// SPDX-License-Identifier: Apache-2.0 // // Copyright 2008-2016 Conrad Sanderson (http://conradsanderson.id.au) // Copyright 2008-2016 National ICT Australia (NICTA) // // Licensed under the Apache License, Version 2.0 (the "License"); // you may not use this file except in compliance with the License. // You may obtain a copy of the License at // http://www.apache.org/licenses/LICENSE-2.0 // // Unless required by applicable law or agreed to in writing, software // distributed under the License is distributed on an "AS IS" BASIS, // WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. // See the License for the specific language governing permissions and // limitations under the License. // ------------------------------------------------------------------------ //! \addtogroup diskio //! @{ //! Generate the first line of the header used for saving matrices in text format. //! Format: "ARMA_MAT_TXT_ABXYZ". //! A is one of: I (for integral types) or F (for floating point types). //! B is one of: U (for unsigned types), S (for signed types), N (for not applicable) or C (for complex types). //! XYZ specifies the width of each element in terms of bytes, eg. "008" indicates eight bytes. template inline std::string diskio::gen_txt_header(const Mat&) { arma_type_check(( is_supported_elem_type::value == false )); const char* ARMA_MAT_TXT_IU001 = "ARMA_MAT_TXT_IU001"; const char* ARMA_MAT_TXT_IS001 = "ARMA_MAT_TXT_IS001"; const char* ARMA_MAT_TXT_IU002 = "ARMA_MAT_TXT_IU002"; const char* ARMA_MAT_TXT_IS002 = "ARMA_MAT_TXT_IS002"; const char* ARMA_MAT_TXT_IU004 = "ARMA_MAT_TXT_IU004"; const char* ARMA_MAT_TXT_IS004 = "ARMA_MAT_TXT_IS004"; const char* ARMA_MAT_TXT_IU008 = "ARMA_MAT_TXT_IU008"; const char* ARMA_MAT_TXT_IS008 = "ARMA_MAT_TXT_IS008"; const char* ARMA_MAT_TXT_FN004 = "ARMA_MAT_TXT_FN004"; const char* ARMA_MAT_TXT_FN008 = "ARMA_MAT_TXT_FN008"; const char* ARMA_MAT_TXT_FC008 = "ARMA_MAT_TXT_FC008"; const char* ARMA_MAT_TXT_FC016 = "ARMA_MAT_TXT_FC016"; char* header = nullptr; if( is_u8::value) { header = const_cast(ARMA_MAT_TXT_IU001); } else if( is_s8::value) { header = const_cast(ARMA_MAT_TXT_IS001); } else if( is_u16::value) { header = const_cast(ARMA_MAT_TXT_IU002); } else if( is_s16::value) { header = const_cast(ARMA_MAT_TXT_IS002); } else if( is_u32::value) { header = const_cast(ARMA_MAT_TXT_IU004); } else if( is_s32::value) { header = const_cast(ARMA_MAT_TXT_IS004); } else if( is_u64::value) { header = const_cast(ARMA_MAT_TXT_IU008); } else if( is_s64::value) { header = const_cast(ARMA_MAT_TXT_IS008); } else if(is_ulng_t_32::value) { header = const_cast(ARMA_MAT_TXT_IU004); } else if(is_slng_t_32::value) { header = const_cast(ARMA_MAT_TXT_IS004); } else if(is_ulng_t_64::value) { header = const_cast(ARMA_MAT_TXT_IU008); } else if(is_slng_t_64::value) { header = const_cast(ARMA_MAT_TXT_IS008); } else if( is_float::value) { header = const_cast(ARMA_MAT_TXT_FN004); } else if( is_double::value) { header = const_cast(ARMA_MAT_TXT_FN008); } else if( is_cx_float::value) { header = const_cast(ARMA_MAT_TXT_FC008); } else if(is_cx_double::value) { header = const_cast(ARMA_MAT_TXT_FC016); } return std::string(header); } //! Generate the first line of the header used for saving matrices in binary format. //! Format: "ARMA_MAT_BIN_ABXYZ". //! A is one of: I (for integral types) or F (for floating point types). //! B is one of: U (for unsigned types), S (for signed types), N (for not applicable) or C (for complex types). //! XYZ specifies the width of each element in terms of bytes, eg. "008" indicates eight bytes. template inline std::string diskio::gen_bin_header(const Mat&) { arma_type_check(( is_supported_elem_type::value == false )); const char* ARMA_MAT_BIN_IU001 = "ARMA_MAT_BIN_IU001"; const char* ARMA_MAT_BIN_IS001 = "ARMA_MAT_BIN_IS001"; const char* ARMA_MAT_BIN_IU002 = "ARMA_MAT_BIN_IU002"; const char* ARMA_MAT_BIN_IS002 = "ARMA_MAT_BIN_IS002"; const char* ARMA_MAT_BIN_IU004 = "ARMA_MAT_BIN_IU004"; const char* ARMA_MAT_BIN_IS004 = "ARMA_MAT_BIN_IS004"; const char* ARMA_MAT_BIN_IU008 = "ARMA_MAT_BIN_IU008"; const char* ARMA_MAT_BIN_IS008 = "ARMA_MAT_BIN_IS008"; const char* ARMA_MAT_BIN_FN004 = "ARMA_MAT_BIN_FN004"; const char* ARMA_MAT_BIN_FN008 = "ARMA_MAT_BIN_FN008"; const char* ARMA_MAT_BIN_FC008 = "ARMA_MAT_BIN_FC008"; const char* ARMA_MAT_BIN_FC016 = "ARMA_MAT_BIN_FC016"; char* header = nullptr; if( is_u8::value) { header = const_cast(ARMA_MAT_BIN_IU001); } else if( is_s8::value) { header = const_cast(ARMA_MAT_BIN_IS001); } else if( is_u16::value) { header = const_cast(ARMA_MAT_BIN_IU002); } else if( is_s16::value) { header = const_cast(ARMA_MAT_BIN_IS002); } else if( is_u32::value) { header = const_cast(ARMA_MAT_BIN_IU004); } else if( is_s32::value) { header = const_cast(ARMA_MAT_BIN_IS004); } else if( is_u64::value) { header = const_cast(ARMA_MAT_BIN_IU008); } else if( is_s64::value) { header = const_cast(ARMA_MAT_BIN_IS008); } else if(is_ulng_t_32::value) { header = const_cast(ARMA_MAT_BIN_IU004); } else if(is_slng_t_32::value) { header = const_cast(ARMA_MAT_BIN_IS004); } else if(is_ulng_t_64::value) { header = const_cast(ARMA_MAT_BIN_IU008); } else if(is_slng_t_64::value) { header = const_cast(ARMA_MAT_BIN_IS008); } else if( is_float::value) { header = const_cast(ARMA_MAT_BIN_FN004); } else if( is_double::value) { header = const_cast(ARMA_MAT_BIN_FN008); } else if( is_cx_float::value) { header = const_cast(ARMA_MAT_BIN_FC008); } else if(is_cx_double::value) { header = const_cast(ARMA_MAT_BIN_FC016); } return std::string(header); } //! Generate the first line of the header used for saving matrices in binary format. //! Format: "ARMA_SPM_BIN_ABXYZ". //! A is one of: I (for integral types) or F (for floating point types). //! B is one of: U (for unsigned types), S (for signed types), N (for not applicable) or C (for complex types). //! XYZ specifies the width of each element in terms of bytes, eg. "008" indicates eight bytes. template inline std::string diskio::gen_bin_header(const SpMat&) { arma_type_check(( is_supported_elem_type::value == false )); const char* ARMA_SPM_BIN_IU001 = "ARMA_SPM_BIN_IU001"; const char* ARMA_SPM_BIN_IS001 = "ARMA_SPM_BIN_IS001"; const char* ARMA_SPM_BIN_IU002 = "ARMA_SPM_BIN_IU002"; const char* ARMA_SPM_BIN_IS002 = "ARMA_SPM_BIN_IS002"; const char* ARMA_SPM_BIN_IU004 = "ARMA_SPM_BIN_IU004"; const char* ARMA_SPM_BIN_IS004 = "ARMA_SPM_BIN_IS004"; const char* ARMA_SPM_BIN_IU008 = "ARMA_SPM_BIN_IU008"; const char* ARMA_SPM_BIN_IS008 = "ARMA_SPM_BIN_IS008"; const char* ARMA_SPM_BIN_FN004 = "ARMA_SPM_BIN_FN004"; const char* ARMA_SPM_BIN_FN008 = "ARMA_SPM_BIN_FN008"; const char* ARMA_SPM_BIN_FC008 = "ARMA_SPM_BIN_FC008"; const char* ARMA_SPM_BIN_FC016 = "ARMA_SPM_BIN_FC016"; char* header = nullptr; if( is_u8::value) { header = const_cast(ARMA_SPM_BIN_IU001); } else if( is_s8::value) { header = const_cast(ARMA_SPM_BIN_IS001); } else if( is_u16::value) { header = const_cast(ARMA_SPM_BIN_IU002); } else if( is_s16::value) { header = const_cast(ARMA_SPM_BIN_IS002); } else if( is_u32::value) { header = const_cast(ARMA_SPM_BIN_IU004); } else if( is_s32::value) { header = const_cast(ARMA_SPM_BIN_IS004); } else if( is_u64::value) { header = const_cast(ARMA_SPM_BIN_IU008); } else if( is_s64::value) { header = const_cast(ARMA_SPM_BIN_IS008); } else if(is_ulng_t_32::value) { header = const_cast(ARMA_SPM_BIN_IU004); } else if(is_slng_t_32::value) { header = const_cast(ARMA_SPM_BIN_IS004); } else if(is_ulng_t_64::value) { header = const_cast(ARMA_SPM_BIN_IU008); } else if(is_slng_t_64::value) { header = const_cast(ARMA_SPM_BIN_IS008); } else if( is_float::value) { header = const_cast(ARMA_SPM_BIN_FN004); } else if( is_double::value) { header = const_cast(ARMA_SPM_BIN_FN008); } else if( is_cx_float::value) { header = const_cast(ARMA_SPM_BIN_FC008); } else if(is_cx_double::value) { header = const_cast(ARMA_SPM_BIN_FC016); } return std::string(header); } //! Generate the first line of the header used for saving cubes in text format. //! Format: "ARMA_CUB_TXT_ABXYZ". //! A is one of: I (for integral types) or F (for floating point types). //! B is one of: U (for unsigned types), S (for signed types), N (for not applicable) or C (for complex types). //! XYZ specifies the width of each element in terms of bytes, eg. "008" indicates eight bytes. template inline std::string diskio::gen_txt_header(const Cube&) { arma_type_check(( is_supported_elem_type::value == false )); const char* ARMA_CUB_TXT_IU001 = "ARMA_CUB_TXT_IU001"; const char* ARMA_CUB_TXT_IS001 = "ARMA_CUB_TXT_IS001"; const char* ARMA_CUB_TXT_IU002 = "ARMA_CUB_TXT_IU002"; const char* ARMA_CUB_TXT_IS002 = "ARMA_CUB_TXT_IS002"; const char* ARMA_CUB_TXT_IU004 = "ARMA_CUB_TXT_IU004"; const char* ARMA_CUB_TXT_IS004 = "ARMA_CUB_TXT_IS004"; const char* ARMA_CUB_TXT_IU008 = "ARMA_CUB_TXT_IU008"; const char* ARMA_CUB_TXT_IS008 = "ARMA_CUB_TXT_IS008"; const char* ARMA_CUB_TXT_FN004 = "ARMA_CUB_TXT_FN004"; const char* ARMA_CUB_TXT_FN008 = "ARMA_CUB_TXT_FN008"; const char* ARMA_CUB_TXT_FC008 = "ARMA_CUB_TXT_FC008"; const char* ARMA_CUB_TXT_FC016 = "ARMA_CUB_TXT_FC016"; char* header = nullptr; if( is_u8::value) { header = const_cast(ARMA_CUB_TXT_IU001); } else if( is_s8::value) { header = const_cast(ARMA_CUB_TXT_IS001); } else if( is_u16::value) { header = const_cast(ARMA_CUB_TXT_IU002); } else if( is_s16::value) { header = const_cast(ARMA_CUB_TXT_IS002); } else if( is_u32::value) { header = const_cast(ARMA_CUB_TXT_IU004); } else if( is_s32::value) { header = const_cast(ARMA_CUB_TXT_IS004); } else if( is_u64::value) { header = const_cast(ARMA_CUB_TXT_IU008); } else if( is_s64::value) { header = const_cast(ARMA_CUB_TXT_IS008); } else if(is_ulng_t_32::value) { header = const_cast(ARMA_CUB_TXT_IU004); } else if(is_slng_t_32::value) { header = const_cast(ARMA_CUB_TXT_IS004); } else if(is_ulng_t_64::value) { header = const_cast(ARMA_CUB_TXT_IU008); } else if(is_slng_t_64::value) { header = const_cast(ARMA_CUB_TXT_IS008); } else if( is_float::value) { header = const_cast(ARMA_CUB_TXT_FN004); } else if( is_double::value) { header = const_cast(ARMA_CUB_TXT_FN008); } else if( is_cx_float::value) { header = const_cast(ARMA_CUB_TXT_FC008); } else if(is_cx_double::value) { header = const_cast(ARMA_CUB_TXT_FC016); } return std::string(header); } //! Generate the first line of the header used for saving cubes in binary format. //! Format: "ARMA_CUB_BIN_ABXYZ". //! A is one of: I (for integral types) or F (for floating point types). //! B is one of: U (for unsigned types), S (for signed types), N (for not applicable) or C (for complex types). //! XYZ specifies the width of each element in terms of bytes, eg. "008" indicates eight bytes. template inline std::string diskio::gen_bin_header(const Cube&) { arma_type_check(( is_supported_elem_type::value == false )); const char* ARMA_CUB_BIN_IU001 = "ARMA_CUB_BIN_IU001"; const char* ARMA_CUB_BIN_IS001 = "ARMA_CUB_BIN_IS001"; const char* ARMA_CUB_BIN_IU002 = "ARMA_CUB_BIN_IU002"; const char* ARMA_CUB_BIN_IS002 = "ARMA_CUB_BIN_IS002"; const char* ARMA_CUB_BIN_IU004 = "ARMA_CUB_BIN_IU004"; const char* ARMA_CUB_BIN_IS004 = "ARMA_CUB_BIN_IS004"; const char* ARMA_CUB_BIN_IU008 = "ARMA_CUB_BIN_IU008"; const char* ARMA_CUB_BIN_IS008 = "ARMA_CUB_BIN_IS008"; const char* ARMA_CUB_BIN_FN004 = "ARMA_CUB_BIN_FN004"; const char* ARMA_CUB_BIN_FN008 = "ARMA_CUB_BIN_FN008"; const char* ARMA_CUB_BIN_FC008 = "ARMA_CUB_BIN_FC008"; const char* ARMA_CUB_BIN_FC016 = "ARMA_CUB_BIN_FC016"; char* header = nullptr; if( is_u8::value) { header = const_cast(ARMA_CUB_BIN_IU001); } else if( is_s8::value) { header = const_cast(ARMA_CUB_BIN_IS001); } else if( is_u16::value) { header = const_cast(ARMA_CUB_BIN_IU002); } else if( is_s16::value) { header = const_cast(ARMA_CUB_BIN_IS002); } else if( is_u32::value) { header = const_cast(ARMA_CUB_BIN_IU004); } else if( is_s32::value) { header = const_cast(ARMA_CUB_BIN_IS004); } else if( is_u64::value) { header = const_cast(ARMA_CUB_BIN_IU008); } else if( is_s64::value) { header = const_cast(ARMA_CUB_BIN_IS008); } else if(is_ulng_t_32::value) { header = const_cast(ARMA_CUB_BIN_IU004); } else if(is_slng_t_32::value) { header = const_cast(ARMA_CUB_BIN_IS004); } else if(is_ulng_t_64::value) { header = const_cast(ARMA_CUB_BIN_IU008); } else if(is_slng_t_64::value) { header = const_cast(ARMA_CUB_BIN_IS008); } else if( is_float::value) { header = const_cast(ARMA_CUB_BIN_FN004); } else