Add data::Load() and data::Save() methods to wrap Armadillo functionality.
Sadly we can't seem to get away from that.
This commit is contained in:
Ryan Curtin
@@ -0,0 +1,30 @@
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cmake_minimum_required(VERSION 2.8)
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# Define the files that we need to compile.
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# Anything not in this list will not be compiled into MLPACK.
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set(SOURCES
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load.hpp
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load_impl.hpp
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save.hpp
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save_impl.hpp
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)
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# add directory name to sources
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set(DIR_SRCS)
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foreach(file ${SOURCES})
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set(DIR_SRCS ${DIR_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/${file})
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endforeach()
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# Append sources (with directory name) to list of all MLPACK sources (used at
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# parent scope).
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set(MLPACK_SRCS ${MLPACK_SRCS} ${DIR_SRCS} PARENT_SCOPE)
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# test executable
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add_executable(load_save_test
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load_save_test.cpp
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)
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# link dependencies of test executable
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target_link_libraries(load_save_test
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mlpack
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boost_unit_test_framework
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)
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@@ -0,0 +1,54 @@
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/**
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* @file load.hpp
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* @author Ryan Curtin
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*
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* Load an Armadillo matrix from file. This is necessary because Armadillo does
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* not transpose matrices on input, and it allows us to give better error
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* output.
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*/
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#ifndef __MLPACK_CORE_DATA_LOAD_HPP
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#define __MLPACK_CORE_DATA_LOAD_HPP
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#include <mlpack/core/io/log.hpp>
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#include <mlpack/core/arma_extend/arma_extend.h> // Includes Armadillo.
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#include <string>
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namespace mlpack {
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namespace data /** Functions to load and save matrices. */ {
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/**
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* Loads a matrix from file, guessing the filetype from the extension. This
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* will transpose the matrix at load time. If the filetype cannot be
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* determined, an error will be given.
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*
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* The supported types of files are the same as found in Armadillo:
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*
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* - CSV (csv_ascii), denoted by .csv, or optionally .txt
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* - ASCII (raw_ascii), denoted by .txt
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* - Armadillo ASCII (arma_ascii), also denoted by .txt
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* - PGM (pgm_binary), denoted by .pgm
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* - PPM (ppm_binary), denoted by .ppm
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* - Raw binary (raw_binary), denoted by .bin
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* - Armadillo binary (arma_binary), denoted by .bin
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*
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* If the file extension is not one of those types, an error will be given.
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* This is preferable to Armadillo's default behavior of loading an unknown
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* filetype as raw_binary, which can have very confusing effects.
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*
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* @param filename Name of file to load.
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* @param matrix Matrix to load contents of file into.
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* @param fatal If an error should be reported as fatal (default false).
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* @return Boolean value indicating success or failure of load.
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*/
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template<typename eT>
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bool Load(const std::string& filename,
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arma::Mat<eT>& matrix,
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bool fatal = false);
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}; // namespace data
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}; // namespace mlpack
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// Include implementation.
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#include "load_impl.hpp"
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#endif
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@@ -0,0 +1,173 @@
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/**
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* @file load_impl.hpp
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* @author Ryan Curtin
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*
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* Implementation of templatized load() function defined in load.hpp.
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*/
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#ifndef __MLPACK_CORE_DATA_LOAD_HPP
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#error "Don't include this file directly; include mlpack/core/data/load.hpp."
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#endif
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#ifndef __MLPACK_CORE_DATA_LOAD_IMPL_HPP
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#define __MLPACK_CORE_DATA_LOAD_IMPL_HPP
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namespace mlpack {
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namespace data {
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template<typename eT>
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bool Load(const std::string& filename, arma::Mat<eT>& matrix, bool fatal)
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{
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// First we will try to discriminate by file extension.
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size_t ext = filename.rfind('.');
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if (ext == std::string::npos)
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{
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if (fatal)
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Log::Fatal << "Cannot determine type of file '" << filename << "'; "
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<< "no extension is present." << std::endl;
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else
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Log::Warn << "Cannot determine type of file '" << filename << "'; "
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<< "no extension is present. Load failed." << std::endl;
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return false;
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}
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std::string extension = filename.substr(ext + 1);
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// Catch nonexistent files by opening the stream ourselves.
