// Copyright (C) 2008-2015 National ICT Australia (NICTA) // // This Source Code Form is subject to the terms of the Mozilla Public // License, v. 2.0. If a copy of the MPL was not distributed with this // file, You can obtain one at http://mozilla.org/MPL/2.0/. // ------------------------------------------------------------------- // // Written by Conrad Sanderson - http://conradsanderson.id.au // Written by Ian Cullinan // Written by Ryan Curtin // Written by Szabolcs Horvat //! \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, e.g. "008" indicates eight bytes. template inline std::string diskio::gen_txt_header(const Mat& x) { arma_type_check(( is_supported_elem_type::value == false )); arma_ignore(x); if(is_u8::value) { return std::string("ARMA_MAT_TXT_IU001"); } else if(is_s8::value) { return std::string("ARMA_MAT_TXT_IS001"); } else if(is_u16::value) { return std::string("ARMA_MAT_TXT_IU002"); } else if(is_s16::value) { return std::string("ARMA_MAT_TXT_IS002"); } else if(is_u32::value) { return std::string("ARMA_MAT_TXT_IU004"); } else if(is_s32::value) { return std::string("ARMA_MAT_TXT_IS004"); } #if defined(ARMA_USE_U64S64) else if(is_u64::value) { return std::string("ARMA_MAT_TXT_IU008"); } else if(is_s64::value) { return std::string("ARMA_MAT_TXT_IS008"); } #endif #if defined(ARMA_ALLOW_LONG) else if(is_ulng_t_32::value) { return std::string("ARMA_MAT_TXT_IU004"); } else if(is_slng_t_32::value) { return std::string("ARMA_MAT_TXT_IS004"); } else if(is_ulng_t_64::value) { return std::string("ARMA_MAT_TXT_IU008"); } else if(is_slng_t_64::value) { return std::string("ARMA_MAT_TXT_IS008"); } #endif else if(is_float::value) { return std::string("ARMA_MAT_TXT_FN004"); } else if(is_double::value) { return std::string("ARMA_MAT_TXT_FN008"); } else if(is_complex_float::value) { return std::string("ARMA_MAT_TXT_FC008"); } else if(is_complex_double::value) { return std::string("ARMA_MAT_TXT_FC016"); } else { return std::string(); } } //! 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, e.g. "008" indicates eight bytes. template inline std::string diskio::gen_bin_header(const Mat& x) { arma_type_check(( is_supported_elem_type::value == false )); arma_ignore(x); if(is_u8::value) { return std::string("ARMA_MAT_BIN_IU001"); } else if(is_s8::value) { return std::string("ARMA_MAT_BIN_IS001"); } else if(is_u16::value) { return std::string("ARMA_MAT_BIN_IU002"); } else if(is_s16::value) { return std::string("ARMA_MAT_BIN_IS002"); } else if(is_u32::value) { return std::string("ARMA_MAT_BIN_IU004"); } else if(is_s32::value) { return std::string("ARMA_MAT_BIN_IS004"); } #if defined(ARMA_USE_U64S64) else if(is_u64::value) { return std::string("ARMA_MAT_BIN_IU008"); } else if(is_s64::value) { return std::string("ARMA_MAT_BIN_IS008"); } #endif #if defined(ARMA_ALLOW_LONG) else if(is_ulng_t_32::value) { return std::string("ARMA_MAT_BIN_IU004"); } else if(is_slng_t_32::value) { return std::string("ARMA_MAT_BIN_IS004"); } else if(is_ulng_t_64::value) { return std::string("ARMA_MAT_BIN_IU008"); } else if(is_slng_t_64::value) { return std::string("ARMA_MAT_BIN_IS008"); } #endif else if(is_float::value) { return std::string("ARMA_MAT_BIN_FN004"); } else if(is_double::value) { return std::string("ARMA_MAT_BIN_FN008"); } else if(is_complex_float::value) { return std::string("ARMA_MAT_BIN_FC008"); } else if(is_complex_double::value) { return std::string("ARMA_MAT_BIN_FC016"); } else { return std::string(); } } //! 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, e.g. "008" indicates eight bytes. template inline std::string diskio::gen_bin_header(const SpMat& x) { arma_type_check(( is_supported_elem_type::value == false )); arma_ignore(x); if(is_u8::value) { return std::string("ARMA_SPM_BIN_IU001"); } else if(is_s8::value) { return std::string("ARMA_SPM_BIN_IS001"); } else if(is_u16::value) { return std::string("ARMA_SPM_BIN_IU002"); } else if(is_s16::value) { return std::string("ARMA_SPM_BIN_IS002"); } else if(is_u32::value) { return std::string("ARMA_SPM_BIN_IU004"); } else if(is_s32::value) { return std::string("ARMA_SPM_BIN_IS004"); } #if defined(ARMA_USE_U64S64) else if(is_u64::value) { return std::string("ARMA_SPM_BIN_IU008"); } else if(is_s64::value) { return std::string("ARMA_SPM_BIN_IS008"); } #endif #if defined(ARMA_ALLOW_LONG) else if(is_ulng_t_32::value) { return std::string("ARMA_SPM_BIN_IU004"); } else if(is_slng_t_32::value) { return std::string("ARMA_SPM_BIN_IS004"); } else if(is_ulng_t_64::value) { return std::string("ARMA_SPM_BIN_IU008"); } else if(is_slng_t_64::value) { return std::string("ARMA_SPM_BIN_IS008"); } #endif else if(is_float::value) { return std::string("ARMA_SPM_BIN_FN004"); } else if(is_double::value) { return std::string("ARMA_SPM_BIN_FN008"); } else if(is_complex_float::value) { return std::string("ARMA_SPM_BIN_FC008"); } else if(is_complex_double::value) { return std::string("ARMA_SPM_BIN_FC016"); } else { return std::string(); } } //! 