if( is_double::value) { header = const_cast(ARMA_CUB_BIN_FN008); } else if( is_cx_float::value) { header = const_cast(ARMA_CUB_BIN_FC008); } else if(is_cx_double::value) { header = const_cast(ARMA_CUB_BIN_FC016); } return std::string(header); } inline file_type diskio::guess_file_type(std::istream& f) { arma_extra_debug_sigprint(); return diskio::guess_file_type_internal(f); } inline file_type diskio::guess_file_type_internal(std::istream& f) { arma_extra_debug_sigprint(); f.clear(); const std::fstream::pos_type pos1 = f.tellg(); f.clear(); f.seekg(0, ios::end); f.clear(); const std::fstream::pos_type pos2 = f.tellg(); const uword N_max = ( (pos1 >= 0) && (pos2 >= 0) && (pos2 > pos1) ) ? uword(pos2 - pos1) : uword(0); f.clear(); f.seekg(pos1); if(N_max == 0) { return file_type_unknown; } const uword N_use = (std::min)(N_max, uword(4096)); podarray data(N_use); data.zeros(); unsigned char* data_mem = data.memptr(); f.clear(); f.read( reinterpret_cast(data_mem), std::streamsize(N_use) ); const bool load_okay = f.good(); f.clear(); f.seekg(pos1); if(load_okay == false) { return file_type_unknown; } bool has_binary = false; bool has_bracket = false; bool has_comma = false; bool has_semicolon = false; for(uword i=0; i= 123) ) { has_binary = true; break; } // the range checking can be made more elaborate if( (val == '(') || (val == ')') ) { has_bracket = true; } if( (val == ';') ) { has_semicolon = true; } if( (val == ',') ) { has_comma = true; } } if(has_binary) { return raw_binary; } // ssv_ascii has to be before csv_ascii; // if the data has semicolons, it suggests a CSV file with semicolon as the separating character; // the semicolon may be used to allow the comma character to represent the decimal seperator (eg. 1,2345 vs 1.2345) if(has_semicolon && (has_bracket == false)) { return ssv_ascii; } if(has_comma && (has_bracket == false)) { return csv_ascii; } return raw_ascii; } //! Append a quasi-random string to the given filename. //! Avoiding use of rand() to preserve its state. inline std::string diskio::gen_tmp_name(const std::string& x) { union { uword val; void* ptr; } u; u.val = uword(0); u.ptr = const_cast(&x); const u16 a = u16( (u.val >> 8) & 0xFFFF ); const u16 b = u16( (std::clock()) & 0xFFFF ); std::ostringstream ss; ss << x << ".tmp_"; ss.setf(std::ios_base::hex, std::ios_base::basefield); ss.width(4); ss.fill('0'); ss << a; ss.width(4); ss.fill('0'); ss << b; return ss.str(); } //! Safely rename a file. //! Before renaming, test if we can write to the final file. //! This should prevent: //! (i) overwriting files that are write protected, //! (ii) overwriting directories. inline bool diskio::safe_rename(const std::string& old_name, const std::string& new_name) { const char* new_name_c_str = new_name.c_str(); std::fstream f(new_name_c_str, std::fstream::out | std::fstream::app); f.put(' '); if(f.good()) { f.close(); } else { return false; } if(std::remove( new_name_c_str) != 0) { return false; } if(std::rename(old_name.c_str(), new_name_c_str) != 0) { return false; } return true; } inline bool diskio::is_readable(const std::string& name) { std::ifstream f; f.open(name, std::fstream::binary); // std::ifstream destructor will close the file return (f.is_open()); } inline void diskio::sanitise_token(std::string& token) { // remove spaces, tabs, carriage returns if(token.length() == 0) { return; } const char c_front = token.front(); const char c_back = token.back(); if( (c_front == ' ') || (c_front == '\t') || (c_front == '\r') || (c_back == ' ') || (c_back == '\t') || (c_back == '\r') ) { token.erase(std::remove_if(token.begin(), token.end(), [](char c) { return ((c == ' ') || (c == '\t') || (c == '\r')); }), token.end()); } } template inline bool diskio::convert_token(eT& val, const std::string& token) { const size_t N = size_t(token.length()); const char* str = token.c_str(); if( (N == 0) || ((N == 1) && (str[0] == '0')) ) { val = eT(0); return true; } if( (N == 3) || (N == 4) ) { const bool neg = (str[0] == '-'); const bool pos = (str[0] == '+'); const size_t offset = ( (neg || pos) && (N == 4) ) ? 1 : 0; const char sig_a = str[offset ]; const char sig_b = str[offset+1]; const char sig_c = str[offset+2]; if( ((sig_a == 'i') || (sig_a == 'I')) && ((sig_b == 'n') || (sig_b == 'N')) && ((sig_c == 'f') || (sig_c == 'F')) ) { val = neg ? cond_rel< is_signed::value >::make_neg(Datum::inf) : Datum::inf; return true; } else if( ((sig_a == 'n') || (sig_a == 'N')) && ((sig_b == 'a') || (sig_b == 'A')) && ((sig_c == 'n') || (sig_c == 'N')) ) { val = Datum::nan; return true; } } // #if (defined(ARMA_HAVE_CXX17) && (__cpp_lib_to_chars >= 201611L)) // { // // std::from_chars() doesn't handle leading whitespace // // std::from_chars() doesn't handle leading + sign // // std::from_chars() handles only the decimal point (.) as the decimal seperator // // const char str0 = str[0]; // const bool start_ok = ((str0 != ' ') && (str0 != '\t') && (str0 != '+')); // // bool has_comma = false; // for(uword i=0; i::value) { val = eT( std::strtod(str, &endptr) ); } else { if(is_signed::value) { // signed integer val = eT( std::strtoll(str, &endptr, 10) ); } else { // unsigned integer if((str[0] == '-') && (N >= 2)) { val = eT(0); if((str[1] == '-') || (str[1] == '+')) { return false; } const char* str_offset1 = &(str[1]); std::strtoull(str_offset1, &endptr, 10); if(str_offset1 == endptr) { return false; } return true; } val = eT( std::strtoull(str, &endptr, 10) ); } } if(str == endptr) { return false; } return true; } template inline bool diskio::convert_token(std::complex& val, const std::string& token) { const size_t N = size_t(token.length()); const size_t Nm1 = N-1; if(N == 0) { val = std::complex(0); return true; } const char* str = token.c_str(); // valid complex number formats: // (real,imag) // (real) // () if( (token[0] != '(') || (token[Nm1] != ')') ) { // no brackets, so treat the token as a non-complex number T val_real; const bool state = diskio::convert_token(val_real, token); // use the non-complex version of this function val = std::complex(val_real); return state; } // does the token contain only the () brackets? if(N <= 2) { val = std::complex(0); return true; } size_t comma_loc = 0; bool comma_found = false; for(size_t i=0; i(val_real); } else { const std::string token_real( &(str[1]), (comma_loc - 1 ) ); const std::string token_imag( &(str[comma_loc+1]), (Nm1 - 1 - comma_loc) ); T val_real; T val_imag; const bool state_real = diskio::convert_token(val_real, token_real); const bool state_imag = diskio::convert_token(val_imag, token_imag); state = (state_real && state_imag); val = std::complex(val_real, val_imag); } return state; } template inline bool diskio::convert_token_strict(eT& val, const std::string& token) { const size_t N = size_t(token.length()); const bool status = (N > 0) ? diskio::convert_token(val, token) : false; if(status == false) { val = Datum::nan; } return status; } template inline std::streamsize diskio::prepare_stream(std::ostream& f) { std::streamsize cell_width = f.width(); if(is_real::value) { f.unsetf(ios::fixed); f.setf(ios::scientific); f.fill(' '); f.precision(16); cell_width = 24; // NOTE: for 'float' the optimum settings are f.precision(8) and cell_width = 15 // NOTE: however, to avoid introducing errors in case single precision data is loaded as double precision, // NOTE: the same settings must be used for both 'float' and 'double' } else if(is_cx::value) { f.unsetf(ios::fixed); f.setf(ios::scientific); f.precision(16); } return cell_width; } //! Save a matrix as raw text (no header, human readable). //! Matrices can be loaded in Matlab and Octave, as long as they don't have complex elements. template inline bool diskio::save_raw_ascii(const Mat& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f; (arma_config::text_as_binary) ? f.open(tmp_name, std::fstream::binary) : f.open(tmp_name); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_raw_ascii(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } //! Save a matrix as raw text (no header, human readable). //! Matrices can be loaded in Matlab and Octave, as long as they don't have complex elements. template inline bool diskio::save_raw_ascii(const Mat& x, std::ostream& f) { arma_extra_debug_sigprint(); const arma_ostream_state stream_state(f); const std::streamsize cell_width = diskio::prepare_stream(f); for(uword row=0; row < x.n_rows; ++row) { for(uword col=0; col < x.n_cols; ++col) { f.put(' '); if(is_real::value) { f.width(cell_width); } arma_ostream::raw_print_elem(f, x.at(row,col)); } f.put('\n'); } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } //! Save a matrix as raw binary (no header) template inline bool diskio::save_raw_binary(const Mat& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f(tmp_name, std::fstream::binary); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_raw_binary(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } template inline bool diskio::save_raw_binary(const Mat& x, std::ostream& f) { arma_extra_debug_sigprint(); f.write( reinterpret_cast(x.mem), std::streamsize(x.n_elem*sizeof(eT)) ); return f.good(); } //! Save a matrix in text format (human readable), //! with a header that indicates the matrix type as well as its dimensions template inline bool diskio::save_arma_ascii(const Mat& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f; (arma_config::text_as_binary) ? f.open(tmp_name, std::fstream::binary) : f.open(tmp_name); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_arma_ascii(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } //! Save a matrix in text format (human readable), //! with a header that indicates the matrix type as well as its dimensions template inline bool diskio::save_arma_ascii(const Mat& x, std::ostream& f) { arma_extra_debug_sigprint(); const arma_ostream_state stream_state(f); f << diskio::gen_txt_header(x) << '\n'; f << x.n_rows << ' ' << x.n_cols << '\n'; const std::streamsize cell_width = diskio::prepare_stream(f); for(uword row=0; row < x.n_rows; ++row) { for(uword col=0; col < x.n_cols; ++col) { f.put(' '); if(is_real::value) { f.width(cell_width); } arma_ostream::raw_print_elem(f, x.at(row,col)); } f.put('\n'); } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } //! Save a matrix in CSV text format (human readable) template inline bool diskio::save_csv_ascii(const Mat& x, const std::string& final_name, const field& header, const bool with_header, const char separator) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f; (arma_config::text_as_binary) ? f.open(tmp_name, std::fstream::binary) : f.open(tmp_name); bool save_okay = f.is_open(); if(save_okay == false) { return false; } if(with_header) { arma_extra_debug_print("diskio::save_csv_ascii(): writing header"); for(uword i=0; i < header.n_elem; ++i) { f << header.at(i); if(i != (header.n_elem-1)) { f.put(separator); } } f.put('\n'); save_okay = f.good(); } if(save_okay) { save_okay = diskio::save_csv_ascii(x, f, separator); } f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } return save_okay; } //! Save a matrix in CSV text format (human readable) template inline bool diskio::save_csv_ascii(const Mat& x, std::ostream& f, const char separator) { arma_extra_debug_sigprint(); const arma_ostream_state stream_state(f); diskio::prepare_stream(f); uword x_n_rows = x.n_rows; uword x_n_cols = x.n_cols; for(uword row=0; row < x_n_rows; ++row) { for(uword col=0; col < x_n_cols; ++col) { arma_ostream::raw_print_elem(f, x.at(row,col)); if( col < (x_n_cols-1) ) { f.put(separator); } } f.put('\n'); } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } //! Save a matrix in CSV text format (human readable); complex numbers stored in "a+bi" format template inline bool diskio::save_csv_ascii(const Mat< std::complex >& x, std::ostream& f, const char separator) { arma_extra_debug_sigprint(); typedef typename std::complex eT; const arma_ostream_state stream_state(f); diskio::prepare_stream(f); uword x_n_rows = x.n_rows; uword x_n_cols = x.n_cols; for(uword row=0; row < x_n_rows; ++row) { for(uword col=0; col < x_n_cols; ++col) { const eT& val = x.at(row,col); const T tmp_r = std::real(val); const T tmp_i = std::imag(val); const T tmp_i_abs = (tmp_i < T(0)) ? T(-tmp_i) : T(tmp_i); const char tmp_sign = (tmp_i < T(0)) ? char('-') : char('+'); arma_ostream::raw_print_elem(f, tmp_r ); f.put(tmp_sign); arma_ostream::raw_print_elem(f, tmp_i_abs); f.put('i'); if( col < (x_n_cols-1) ) { f.put(separator); } } f.put('\n'); } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } template inline bool diskio::save_coord_ascii(const Mat& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f; (arma_config::text_as_binary) ? f.open(tmp_name, std::fstream::binary) : f.open(tmp_name); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_coord_ascii(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } template inline bool diskio::save_coord_ascii(const Mat& x, std::ostream& f) { arma_extra_debug_sigprint(); const arma_ostream_state stream_state(f); diskio::prepare_stream(f); for(uword col=0; col < x.n_cols; ++col) for(uword row=0; row < x.n_rows; ++row) { const eT val = x.at(row,col); if(val != eT(0)) { f << row << ' ' << col << ' ' << val << '\n'; } } // make sure it's possible to figure out the matrix size later if( (x.n_rows > 0) && (x.n_cols > 0) ) { const uword max_row = (x.n_rows > 0) ? x.n_rows-1 : 0; const uword max_col = (x.n_cols > 0) ? x.n_cols-1 : 0; if( x.at(max_row, max_col) == eT(0) ) { f << max_row << ' ' << max_col << " 0\n"; } } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } template inline bool diskio::save_coord_ascii(const Mat< std::complex >& x, std::ostream& f) { arma_extra_debug_sigprint(); typedef typename std::complex eT; const arma_ostream_state stream_state(f); diskio::prepare_stream(f); const eT eT_zero = eT(0); for(uword col=0; col < x.n_cols; ++col) for(uword row=0; row < x.n_rows; ++row) { const eT& val = x.at(row,col); if(val != eT_zero) { f << row << ' ' << col << ' ' << val.real() << ' ' << val.imag() << '\n'; } } // make sure it's possible to figure out the matrix size later if( (x.n_rows > 0) && (x.n_cols > 0) ) { const uword max_row = (x.n_rows > 0) ? x.n_rows-1 : 0; const uword max_col = (x.n_cols > 0) ? x.n_cols-1 : 0; if( x.at(max_row, max_col) == eT_zero ) { f << max_row << ' ' << max_col << " 0 0\n"; } } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } //! Save a matrix in binary format, //! with a header that stores the matrix type as well as its dimensions template inline bool diskio::save_arma_binary(const Mat& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f(tmp_name, std::fstream::binary); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_arma_binary(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } //! Save a matrix in binary format, //! with a header that stores the matrix type as well as its dimensions template inline bool diskio::save_arma_binary(const Mat& x, std::ostream& f) { arma_extra_debug_sigprint(); f << diskio::gen_bin_header(x) << '\n'; f << x.n_rows << ' ' << x.n_cols << '\n'; f.write( reinterpret_cast(x.mem), std::streamsize(x.n_elem*sizeof(eT)) ); return f.good(); } //! Save a matrix as a PGM greyscale image template inline bool diskio::save_pgm_binary(const Mat& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::fstream f(tmp_name, std::fstream::out | std::fstream::binary); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_pgm_binary(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } //! Save a matrix as a PGM greyscale image template inline bool diskio::save_pgm_binary(const Mat& x, std::ostream& f) { arma_extra_debug_sigprint(); f << "P5" << '\n'; f << x.n_cols << ' ' << x.n_rows << '\n'; f << 255 << '\n'; const uword n_elem = x.n_rows * x.n_cols; podarray tmp(n_elem); uword i = 0; for(uword row=0; row < x.n_rows; ++row) for(uword col=0; col < x.n_cols; ++col) { tmp[i] = u8( x.at(row,col) ); // TODO: add round() ? ++i; } f.write(reinterpret_cast(tmp.mem), std::streamsize(n_elem) ); return f.good(); } //! Save a matrix as a PGM greyscale image template inline bool diskio::save_pgm_binary(const Mat< std::complex >& x, const std::string& final_name) { arma_extra_debug_sigprint(); const uchar_mat tmp = conv_to::from(x); return diskio::save_pgm_binary(tmp, final_name); } //! Save a matrix as a PGM greyscale image template inline bool diskio::save_pgm_binary(const Mat< std::complex >& x, std::ostream& f) { arma_extra_debug_sigprint(); const uchar_mat tmp = conv_to::from(x); return diskio::save_pgm_binary(tmp, f); } //! Save a matrix as part of a HDF5 file template inline bool diskio::save_hdf5_binary(const Mat& x, const hdf5_name& spec, std::string& err_msg) { arma_extra_debug_sigprint(); #if defined(ARMA_USE_HDF5) { hdf5_misc::hdf5_suspend_printing_errors hdf5_print_suspender; bool save_okay = false; const bool append = bool(spec.opts.flags & hdf5_opts::flag_append); const bool replace = bool(spec.opts.flags & hdf5_opts::flag_replace); const bool use_existing_file = ((append || replace) && (H5Fis_hdf5(spec.filename.c_str()) > 0)); const std::string tmp_name = (use_existing_file) ? std::string() : diskio::gen_tmp_name(spec.filename); // Set up the file according to HDF5's preferences hid_t file = (use_existing_file) ? H5Fopen(spec.filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT) : H5Fcreate(tmp_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); if(file < 0) { return false; } // We need to create a dataset, datatype, and dataspace hsize_t dims[2]; dims[1] = x.n_rows; dims[0] = x.n_cols; hid_t dataspace = H5Screate_simple(2, dims, NULL); // treat the matrix as a 2d array dataspace hid_t datatype = hdf5_misc::get_hdf5_type(); // If this returned something invalid, well, it's time to crash. arma_check(datatype == -1, "Mat::save(): unknown datatype for HDF5"); // MATLAB forces the users to specify a name at save time for HDF5; // Octave will use the default of 'dataset' unless otherwise specified. // If the user hasn't specified a dataset name, we will use 'dataset' // We may have to split out the group name from the dataset name. std::vector groups; std::string full_name = spec.dsname; size_t loc; while((loc = full_name.find("/")) != std::string::npos) { // Create another group... if(loc != 0) // Ignore the first /, if there is a leading /. { hid_t gid = H5Gcreate((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); if((gid < 0) && use_existing_file) { gid = H5Gopen((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT); } groups.push_back(gid); } full_name = full_name.substr(loc + 1); } const std::string dataset_name = full_name.empty() ? std::string("dataset") : full_name; const hid_t last_group = (groups.size() == 0) ? file : groups[groups.size() - 1]; if(use_existing_file && replace) { H5Ldelete(last_group, dataset_name.c_str(), H5P_DEFAULT); // NOTE: H5Ldelete() in HDF5 v1.8 doesn't reclaim the deleted space; use h5repack to reclaim space: h5repack oldfile.h5 newfile.h5 // NOTE: has this behaviour changed in HDF5 1.10 ? // NOTE: https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2017-August/010482.html // NOTE: https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2017-August/010486.html } hid_t dataset = H5Dcreate(last_group, dataset_name.c_str(), datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); if(dataset < 0) { save_okay = false; err_msg = "failed to create dataset"; } else { save_okay = (H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, x.mem) >= 0); H5Dclose(dataset); } H5Tclose(datatype); H5Sclose(dataspace); for(size_t i = 0; i < groups.size(); ++i) { H5Gclose(groups[i]); } H5Fclose(file); if((use_existing_file == false) && (save_okay == true)) { save_okay = diskio::safe_rename(tmp_name, spec.filename); } return save_okay; } #else { arma_ignore(x); arma_ignore(spec); arma_ignore(err_msg); arma_stop_logic_error("Mat::save(): use of HDF5 must be enabled"); return false; } #endif } //! Load a matrix as raw text (no header, human readable). //! Can read matrices saved as text in Matlab and Octave. //! NOTE: this is much slower than reading a file with a header. template inline bool diskio::load_raw_ascii(Mat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; (arma_config::text_as_binary) ? f.open(name, std::fstream::binary) : f.open(name); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_raw_ascii(x, f, err_msg); f.close(); } return load_okay; } //! Load a matrix as raw text (no header, human readable). //! Can read matrices saved as text in Matlab and Octave. //! NOTE: this is much slower than reading a file with a header. template inline bool diskio::load_raw_ascii(Mat& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); bool load_okay = f.good(); f.clear(); const std::fstream::pos_type pos1 = f.tellg(); // // work out the size uword f_n_rows = 0; uword f_n_cols = 0; bool f_n_cols_found = false; std::string line_string; std::stringstream line_stream; std::string token; while( f.good() && load_okay ) { std::getline(f, line_string); // TODO: does it make sense to stop processing the file if an empty line is found ? if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_n_cols = 0; while(line_stream >> token) { ++line_n_cols; } if(f_n_cols_found == false) { f_n_cols = line_n_cols; f_n_cols_found = true; } else { if(line_n_cols != f_n_cols) { load_okay = false; err_msg = "inconsistent number of columns"; } } ++f_n_rows; } if(load_okay) { f.clear(); f.seekg(pos1); if(f.fail() || (f.tellg() != pos1)) { err_msg = "seek failure"; return false; } try { x.set_size(f_n_rows, f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } for(uword row=0; ((row < x.n_rows) && load_okay); ++row) for(uword col=0; ((col < x.n_cols) && load_okay); ++col) { f >> token; if(diskio::convert_token(x.at(row,col), token) == false) { load_okay = false; err_msg = "data interpretation failure"; } } } // an empty file indicates an empty matrix if( (f_n_cols_found == false) && (load_okay == true) ) { x.reset(); } return load_okay; } //! Load a matrix in binary format (no header); //! the matrix is assumed to have one column template inline bool diskio::load_raw_binary(Mat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; f.open(name, std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_raw_binary(x, f, err_msg); f.close(); } return load_okay; } template inline bool diskio::load_raw_binary(Mat& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); f.clear(); const std::streampos pos1 = f.tellg(); f.clear(); f.seekg(0, ios::end); f.clear(); const std::streampos pos2 = f.tellg(); const uword N = ( (pos1 >= 0) && (pos2 >= 0) ) ? uword(pos2 - pos1) : 0; f.clear(); //f.seekg(0, ios::beg); f.seekg(pos1); if(f.fail() || (f.tellg() != pos1)) { err_msg = "seek failure"; return false; } try { x.set_size(N / uword(sizeof(eT)), 1); } catch(...) { err_msg = "not enough memory"; return false; } f.clear(); f.read( reinterpret_cast(x.memptr()), std::streamsize(x.n_elem * uword(sizeof(eT))) ); return f.good(); } //! Load a matrix in text format (human readable), //! with a header that indicates the matrix type as well as its dimensions template inline bool diskio::load_arma_ascii(Mat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; (arma_config::text_as_binary) ? f.open(name, std::fstream::binary) : f.open(name); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_arma_ascii(x, f, err_msg); f.close(); } return load_okay; } //! Load a matrix in text format (human readable), //! with a header that indicates the matrix type as well as its dimensions template inline bool diskio::load_arma_ascii(Mat& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); std::streampos pos = f.tellg(); bool load_okay = true; std::string f_header; uword f_n_rows; uword f_n_cols; f >> f_header; f >> f_n_rows; f >> f_n_cols; if(f_header == diskio::gen_txt_header(x)) { try { x.zeros(f_n_rows, f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } std::string token; for(uword row=0; row < x.n_rows; ++row) for(uword col=0; col < x.n_cols; ++col) { f >> token; diskio::convert_token( x.at(row,col), token ); } load_okay = f.good(); } else { load_okay = false; err_msg = "incorrect header"; } // allow automatic conversion of u32/s32 matrices into u64/s64 matrices if(load_okay == false) { if( (sizeof(eT) == 8) && is_same_type::yes ) { Mat tmp; std::string junk; f.clear(); f.seekg(pos); load_okay = diskio::load_arma_ascii(tmp, f, junk); if(load_okay) { x = conv_to< Mat >::from(tmp); } } else if( (sizeof(eT) == 8) && is_same_type::yes ) { Mat tmp; std::string junk; f.clear(); f.seekg(pos); load_okay = diskio::load_arma_ascii(tmp, f, junk); if(load_okay) { x = conv_to< Mat >::from(tmp); } } } return load_okay; } //! Load a matrix in CSV text format (human readable) template inline bool diskio::load_csv_ascii(Mat& x, const std::string& name, std::string& err_msg, field& header, const bool