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std::fstream stream;
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stream.open(filename.c_str(), std::fstream::in);
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if (!stream.is_open())
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{
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if (fatal)
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Log::Fatal << "Cannot open file '" << filename << "'. " << std::endl;
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else
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Log::Warn << "Cannot open file '" << filename << "'; load failed."
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<< std::endl;
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return false;
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}
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bool unknown_type = false;
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arma::file_type load_type;
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std::string string_type;
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if (extension == "csv")
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{
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load_type = arma::csv_ascii;
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string_type = "CSV data";
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}
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else if (extension == "txt")
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{
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// This could be raw ASCII or Armadillo ASCII (ASCII with size header).
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// We'll let Armadillo do its guessing (although we have to check if it is
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// arma_ascii ourselves) and see what we come up with.
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// This is taken from load_auto_detect() in diskio_meat.hpp
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const std::string ARMA_MAT_TXT = "ARMA_MAT_TXT";
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char* raw_header = new char[ARMA_MAT_TXT.length() + 1];
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std::streampos pos = stream.tellg();
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stream.read(raw_header, std::streamsize(ARMA_MAT_TXT.length()));
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raw_header[ARMA_MAT_TXT.length()] = '\0';
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stream.clear();
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stream.seekg(pos); // Reset stream position after peeking.
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if (std::string(raw_header) == ARMA_MAT_TXT)
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{
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load_type = arma::arma_ascii;
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string_type = "Armadillo ASCII formatted data";
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}
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else // It's not arma_ascii. Now we let Armadillo guess.
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{
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load_type = arma::diskio::guess_file_type(stream);
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if (load_type == arma::raw_ascii) // Raw ASCII (space-separated).
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string_type = "raw ASCII formatted data";
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else if (load_type == arma::csv_ascii) // CSV can be .txt too.
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string_type = "CSV data";
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else // Unknown .txt... we will throw an error.
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unknown_type = true;
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}
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delete[] raw_header;
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}
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else if (extension == "bin")
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{
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// This could be raw binary or Armadillo binary (binary with header). We
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// will check to see if it is Armadillo binary.
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const std::string ARMA_MAT_BIN = "ARMA_MAT_BIN";
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char *raw_header = new char[ARMA_MAT_BIN.length() + 1];
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std::streampos pos = stream.tellg();
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stream.read(raw_header, std::streamsize(ARMA_MAT_BIN.length()));
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raw_header[ARMA_MAT_BIN.length()] = '\0';
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stream.clear();
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stream.seekg(pos); // Reset stream position after peeking.
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if (std::string(raw_header) == ARMA_MAT_BIN)
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{
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string_type = "Armadillo binary formatted data";
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load_type = arma::arma_binary;
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}
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else // We can only assume it's raw binary.
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{
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string_type = "raw binary formatted data";
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load_type = arma::raw_binary;
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}
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delete[] raw_header;
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}
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else if (extension == "pgm")
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{
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load_type = arma::pgm_binary;
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string_type = "PGM data";
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}
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else // Unknown extension...
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{
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unknown_type = true;
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}
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// Provide error if we don't know the type.
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if (unknown_type)
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{
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if (fatal)
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Log::Fatal << "Unable to detect type of '" << filename << "'; "
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<< "incorrect extension?" << std::endl;
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else
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Log::Warn << "Unable to detect type of '" << filename << "'; load failed."
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<< " Incorrect extension?" << std::endl;
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return false;
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}
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// Try to load the file; but if it's raw_binary, it could be a problem.
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if (load_type == arma::raw_binary)
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Log::Warn << "Loading '" << filename << "' as " << string_type << "; "
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<< "but this may not be the actual filetype!" << std::endl;
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else
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Log::Info << "Loading '" << filename << "' as " << string_type << "."
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<< std::endl;
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bool success = matrix.load(stream, load_type);
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if (!success)
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{
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if (fatal)
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Log::Fatal << "Loading from '" << filename << "' failed." << std::endl;
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else
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Log::Warn << "Loading from '" << filename << "' failed." << std::endl;
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}
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// Now transpose the matrix.
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matrix = trans(matrix);
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// Finally, return the success indicator.
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return success;
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}
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}; // namespace data
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}; // namespace mlpack
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#endif
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@@ -0,0 +1,311 @@
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/**
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* @file load_save_test.cpp
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* @author Ryan Curtin
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*
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* Tests for data::Load() and data::Save().
