| /* |
| 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_H |
| #define NPY_H |
| |
| #include <complex> |
| #include <fstream> |
| #include <string> |
| #include <iostream> |
| #include <sstream> |
| #include <cstdint> |
| #include <cstring> |
| #include <vector> |
| #include <stdexcept> |
| #include <algorithm> |
| #include <regex> |
| #include <unordered_map> |
| |
| |
| 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 char host_endian_char = ( big_endian ? |
| big_endian_char : |
| little_endian_char ); |
| |
| /* npy array length */ |
| typedef unsigned long int ndarray_len_t; |
| |
| inline void write_magic(std::ostream& ostream, unsigned char v_major=1, unsigned char v_minor=0) { |
| ostream.write(magic_string, magic_string_length); |
| ostream.put(v_major); |
| ostream.put(v_minor); |
| } |
| |
| inline void read_magic(std::istream& istream, unsigned char& v_major, unsigned char& v_minor) { |
| 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."); |
| |
| v_major = buf[magic_string_length]; |
| v_minor = buf[magic_string_length+1]; |
| } |
| |
| // typestring magic |
| struct Typestring { |
| private: |
| char c_endian; |
| char c_type; |
| int len; |
| |
| public: |
| inline std::string str() { |
| const size_t max_buflen = 16; |
| char buf[max_buflen]; |
| std::sprintf(buf, "%c%c%u", c_endian, c_type, len); |
| return std::string(buf); |
| } |
| |
| Typestring(const std::vector<float>& v) |
| :c_endian {host_endian_char}, c_type {'f'}, len {sizeof(float)} {} |
| Typestring(const std::vector<double>& v) |
| :c_endian {host_endian_char}, c_type {'f'}, len {sizeof(double)} {} |
| Typestring(const std::vector<long double>& v) |
| :c_endian {host_endian_char}, c_type {'f'}, len {sizeof(long double)} {} |
| |
| Typestring(const std::vector<char>& v) |
| :c_endian {no_endian_char}, c_type {'i'}, len {sizeof(char)} {} |
| Typestring(const std::vector<short>& v) |
| :c_endian {host_endian_char}, c_type {'i'}, len {sizeof(short)} {} |
| Typestring(const std::vector<int>& v) |
| :c_endian {host_endian_char}, c_type {'i'}, len {sizeof(int)} {} |
| Typestring(const std::vector<long>& v) |
| :c_endian {host_endian_char}, c_type {'i'}, len {sizeof(long)} {} |
| Typestring(const std::vector<long long>& v) :c_endian {host_endian_char}, c_type {'i'}, len {sizeof(long long)} {} |
| |
| Typestring(const std::vector<unsigned char>& v) |
| :c_endian {no_endian_char}, c_type {'u'}, len {sizeof(unsigned char)} {} |
| Typestring(const std::vector<unsigned short>& v) |
| :c_endian {host_endian_char}, c_type {'u'}, len {sizeof(unsigned short)} {} |
| Typestring(const std::vector<unsigned int>& v) |
| :c_endian {host_endian_char}, c_type {'u'}, len {sizeof(unsigned int)} {} |
| Typestring(const std::vector<unsigned long>& v) |
| :c_endian {host_endian_char}, c_type {'u'}, len {sizeof(unsigned long)} {} |
| Typestring(const std::vector<unsigned long long>& v) |
| :c_endian {host_endian_char}, c_type {'u'}, len {sizeof(unsigned long long)} {} |
| |
| Typestring(const std::vector<std::complex<float>>& v) |
| :c_endian {host_endian_char}, c_type {'c'}, len {sizeof(std::complex<float>)} {} |
| Typestring(const std::vector<std::complex<double>>& v) |
| :c_endian {host_endian_char}, c_type {'c'}, len {sizeof(std::complex<double>)} {} |
| Typestring(const std::vector<std::complex<long double>>& v) |
| :c_endian {host_endian_char}, c_type {'c'}, len {sizeof(std::complex<long double>)} {} |
| }; |
| |
| inline void parse_typestring( std::string typestring){ |
| std::regex re ("'([<>|])([ifuc])(\\d+)'"); |
| std::smatch sm; |
| |
| std::regex_match(typestring, sm, re ); |
| |
| if ( sm.size() != 4 ) { |