with_header, const char separator, const bool strict) { arma_extra_debug_sigprint(); std::ifstream f; (arma_config::text_as_binary) ? f.open(name, std::fstream::binary) : f.open(name); bool load_okay = f.is_open(); if(load_okay == false) { return false; } if(with_header) { arma_extra_debug_print("diskio::load_csv_ascii(): reading header"); std::string header_line; std::stringstream header_stream; std::vector header_tokens; std::getline(f, header_line); load_okay = f.good(); if(load_okay) { std::string token; header_stream.clear(); header_stream.str(header_line); uword header_n_tokens = 0; while(header_stream.good()) { std::getline(header_stream, token, separator); diskio::sanitise_token(token); ++header_n_tokens; header_tokens.push_back(token); } if(header_n_tokens == uword(0)) { header.reset(); } else { header.set_size(1,header_n_tokens); for(uword i=0; i < header_n_tokens; ++i) { header.at(i) = header_tokens[i]; } } } } if(load_okay) { load_okay = diskio::load_csv_ascii(x, f, err_msg, separator, strict); } f.close(); return load_okay; } //! Load a matrix in CSV text format (human readable) template inline bool diskio::load_csv_ascii(Mat& x, std::istream& f, std::string& err_msg, const char separator, const bool strict) { arma_extra_debug_sigprint(); // TODO: replace with more efficient implementation if(f.good() == false) { return false; } f.clear(); const std::fstream::pos_type pos1 = f.tellg(); // // work out the size uword f_n_rows = 0; uword f_n_cols = 0; std::string line_string; std::stringstream line_stream; std::string token; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_n_cols = 0; while(line_stream.good()) { std::getline(line_stream, token, separator); ++line_n_cols; } if(f_n_cols < line_n_cols) { f_n_cols = line_n_cols; } ++f_n_rows; } f.clear(); f.seekg(pos1); if(f.fail() || (f.tellg() != pos1)) { err_msg = "seek failure"; return false; } try { x.zeros(f_n_rows, f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } if(strict) { x.fill(Datum::nan); } // take into account that each row may have a unique number of columns const bool use_mp = (arma_config::openmp) && (f_n_rows >= 2) && (f_n_cols >= 64); field token_array; bool token_array_ok = false; if(use_mp) { try { token_array.set_size(f_n_cols); for(uword i=0; i < f_n_cols; ++i) { token_array(i).reserve(32); } token_array_ok = true; } catch(...) { token_array.reset(); } } if(use_mp && token_array_ok) { #if defined(ARMA_USE_OPENMP) { uword row = 0; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); for(uword i=0; i < f_n_cols; ++i) { token_array(i).clear(); } uword line_stream_col = 0; while(line_stream.good()) { std::getline(line_stream, token_array(line_stream_col), separator); ++line_stream_col; } const int n_threads = mp_thread_limit::get(); #pragma omp parallel for schedule(static) num_threads(n_threads) for(uword col=0; col < line_stream_col; ++col) { eT& out_val = x.at(row,col); (strict) ? diskio::convert_token_strict( out_val, token_array(col) ) : diskio::convert_token( out_val, token_array(col) ); } ++row; } } #endif } else // serial implementation { uword row = 0; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword col = 0; while(line_stream.good()) { std::getline(line_stream, token, separator); eT& out_val = x.at(row,col); (strict) ? diskio::convert_token_strict( out_val, token ) : diskio::convert_token( out_val, token ); ++col; } ++row; } } return true; } //! Load a matrix in CSV text format (human readable); complex numbers stored in "a+bi" format template inline bool diskio::load_csv_ascii(Mat< std::complex >& x, std::istream& f, std::string& err_msg, const char separator, const bool strict) { arma_extra_debug_sigprint(); // TODO: replace with more efficient implementation if(f.good() == false) { return false; } f.clear(); const std::fstream::pos_type pos1 = f.tellg(); // // work out the size uword f_n_rows = 0; uword f_n_cols = 0; std::string line_string; std::stringstream line_stream; std::string token; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_n_cols = 0; while(line_stream.good()) { std::getline(line_stream, token, separator); ++line_n_cols; } if(f_n_cols < line_n_cols) { f_n_cols = line_n_cols; } ++f_n_rows; } f.clear(); f.seekg(pos1); if(f.fail() || (f.tellg() != pos1)) { err_msg = "seek failure"; return false; } try { x.zeros(f_n_rows, f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } if(strict) { x.fill(Datum< std::complex >::nan); } // take into account that each row may have a unique number of columns uword row = 0; std::string str_real; std::string str_imag; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword col = 0; while(line_stream.good()) { std::getline(line_stream, token, separator); diskio::sanitise_token(token); const size_t token_len = size_t( token.length() ); if(token_len == 0) { col++; continue; } // handle special cases: inf and nan, without the imaginary part if( (token_len == 3) || (token_len == 4) ) { const char* str = token.c_str(); const bool neg = (str[0] == '-'); const bool pos = (str[0] == '+'); const size_t offset = ( (neg || pos) && (token_len == 4) ) ? 1 : 0; const char sig_a = str[offset ]; const char sig_b = str[offset+1]; const char sig_c = str[offset+2]; bool found_val_real = false; T val_real = T(0); if( ((sig_a == 'i') || (sig_a == 'I')) && ((sig_b == 'n') || (sig_b == 'N')) && ((sig_c == 'f') || (sig_c == 'F')) ) { val_real = (neg) ? -(Datum::inf) : Datum::inf; found_val_real = true; } else if( ((sig_a == 'n') || (sig_a == 'N')) && ((sig_b == 'a') || (sig_b == 'A')) && ((sig_c == 'n') || (sig_c == 'N')) ) { val_real = Datum::nan; found_val_real = true; } if(found_val_real) { const T val_imag = (strict) ? T(Datum::nan) : T(0); x.at(row,col) = std::complex(val_real, val_imag); col++; continue; // get next token } } bool found_x = false; std::string::size_type loc_x = 0; // location of the separator (+ or -) between the real and imaginary part std::string::size_type loc_i = token.find_last_of('i'); // location of the imaginary part indicator if(loc_i == std::string::npos) { str_real = token; str_imag.clear(); } else { bool found_plus = false; bool found_minus = false; std::string::size_type loc_plus = token.find_last_of('+'); if(loc_plus != std::string::npos) { if(loc_plus >= 1) { const char prev_char = token.at(loc_plus-1); // make sure we're not looking at the sign of the exponent if( (prev_char != 'e') && (prev_char != 'E') ) { found_plus = true; } else { // search again, omitting the exponent loc_plus = token.find_last_of('+', loc_plus-1); if(loc_plus != std::string::npos) { found_plus = true; } } } else { // loc_plus == 0, meaning we're at the start of the string found_plus = true; } } std::string::size_type loc_minus = token.find_last_of('-'); if(loc_minus != std::string::npos) { if(loc_minus >= 1) { const char prev_char = token.at(loc_minus-1); // make sure we're not looking at the sign of the exponent if( (prev_char != 'e') && (prev_char != 'E') ) { found_minus = true; } else { // search again, omitting the exponent loc_minus = token.find_last_of('-', loc_minus-1); if(loc_minus != std::string::npos) { found_minus = true; } } } else { // loc_minus == 0, meaning we're at the start of the string found_minus = true; } } if(found_plus && found_minus) { if( (loc_i > loc_plus) && (loc_i > loc_minus) ) { // choose the sign closest to the "i" to be the separator between the real and imaginary part loc_x = ( (loc_i - loc_plus) < (loc_i - loc_minus) ) ? loc_plus : loc_minus; found_x = true; } } else if(found_plus ) { loc_x = loc_plus; found_x = true; } else if(found_minus) { loc_x = loc_minus; found_x = true; } if(found_x) { if( loc_x > 0 ) { str_real = token.substr(0,loc_x); } else { str_real.clear(); } if((loc_x+1) < token.size()) { str_imag = token.substr(loc_x, token.size()-loc_x-1); } else { str_imag.clear(); } } else { str_real.clear(); str_imag.clear(); } } T val_real = T(0); T val_imag = T(0); (strict) ? diskio::convert_token_strict(val_real, str_real) : diskio::convert_token(val_real, str_real); (strict) ? diskio::convert_token_strict(val_imag, str_imag) : diskio::convert_token(val_imag, str_imag); x.at(row,col) = std::complex(val_real, val_imag); ++col; } ++row; } return true; } template inline bool diskio::load_coord_ascii(Mat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; (arma_config::text_as_binary) ? f.open(name, std::fstream::binary) : f.open(name); bool load_okay = f.is_open(); if(load_okay == false) { return false; } if(load_okay) { load_okay = diskio::load_coord_ascii(x, f, err_msg); } f.close(); return load_okay; } //! Load a matrix in CSV text format (human readable) template inline bool diskio::load_coord_ascii(Mat& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); if(f.good() == false) { return false; } f.clear(); const std::fstream::pos_type pos1 = f.tellg(); // work out the size uword f_n_rows = 0; uword f_n_cols = 0; bool size_found = false; std::string line_string; std::stringstream line_stream; std::string token; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_row = 0; uword line_col = 0; // a valid line in co-ord format has at least 2 entries line_stream >> line_row; if(line_stream.good() == false) { err_msg = "incorrect format"; return false; } line_stream >> line_col; size_found = true; if(f_n_rows < line_row) { f_n_rows = line_row; } if(f_n_cols < line_col) { f_n_cols = line_col; } } // take into account that indices start at 0 if(size_found) { ++f_n_rows; ++f_n_cols; } f.clear(); f.seekg(pos1); if(f.fail() || (f.tellg() != pos1)) { err_msg = "seek failure"; return false; } try { Mat tmp(f_n_rows, f_n_cols, arma_zeros_indicator()); while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_row = 0; uword line_col = 0; line_stream >> line_row; line_stream >> line_col; eT val = eT(0); line_stream >> token; if(line_stream.fail() == false) { diskio::convert_token( val, token ); } if(val != eT(0)) { tmp(line_row,line_col) = val; } } x.steal_mem(tmp); } catch(...) { err_msg = "not enough memory"; return false; } return true; } template inline bool diskio::load_coord_ascii(Mat< std::complex >& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); if(f.good() == false) { return false; } f.clear(); const std::fstream::pos_type pos1 = f.tellg(); // work out the size uword f_n_rows = 0; uword f_n_cols = 0; bool size_found = false; std::string line_string; std::stringstream line_stream; std::string token_real; std::string token_imag; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_row = 0; uword line_col = 0; // a valid line in co-ord format has at least 2 entries line_stream >> line_row; if(line_stream.good() == false) { err_msg = "incorrect format"; return false; } line_stream >> line_col; size_found = true; if(f_n_rows < line_row) f_n_rows = line_row; if(f_n_cols < line_col) f_n_cols = line_col; } // take into account that indices start at 0 if(size_found) { ++f_n_rows; ++f_n_cols; } f.clear(); f.seekg(pos1); if(f.fail() || (f.tellg() != pos1)) { err_msg = "seek failure"; return false; } try { Mat< std::complex > tmp(f_n_rows, f_n_cols, arma_zeros_indicator()); while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_row = 0; uword line_col = 0; line_stream >> line_row; line_stream >> line_col; T val_real = T(0); T val_imag = T(0); line_stream >> token_real; if(line_stream.fail() == false) { diskio::convert_token( val_real, token_real ); } line_stream >> token_imag; if(line_stream.fail() == false) { diskio::convert_token( val_imag, token_imag ); } if( (val_real != T(0)) || (val_imag != T(0)) ) { tmp(line_row,line_col) = std::complex(val_real, val_imag); } } x.steal_mem(tmp); } catch(...) { err_msg = "not enough memory"; return false; } return true; } //! Load a matrix in binary format, //! with a header that indicates the matrix type as well as its dimensions template inline bool diskio::load_arma_binary(Mat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; f.open(name, std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_arma_binary(x, f, err_msg); f.close(); } return load_okay; } template inline bool diskio::load_arma_binary(Mat& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); std::streampos pos = f.tellg(); bool load_okay = true; std::string f_header; uword f_n_rows; uword f_n_cols; f >> f_header; f >> f_n_rows; f >> f_n_cols; if(f_header == diskio::gen_bin_header(x)) { //f.seekg(1, ios::cur); // NOTE: this may not be portable, as on a Windows machine a newline could be two