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*/
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#include <sstream>
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#include "load.hpp"
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#include "save.hpp"
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#define BOOST_TEST_MODULE LoadSaveTest
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#include <boost/test/unit_test.hpp>
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using namespace mlpack;
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/**
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* Make sure failure occurs when no extension given.
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*/
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BOOST_AUTO_TEST_CASE(NoExtensionLoad) {
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arma::mat out;
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BOOST_REQUIRE(data::Load("noextension", out) == false);
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}
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/**
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* Make sure failure occurs when no extension given.
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*/
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BOOST_AUTO_TEST_CASE(NoExtensionSave) {
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arma::mat out;
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BOOST_REQUIRE(data::Save("noextension", out) == false);
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}
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/**
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* Make sure load fails if the file does not exist.
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*/
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BOOST_AUTO_TEST_CASE(NotExistLoad) {
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arma::mat out;
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BOOST_REQUIRE(data::Load("nonexistentfile_______________.csv", out) == false);
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}
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/**
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* Make sure a CSV is loaded correctly.
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*/
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BOOST_AUTO_TEST_CASE(LoadCSVTest) {
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std::fstream f;
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f.open("test_file.csv", std::fstream::out);
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f << "1, 2, 3, 4" << std::endl;
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f << "5, 6, 7, 8" << std::endl;
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f.close();
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arma::mat test;
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BOOST_REQUIRE(data::Load("test_file.csv", test) == true);
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BOOST_REQUIRE_EQUAL(test.n_rows, 4);
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BOOST_REQUIRE_EQUAL(test.n_cols, 2);
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for (int i = 0; i < 8; i++)
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BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
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// Remove the file.
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remove("test_file.csv");
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}
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/**
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* Make sure a CSV is saved correctly.
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*/
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BOOST_AUTO_TEST_CASE(SaveCSVTest) {
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arma::mat test = "1 5;"
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"2 6;"
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"3 7;"
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"4 8;";
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BOOST_REQUIRE(data::Save("test_file.csv", test) == true);
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// Load it in and make sure it is the same.
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BOOST_REQUIRE(data::Load("test_file.csv", test) == true);
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BOOST_REQUIRE_EQUAL(test.n_rows, 4);
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BOOST_REQUIRE_EQUAL(test.n_cols, 2);
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for (int i = 0; i < 8; i++)
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BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
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// Remove the file.
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remove("test_file.csv");
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}
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/**
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* Make sure arma_ascii is loaded correctly.
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*/
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BOOST_AUTO_TEST_CASE(LoadArmaASCIITest) {
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arma::mat test = "1 5;"
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"2 6;"
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"3 7;"
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"4 8;";
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arma::mat testTrans = trans(test);
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BOOST_REQUIRE(testTrans.save("test_file.txt", arma::arma_ascii));
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BOOST_REQUIRE(data::Load("test_file.txt", test) == true);
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BOOST_REQUIRE_EQUAL(test.n_rows, 4);
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BOOST_REQUIRE_EQUAL(test.n_cols, 2);
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for (int i = 0; i < 8; i++)
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BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
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// Remove the file.
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remove("test_file.txt");
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}
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/**
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* Make sure a CSV is saved correctly.
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*/
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BOOST_AUTO_TEST_CASE(SaveArmaASCIITest) {
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arma::mat test = "1 5;"
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"2 6;"
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"3 7;"
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"4 8;";
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BOOST_REQUIRE(data::Save("test_file.txt", test) == true);
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// Load it in and make sure it is the same.
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BOOST_REQUIRE(data::Load("test_file.txt", test) == true);
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BOOST_REQUIRE_EQUAL(test.n_rows, 4);
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BOOST_REQUIRE_EQUAL(test.n_cols, 2);
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for (int i = 0; i < 8; i++)
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BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
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// Remove the file.
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remove("test_file.txt");
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}
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/**
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* Make sure raw_ascii is loaded correctly.
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*/
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BOOST_AUTO_TEST_CASE(LoadRawASCIITest) {
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std::fstream f;
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f.open("test_file.txt", std::fstream::out);
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f << "1 2 3 4" << std::endl;
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f << "5 6 7 8" << std::endl;
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f.close();
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arma::mat test;
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BOOST_REQUIRE(data::Load("test_file.txt", test) == true);
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BOOST_REQUIRE_EQUAL(test.n_rows, 4);
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BOOST_REQUIRE_EQUAL(test.n_cols, 2);
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for (int i = 0; i < 8; i++)
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BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
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// Remove the file.