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, e.g. "008" indicates eight bytes. template inline std::string diskio::gen_txt_header(const Cube& x) { arma_type_check(( is_supported_elem_type::value == false )); arma_ignore(x); if(is_u8::value) { return std::string("ARMA_CUB_TXT_IU001"); } else if(is_s8::value) { return std::string("ARMA_CUB_TXT_IS001"); } else if(is_u16::value) { return std::string("ARMA_CUB_TXT_IU002"); } else if(is_s16::value) { return std::string("ARMA_CUB_TXT_IS002"); } else if(is_u32::value) { return std::string("ARMA_CUB_TXT_IU004"); } else if(is_s32::value) { return std::string("ARMA_CUB_TXT_IS004"); } #if defined(ARMA_USE_U64S64) else if(is_u64::value) { return std::string("ARMA_CUB_TXT_IU008"); } else if(is_s64::value) { return std::string("ARMA_CUB_TXT_IS008"); } #endif #if defined(ARMA_ALLOW_LONG) else if(is_ulng_t_32::value) { return std::string("ARMA_CUB_TXT_IU004"); } else if(is_slng_t_32::value) { return std::string("ARMA_CUB_TXT_IS004"); } else if(is_ulng_t_64::value) { return std::string("ARMA_CUB_TXT_IU008"); } else if(is_slng_t_64::value) { return std::string("ARMA_CUB_TXT_IS008"); } #endif else if(is_float::value) { return std::string("ARMA_CUB_TXT_FN004"); } else if(is_double::value) { return std::string("ARMA_CUB_TXT_FN008"); } else if(is_complex_float::value) { return std::string("ARMA_CUB_TXT_FC008"); } else if(is_complex_double::value) { return std::string("ARMA_CUB_TXT_FC016"); } else { return std::string(); } } //! 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, e.g. "008" indicates eight bytes. template inline std::string diskio::gen_bin_header(const Cube& x) { arma_type_check(( is_supported_elem_type::value == false )); arma_ignore(x); if(is_u8::value) { return std::string("ARMA_CUB_BIN_IU001"); } else if(is_s8::value) { return std::string("ARMA_CUB_BIN_IS001"); } else if(is_u16::value) { return std::string("ARMA_CUB_BIN_IU002"); } else if(is_s16::value) { return std::string("ARMA_CUB_BIN_IS002"); } else if(is_u32::value) { return std::string("ARMA_CUB_BIN_IU004"); } else if(is_s32::value) { return std::string("ARMA_CUB_BIN_IS004"); } #if defined(ARMA_USE_U64S64) else if(is_u64::value) { return std::string("ARMA_CUB_BIN_IU008"); } else if(is_s64::value) { return std::string("ARMA_CUB_BIN_IS008"); } #endif #if defined(ARMA_ALLOW_LONG) else if(is_ulng_t_32::value) { return std::string("ARMA_CUB_BIN_IU004"); } else if(is_slng_t_32::value) { return std::string("ARMA_CUB_BIN_IS004"); } else if(is_ulng_t_64::value) { return std::string("ARMA_CUB_BIN_IU008"); } else if(is_slng_t_64::value) { return std::string("ARMA_CUB_BIN_IS008"); } #endif else if(is_float::value) { return std::string("ARMA_CUB_BIN_FN004"); } else if(is_double::value) { return std::string("ARMA_CUB_BIN_FN008"); } else if(is_complex_float::value) { return std::string("ARMA_CUB_BIN_FC008"); } else if(is_complex_double::value) { return std::string("ARMA_CUB_BIN_FC016"); } else { return std::string(); } } inline file_type diskio::guess_file_type(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 = ( (pos1 >= 0) && (pos2 >= 0) && (pos2 > pos1) ) ? uword(pos2 - pos1) : 0; f.clear(); f.seekg(pos1); if(N == 0) { return file_type_unknown; } podarray data(N); data.zeros(); unsigned char* ptr = data.memptr(); f.clear(); f.read( reinterpret_cast(ptr), std::streamsize(N) ); const bool load_okay = f.good(); f.clear(); f.seekg(pos1); bool has_binary = false; bool has_bracket = false; bool has_comma = false; if(load_okay == true) { 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_comma = true; } } } else { return file_type_unknown; } if(has_binary) { return raw_binary; } if(has_comma && (has_bracket == false)) { return csv_ascii; } return raw_ascii; } //! Append a quasi-random string to the given filename. //! The rand() function is deliberately not used, //! as rand() has an internal state that changes //! from call to call. Such states should not be //! modified in scientific applications, where the //! results should be reproducable and not affected //! by saving data. inline arma_cold 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); std::stringstream ss; ss << x << ".tmp_" << std::hex << std::noshowbase << (u.val) << (std::clock()); 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 arma_cold bool diskio::safe_rename(const std::string& old_name, const std::string& new_name) { std::fstream f(new_name.c_str(), std::fstream::out | std::fstream::app); f.put(' '); bool save_okay = f.good(); f.close(); if(save_okay == true) { std::remove(new_name.c_str()); const int mv_result = std::rename(old_name.c_str(), new_name.c_str()); save_okay = (mv_result == 0); } return save_okay; } template inline bool diskio::convert_naninf(eT& val, const std::string& token) { // see if the token represents a NaN or Inf if( (token.length() == 3) || (token.length() == 4) ) { const bool neg = (token[0] == '-'); const bool pos = (token[0] == '+'); const size_t offset = ( (neg || pos) && (token.length() == 4) ) ? 