characters f.get(); try { x.set_size(f_n_rows,f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } f.read( reinterpret_cast(x.memptr()), std::streamsize(x.n_elem*sizeof(eT)) ); load_okay = f.good(); } else { load_okay = false; err_msg = "incorrect header"; } // allow automatic conversion of u32/s32 matrices into u64/s64 matrices if(load_okay == false) { if( (sizeof(eT) == 8) && is_same_type::yes ) { Mat tmp; std::string junk; f.clear(); f.seekg(pos); load_okay = diskio::load_arma_binary(tmp, f, junk); if(load_okay) { x = conv_to< Mat >::from(tmp); } } else if( (sizeof(eT) == 8) && is_same_type::yes ) { Mat tmp; std::string junk; f.clear(); f.seekg(pos); load_okay = diskio::load_arma_binary(tmp, f, junk); if(load_okay) { x = conv_to< Mat >::from(tmp); } } } return load_okay; } inline void diskio::pnm_skip_comments(std::istream& f) { while( isspace(f.peek()) ) { while( isspace(f.peek()) ) { f.get(); } if(f.peek() == '#') { while( (f.peek() != '\r') && (f.peek() != '\n') ) { f.get(); } } } } //! Load a PGM greyscale image as a matrix template inline bool diskio::load_pgm_binary(Mat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::fstream f; f.open(name, std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_pgm_binary(x, f, err_msg); f.close(); } return load_okay; } //! Load a PGM greyscale image as a matrix template inline bool diskio::load_pgm_binary(Mat& x, std::istream& f, std::string& err_msg) { bool load_okay = true; std::string f_header; f >> f_header; if(f_header == "P5") { uword f_n_rows = 0; uword f_n_cols = 0; int f_maxval = 0; diskio::pnm_skip_comments(f); f >> f_n_cols; diskio::pnm_skip_comments(f); f >> f_n_rows; diskio::pnm_skip_comments(f); f >> f_maxval; f.get(); if( (f_maxval > 0) && (f_maxval <= 65535) ) { try { x.set_size(f_n_rows,f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } if(f_maxval <= 255) { const uword n_elem = f_n_cols*f_n_rows; podarray tmp(n_elem); f.read( reinterpret_cast(tmp.memptr()), std::streamsize(n_elem) ); uword i = 0; //cout << "f_n_cols = " << f_n_cols << endl; //cout << "f_n_rows = " << f_n_rows << endl; for(uword row=0; row < f_n_rows; ++row) for(uword col=0; col < f_n_cols; ++col) { x.at(row,col) = eT(tmp[i]); ++i; } } else { const uword n_elem = f_n_cols*f_n_rows; podarray tmp(n_elem); f.read( reinterpret_cast(tmp.memptr()), std::streamsize(n_elem*2) ); uword i = 0; for(uword row=0; row < f_n_rows; ++row) for(uword col=0; col < f_n_cols; ++col) { x.at(row,col) = eT(tmp[i]); ++i; } } } else { load_okay = false; err_msg = "functionality unimplemented"; } if(f.good() == false) { load_okay = false; } } else { load_okay = false; err_msg = "unsupported header"; } return load_okay; } //! Load a PGM greyscale image as a matrix template inline bool diskio::load_pgm_binary(Mat< std::complex >& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); uchar_mat tmp; const bool load_okay = diskio::load_pgm_binary(tmp, name, err_msg); x = conv_to< Mat< std::complex > >::from(tmp); return load_okay; } //! Load a PGM greyscale image as a matrix template inline bool diskio::load_pgm_binary(Mat< std::complex >& x, std::istream& is, std::string& err_msg) { arma_extra_debug_sigprint(); uchar_mat tmp; const bool load_okay = diskio::load_pgm_binary(tmp, is, err_msg); x = conv_to< Mat< std::complex > >::from(tmp); return load_okay; } //! Load a HDF5 file as a matrix template inline bool diskio::load_hdf5_binary(Mat& x, const hdf5_name& spec, std::string& err_msg) { arma_extra_debug_sigprint(); #if defined(ARMA_USE_HDF5) { if(diskio::is_readable(spec.filename) == false) { return false; } hdf5_misc::hdf5_suspend_printing_errors hdf5_print_suspender; bool load_okay = false; hid_t fid = H5Fopen(spec.filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT); if(fid >= 0) { // MATLAB HDF5 dataset names are user-specified; // Octave tends to store the datasets in a group, with the actual dataset being referred to as "value". // If the user hasn't specified a dataset, we will search for "dataset" and "value", // and if those are not found we will take the first dataset we do find. std::vector searchNames; const bool exact = (spec.dsname.empty() == false); if(exact) { searchNames.push_back(spec.dsname); } else { searchNames.push_back("dataset"); searchNames.push_back("value" ); } hid_t dataset = hdf5_misc::search_hdf5_file(searchNames, fid, 2, exact); if(dataset >= 0) { hid_t filespace = H5Dget_space(dataset); // This must be <= 2 due to our search rules. const int ndims = H5Sget_simple_extent_ndims(filespace); hsize_t dims[2]; const herr_t query_status = H5Sget_simple_extent_dims(filespace, dims, NULL); // arma_check(query_status < 0, "Mat::load(): cannot get size of HDF5 dataset"); if(query_status < 0) { err_msg = "cannot get size of HDF5 dataset"; H5Sclose(filespace); H5Dclose(dataset); H5Fclose(fid); return false; } if(ndims == 1) { dims[1] = 1; } // Vector case; fake second dimension (one column). try { x.set_size(dims[1], dims[0]); } catch(...) { err_msg = "not enough memory"; return false; } // Now we have to see what type is stored to figure out how to load it. hid_t datatype = H5Dget_type(dataset); hid_t mat_type = hdf5_misc::get_hdf5_type(); // If these are the same type, it is simple. if(H5Tequal(datatype, mat_type) > 0) { // Load directly; H5S_ALL used so that we load the entire dataset. hid_t read_status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(x.memptr())); if(read_status >= 0) { load_okay = true; } } else { // Load into another array and convert its type accordingly. hid_t read_status = hdf5_misc::load_and_convert_hdf5(x.memptr(), dataset, datatype, x.n_elem); if(read_status >= 0) { load_okay = true; } } // Now clean up. H5Tclose(datatype); H5Tclose(mat_type); H5Sclose(filespace); } H5Dclose(dataset); H5Fclose(fid); if(load_okay == false) { err_msg = "unsupported or missing HDF5 data"; } } else { err_msg = "cannot open"; } return load_okay; } #else { arma_ignore(x); arma_ignore(spec); arma_ignore(err_msg); arma_stop_logic_error("Mat::load(): use of HDF5 must be enabled"); return false; } #endif } //! Try to load a matrix by automatically determining its type template inline bool diskio::load_auto_detect(Mat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); if(diskio::is_readable(name) == false) { return false; } #if defined(ARMA_USE_HDF5) // We're currently using the C bindings for the HDF5 library, which don't support C++ streams if( H5Fis_hdf5(name.c_str()) ) { return load_hdf5_binary(x, name, err_msg); } #endif std::fstream f; f.open(name, std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_auto_detect(x, f, err_msg); f.close(); } return load_okay; } //! Try to load a matrix by automatically determining its type template inline bool diskio::load_auto_detect(Mat& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); const char* ARMA_MAT_TXT_str = "ARMA_MAT_TXT"; const char* ARMA_MAT_BIN_str = "ARMA_MAT_BIN"; const char* P5_str = "P5"; const uword ARMA_MAT_TXT_len = uword(12); const uword ARMA_MAT_BIN_len = uword(12); const uword P5_len = uword(2); podarray header(ARMA_MAT_TXT_len + 1); char* header_mem = header.memptr(); std::streampos pos = f.tellg(); f.read( header_mem, std::streamsize(ARMA_MAT_TXT_len) ); f.clear(); f.seekg(pos); header_mem[ARMA_MAT_TXT_len] = '\0'; if( std::strncmp(ARMA_MAT_TXT_str, header_mem, size_t(ARMA_MAT_TXT_len)) == 0 ) { return load_arma_ascii(x, f, err_msg); } else if( std::strncmp(ARMA_MAT_BIN_str, header_mem, size_t(ARMA_MAT_BIN_len)) == 0 ) { return load_arma_binary(x, f, err_msg); } else if( std::strncmp(P5_str, header_mem, size_t(P5_len)) == 0 ) { return load_pgm_binary(x, f, err_msg); } else { const file_type ft = guess_file_type_internal(f); switch(ft) { case csv_ascii: return load_csv_ascii(x, f, err_msg, char(','), false); break; case ssv_ascii: return load_csv_ascii(x, f, err_msg, char(';'), false); break; case raw_binary: return load_raw_binary(x, f, err_msg); break; case raw_ascii: return load_raw_ascii(x, f, err_msg); break; default: err_msg = "unknown data"; return false; } } return false; } // // sparse matrices // //! Save a sparse matrix in CSV format template inline bool diskio::save_csv_ascii(const SpMat& x, const std::string& final_name, const field& header, const bool with_header, const char separator) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f; (arma_config::text_as_binary) ? f.open(tmp_name, std::fstream::binary) : f.open(tmp_name); bool save_okay = f.is_open(); if(save_okay == false) { return false; } if(with_header) { arma_extra_debug_print("diskio::save_csv_ascii(): writing header"); for(uword i=0; i < header.n_elem; ++i) { f << header(i); if(i != (header.n_elem-1)) { f.put(separator); } } f.put('\n'); save_okay = f.good(); } if(save_okay) { save_okay = diskio::save_csv_ascii(x, f, separator); } f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } return save_okay; } //! Save a sparse matrix in CSV format template inline bool diskio::save_csv_ascii(const SpMat& x, std::ostream& f, const char separator) { arma_extra_debug_sigprint(); const arma_ostream_state stream_state(f); diskio::prepare_stream(f); x.sync(); uword x_n_rows = x.n_rows; uword x_n_cols = x.n_cols; const eT eT_zero = eT(0); for(uword row=0; row < x_n_rows; ++row) { for(uword col=0; col < x_n_cols; ++col) { const eT val = x.at(row,col); if(val == eT_zero) { f.put('0'); } else { arma_ostream::raw_print_elem(f, val); } if( col < (x_n_cols-1) ) { f.put(separator); } } f.put('\n'); } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } //! Save a sparse matrix in CSV format (complex numbers) template inline bool diskio::save_csv_ascii(const SpMat< std::complex >& x, std::ostream& f, const char separator) { arma_extra_debug_sigprint(); arma_ignore(x); arma_ignore(f); arma_ignore(separator); arma_debug_warn_level(1, "saving complex sparse matrices as csv_ascii not yet implemented"); return false; } //! Save a matrix in ASCII coord format template inline bool diskio::save_coord_ascii(const SpMat& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f; (arma_config::text_as_binary) ? f.open(tmp_name, std::fstream::binary) : f.open(tmp_name); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_coord_ascii(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } //! Save a matrix in ASCII coord format template inline bool diskio::save_coord_ascii(const SpMat& x, std::ostream& f) { arma_extra_debug_sigprint(); const arma_ostream_state stream_state(f); diskio::prepare_stream(f); typename SpMat::const_iterator iter = x.begin(); typename SpMat::const_iterator iter_end = x.end(); for(; iter != iter_end; ++iter) { const eT val = (*iter); f << iter.row() << ' ' << iter.col() << ' ' << val << '\n'; } // make sure it's possible to figure out the matrix size later if( (x.n_rows > 0) && (x.n_cols > 0) ) { const uword max_row = (x.n_rows > 0) ? x.n_rows-1 : 0; const uword max_col = (x.n_cols > 0) ? x.n_cols-1 : 0; if( x.at(max_row, max_col) == eT(0) ) { f << max_row << ' ' << max_col << " 0\n"; } } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } //! Save a matrix in ASCII coord format (complex numbers) template inline bool diskio::save_coord_ascii(const SpMat< std::complex >& x, std::ostream& f) { arma_extra_debug_sigprint(); typedef typename std::complex eT; const arma_ostream_state stream_state(f); diskio::prepare_stream(f); typename SpMat::const_iterator iter = x.begin(); typename SpMat::const_iterator iter_end = x.end(); for(; iter != iter_end; ++iter) { const eT val = (*iter); f << iter.row() << ' ' << iter.col() << ' ' << val.real() << ' ' << val.imag() << '\n'; } // make sure it's possible to figure out the matrix size later if( (x.n_rows > 0) && (x.n_cols > 0) ) { const uword max_row = (x.n_rows > 0) ? x.n_rows-1 : 0; const uword max_col = (x.n_cols > 0) ? x.n_cols-1 : 0; if( x.at(max_row, max_col) == eT(0) ) { f << max_row << ' ' << max_col << " 0 0\n"; } } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } //! Save a matrix in binary format, //! with a header that stores the matrix type as well as its dimensions template inline bool diskio::save_arma_binary(const SpMat& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f(tmp_name, std::fstream::binary); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_arma_binary(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } //! Save a matrix in binary format, //! with a header that stores the matrix type as well as its dimensions template inline bool