| /* |
| 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. |
| */ |
| |
| #include <complex> |
| #include <fstream> |
| #include <string> |
| #include <iostream> |
| #include <sstream> |
| #include <cstdint> |
| #include <vector> |
| #include <stdexcept> |
| #include <algorithm> |
| #include <regex> |
| |
| |
| 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 ); |
| |
| 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 = new char[magic_string_length+2]; |
| istream.read(buf, magic_string_length+2); |
| |
| if(!istream) { |
| throw std::runtime_error("io error: failed reading file"); |
| } |
| |
| for (size_t i=0; i < magic_string_length; i++) { |
| if(buf[i] != magic_string[i]) { |
| throw std::runtime_error("this file do not have a valid npy format."); |
| } |
| } |
| |
| *v_major = buf[magic_string_length]; |
| *v_minor = buf[magic_string_length+1]; |
| delete[] buf; |
| } |
| |
| // 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(std::vector<float>& v) :c_endian {host_endian_char}, c_type {'f'}, len {sizeof(float)} {} |
| Typestring(std::vector<double>& v) :c_endian {host_endian_char}, c_type {'f'}, len {sizeof(double)} {} |
| Typestring(std::vector<long double>& v) :c_endian {host_endian_char}, c_type {'f'}, len {sizeof(long double)} {} |
| |
| Typestring(std::vector<char>& v) :c_endian {no_endian_char}, c_type {'i'}, len {sizeof(char)} {} |
| Typestring(std::vector<short>& v) :c_endian {host_endian_char}, c_type {'i'}, len {sizeof(short)} {} |
| Typestring(std::vector<int>& v) :c_endian {host_endian_char}, c_type {'i'}, len {sizeof(int)} {} |
| Typestring(std::vector<long>& v) :c_endian {host_endian_char}, c_type {'i'}, len {sizeof(long)} {} |
| Typestring(std::vector<long long>& v) :c_endian {host_endian_char}, c_type {'i'}, len {sizeof(long long)} {} |
| |
| Typestring(std::vector<unsigned char>& v) :c_endian {no_endian_char}, c_type {'u'}, len {sizeof(unsigned char)} {} |
| Typestring(std::vector<unsigned short>& v) :c_endian {host_endian_char}, c_type {'u'}, len {sizeof(unsigned short)} {} |
| Typestring(std::vector<unsigned int>& v) :c_endian {host_endian_char}, c_type {'u'}, len {sizeof(unsigned int)} {} |
| Typestring(std::vector<unsigned long>& v) :c_endian {host_endian_char}, c_type {'u'}, len {sizeof(unsigned long)} {} |
| Typestring(std::vector<unsigned long long>& v) :c_endian {host_endian_char}, c_type {'u'}, len {sizeof(unsigned long long)} {} |
| |
| Typestring(std::vector<std::complex<float>>& v) :c_endian {host_endian_char}, c_type {'c'}, len {sizeof(std::complex<float>)} {} |
| Typestring(std::vector<std::complex<double>>& v) :c_endian {host_endian_char}, c_type {'c'}, len {sizeof(std::complex<double>)} {} |
| Typestring(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"); |
| } |
| } |
| |
| /* Helpers for the improvised parser */ |
| inline std::string unwrap_s(std::string s, char delim_front, char delim_back) { |
| if ((s.back() == delim_back) && (s.front() == delim_front)) |
| return s.substr(1, s.length()-2); |
| else |
| throw std::runtime_error("unable to unwrap"); |
| } |
| |
| inline std::string get_value_from_map(std::string mapstr) { |
| size_t sep_pos = mapstr.find_first_of(":"); |
| if (sep_pos == std::string::npos) |
| return ""; |
| |
| return mapstr.substr(sep_pos+1); |
| } |
| |
| inline void pop_char(std::string& s, char c) { |
| if (s.back() == c) |
| s.pop_back(); |
| } |
| |
| inline void ParseHeader(std::string header, std::string& descr, bool *fortran_order, std::vector<unsigned long>& 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(); |
| |
| // remove all whitespaces |
| header.erase(std::remove(header.begin(), header.end(), ' '), header.end()); |
| |
| // unwrap dictionary |
| header = unwrap_s(header, '{', '}'); |
| |
| // find the positions of the 3 dictionary keys |
| size_t keypos_descr = header.find("'descr'"); |
| size_t keypos_fortran = header.find("'fortran_order'"); |
| size_t keypos_shape = header.find("'shape'"); |
| |
| // make sure all the keys are present |
| if (keypos_descr == std::string::npos) |
| throw std::runtime_error("missing 'descr' key"); |
| if (keypos_fortran == std::string::npos) |
| throw std::runtime_error("missing 'fortran_order' key"); |
| if (keypos_shape == std::string::npos) |
| throw std::runtime_error("missing 'shape' key"); |
| |
| // Make sure the keys are in order. |
| // Note that this violates the standard, which states that readers *must* not |
| // depend on the correct order here. |
| // TODO: fix |
| if (keypos_descr >= keypos_fortran || keypos_fortran >= keypos_shape) |
| throw std::runtime_error("header keys in wrong order"); |
| |
| // get the 3 key-value pairs |
| std::string keyvalue_descr; |
| keyvalue_descr = header.substr(keypos_descr, keypos_fortran - keypos_descr); |
| pop_char(keyvalue_descr, ','); |
| |
| std::string keyvalue_fortran; |
| keyvalue_fortran = header.substr(keypos_fortran, keypos_shape - keypos_fortran); |
| pop_char(keyvalue_fortran, ','); |
| |