1 : 0; const std::string token2 = token.substr(offset, 3); if( (token2 == "inf") || (token2 == "Inf") || (token2 == "INF") ) { val = neg ? cond_rel< is_signed::value >::make_neg(Datum::inf) : Datum::inf; return true; } else if( (token2 == "nan") || (token2 == "Nan") || (token2 == "NaN") || (token2 == "NAN") ) { val = Datum::nan; return true; } } return false; } template inline bool diskio::convert_naninf(std::complex& val, const std::string& token) { if( token.length() >= 5 ) { std::stringstream ss( token.substr(1, token.length()-2) ); // strip '(' at the start and ')' at the end std::string token_real; std::string token_imag; std::getline(ss, token_real, ','); std::getline(ss, token_imag); std::stringstream ss_real(token_real); std::stringstream ss_imag(token_imag); T val_real = T(0); T val_imag = T(0); ss_real >> val_real; ss_imag >> val_imag; bool success_real = true; bool success_imag = true; if(ss_real.fail() == true) { success_real = diskio::convert_naninf( val_real, token_real ); } if(ss_imag.fail() == true) { success_imag = diskio::convert_naninf( val_imag, token_imag ); } val = std::complex(val_real, val_imag); return (success_real && success_imag); } return false; } //! 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::fstream f(tmp_name.c_str(), std::fstream::out); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_raw_ascii(x, f); f.flush(); f.close(); if(save_okay == true) { 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(); uword cell_width; // TODO: need sane values for complex numbers if( (is_float::value) || (is_double::value) ) { f.setf(ios::scientific); f.precision(12); cell_width = 20; } for(uword row=0; row < x.n_rows; ++row) { for(uword col=0; col < x.n_cols; ++col) { f.put(' '); if( (is_float::value) || (is_double::value) ) { f.width(cell_width); } arma_ostream::print_elem(f, x.at(row,col), false); } f.put('\n'); } return f.good(); } //! 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.c_str(), std::fstream::binary); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_raw_binary(x, f); f.flush(); f.close(); if(save_okay == true) { 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(tmp_name.c_str()); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_arma_ascii(x, f); f.flush(); f.close(); if(save_okay == true) { 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 ios::fmtflags orig_flags = f.flags(); f << diskio::gen_txt_header(x) << '\n'; f << x.n_rows << ' ' << x.n_cols << '\n'; uword cell_width; // TODO: need sane values for complex numbers if( (is_float::value) || (is_double::value) ) { f.setf(ios::scientific); f.precision(12); cell_width = 20; } for(uword row=0; row < x.n_rows; ++row) { for(uword col=0; col < x.n_cols; ++col) { f.put(' '); if( (is_float::value) || (is_double::value) ) { f.width(cell_width); } arma_ostream::print_elem(f, x.at(row,col), false); } f.put('\n'); } const bool save_okay = f.good(); f.flags(orig_flags); 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) { arma_extra_debug_sigprint(); const std::string tmp_name = diskio::gen_tmp_name(final_name); std::ofstream f(tmp_name.c_str()); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_csv_ascii(x, f); f.flush(); f.close(); if(save_okay == true) { 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) { arma_extra_debug_sigprint(); const ios::fmtflags orig_flags = f.flags(); // TODO: need sane values for complex numbers if( (is_float::value) || (is_double::value) ) { f.setf(ios::scientific); f.precision(12); } 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::print_elem(f, x.at(row,col), false); if( col < (x_n_cols-1) ) { f.put(','); } } f.put('\n'); } const bool save_okay = f.good(); f.flags(orig_flags); 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.c_str(), std::fstream::binary); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_arma_binary(x, f); f.flush(); f.close(); if(save_okay == true) { 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.c_str(), std::fstream::out | std::fstream::binary); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_pgm_binary(x, f); f.flush(); f.close(); if(save_okay == true) { save_okay = diskio::safe_rename(tmp_name, final_name); } } return save_okay; } // // TODO: // add functionality to save the image in a normalised format, // i.e. scaled so that every value falls in the [0,255] range. //! 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 std::string& final_name) { arma_extra_debug_sigprint(); #if defined(ARMA_USE_HDF5) { #if !defined(ARMA_PRINT_HDF5_ERRORS) { // Disable annoying HDF5 error messages. arma_H5Eset_auto(H5E_DEFAULT, NULL, NULL); } #endif bool save_okay = false; const std::string tmp_name = diskio::gen_tmp_name(final_name); // Set up the file according to HDF5's preferences hid_t file = arma_H5Fcreate(tmp_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); // 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 = arma_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, so we will // use that. hid_t dataset = arma_H5Dcreate(file, "dataset", datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); // H5Dwrite does not make a distinction between row-major and column-major; // it just writes the memory. MATLAB and Octave store HDF5 matrices as // column-major, though, so we can save ours like that too and not need to // transpose. herr_t status = arma_H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, x.mem); save_okay = (status >= 0); arma_H5Dclose(dataset); arma_H5Tclose(datatype); arma_H5Sclose(dataspace); arma_H5Fclose(file); if(save_okay == true) { save_okay = diskio::safe_rename(tmp_name, final_name); } return save_okay; } #else { arma_ignore(x); arma_ignore(final_name); arma_stop("Mat::save(): use of HDF5 needs to 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::fstream f; f.open(name.c_str(), std::fstream::in); bool load_okay = f.is_open(); if(load_okay == true) { 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::string token; std::stringstream line_stream; while( (f.good() == true) && (load_okay == true) ) { 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 >> 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) { err_msg = "inconsistent number of columns in "; load_okay = false; } } ++f_n_rows; } if(load_okay == true) { f.clear(); f.seekg(pos1); x.set_size(f_n_rows, f_n_cols); std::stringstream ss; for(uword row=0; (row < x.n_rows) && (load_okay == true); ++row) { for(uword col=0; (col < x.n_cols) && (load_okay == true); ++col) { f >> token; if( (is_signed::value == false) && (token.length() > 0) && (token[0] == '-') ) { x.at(row,col) = eT(0); } else { ss.clear(); ss.str(token); eT val = eT(0); ss >> val; if(ss.fail() == false) { x.at(row,col) = val; } else { const bool success = diskio::convert_naninf( x.at(row,col), token ); if(success == false) { load_okay = false; err_msg = "couldn't interpret data in "; } } } } } } // 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.c_str(), std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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(); arma_ignore(err_msg); 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); x.set_size(N / sizeof(eT), 1); f.clear(); f.read( reinterpret_cast(x.memptr()), std::streamsize(N) ); 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(name.c_str()); bool load_okay = f.is_open(); if(load_okay == true) { 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)) { x.zeros(f_n_rows, f_n_cols); std::string token; std::stringstream ss; for(uword row=0; row < x.n_rows; ++row) { for(uword col=0; col < x.n_cols; ++col) { f >> token; ss.clear(); ss.str(token); eT val = eT(0); ss >> val; if(ss.fail() == false) { x.at(row,col) = val; } else { diskio::convert_naninf( x.at(row,col), token ); } } } load_okay = f.good(); } else { load_okay = false; err_msg = "incorrect header in "; } // 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) { arma_extra_debug_sigprint(); std::fstream f; f.open(name.c_str(), std::fstream::in); bool load_okay = f.is_open(); if(load_okay == true) { load_okay = diskio::load_csv_ascii(x, f, err_msg); 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&) { 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; std::string line_string; std::string token; std::stringstream line_stream; while( (f.good() == true) && (load_okay == true) ) { 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() == true) { std::getline(line_stream, token, ','); ++line_n_cols; } if(f_n_cols < line_n_cols) { f_n_cols = line_n_cols; } ++f_n_rows; } f.clear(); f.seekg(pos1); x.zeros(f_n_rows, f_n_cols); uword row = 0; std::stringstream ss; while(f.good() == true) { 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() == true) { std::getline(line_stream, token, ','); if( (is_signed::value == false) && (token.length() > 0) && (token[0] == '-') ) { x.at(row,col) = eT(0); } else { ss.clear(); ss.str(token); eT val = eT(0); ss >> val; if(ss.fail() == false) { x.at(row,col) = val; } else { diskio::convert_naninf( x.at(row,col), token ); } } ++col; } ++row; } return load_okay; } //! 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.c_str(), std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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(); x.set_size(f_n_rows,f_n_cols); 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 in "; } // 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.c_str(), std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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) ) { x.set_size(f_n_rows,f_n_cols); 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 = "currently no code available to handle loading "; } if(f.good() == false) { load_okay = false; } } else { load_okay = false; err_msg = "unsupported header in "; } 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 std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); #if defined(ARMA_USE_HDF5) { // These may be necessary to store the error handler (if we need to). herr_t (*old_func)(hid_t, void*); void *old_client_data; #if !defined(ARMA_PRINT_HDF5_ERRORS) { // Save old error handler. arma_H5Eget_auto(H5E_DEFAULT, &old_func, &old_client_data); // Disable annoying HDF5 error messages. arma_H5Eset_auto(H5E_DEFAULT, NULL, NULL); } #endif bool load_okay = false; hid_t fid = arma_H5Fopen(name.