diskio::save_arma_binary(const SpMat& x, std::ostream& f) { arma_extra_debug_sigprint(); f << diskio::gen_bin_header(x) << '\n'; f << x.n_rows << ' ' << x.n_cols << ' ' << x.n_nonzero << '\n'; f.write( reinterpret_cast(x.values), std::streamsize(x.n_nonzero*sizeof(eT)) ); f.write( reinterpret_cast(x.row_indices), std::streamsize(x.n_nonzero*sizeof(uword)) ); f.write( reinterpret_cast(x.col_ptrs), std::streamsize((x.n_cols+1)*sizeof(uword)) ); return f.good(); } template inline bool diskio::load_csv_ascii(SpMat& x, const std::string& name, std::string& err_msg, field& header, const bool with_header, const char separator) { arma_extra_debug_sigprint(); std::ifstream f; (arma_config::text_as_binary) ? f.open(name, std::fstream::binary) : f.open(name); bool load_okay = f.is_open(); if(load_okay == false) { return false; } if(with_header) { arma_extra_debug_print("diskio::load_csv_ascii(): reading header"); std::string header_line; std::stringstream header_stream; std::vector header_tokens; std::getline(f, header_line); load_okay = f.good(); if(load_okay) { std::string token; header_stream.clear(); header_stream.str(header_line); uword header_n_tokens = 0; while(header_stream.good()) { std::getline(header_stream, token, separator); diskio::sanitise_token(token); ++header_n_tokens; header_tokens.push_back(token); } if(header_n_tokens == uword(0)) { header.reset(); } else { header.set_size(1,header_n_tokens); for(uword i=0; i < header_n_tokens; ++i) { header.at(i) = header_tokens[i]; } } } } if(load_okay) { load_okay = diskio::load_csv_ascii(x, f, err_msg, separator); } f.close(); return load_okay; } template inline bool diskio::load_csv_ascii(SpMat& x, std::istream& f, std::string& err_msg, const char separator) { arma_extra_debug_sigprint(); // TODO: replace with more efficient implementation if(f.good() == false) { return false; } f.clear(); const std::fstream::pos_type pos1 = f.tellg(); // // work out the size uword f_n_rows = 0; uword f_n_cols = 0; std::string line_string; std::stringstream line_stream; std::string token; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_n_cols = 0; while(line_stream.good()) { std::getline(line_stream, token, separator); ++line_n_cols; } if(f_n_cols < line_n_cols) { f_n_cols = line_n_cols; } ++f_n_rows; } f.clear(); f.seekg(pos1); if(f.fail() || (f.tellg() != pos1)) { err_msg = "seek failure"; return false; } try { MapMat tmp(f_n_rows, f_n_cols); uword row = 0; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword col = 0; while(line_stream.good()) { std::getline(line_stream, token, separator); eT val = eT(0); diskio::convert_token( val, token ); if(val != eT(0)) { tmp(row,col) = val; } ++col; } ++row; } x = tmp; } catch(...) { err_msg = "not enough memory"; return false; } return true; } template inline bool diskio::load_csv_ascii(SpMat< std::complex >& x, std::istream& f, std::string& err_msg, const char separator) { arma_extra_debug_sigprint(); arma_ignore(x); arma_ignore(f); arma_ignore(err_msg); arma_ignore(separator); arma_debug_warn_level(1, "loading complex sparse matrices as csv_ascii not yet implemented"); return false; } template inline bool diskio::load_coord_ascii(SpMat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; (arma_config::text_as_binary) ? f.open(name, std::fstream::binary) : f.open(name); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_coord_ascii(x, f, err_msg); f.close(); } return load_okay; } template inline bool diskio::load_coord_ascii(SpMat& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); if(f.good() == false) { return false; } f.clear(); const std::fstream::pos_type pos1 = f.tellg(); // work out the size uword f_n_rows = 0; uword f_n_cols = 0; bool size_found = false; std::string line_string; std::stringstream line_stream; std::string token; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_row = 0; uword line_col = 0; // a valid line in co-ord format has at least 2 entries line_stream >> line_row; if(line_stream.good() == false) { err_msg = "incorrect format"; return false; } line_stream >> line_col; size_found = true; if(f_n_rows < line_row) { f_n_rows = line_row; } if(f_n_cols < line_col) { f_n_cols = line_col; } } // take into account that indices start at 0 if(size_found) { ++f_n_rows; ++f_n_cols; } f.clear(); f.seekg(pos1); if(f.fail() || (f.tellg() != pos1)) { err_msg = "seek failure"; return false; } try { MapMat tmp(f_n_rows, f_n_cols); while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_row = 0; uword line_col = 0; line_stream >> line_row; line_stream >> line_col; eT val = eT(0); line_stream >> token; if(line_stream.fail() == false) { diskio::convert_token( val, token ); } if(val != eT(0)) { tmp(line_row,line_col) = val; } } x = tmp; } catch(...) { err_msg = "not enough memory"; return false; } return true; } template inline bool diskio::load_coord_ascii(SpMat< std::complex >& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); if(f.good() == false) { return false; } f.clear(); const std::fstream::pos_type pos1 = f.tellg(); // work out the size uword f_n_rows = 0; uword f_n_cols = 0; bool size_found = false; std::string line_string; std::stringstream line_stream; std::string token_real; std::string token_imag; while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_row = 0; uword line_col = 0; // a valid line in co-ord format has at least 2 entries line_stream >> line_row; if(line_stream.good() == false) { err_msg = "incorrect format"; return false; } line_stream >> line_col; size_found = true; if(f_n_rows < line_row) f_n_rows = line_row; if(f_n_cols < line_col) f_n_cols = line_col; } // take into account that indices start at 0 if(size_found) { ++f_n_rows; ++f_n_cols; } f.clear(); f.seekg(pos1); if(f.fail() || (f.tellg() != pos1)) { err_msg = "seek failure"; return false; } try { MapMat< std::complex > tmp(f_n_rows, f_n_cols); while(f.good()) { std::getline(f, line_string); if(line_string.size() == 0) { break; } line_stream.clear(); line_stream.str(line_string); uword line_row = 0; uword line_col = 0; line_stream >> line_row; line_stream >> line_col; T val_real = T(0); T val_imag = T(0); line_stream >> token_real; if(line_stream.fail() == false) { diskio::convert_token( val_real, token_real ); } line_stream >> token_imag; if(line_stream.fail() == false) { diskio::convert_token( val_imag, token_imag ); } if( (val_real != T(0)) || (val_imag != T(0)) ) { tmp(line_row,line_col) = std::complex(val_real, val_imag); } } x = tmp; } catch(...) { err_msg = "not enough memory"; return false; } return true; } //! Load a matrix in binary format, //! with a header that indicates the matrix type as well as its dimensions template inline bool diskio::load_arma_binary(SpMat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; f.open(name, std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_arma_binary(x, f, err_msg); f.close(); } return load_okay; } template inline bool diskio::load_arma_binary(SpMat& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); bool load_okay = true; std::string f_header; f >> f_header; if(f_header == diskio::gen_bin_header(x)) { uword f_n_rows; uword f_n_cols; uword f_n_nz; f >> f_n_rows; f >> f_n_cols; f >> f_n_nz; //f.seekg(1, ios::cur); // NOTE: this may not be portable, as on a Windows machine a newline could be two characters f.get(); try { x.reserve(f_n_rows, f_n_cols, f_n_nz); } catch(...) { err_msg = "not enough memory"; return false; } f.read( reinterpret_cast(access::rwp(x.values)), std::streamsize(x.n_nonzero*sizeof(eT)) ); std::streampos pos = f.tellg(); f.read( reinterpret_cast(access::rwp(x.row_indices)), std::streamsize(x.n_nonzero*sizeof(uword)) ); f.read( reinterpret_cast(access::rwp(x.col_ptrs)), std::streamsize((x.n_cols+1)*sizeof(uword)) ); bool check1 = true; for(uword i=0; i < x.n_nonzero; ++i) { if(x.values[i] == eT(0)) { check1 = false; break; } } bool check2 = true; for(uword i=0; i < x.n_cols; ++i) { if(x.col_ptrs[i+1] < x.col_ptrs[i]) { check2 = false; break; } } bool check3 = (x.col_ptrs[x.n_cols] == x.n_nonzero); if((check1 == true) && ((check2 == false) || (check3 == false))) { if(sizeof(uword) == 8) { arma_extra_debug_print("detected inconsistent data while loading; re-reading integer parts as u32"); // inconstency could be due to a different uword size used during saving, // so try loading the row_indices and col_ptrs under the assumption of 32 bit unsigned integers f.clear(); f.seekg(pos); podarray tmp_a(x.n_nonzero ); tmp_a.zeros(); podarray tmp_b(x.n_cols + 1); tmp_b.zeros(); f.read( reinterpret_cast(tmp_a.memptr()), std::streamsize( x.n_nonzero * sizeof(u32)) ); f.read( reinterpret_cast(tmp_b.memptr()), std::streamsize((x.n_cols + 1) * sizeof(u32)) ); check2 = true; for(uword i=0; i < x.n_cols; ++i) { if(tmp_b[i+1] < tmp_b[i]) { check2 = false; break; } } check3 = (tmp_b[x.n_cols] == x.n_nonzero); load_okay = f.good(); if( load_okay && (check2 == true) && (check3 == true) ) { arma_extra_debug_print("reading integer parts as u32 succeeded"); arrayops::convert(access::rwp(x.row_indices), tmp_a.memptr(), x.n_nonzero ); arrayops::convert(access::rwp(x.col_ptrs), tmp_b.memptr(), x.n_cols + 1); } else { arma_extra_debug_print("reading integer parts as u32 failed"); } } } if((check1 == false) || (check2 == false) || (check3 == false)) { load_okay = false; err_msg = "inconsistent data"; } else { load_okay = f.good(); } } else { load_okay = false; err_msg = "incorrect header"; } return load_okay; } // cubes //! Save a cube as raw text (no header, human readable). template inline bool diskio::save_raw_ascii(const Cube& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f; (arma_config::text_as_binary) ? f.open(tmp_name, std::fstream::binary) : f.open(tmp_name); bool save_okay = f.is_open(); if(save_okay) { save_okay = save_raw_ascii(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } //! Save a cube as raw text (no header, human readable). template inline bool diskio::save_raw_ascii(const Cube& x, std::ostream& f) { arma_extra_debug_sigprint(); const arma_ostream_state stream_state(f); const std::streamsize cell_width = diskio::prepare_stream(f); for(uword slice=0; slice < x.n_slices; ++slice) { for(uword row=0; row < x.n_rows; ++row) { for(uword col=0; col < x.n_cols; ++col) { f.put(' '); if(is_real::value) { f.width(cell_width); } arma_ostream::raw_print_elem(f, x.at(row,col,slice)); } f.put('\n'); } } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } //! Save a cube as raw binary (no header) template inline bool diskio::save_raw_binary(const Cube& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f(tmp_name, std::fstream::binary); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_raw_binary(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } template inline bool diskio::save_raw_binary(const Cube& x, std::ostream& f) { arma_extra_debug_sigprint(); f.write( reinterpret_cast(x.mem), std::streamsize(x.n_elem*sizeof(eT)) ); return f.good(); } //! Save a cube in text format (human readable), //! with a header that indicates the cube type as well as its dimensions template inline bool diskio::save_arma_ascii(const Cube& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f; (arma_config::text_as_binary) ? f.open(tmp_name, std::fstream::binary) : f.open(tmp_name); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_arma_ascii(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } //! Save a cube in text format (human readable), //! with a header that indicates the cube type as well as its dimensions template inline bool diskio::save_arma_ascii(const Cube& x, std::ostream& f) { arma_extra_debug_sigprint(); const arma_ostream_state stream_state(f); f << diskio::gen_txt_header(x) << '\n'; f << x.n_rows << ' ' << x.n_cols << ' ' << x.n_slices << '\n'; const std::streamsize cell_width = diskio::prepare_stream(f); for(uword slice=0; slice < x.n_slices; ++slice) { for(uword row=0; row < x.n_rows; ++row) { for(uword col=0; col < x.n_cols; ++col) { f.put(' '); if(is_real::value) { f.width(cell_width); } arma_ostream::raw_print_elem(f, x.at(row,col,slice)); } f.put('\n'); } } const bool save_okay = f.good(); stream_state.restore(f); return save_okay; } //! Save a cube in binary format, //! with a header that stores the cube type as well as its dimensions template inline bool diskio::save_arma_binary(const Cube& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f(tmp_name, std::fstream::binary); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_arma_binary(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } //! Save