr), val) != std::end(arr); |
| } |
| |
| inline dtype_t parse_descr(std::string typestring) { |
| if (typestring.length() < 3) { |
| throw std::runtime_error("invalid typestring (length)"); |
| } |
| |
| char byteorder_c = typestring.at(0); |
| char kind_c = typestring.at(1); |
| std::string itemsize_s = typestring.substr(2); |
| |
| if (!in_array(byteorder_c, endian_chars)) { |
| throw std::runtime_error("invalid typestring (byteorder)"); |
| } |
| |
| if (!in_array(kind_c, numtype_chars)) { |
| throw std::runtime_error("invalid typestring (kind)"); |
| } |
| |
| if (!is_digits(itemsize_s)) { |
| throw std::runtime_error("invalid typestring (itemsize)"); |
| } |
| unsigned int itemsize = std::stoul(itemsize_s); |
| |
| return {byteorder_c, kind_c, itemsize}; |
| } |
| |
| namespace pyparse { |
| |
| /** |
| Removes leading and trailing whitespaces |
| */ |
| inline std::string trim(const std::string &str) { |
| const std::string whitespace = " \t"; |
| auto begin = str.find_first_not_of(whitespace); |
| |
| if (begin == std::string::npos) |
| return ""; |
| |
| auto end = str.find_last_not_of(whitespace); |
| |
| return str.substr(begin, end - begin + 1); |
| } |
| |
| |
| inline std::string get_value_from_map(const std::string &mapstr) { |
| size_t sep_pos = mapstr.find_first_of(":"); |
| if (sep_pos == std::string::npos) |
| return ""; |
| |
| std::string tmp = mapstr.substr(sep_pos + 1); |
| return trim(tmp); |
| } |
| |
| /** |
| Parses the string representation of a Python dict |
| |
| The keys need to be known and may not appear anywhere else in the data. |
| */ |
| inline std::unordered_map <std::string, std::string> parse_dict(std::string in, const std::vector <std::string> &keys) { |
| std::unordered_map <std::string, std::string> map; |
| |
| if (keys.size() == 0) |
| return map; |
| |
| in = trim(in); |
| |
| // unwrap dictionary |
| if ((in.front() == '{') && (in.back() == '}')) |
| in = in.substr(1, in.length() - 2); |
| else |
| throw std::runtime_error("Not a Python dictionary."); |
| |
| std::vector <std::pair<size_t, std::string>> positions; |
| |
| for (auto const &value : keys) { |
| size_t pos = in.find("'" + value + "'"); |
| |
| if (pos == std::string::npos) |
| throw std::runtime_error("Missing '" + value + "' key."); |
| |
| std::pair <size_t, std::string> position_pair{pos, value}; |
| positions.push_back(position_pair); |
| } |
| |
| // sort by position in dict |
| std::sort(positions.begin(), positions.end()); |
| |
| for (size_t i = 0; i < positions.size(); ++i) { |
| std::string raw_value; |
| size_t begin{positions[i].first}; |
| size_t end{std::string::npos}; |
| |
| std::string key = positions[i].second; |
| |
| if (i + 1 < positions.size()) |
| end = positions[i + 1].first; |
| |
| raw_value = in.substr(begin, end - begin); |
| |
| raw_value = trim(raw_value); |
| |
| if (raw_value.back() == ',') |
| raw_value.pop_back(); |
| |
| map[key] = get_value_from_map(raw_value); |
| } |
| |
| return map; |
| } |
| |
| /** |
| Parses the string representation of a Python boolean |
| */ |
| inline bool parse_bool(const std::string &in) { |
| if (in == "True") |
| return true; |
| if (in == "False") |
| return false; |
| |
| throw std::runtime_error("Invalid python boolan."); |
| } |
| |
| /** |
| Parses the string representation of a Python str |
| */ |
| inline std::string parse_str(const std::string &in) { |
| if ((in.front() == '\'') && (in.back() == '\'')) |
| return in.substr(1, in.length() - 2); |
| |
| throw std::runtime_error("Invalid python string."); |
| } |
| |
| /** |
| Parses the string represenatation of a Python tuple into a vector of its items |
| */ |
| inline std::vector <std::string> parse_tuple(std::string in) { |
| std::vector <std::string> v; |
| const char seperator = ','; |
| |
| in = trim(in); |
| |
| if ((in.front() == '(') && (in.back() == ')')) |
| in = in.substr(1, in.length() - 2); |
| else |
| throw std::runtime_error("Invalid Python tuple."); |
| |
| std::istringstream iss(in); |
| |
| for (std::string token; std::getline(iss, token, seperator);) { |
| v.push_back(token); |
| } |
| |
| return v; |
| } |
| |