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". // So 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; searchNames.push_back("dataset"); searchNames.push_back("value"); hid_t dataset = hdf5_misc::search_hdf5_file(searchNames, fid, 2, false); if(dataset >= 0) { hid_t filespace = arma_H5Dget_space(dataset); // This must be <= 2 due to our search rules. const int ndims = arma_H5Sget_simple_extent_ndims(filespace); hsize_t dims[2]; const herr_t query_status = arma_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 in "; arma_H5Sclose(filespace); arma_H5Dclose(dataset); arma_H5Fclose(fid); #if !defined(ARMA_PRINT_HDF5_ERRORS) { // Restore HDF5 error handler. arma_H5Eset_auto(H5E_DEFAULT, old_func, old_client_data); } #endif return false; } if(ndims == 1) { dims[1] = 1; } // Vector case; fake second dimension (one column). x.set_size(dims[1], dims[0]); // Now we have to see what type is stored to figure out how to load it. hid_t datatype = arma_H5Dget_type(dataset); hid_t mat_type = hdf5_misc::get_hdf5_type(); // If these are the same type, it is simple. if(arma_H5Tequal(datatype, mat_type) > 0) { // Load directly; H5S_ALL used so that we load the entire dataset. hid_t read_status = arma_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. arma_H5Tclose(datatype); arma_H5Tclose(mat_type); arma_H5Sclose(filespace); } arma_H5Dclose(dataset); arma_H5Fclose(fid); if(load_okay == false) { err_msg = "unsupported or incorrect HDF5 data in "; } } else { err_msg = "cannot open file "; } #if !defined(ARMA_PRINT_HDF5_ERRORS) { // Restore HDF5 error handler. arma_H5Eset_auto(H5E_DEFAULT, old_func, old_client_data); } #endif return load_okay; } #else { arma_ignore(x); arma_ignore(name); arma_ignore(err_msg); arma_stop("Mat::load(): use of HDF5 needs to 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 defined(ARMA_USE_HDF5) // We're currently using the C bindings for the HDF5 library, which don't support C++ streams if( arma_H5Fis_hdf5(name.c_str()) ) { return load_hdf5_binary(x, name, err_msg); } #endif std::fstream f; f.open(name.c_str(), std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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(); static const std::string ARMA_MAT_TXT = "ARMA_MAT_TXT"; static const std::string ARMA_MAT_BIN = "ARMA_MAT_BIN"; static const std::string P5 = "P5"; podarray raw_header( uword(ARMA_MAT_TXT.length()) + 1); std::streampos pos = f.tellg(); f.read( raw_header.memptr(), std::streamsize(ARMA_MAT_TXT.length()) ); raw_header[uword(ARMA_MAT_TXT.length())] = '\0'; f.clear(); f.seekg(pos); const std::string header = raw_header.mem; if(ARMA_MAT_TXT == header.substr(0,ARMA_MAT_TXT.length())) { return load_arma_ascii(x, f, err_msg); } else if(ARMA_MAT_BIN == header.substr(0,ARMA_MAT_BIN.length())) { return load_arma_binary(x, f, err_msg); } else if(P5 == header.substr(0,P5.length())) { return load_pgm_binary(x, f, err_msg); } else { const file_type ft = guess_file_type(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 in "; return false; } } return false; } // // sparse matrices // //! 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(tmp_name.c_str()); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_coord_ascii(x, f); f.flush(); f.close(); if(save_okay == true) { 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 ios::fmtflags orig_flags = f.flags(); typename SpMat::const_iterator iter = x.begin(); typename SpMat::const_iterator iter_end = x.end(); for(; iter != iter_end; ++iter) { f.setf(ios::fixed); f << iter.row() << ' ' << iter.col() << ' '; if( (is_float::value) || (is_double::value) ) { f.setf(ios::scientific); f.precision(12); } f << (*iter) << '\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.setf(ios::fixed); f << max_row << ' ' << max_col << " 0\n"; } } const bool save_okay = f.good(); f.flags(orig_flags); 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(); const ios::fmtflags orig_flags = f.flags(); typedef typename std::complex eT; typename SpMat::const_iterator iter = x.begin(); typename SpMat::const_iterator iter_end = x.end(); for(; iter != iter_end; ++iter) { f.setf(ios::fixed); f << iter.row() << ' ' << iter.col() << ' '; if( (is_float::value) || (is_double::value) ) { f.setf(ios::scientific); f.precision(12); } const eT val = (*iter); f << 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.setf(ios::fixed); f << max_row << ' ' << max_col << " 0 0\n"; } } const bool save_okay = f.good(); f.flags(orig_flags); 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.c_str(), std::fstream::binary); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_arma_binary(x, f); f.flush(); f.close(); if(save_okay == true) { 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_coord_ascii(SpMat& x, const std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); std::fstream f; f.open(name.c_str(), std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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(); arma_ignore(err_msg); 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; uword f_n_nz = 0; bool size_found = false; std::string line_string; std::string token; std::stringstream line_stream; std::stringstream ss; uword last_line_row = 0; uword last_line_col = 0; bool first_line = true; bool weird_format = false; while( (f.good() == true) && (load_okay == true) ) { 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) { load_okay = false; break; } 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; if(first_line == true) { first_line = false; } else { if( (line_col < last_line_col) || ((line_row <= last_line_row) && (line_col <= last_line_col)) ) { weird_format = true; } } last_line_row = line_row; last_line_col = line_col; if(line_stream.good() == true) { eT final_val = eT(0); line_stream >> token; if(line_stream.fail() == false) { eT val = eT(0); ss.clear(); ss.str(token); ss >> val; if(ss.fail() == false) { final_val = val; } else { val = eT(0); const bool success = diskio::convert_naninf( val, token ); if(success == true) { final_val = val; } } } if(final_val != eT(0)) { ++f_n_nz; } } } if(size_found == true) { // take into account that indices start at 0 f_n_rows++; f_n_cols++; } if(load_okay == true) { f.clear(); f.seekg(pos1); x.set_size(f_n_rows, f_n_cols); if(weird_format == false) { x.mem_resize(f_n_nz); } uword pos = 0; while(f.good() == true) { 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 final_val = eT(0); line_stream >> token; if(line_stream.fail() == false) { eT val = eT(0); ss.clear(); ss.str(token); ss >> val; if(ss.fail() == false) { final_val = val; } else { val = eT(0); const bool success = diskio::convert_naninf( val, token ); if(success == true) { final_val = val; } } } if(final_val != eT(0)) { if(weird_format == false) { access::rw(x.row_indices[pos]) = line_row; access::rw(x.values[pos]) = final_val; ++access::rw(x.col_ptrs[line_col + 1]); ++pos; } else { x.at(line_row,line_col) = final_val; } } } if(weird_format == false) { for(uword c = 1; c <= f_n_cols; ++c) { access::rw(x.col_ptrs[c]) += x.col_ptrs[c - 1]; } } } return load_okay; } template inline bool diskio::load_coord_ascii(SpMat< std::complex >& x, std::istream& f, std::string& err_msg) { arma_extra_debug_sigprint(); arma_ignore(err_msg); 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; uword f_n_nz = 0; bool size_found = false; std::string line_string; std::string token_real; std::string token_imag; std::stringstream line_stream; std::stringstream ss; uword last_line_row = 0; uword last_line_col = 0; bool first_line = true; bool weird_format = false; while( (f.good() == true) && (load_okay == true) ) { 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) { load_okay = false; break; } 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; if(first_line == true) { first_line = false; } else { if( (line_col < last_line_col) || ((line_row <= last_line_row) && (line_col <= last_line_col)) ) { weird_format = true; } } last_line_row = line_row; last_line_col = line_col; if(line_stream.good() == true) { T final_val_real = T(0); T final_val_imag = T(0); line_stream >> token_real; if(line_stream.fail() == false) { T val_real = T(0); ss.clear(); ss.str(token_real); ss >> val_real; if(ss.fail() == false) { final_val_real = val_real; } else { val_real = T(0); const bool success = diskio::convert_naninf( val_real, token_real ); if(success == true) { final_val_real = val_real; } } } line_stream >> token_imag; if(line_stream.fail() == false) { T val_imag = T(0); ss.clear(); ss.str(token_imag); ss >> val_imag; if(ss.fail() == false) { final_val_imag = val_imag; } else { val_imag = T(0); const bool success = diskio::convert_naninf( val_imag, token_imag ); if(success == true) { final_val_imag = val_imag; } } } if( (final_val_real != T(0)) || (final_val_imag != T(0)) ) { ++f_n_nz; } } } if(size_found == true) { // take into account that indices start at 0 f_n_rows++; f_n_cols++; } if(load_okay == true) { f.clear(); f.seekg(pos1); x.set_size(f_n_rows, f_n_cols); if(weird_format == false) { x.mem_resize(f_n_nz); } uword pos = 0; while(f.good() == true) { 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 final_val_real = T(0); T final_val_imag = T(0); line_stream >> token_real; if(line_stream.fail() == false) { T val_real = T(0); ss.clear(); ss.str(token_real); ss >> val_real; if(ss.fail() == false) { final_val_real = val_real; } else { val_real = T(0); const bool success = diskio::convert_naninf( val_real, token_real ); if(success == true) { final_val_real = val_real; } } } line_stream >> token_imag; if(line_stream.fail() == false) { T val_imag = T(0); ss.clear(); ss.str(token_imag); ss >> val_imag; if(ss.fail() == false) { final_val_imag = val_imag; } else { val_imag = T(0); const bool success = diskio::convert_naninf( val_imag, token_imag ); if(success == true) { final_val_imag = val_imag; } } } if( (final_val_real != T(0)) || (final_val_imag != T(0)) ) { if(weird_format == false) { access::rw(x.row_indices[pos]) = line_row; access::rw(x.values[pos]) = std::complex(final_val_real, final_val_imag); ++access::rw(x.col_ptrs[line_col + 1]); ++pos; } else { x.at(line_row,line_col) = std::complex(final_val_real, final_val_imag); } } } if(weird_format == false) { for(uword c = 1; c <= f_n_cols; ++c) { access::rw(x.col_ptrs[c]) += x.col_ptrs[c - 1]; } } } return load_okay; } //! 