a cube in binary format, //! with a header that stores the cube type as well as its dimensions template inline bool diskio::save_arma_binary(const Cube& x, std::ostream& f) { arma_extra_debug_sigprint(); f << diskio::gen_bin_header(x) << '\n'; f << x.n_rows << ' ' << x.n_cols << ' ' << x.n_slices << '\n'; f.write( reinterpret_cast(x.mem), std::streamsize(x.n_elem*sizeof(eT)) ); return f.good(); } //! Save a cube as part of a HDF5 file template inline bool diskio::save_hdf5_binary(const Cube& x, const hdf5_name& spec, std::string& err_msg) { arma_extra_debug_sigprint(); #if defined(ARMA_USE_HDF5) { hdf5_misc::hdf5_suspend_printing_errors hdf5_print_suspender; bool save_okay = false; const bool append = bool(spec.opts.flags & hdf5_opts::flag_append); const bool replace = bool(spec.opts.flags & hdf5_opts::flag_replace); const bool use_existing_file = ((append || replace) && (H5Fis_hdf5(spec.filename.c_str()) > 0)); const std::string tmp_name = (use_existing_file) ? std::string() : diskio::gen_tmp_name(spec.filename); // Set up the file according to HDF5's preferences hid_t file = (use_existing_file) ? H5Fopen(spec.filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT) : H5Fcreate(tmp_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); if(file < 0) { return false; } // We need to create a dataset, datatype, and dataspace hsize_t dims[3]; dims[2] = x.n_rows; dims[1] = x.n_cols; dims[0] = x.n_slices; hid_t dataspace = H5Screate_simple(3, dims, NULL); // treat the cube as a 3d array dataspace hid_t datatype = hdf5_misc::get_hdf5_type(); // If this returned something invalid, well, it's time to crash. arma_check(datatype == -1, "Cube::save(): unknown datatype for HDF5"); // MATLAB forces the users to specify a name at save time for HDF5; // Octave will use the default of 'dataset' unless otherwise specified. // If the user hasn't specified a dataset name, we will use 'dataset' // We may have to split out the group name from the dataset name. std::vector groups; std::string full_name = spec.dsname; size_t loc; while((loc = full_name.find("/")) != std::string::npos) { // Create another group... if(loc != 0) // Ignore the first /, if there is a leading /. { hid_t gid = H5Gcreate((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); if((gid < 0) && use_existing_file) { gid = H5Gopen((groups.size() == 0) ? file : groups[groups.size() - 1], full_name.substr(0, loc).c_str(), H5P_DEFAULT); } groups.push_back(gid); } full_name = full_name.substr(loc + 1); } const std::string dataset_name = full_name.empty() ? std::string("dataset") : full_name; const hid_t last_group = (groups.size() == 0) ? file : groups[groups.size() - 1]; if(use_existing_file && replace) { H5Ldelete(last_group, dataset_name.c_str(), H5P_DEFAULT); // NOTE: H5Ldelete() in HDF5 v1.8 doesn't reclaim the deleted space; use h5repack to reclaim space: h5repack oldfile.h5 newfile.h5 // NOTE: has this behaviour changed in HDF5 1.10 ? // NOTE: https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2017-August/010482.html // NOTE: https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2017-August/010486.html } hid_t dataset = H5Dcreate(last_group, dataset_name.c_str(), datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); if(dataset < 0) { save_okay = false; err_msg = "failed to create dataset"; } else { save_okay = (H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, x.mem) >= 0); H5Dclose(dataset); } H5Tclose(datatype); H5Sclose(dataspace); for(size_t i = 0; i < groups.size(); ++i) { H5Gclose(groups[i]); } H5Fclose(file); if((use_existing_file == false) && (save_okay == true)) { save_okay = diskio::safe_rename(tmp_name, spec.filename); } return save_okay; } #else { arma_ignore(x); arma_ignore(spec); arma_ignore(err_msg); arma_stop_logic_error("Cube::save(): use of HDF5 must be enabled"); return false; } #endif } //! Load a cube as raw text (no header, human readable). //! NOTE: this is much slower than reading a file with a header. template inline bool diskio::load_raw_ascii(Cube& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); Mat tmp; const bool load_okay = diskio::load_raw_ascii(tmp, name, err_msg); if(load_okay) { if(tmp.is_empty() == false) { try { x.set_size(tmp.n_rows, tmp.n_cols, 1); } catch(...) { err_msg = "not enough memory"; return false; } x.slice(0) = tmp; } else { x.reset(); } } return load_okay; } //! Load a cube as raw text (no header, human readable). //! NOTE: this is much slower than reading a file with a header. template inline bool diskio::load_raw_ascii(Cube& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); Mat tmp; const bool load_okay = diskio::load_raw_ascii(tmp, f, err_msg); if(load_okay) { if(tmp.is_empty() == false) { try { x.set_size(tmp.n_rows, tmp.n_cols, 1); } catch(...) { err_msg = "not enough memory"; return false; } x.slice(0) = tmp; } else { x.reset(); } } return load_okay; } //! Load a cube in binary format (no header); //! the cube is assumed to have one slice with one column template inline bool diskio::load_raw_binary(Cube& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; f.open(name, std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_raw_binary(x, f, err_msg); f.close(); } return load_okay; } template inline bool diskio::load_raw_binary(Cube& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); f.clear(); const std::streampos pos1 = f.tellg(); f.clear(); f.seekg(0, ios::end); f.clear(); const std::streampos pos2 = f.tellg(); const uword N = ( (pos1 >= 0) && (pos2 >= 0) ) ? uword(pos2 - pos1) : 0; f.clear(); //f.seekg(0, ios::beg); f.seekg(pos1); try { x.set_size(N / uword(sizeof(eT)), 1, 1); } catch(...) { err_msg = "not enough memory"; return false; } f.clear(); f.read( reinterpret_cast(x.memptr()), std::streamsize(x.n_elem * uword(sizeof(eT))) ); return f.good(); } //! Load a cube in text format (human readable), //! with a header that indicates the cube type as well as its dimensions template inline bool diskio::load_arma_ascii(Cube& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; (arma_config::text_as_binary) ? f.open(name, std::fstream::binary) : f.open(name); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_arma_ascii(x, f, err_msg); f.close(); } return load_okay; } //! Load a cube in text format (human readable), //! with a header that indicates the cube type as well as its dimensions template inline bool diskio::load_arma_ascii(Cube& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); std::streampos pos = f.tellg(); bool load_okay = true; std::string f_header; uword f_n_rows; uword f_n_cols; uword f_n_slices; f >> f_header; f >> f_n_rows; f >> f_n_cols; f >> f_n_slices; if(f_header == diskio::gen_txt_header(x)) { try { x.set_size(f_n_rows, f_n_cols, f_n_slices); } catch(...) { err_msg = "not enough memory"; return false; } for(uword slice = 0; slice < x.n_slices; ++slice) for(uword row = 0; row < x.n_rows; ++row ) for(uword col = 0; col < x.n_cols; ++col ) { f >> x.at(row,col,slice); } load_okay = f.good(); } else { load_okay = false; err_msg = "incorrect header"; } // allow automatic conversion of u32/s32 cubes into u64/s64 cubes if(load_okay == false) { if( (sizeof(eT) == 8) && is_same_type::yes ) { Cube tmp; std::string junk; f.clear(); f.seekg(pos); load_okay = diskio::load_arma_ascii(tmp, f, junk); if(load_okay) { x = conv_to< Cube >::from(tmp); } } else if( (sizeof(eT) == 8) && is_same_type::yes ) { Cube tmp; std::string junk; f.clear(); f.seekg(pos); load_okay = diskio::load_arma_ascii(tmp, f, junk); if(load_okay) { x = conv_to< Cube >::from(tmp); } } } return load_okay; } //! Load a cube in binary format, //! with a header that indicates the cube type as well as its dimensions template inline bool diskio::load_arma_binary(Cube& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f; f.open(name, std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_arma_binary(x, f, err_msg); f.close(); } return load_okay; } template inline bool diskio::load_arma_binary(Cube& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); std::streampos pos = f.tellg(); bool load_okay = true; std::string f_header; uword f_n_rows; uword f_n_cols; uword f_n_slices; f >> f_header; f >> f_n_rows; f >> f_n_cols; f >> f_n_slices; if(f_header == diskio::gen_bin_header(x)) { //f.seekg(1, ios::cur); // NOTE: this may not be portable, as on a Windows machine a newline could be two characters f.get(); try { x.set_size(f_n_rows, f_n_cols, f_n_slices); } catch(...) { err_msg = "not enough memory"; return false; } f.read( reinterpret_cast(x.memptr()), std::streamsize(x.n_elem*sizeof(eT)) ); load_okay = f.good(); } else { load_okay = false; err_msg = "incorrect header"; } // allow automatic conversion of u32/s32 cubes into u64/s64 cubes if(load_okay == false) { if( (sizeof(eT) == 8) && is_same_type::yes ) { Cube tmp; std::string junk; f.clear(); f.seekg(pos); load_okay = diskio::load_arma_binary(tmp, f, junk); if(load_okay) { x = conv_to< Cube >::from(tmp); } } else if( (sizeof(eT) == 8) && is_same_type::yes ) { Cube tmp; std::string junk; f.clear(); f.seekg(pos); load_okay = diskio::load_arma_binary(tmp, f, junk); if(load_okay) { x = conv_to< Cube >::from(tmp); } } } return load_okay; } //! Load a HDF5 file as a cube template inline bool diskio::load_hdf5_binary(Cube& x, const hdf5_name& spec, std::string& err_msg) { arma_extra_debug_sigprint(); #if defined(ARMA_USE_HDF5) { if(diskio::is_readable(spec.filename) == false) { return false; } hdf5_misc::hdf5_suspend_printing_errors hdf5_print_suspender; bool load_okay = false; hid_t fid = H5Fopen(spec.filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT); if(fid >= 0) { // MATLAB HDF5 dataset names are user-specified; // Octave tends to store the datasets in a group, with the actual dataset being referred to as "value". // If the user hasn't specified a dataset, we will search for "dataset" and "value", // and if those are not found we will take the first dataset we do find. std::vector searchNames; const bool exact = (spec.dsname.empty() == false); if(exact) { searchNames.push_back(spec.dsname); } else { searchNames.push_back("dataset"); searchNames.push_back("value" ); } hid_t dataset = hdf5_misc::search_hdf5_file(searchNames, fid, 3, exact); if(dataset >= 0) { hid_t filespace = H5Dget_space(dataset); // This must be <= 3 due to our search rules. const int ndims = H5Sget_simple_extent_ndims(filespace); hsize_t dims[3]; const herr_t query_status = H5Sget_simple_extent_dims(filespace, dims, NULL); // arma_check(query_status < 0, "Cube::load(): cannot get size of HDF5 dataset"); if(query_status < 0) { err_msg = "cannot get size of HDF5 dataset"; H5Sclose(filespace); H5Dclose(dataset); H5Fclose(fid); return false; } if(ndims == 1) { dims[1] = 1; dims[2] = 1; } // Vector case; one row/colum, several slices if(ndims == 2) { dims[2] = 1; } // Matrix case; one column, several rows/slices try { x.set_size(dims[2], dims[1], dims[0]); } catch(...) { err_msg = "not enough memory"; return false; } // Now we have to see what type is stored to figure out how to load it. hid_t datatype = H5Dget_type(dataset); hid_t mat_type = hdf5_misc::get_hdf5_type(); // If these are the same type, it is simple. if(H5Tequal(datatype, mat_type) > 0) { // Load directly; H5S_ALL used so that we load the entire dataset. hid_t read_status = H5Dread(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, void_ptr(x.memptr())); if(read_status >= 0) { load_okay = true; } } else { // Load into another array and convert its type accordingly. hid_t read_status = hdf5_misc::load_and_convert_hdf5(x.memptr(), dataset, datatype, x.n_elem); if(read_status >= 0) { load_okay = true; } } // Now clean up. H5Tclose(datatype); H5Tclose(mat_type); H5Sclose(filespace); } H5Dclose(dataset); H5Fclose(fid); if(load_okay == false) { err_msg = "unsupported or missing HDF5 data"; } } else { err_msg = "cannot open"; } return load_okay; } #else { arma_ignore(x); arma_ignore(spec); arma_ignore(err_msg); arma_stop_logic_error("Cube::load(): use of HDF5 must be enabled"); return false; } #endif } //! Try to load a cube by automatically determining its type template inline bool diskio::load_auto_detect(Cube& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); if(diskio::is_readable(name) == false) { return false; } #if defined(ARMA_USE_HDF5) // We're currently using the C bindings