| throw std::runtime_error("invalid typestring"); |
| } |
| } |
| |
| 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, 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 void parse_header(std::string header, std::string& descr, bool& fortran_order, std::vector<ndarray_len_t>& shape) { |
| /* |
| 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"]; |
| |
| // TODO: extract info from typestring |
| parse_typestring(descr_s); |
| // remove |
| descr = npy::pyparse::parse_str(descr_s); |
| |
| // convert literal Python bool to C++ bool |
| fortran_order = npy::pyparse::parse_bool(fortran_s); |
| |
| // parse the shape tuple |
| auto shape_v = npy::pyparse::parse_tuple(shape_s); |
| if (shape_v.size() == 0) |
| throw std::runtime_error("invalid shape tuple in header"); |
| |
| for ( auto item : shape_v ) { |
| std::stringstream stream(item); |
| unsigned long value; |
| stream >> value; |
| ndarray_len_t dim = static_cast<ndarray_len_t>(value); |
| shape.push_back(dim); |
| } |
| } |
| |
| |
| 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 std::string& descr, bool fortran_order, const std::vector<ndarray_len_t>& shape_v) |
| { |
| std::string header_dict = write_header_dict(descr, fortran_order, shape_v); |
| |
| size_t length = magic_string_length + 2 + 2 + header_dict.length() + 1; |
| |
| unsigned char version[2] = {1, 0}; |
| if (length >= 255*255) { |
| length = magic_string_length + 2 + 4 + header_dict.length() + 1; |
| version[0] = 2; |
| version[1] = 0; |
| } |
| size_t padding_len = 16 - length % 16; |
| std::string padding (padding_len, ' '); |
| |
| // write magic |
| write_magic(out, version[0], version[1]); |
| |
| // write header length |
| if (version[0] == 1 && version[1] == 0) { |
| char header_len_le16[2]; |
| uint16_t header_len = 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{ |
| char header_len_le32[4]; |
| uint32_t header_len = 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 |
| unsigned char v_major, v_minor; |
| read_magic(istream, v_major, v_minor); |
| |
| uint32_t header_length; |
| if(v_major == 1 && v_minor == 0){ |
| |
| char header_len_le16[2]; |
| istream.read(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: display warning |
| } |
| }else if(v_major == 2 && v_minor == 0) { |
| char header_len_le32[4]; |
| istream.read(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: display warning |
| } |
| }else{ |
| throw std::runtime_error("unsupported file format version"); |
| } |
| |
| auto buf_v = std::vector<char>(); |
| buf_v.reserve(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 std::vector<Scalar>& data) |
| { |
| Typestring typestring_o(data); |
| std::string typestring = typestring_o.str(); |
| |
| 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); |
| write_header(stream, typestring, fortran_order, shape_v); |
| |
| auto size = static_cast<size_t>(comp_size(shape_v)); |
| |
| stream.write(reinterpret_cast<const char*>(data.data()), sizeof(Scalar) * size); |
| } |
| |
| |
| template<typename Scalar> |
| inline void LoadArrayFromNumpy(const std::string& filename, std::vector<unsigned long>& shape, 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 = read_header(stream); |
| |
| // parse header |
| bool fortran_order; |
| std::string typestr; |
| |
| parse_header(header, typestr, fortran_order, shape); |
| |
| // check if the typestring matches the given one |
| Typestring typestring_o {data}; |
| std::string expect_typestr = typestring_o.str(); |
| if (typestr != expect_typestr) { |
| throw std::runtime_error("formatting error: typestrings not matching"); |
| } |
| |
| |
| // 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_H |