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.c_str(), std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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(); x.set_size(f_n_rows, f_n_cols); x.mem_resize(f_n_nz); 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 in "; } else { load_okay = f.good(); } } else { load_okay = false; err_msg = "incorrect header in "; } 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::fstream f(tmp_name.c_str(), std::fstream::out); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = save_raw_ascii(x, f); f.flush(); f.close(); if(save_okay == true) { 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(); uword cell_width; // TODO: need sane values for complex numbers if( (is_float::value) || (is_double::value) ) { f.setf(ios::scientific); f.precision(12); cell_width = 20; } 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_float::value) || (is_double::value) ) { f.width(cell_width); } arma_ostream::print_elem(f, x.at(row,col,slice), false); } f.put('\n'); } } return f.good(); } //! 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.c_str(), std::fstream::binary); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_raw_binary(x, f); f.flush(); f.close(); if(save_okay == true) { 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(tmp_name.c_str()); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_arma_ascii(x, f); f.flush(); f.close(); if(save_okay == true) { 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 ios::fmtflags orig_flags = f.flags(); f << diskio::gen_txt_header(x) << '\n'; f << x.n_rows << ' ' << x.n_cols << ' ' << x.n_slices << '\n'; uword cell_width; // TODO: need sane values for complex numbers if( (is_float::value) || (is_double::value) ) { f.setf(ios::scientific); f.precision(12); cell_width = 20; } 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_float::value) || (is_double::value) ) { f.width(cell_width); } arma_ostream::print_elem(f, x.at(row,col,slice), false); } f.put('\n'); } } const bool save_okay = f.good(); f.flags(orig_flags); 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.c_str(), std::fstream::binary); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_arma_binary(x, f); f.flush(); f.close(); if(save_okay == true) { 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 std::string& final_name) { arma_extra_debug_sigprint(); #if defined(ARMA_USE_HDF5) { #if !defined(ARMA_PRINT_HDF5_ERRORS) { // Disable annoying HDF5 error messages. arma_H5Eset_auto(H5E_DEFAULT, NULL, NULL); } #endif bool save_okay = false; const std::string tmp_name = diskio::gen_tmp_name(final_name); // Set up the file according to HDF5's preferences hid_t file = arma_H5Fcreate(tmp_name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); // 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 = arma_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, so we will // use that. hid_t dataset = arma_H5Dcreate(file, "dataset", datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT); herr_t status = arma_H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, x.mem); save_okay = (status >= 0); arma_H5Dclose(dataset); arma_H5Tclose(datatype); arma_H5Sclose(dataspace); arma_H5Fclose(file); if(save_okay == true) { save_okay = diskio::safe_rename(tmp_name, final_name); } return save_okay; } #else { arma_ignore(x); arma_ignore(final_name); arma_stop("Cube::save(): use of HDF5 needs to 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 == true) { if(tmp.is_empty() == false) { x.set_size(tmp.n_rows, tmp.n_cols, 1); 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 == true) { if(tmp.is_empty() == false) { x.set_size(tmp.n_rows, tmp.n_cols, 1); 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.c_str(), std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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(); arma_ignore(err_msg); 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); x.set_size(N / sizeof(eT), 1, 1); f.clear(); f.read( reinterpret_cast(x.memptr()), std::streamsize(N) ); 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(name.c_str()); bool load_okay = f.is_open(); if(load_okay == true) { 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)) { x.set_size(f_n_rows, f_n_cols, f_n_slices); 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 in "; } // 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.c_str(), std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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(); x.set_size(f_n_rows, f_n_cols, f_n_slices); 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 in "; } // 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 std::string& name, std::string& err_msg) { arma_extra_debug_sigprint(); #if defined(ARMA_USE_HDF5) { // These may be necessary to store the error handler (if we need to). herr_t (*old_func)(hid_t, void*); void *old_client_data; #if !defined(ARMA_PRINT_HDF5_ERRORS) { // Save old error handler. arma_H5Eget_auto(H5E_DEFAULT, &old_func, &old_client_data); // Disable annoying HDF5 error messages. arma_H5Eset_auto(H5E_DEFAULT, NULL, NULL); } #endif bool load_okay = false; hid_t fid = arma_H5Fopen(name.