for the HDF5 library, which don't support C++ streams if( H5Fis_hdf5(name.c_str()) ) { return load_hdf5_binary(x, name, err_msg); } #endif std::fstream f; f.open(name, std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_auto_detect(x, f, err_msg); f.close(); } return load_okay; } //! Try to load a cube by automatically determining its type template inline bool diskio::load_auto_detect(Cube& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); const char* ARMA_CUB_TXT_str = "ARMA_CUB_TXT"; const char* ARMA_CUB_BIN_str = "ARMA_CUB_BIN"; const char* P6_str = "P6"; const uword ARMA_CUB_TXT_len = uword(12); const uword ARMA_CUB_BIN_len = uword(12); const uword P6_len = uword(2); podarray header(ARMA_CUB_TXT_len + 1); char* header_mem = header.memptr(); std::streampos pos = f.tellg(); f.read( header_mem, std::streamsize(ARMA_CUB_TXT_len) ); f.clear(); f.seekg(pos); header_mem[ARMA_CUB_TXT_len] = '\0'; if( std::strncmp(ARMA_CUB_TXT_str, header_mem, size_t(ARMA_CUB_TXT_len)) == 0 ) { return load_arma_ascii(x, f, err_msg); } else if( std::strncmp(ARMA_CUB_BIN_str, header_mem, size_t(ARMA_CUB_BIN_len)) == 0 ) { return load_arma_binary(x, f, err_msg); } else if( std::strncmp(P6_str, header_mem, size_t(P6_len)) == 0 ) { return load_ppm_binary(x, f, err_msg); } else { const file_type ft = guess_file_type_internal(f); switch(ft) { // case csv_ascii: // return load_csv_ascii(x, f, err_msg); // break; case raw_binary: return load_raw_binary(x, f, err_msg); break; case raw_ascii: return load_raw_ascii(x, f, err_msg); break; default: err_msg = "unknown data"; return false; } } return false; } // fields template inline bool diskio::save_arma_binary(const field& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f( tmp_name, std::fstream::binary ); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_arma_binary(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } template inline bool diskio::save_arma_binary(const field& x, std::ostream& f) { arma_extra_debug_sigprint(); arma_type_check(( (is_Mat::value == false) && (is_Cube::value == false) )); if(x.n_slices <= 1) { f << "ARMA_FLD_BIN" << '\n'; f << x.n_rows << '\n'; f << x.n_cols << '\n'; } else { f << "ARMA_FL3_BIN" << '\n'; f << x.n_rows << '\n'; f << x.n_cols << '\n'; f << x.n_slices << '\n'; } bool save_okay = true; for(uword i=0; i inline bool diskio::load_arma_binary(field& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f( name, std::fstream::binary ); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_arma_binary(x, f, err_msg); f.close(); } return load_okay; } template inline bool diskio::load_arma_binary(field& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); arma_type_check(( (is_Mat::value == false) && (is_Cube::value == false) )); bool load_okay = true; std::string f_type; f >> f_type; if(f_type == "ARMA_FLD_BIN") { uword f_n_rows; uword f_n_cols; f >> f_n_rows; f >> f_n_cols; try { x.set_size(f_n_rows, f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } f.get(); for(uword i=0; i> f_n_rows; f >> f_n_cols; f >> f_n_slices; try { x.set_size(f_n_rows, f_n_cols, f_n_slices); } catch(...) { err_msg = "not enough memory"; return false; } f.get(); for(uword i=0; i& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f( tmp_name, std::fstream::binary ); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_std_string(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } inline bool diskio::save_std_string(const field& x, std::ostream& f) { arma_extra_debug_sigprint(); for(uword row=0; row& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::ifstream f(name); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_std_string(x, f, err_msg); f.close(); } return load_okay; } inline bool diskio::load_std_string(field& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); bool load_okay = true; // // work out the size uword f_n_rows = 0; uword f_n_cols = 0; bool f_n_cols_found = false; std::string line_string; std::string token; while( f.good() && load_okay ) { std::getline(f, line_string); if(line_string.size() == 0) { break; } std::stringstream line_stream(line_string); uword line_n_cols = 0; while(line_stream >> token) { line_n_cols++; } if(f_n_cols_found == false) { f_n_cols = line_n_cols; f_n_cols_found = true; } else { if(line_n_cols != f_n_cols) { load_okay = false; err_msg = "inconsistent number of columns"; } } ++f_n_rows; } if(load_okay) { f.clear(); f.seekg(0, ios::beg); //f.seekg(start); try { x.set_size(f_n_rows, f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } for(uword row=0; row < x.n_rows; ++row) for(uword col=0; col < x.n_cols; ++col) { f >> x.at(row,col); } } if(f.good() == false) { load_okay = false; } return load_okay; } //! Try to load a field by automatically determining its type template inline bool diskio::load_auto_detect(field& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::fstream f; f.open(name, std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_auto_detect(x, f, err_msg); f.close(); } return load_okay; } //! Try to load a field by automatically determining its type template inline bool diskio::load_auto_detect(field& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); arma_type_check(( is_Mat::value == false )); static const std::string ARMA_FLD_BIN = "ARMA_FLD_BIN"; static const std::string ARMA_FL3_BIN = "ARMA_FL3_BIN"; static const std::string P6 = "P6"; podarray raw_header(uword(ARMA_FLD_BIN.length()) + 1); std::streampos pos = f.tellg(); f.read( raw_header.memptr(), std::streamsize(ARMA_FLD_BIN.length()) ); f.clear(); f.seekg(pos); raw_header[uword(ARMA_FLD_BIN.length())] = '\0'; const std::string header = raw_header.mem; if(ARMA_FLD_BIN == header.substr(0, ARMA_FLD_BIN.length())) { return load_arma_binary(x, f, err_msg); } else if(ARMA_FL3_BIN == header.substr(0, ARMA_FL3_BIN.length())) { return load_arma_binary(x, f, err_msg); } else if(P6 == header.substr(0, P6.length())) { return load_ppm_binary(x, f, err_msg); } else { err_msg = "unsupported header"; return false; } } // // handling of PPM images by cubes template inline bool diskio::load_ppm_binary(Cube& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::fstream f; f.open(name, std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_ppm_binary(x, f, err_msg); f.close(); } return load_okay; } template inline bool diskio::load_ppm_binary(Cube& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); bool load_okay = true; std::string f_header; f >> f_header; if(f_header == "P6") { uword f_n_rows = 0; uword f_n_cols = 0; int f_maxval = 0; diskio::pnm_skip_comments(f); f >> f_n_cols; diskio::pnm_skip_comments(f); f >> f_n_rows; diskio::pnm_skip_comments(f); f >> f_maxval; f.get(); if( (f_maxval > 0) && (f_maxval <= 65535) ) { try { x.set_size(f_n_rows, f_n_cols, 3); } catch(...) { err_msg = "not enough memory"; return false; } if(f_maxval <= 255) { const uword n_elem = 3*f_n_cols*f_n_rows; podarray tmp(n_elem); f.read( reinterpret_cast(tmp.memptr()), std::streamsize(n_elem) ); uword i = 0; //cout << "f_n_cols = " << f_n_cols << endl; //cout << "f_n_rows = " << f_n_rows << endl; for(uword row=0; row < f_n_rows; ++row) for(uword col=0; col < f_n_cols; ++col) { x.at(row,col,0) = eT(tmp[i+0]); x.at(row,col,1) = eT(tmp[i+1]); x.at(row,col,2) = eT(tmp[i+2]); i+=3; } } else { const uword n_elem = 3*f_n_cols*f_n_rows; podarray tmp(n_elem); f.read( reinterpret_cast(tmp.memptr()), std::streamsize(2*n_elem) ); uword i = 0; for(uword row=0; row < f_n_rows; ++row) for(uword col=0; col < f_n_cols; ++col) { x.at(row,col,0) = eT(tmp[i+0]); x.at(row,col,1) = eT(tmp[i+1]); x.at(row,col,2) = eT(tmp[i+2]); i+=3; } } } else { load_okay = false; err_msg = "functionality unimplemented"; } if(f.good() == false) { load_okay = false; } } else { load_okay = false; err_msg = "unsupported header"; } return load_okay; } template inline bool diskio::save_ppm_binary(const Cube& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f( tmp_name, std::fstream::binary ); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_ppm_binary(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } template inline bool diskio::save_ppm_binary(const Cube& x, std::ostream& f) { arma_extra_debug_sigprint(); arma_debug_check( (x.n_slices != 3), "diskio::save_ppm_binary(): given cube must have exactly 3 slices" ); const uword n_elem = 3 * x.n_rows * x.n_cols; podarray tmp(n_elem); uword i = 0; for(uword row=0; row < x.n_rows; ++row) { for(uword col=0; col < x.n_cols; ++col) { tmp[i+0] = u8( access::tmp_real( x.at(row,col,0) ) ); tmp[i+1] = u8( access::tmp_real( x.at(row,col,1) ) ); tmp[i+2] = u8( access::tmp_real( x.at(row,col,2) ) ); i+=3; } } f << "P6" << '\n'; f << x.n_cols << '\n'; f << x.n_rows << '\n'; f << 255 << '\n'; f.write( reinterpret_cast(tmp.mem), std::streamsize(n_elem) ); return f.good(); } // // handling of PPM images by fields template inline bool diskio::load_ppm_binary(field& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::fstream f; f.open(name, std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay) { load_okay = diskio::load_ppm_binary(x, f, err_msg); f.close(); } return load_okay; } template inline bool diskio::load_ppm_binary(field& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); arma_type_check(( is_Mat::value == false )); typedef typename T1::elem_type eT; bool load_okay = true; std::string f_header; f >> f_header; if(f_header == "P6") { uword f_n_rows = 0; uword f_n_cols = 0; int f_maxval = 0; diskio::pnm_skip_comments(f); f >> f_n_cols; diskio::pnm_skip_comments(f); f >> f_n_rows; diskio::pnm_skip_comments(f); f >> f_maxval; f.get(); if( (f_maxval > 0) && (f_maxval <= 65535) ) { x.set_size(3); Mat& R = x(0); Mat& G = x(1); Mat& B = x(2); try { R.set_size(f_n_rows,f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } try { G.set_size(f_n_rows,f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } try { B.set_size(f_n_rows,f_n_cols); } catch(...) { err_msg = "not enough memory"; return false; } if(f_maxval <= 255) { const uword n_elem = 3*f_n_cols*f_n_rows; podarray tmp(n_elem); f.read( reinterpret_cast(tmp.memptr()), std::streamsize(n_elem) ); uword i = 0; //cout << "f_n_cols = " << f_n_cols << endl; //cout << "f_n_rows = " << f_n_rows << endl; for(uword row=0; row < f_n_rows; ++row) { for(uword col=0; col < f_n_cols; ++col) { R.at(row,col) = eT(tmp[i+0]); G.at(row,col) = eT(tmp[i+1]); B.at(row,col) = eT(tmp[i+2]); i+=3; } } } else { const uword n_elem = 3*f_n_cols*f_n_rows; podarray tmp(n_elem); f.read( reinterpret_cast(tmp.memptr()), std::streamsize(2*n_elem) ); uword i = 0; for(uword row=0; row < f_n_rows; ++row) for(uword col=0; col < f_n_cols; ++col) { R.at(row,col) = eT(tmp[i+0]); G.at(row,col) = eT(tmp[i+1]); B.at(row,col) = eT(tmp[i+2]); i+=3; } } } else { load_okay = false; err_msg = "functionality unimplemented"; } if(f.good() == false) { load_okay = false; } } else { load_okay = false; err_msg = "unsupported header"; } return load_okay; } template inline bool diskio::save_ppm_binary(const field& x, const std::string& final_name) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f( tmp_name, std::fstream::binary ); bool save_okay = f.is_open(); if(save_okay) { save_okay = diskio::save_ppm_binary(x, f); f.flush(); f.close(); if(save_okay) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } template inline bool diskio::save_ppm_binary(const field& x, std::ostream& f) { arma_extra_debug_sigprint(); arma_type_check(( is_Mat::value == false )); typedef typename T1::elem_type eT; arma_debug_check( (x.n_elem != 3), "diskio::save_ppm_binary(): given field must have exactly 3 matrices of equal size" ); bool same_size = true; for(uword i=1; i<3; ++i) { if( (x(0).n_rows != x(i).n_rows) || (x(0).n_cols != x(i).n_cols) ) { same_size = false; break; } } arma_debug_check( (same_size != true), "diskio::save_ppm_binary(): given field must have exactly 3 matrices of equal size" ); const Mat& R = x(0); const Mat& G = x(1); const Mat& B = x(2); f << "P6" << '\n'; f << R.n_cols << '\n'; f << R.n_rows << '\n'; f << 255 << '\n'; const uword n_elem = 3 * R.n_rows * R.n_cols; podarray tmp(n_elem); uword i = 0; for(uword row=0; row < R.n_rows; ++row) for(uword col=0; col < R.n_cols; ++col) { tmp[i+0] = u8( access::tmp_real( R.at(row,col) ) ); tmp[i+1] = u8( access::tmp_real( G.at(row,col) ) ); tmp[i+2] = u8( access::tmp_real( B.at(row,col) ) ); i+=3; } f.write( reinterpret_cast(tmp.mem), std::streamsize(n_elem) ); return f.good(); } //! @}