| template<typename T> |
| inline std::string write_tuple(const std::vector <T> &v) { |
| if (v.size() == 0) |
| return "()"; |
| |
| std::ostringstream ss; |
| |
| if (v.size() == 1) { |
| ss << "(" << v.front() << ",)"; |
| } else { |
| const std::string delimiter = ", "; |
| // v.size() > 1 |
| ss << "("; |
| std::copy(v.begin(), v.end() - 1, std::ostream_iterator<T>(ss, delimiter.c_str())); |
| ss << v.back(); |
| ss << ")"; |
| } |
| |
| return ss.str(); |
| } |
| |
| inline std::string write_boolean(bool b) { |
| if (b) |
| return "True"; |
| else |
| return "False"; |
| } |
| |
| } // namespace pyparse |
| |
| |
| inline header_t parse_header(std::string header) { |
| /* |
| The first 6 bytes are a magic string: exactly "x93NUMPY". |
| The next 1 byte is an unsigned byte: the major version number of the file format, e.g. x01. |
| 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. |
| The next 2 bytes form a little-endian unsigned short int: the length of the header data HEADER_LEN. |
| 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. |
| The dictionary contains three keys: |
| |
| "descr" : dtype.descr |
| An object that can be passed as an argument to the numpy.dtype() constructor to create the array's dtype. |
| "fortran_order" : bool |
| 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. |
| "shape" : tuple of int |
| The shape of the array. |
| For repeatability and readability, this dictionary is formatted using pprint.pformat() so the keys are in alphabetic order. |
| */ |
| |
| // remove trailing newline |
| if (header.back() != '\n') |
| throw std::runtime_error("invalid header"); |
| header.pop_back(); |
| |
| // parse the dictionary |
| std::vector <std::string> keys{"descr", "fortran_order", "shape"}; |
| auto dict_map = npy::pyparse::parse_dict(header, keys); |
| |
| if (dict_map.size() == 0) |
| throw std::runtime_error("invalid dictionary in header"); |
| |
| std::string descr_s = dict_map["descr"]; |
| std::string fortran_s = dict_map["fortran_order"]; |
| std::string shape_s = dict_map["shape"]; |
| |
| std::string descr = npy::pyparse::parse_str(descr_s); |
| dtype_t dtype = parse_descr(descr); |
| |
| // convert literal Python bool to C++ bool |
| bool fortran_order = npy::pyparse::parse_bool(fortran_s); |
| |
| // parse the shape tuple |
| auto shape_v = npy::pyparse::parse_tuple(shape_s); |
| |
| std::vector <ndarray_len_t> shape; |
| for (auto item : shape_v) { |
| ndarray_len_t dim = static_cast<ndarray_len_t>(std::stoul(item)); |
| shape.push_back(dim); |
| } |
| |
| return {dtype, fortran_order, shape}; |
| } |
| |
| |
| inline std::string |
| write_header_dict(const std::string &descr, bool fortran_order, const std::vector <ndarray_len_t> &shape) { |
| std::string s_fortran_order = npy::pyparse::write_boolean(fortran_order); |
| std::string shape_s = npy::pyparse::write_tuple(shape); |
| |
| return "{'descr': '" + descr + "', 'fortran_order': " + s_fortran_order + ", 'shape': " + shape_s + ", }"; |
| } |
| |
| inline void write_header(std::ostream &out, const header_t &header) { |
| std::string header_dict = write_header_dict(header.dtype.str(), header.fortran_order, header.shape); |
| |
| size_t length = magic_string_length + 2 + 2 + header_dict.length() + 1; |
| |
| version_t version{1, 0}; |
| if (length >= 255 * 255) { |
| length = magic_string_length + 2 + 4 + header_dict.length() + 1; |
| version = {2, 0}; |
| } |
| size_t padding_len = 16 - length % 16; |
| std::string padding(padding_len, ' '); |
| |
| // write magic |
| write_magic(out, version); |
| |
| // write header length |
| if (version == version_t{1, 0}) { |
| uint8_t header_len_le16[2]; |
| uint16_t header_len = static_cast<uint16_t>(header_dict.length() + padding.length() + 1); |
| |
| header_len_le16[0] = (header_len >> 0) & 0xff; |
| header_len_le16[1] = (header_len >> 8) & 0xff; |
| out.write(reinterpret_cast<char *>(header_len_le16), 2); |
| } else { |
| uint8_t header_len_le32[4]; |
| uint32_t header_len = static_cast<uint32_t>(header_dict.length() + padding.length() + 1); |
| |
| header_len_le32[0] = (header_len >> 0) & 0xff; |
| header_len_le32[1] = (header_len >> 8) & 0xff; |