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". // So 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; searchNames.push_back("dataset"); searchNames.push_back("value"); hid_t dataset = hdf5_misc::search_hdf5_file(searchNames, fid, 3, false); if(dataset >= 0) { hid_t filespace = arma_H5Dget_space(dataset); // This must be <= 3 due to our search rules. const int ndims = arma_H5Sget_simple_extent_ndims(filespace); hsize_t dims[3]; const herr_t query_status = arma_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 in "; arma_H5Sclose(filespace); arma_H5Dclose(dataset); arma_H5Fclose(fid); #if !defined(ARMA_PRINT_HDF5_ERRORS) { // Restore HDF5 error handler. arma_H5Eset_auto(H5E_DEFAULT, old_func, old_client_data); } #endif 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 x.set_size(dims[2], dims[1], dims[0]); // Now we have to see what type is stored to figure out how to load it. hid_t datatype = arma_H5Dget_type(dataset); hid_t mat_type = hdf5_misc::get_hdf5_type(); // If these are the same type, it is simple. if(arma_H5Tequal(datatype, mat_type) > 0) { // Load directly; H5S_ALL used so that we load the entire dataset. hid_t read_status = arma_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. arma_H5Tclose(datatype); arma_H5Tclose(mat_type); arma_H5Sclose(filespace); } arma_H5Dclose(dataset); arma_H5Fclose(fid); if(load_okay == false) { err_msg = "unsupported or incorrect HDF5 data in "; } } else { err_msg = "cannot open file "; } #if !defined(ARMA_PRINT_HDF5_ERRORS) { // Restore HDF5 error handler. arma_H5Eset_auto(H5E_DEFAULT, old_func, old_client_data); } #endif return load_okay; } #else { arma_ignore(x); arma_ignore(name); arma_ignore(err_msg); arma_stop("Cube::load(): use of HDF5 needs to 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 defined(ARMA_USE_HDF5) // We're currently using the C bindings for the HDF5 library, which don't support C++ streams if( arma_H5Fis_hdf5(name.c_str()) ) { return load_hdf5_binary(x, name, err_msg); } #endif std::fstream f; f.open(name.c_str(), std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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(); static const std::string ARMA_CUB_TXT = "ARMA_CUB_TXT"; static const std::string ARMA_CUB_BIN = "ARMA_CUB_BIN"; static const std::string P6 = "P6"; podarray raw_header(uword(ARMA_CUB_TXT.length()) + 1); std::streampos pos = f.tellg(); f.read( raw_header.memptr(), std::streamsize(ARMA_CUB_TXT.length()) ); raw_header[uword(ARMA_CUB_TXT.length())] = '\0'; f.clear(); f.seekg(pos); const std::string header = raw_header.mem; if(ARMA_CUB_TXT == header.substr(0, ARMA_CUB_TXT.length())) { return load_arma_ascii(x, f, err_msg); } else if(ARMA_CUB_BIN == header.substr(0, ARMA_CUB_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 { const file_type ft = guess_file_type(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 in "; 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.c_str(), std::fstream::binary ); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_arma_binary(x, f); f.flush(); f.close(); if(save_okay == true) { 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.c_str(), std::fstream::binary ); bool load_okay = f.is_open(); if(load_okay == true) { 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; x.set_size(f_n_rows, f_n_cols); f.get(); for(uword i=0; i> f_n_rows; f >> f_n_cols; f >> f_n_slices; x.set_size(f_n_rows, f_n_cols, f_n_slices); 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.c_str(), std::fstream::binary ); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_std_string(x, f); f.flush(); f.close(); if(save_okay == true) { 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.c_str() ); bool load_okay = f.is_open(); if(load_okay == true) { 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() == true) && (load_okay == true) ) { 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 in "; } } ++f_n_rows; } if(load_okay == true) { f.clear(); f.seekg(0, ios::beg); //f.seekg(start); x.set_size(f_n_rows, f_n_cols); 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.c_str(), std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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 in "; 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.c_str(), std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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) ) { x.set_size(f_n_rows, f_n_cols, 3); 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 = "currently no code available to handle loading "; } if(f.good() == false) { load_okay = false; } } else { load_okay = false; err_msg = "unsupported header in "; } 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.c_str(), std::fstream::binary ); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_ppm_binary(x, f); f.flush(); f.close(); if(save_okay == true) { 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.c_str(), std::fstream::in | std::fstream::binary); bool load_okay = f.is_open(); if(load_okay == true) { 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); R.set_size(f_n_rows,f_n_cols); G.set_size(f_n_rows,f_n_cols); B.set_size(f_n_rows,f_n_cols); 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 = "currently no code available to handle loading "; } if(f.good() == false) { load_okay = false; } } else { load_okay = false; err_msg = "unsupported header in "; } 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.c_str(), std::fstream::binary ); bool save_okay = f.is_open(); if(save_okay == true) { save_okay = diskio::save_ppm_binary(x, f); f.flush(); f.close(); if(save_okay == true) { 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(); } //! @}