| std::string keyvalue_shape; |
| keyvalue_shape = header.substr(keypos_shape, std::string::npos); |
| pop_char(keyvalue_shape, ','); |
| |
| // get the values (right side of `:') |
| std::string descr_s = get_value_from_map(keyvalue_descr); |
| std::string fortran_s = get_value_from_map(keyvalue_fortran); |
| std::string shape_s = get_value_from_map(keyvalue_shape); |
| |
| parse_typestring(descr_s); |
| descr = unwrap_s(descr_s, '\'', '\''); |
| |
| // convert literal Python bool to C++ bool |
| if (fortran_s == "True") |
| *fortran_order = true; |
| else if (fortran_s == "False") |
| *fortran_order = false; |
| else |
| throw std::runtime_error("invalid fortran_order value"); |
| |
| // parse the shape Python tuple ( x, y, z,) |
| |
| // first clear the vector |
| shape.clear(); |
| shape_s = unwrap_s(shape_s, '(', ')'); |
| |
| // a tokenizer would be nice... |
| size_t pos = 0; |
| size_t pos_next; |
| for(;;) { |
| pos_next = shape_s.find_first_of(',', pos); |
| std::string dim_s; |
| if (pos_next != std::string::npos) |
| dim_s = shape_s.substr(pos, pos_next - pos); |
| else |
| dim_s = shape_s.substr(pos); |
| pop_char(dim_s, ','); |
| if (dim_s.length() == 0) { |
| if (pos_next != std::string::npos) |
| throw std::runtime_error("invalid shape"); |
| }else{ |
| std::stringstream ss; |
| ss << dim_s; |
| unsigned long tmp; |
| ss >> tmp; |
| shape.push_back(tmp); |
| } |
| if (pos_next != std::string::npos) |
| pos = ++pos_next; |
| else |
| break; |
| } |
| } |
| |
| inline void WriteHeader(std::ostream& out, const std::string& descr, bool fortran_order, unsigned int n_dims, const unsigned long shape[]) |
| { |
| std::ostringstream ss_header; |
| std::string s_fortran_order; |
| if (fortran_order) |
| s_fortran_order = "True"; |
| else |
| s_fortran_order = "False"; |
| |
| std::ostringstream ss_shape; |
| ss_shape << "("; |
| for (unsigned int n=0; n < n_dims; n++){ |
| ss_shape << shape[n] << ", "; |
| } |
| ss_shape << ")"; |
| |
| ss_header << "{'descr': '" << descr << "', 'fortran_order': " << s_fortran_order << ", 'shape': " << ss_shape.str() << " }"; |
| |
| size_t header_len_pre = ss_header.str().length() + 1; |
| size_t metadata_len = magic_string_length + 2 + 2 + header_len_pre; |
| |
| unsigned char version[2] = {1, 0}; |
| if (metadata_len >= 255*255) { |
| metadata_len = magic_string_length + 2 + 4 + header_len_pre; |
| version[0] = 2; |
| version[1] = 0; |
| } |
| size_t padding_len = 16 - metadata_len % 16; |
| std::string padding (padding_len, ' '); |
| ss_header << padding; |
| ss_header << '\n'; |
| |
| std::string header = ss_header.str(); |
| |
| // 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.length(); |
| |
| 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.length(); |
| |
| 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; |
| } |
| |
| inline std::string read_header_1_0(std::istream& istream) { |
| // read header length and convert from little endian |
| char header_len_le16[2]; |
| istream.read(header_len_le16, 2); |
| |
| uint16_t 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 |
| } |
| |
| char *buf = new char[header_length]; |
| istream.read(buf, header_length); |
| std::string header (buf, header_length); |
| delete[] buf; |
| |
| return header; |
| } |
| |
| inline std::string read_header_2_0(std::istream& istream) { |
| // read header length and convert from little endian |
| char header_len_le32[4]; |
| istream.read(header_len_le32, 4); |
| |
| uint32_t 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 |
| } |
| |
| char *buf = new char[header_length]; |
| istream.read(buf, header_length); |
| std::string header (buf, header_length); |
| delete[] buf; |
| |
| return header; |
| } |
| |
| template<typename Scalar> |
| 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."); |
| } |
| WriteHeader(stream, typestring, fortran_order, n_dims, shape); |
| |
| size_t size = 1; |
| for (unsigned int i=0; i<n_dims; ++i) |
| size *= shape[i]; |
| stream.write(reinterpret_cast<const char*>(&data[0]), sizeof(Scalar) * size); |
| } |
| |
| |
| /** |
| |
| */ |
| template<typename Scalar> |
| 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."); |
| } |
| // check magic bytes an version number |
| unsigned char v_major, v_minor; |
| read_magic(stream, &v_major, &v_minor); |
| |
| std::string header; |
| |
| if(v_major == 1 && v_minor == 0){ |
| header = read_header_1_0(stream); |
| }else if(v_major == 2 && v_minor == 0) { |
| header = read_header_2_0(stream); |
| }else{ |
| throw std::runtime_error("unsupported file format version"); |
| } |
| |
| // parse header |
| bool fortran_order; |
| std::string typestr; |
| |
| ParseHeader(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 |
| size_t total_size = 1; |
| for(size_t i=0; i<shape.size(); ++i) { |
| total_size *= shape[i]; |
| } |
| data.resize(total_size); |
| |
| // read the data |
| stream.read(reinterpret_cast<char*>(&data[0]), sizeof(Scalar)*total_size); |
| } |
| |
| } // namespace npy |