| header_len_le32[2] = (header_len >> 16) & 0xff; |
| header_len_le32[3] = (header_len >> 24) & 0xff; |
| out.write(reinterpret_cast<char *>(header_len_le32), 4); |
| } |
| |
| out << header_dict << padding << '\n'; |
| } |
| |
| inline std::string read_header(std::istream &istream) { |
| // check magic bytes an version number |
| version_t version = read_magic(istream); |
| |
| uint32_t header_length; |
| if (version == version_t{1, 0}) { |
| uint8_t header_len_le16[2]; |
| istream.read(reinterpret_cast<char *>(header_len_le16), 2); |
| header_length = (header_len_le16[0] << 0) | (header_len_le16[1] << 8); |
| |
| if ((magic_string_length + 2 + 2 + header_length) % 16 != 0) { |
| // TODO(llohse): display warning |
| } |
| } else if (version == version_t{2, 0}) { |
| uint8_t header_len_le32[4]; |
| istream.read(reinterpret_cast<char *>(header_len_le32), 4); |
| |
| header_length = (header_len_le32[0] << 0) | (header_len_le32[1] << 8) |
| | (header_len_le32[2] << 16) | (header_len_le32[3] << 24); |
| |
| if ((magic_string_length + 2 + 4 + header_length) % 16 != 0) { |
| // TODO(llohse): display warning |
| } |
| } else { |
| throw std::runtime_error("unsupported file format version"); |
| } |
| |
| auto buf_v = std::vector<char>(header_length); |
| istream.read(buf_v.data(), header_length); |
| std::string header(buf_v.data(), header_length); |
| |
| return header; |
| } |
| |
| inline ndarray_len_t comp_size(const std::vector <ndarray_len_t> &shape) { |
| ndarray_len_t size = 1; |
| for (ndarray_len_t i : shape) |
| size *= i; |
| |
| return size; |
| } |
| |
| template<typename Scalar> |
| inline void |
| SaveArrayAsNumpy(const std::string &filename, bool fortran_order, unsigned int n_dims, const unsigned long shape[], |
| const Scalar* data) { |
| // static_assert(has_typestring<Scalar>::value, "scalar type not understood"); |
| const dtype_t dtype = dtype_map.at(std::type_index(typeid(Scalar))); |
| |
| std::ofstream stream(filename, std::ofstream::binary); |
| if (!stream) { |
| throw std::runtime_error("io error: failed to open a file."); |
| } |
| |
| std::vector <ndarray_len_t> shape_v(shape, shape + n_dims); |
| header_t header{dtype, fortran_order, shape_v}; |
| write_header(stream, header); |
| |
| auto size = static_cast<size_t>(comp_size(shape_v)); |
| |
| stream.write(reinterpret_cast<const char *>(data), sizeof(Scalar) * size); |
| } |
| |
| template<typename Scalar> |
| inline void |
| SaveArrayAsNumpy(const std::string &filename, bool fortran_order, unsigned int n_dims, const unsigned long shape[], |
| const std::vector <Scalar> &data) { |
| SaveArrayAsNumpy(filename, fortran_order, n_dims, shape, data.data()); |
| } |
| |
| template<typename Scalar> |
| inline void |
| LoadArrayFromNumpy(const std::string &filename, std::vector<unsigned long> &shape, std::vector <Scalar> &data) { |
| bool fortran_order; |
| LoadArrayFromNumpy<Scalar>(filename, shape, fortran_order, data); |
| } |
| |
| template<typename Scalar> |
| inline void LoadArrayFromNumpy(const std::string &filename, std::vector<unsigned long> &shape, bool &fortran_order, |
| std::vector <Scalar> &data) { |
| std::ifstream stream(filename, std::ifstream::binary); |
| if (!stream) { |
| throw std::runtime_error("io error: failed to open a file."); |
| } |
| |
| std::string header_s = read_header(stream); |
| |
| // parse header |
| header_t header = parse_header(header_s); |
| |
| // check if the typestring matches the given one |
| // static_assert(has_typestring<Scalar>::value, "scalar type not understood"); |
| const dtype_t dtype = dtype_map.at(std::type_index(typeid(Scalar))); |
| |
| if (header.dtype.tie() != dtype.tie()) { |
| throw std::runtime_error("formatting error: typestrings not matching"); |
| } |
| |
| shape = header.shape; |
| fortran_order = header.fortran_order; |
| |
| // compute the data size based on the shape |
| auto size = static_cast<size_t>(comp_size(shape)); |
| data.resize(size); |
| |
| // read the data |
| stream.read(reinterpret_cast<char *>(data.data()), sizeof(Scalar) * size); |
| } |
| |
| } // namespace npy |
| |
| #endif // NPY_HPP_ |