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remove("test_file.txt");
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}
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/**
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* Make sure CSV is loaded correctly as .txt.
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*/
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BOOST_AUTO_TEST_CASE(LoadCSVTxtTest) {
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std::fstream f;
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f.open("test_file.txt", std::fstream::out);
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f << "1, 2, 3, 4" << std::endl;
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f << "5, 6, 7, 8" << std::endl;
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f.close();
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arma::mat test;
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BOOST_REQUIRE(data::Load("test_file.txt", test) == true);
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BOOST_REQUIRE_EQUAL(test.n_rows, 4);
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BOOST_REQUIRE_EQUAL(test.n_cols, 2);
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for (int i = 0; i < 8; i++)
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BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
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// Remove the file.
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remove("test_file.txt");
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}
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/**
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* Make sure arma_binary is loaded correctly.
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*/
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BOOST_AUTO_TEST_CASE(LoadArmaBinaryTest) {
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arma::mat test = "1 5;"
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"2 6;"
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"3 7;"
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"4 8;";
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arma::mat testTrans = trans(test);
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BOOST_REQUIRE(testTrans.quiet_save("test_file.bin", arma::arma_binary)
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== true);
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// Now reload through our interface.
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BOOST_REQUIRE(data::Load("test_file.bin", test) == true);
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BOOST_REQUIRE_EQUAL(test.n_rows, 4);
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BOOST_REQUIRE_EQUAL(test.n_cols, 2);
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for (int i = 0; i < 8; i++)
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BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
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// Remove the file.
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remove("test_file.bin");
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}
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/**
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* Make sure arma_binary is saved correctly.
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*/
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BOOST_AUTO_TEST_CASE(SaveArmaBinaryTest) {
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arma::mat test = "1 5;"
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"2 6;"
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"3 7;"
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"4 8;";
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BOOST_REQUIRE(data::Save("test_file.bin", test) == true);
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BOOST_REQUIRE(data::Load("test_file.bin", test) == true);
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BOOST_REQUIRE_EQUAL(test.n_rows, 4);
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BOOST_REQUIRE_EQUAL(test.n_cols, 2);
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for (int i = 0; i < 8; i++)
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BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
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// Remove the file.
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remove("test_file.bin");
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}
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/**
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* Make sure raw_binary is loaded correctly.
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*/
|
||||
BOOST_AUTO_TEST_CASE(LoadRawBinaryTest) {
|
||||
arma::mat test = "1 2;"
|
||||
"3 4;"
|
||||
"5 6;"
|
||||
"7 8;";
|
||||
|
||||
arma::mat testTrans = trans(test);
|
||||
BOOST_REQUIRE(testTrans.quiet_save("test_file.bin", arma::raw_binary)
|
||||
== true);
|
||||
|
||||
// Now reload through our interface.
|
||||
BOOST_REQUIRE(data::Load("test_file.bin", test) == true);
|
||||
|
||||
BOOST_REQUIRE_EQUAL(test.n_rows, 1);
|
||||
BOOST_REQUIRE_EQUAL(test.n_cols, 8);
|
||||
|
||||
for (int i = 0; i < 8; i++)
|
||||
BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
|
||||
|
||||
// Remove the file.
|
||||
remove("test_file.bin");
|
||||
}
|
||||
|
||||
/**
|
||||
* Make sure load as PGM is successful.
|
||||
*/
|
||||
BOOST_AUTO_TEST_CASE(LoadPGMBinaryTest) {
|
||||
arma::mat test = "1 5;"
|
||||
"2 6;"
|
||||
"3 7;"
|
||||
"4 8;";
|
||||
|
||||
arma::mat testTrans = trans(test);
|
||||
BOOST_REQUIRE(testTrans.quiet_save("test_file.pgm", arma::pgm_binary)
|
||||
== true);
|
||||
|
||||
// Now reload through our interface.
|
||||
BOOST_REQUIRE(data::Load("test_file.pgm", test) == true);
|
||||
|
||||
BOOST_REQUIRE_EQUAL(test.n_rows, 4);
|
||||
BOOST_REQUIRE_EQUAL(test.n_cols, 2);
|
||||
|
||||
for (int i = 0; i < 8; i++)
|
||||
BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
|
||||
|
||||
// Remove the file.
|
||||
remove("test_file.pgm");
|
||||
}
|
||||
|
||||
/**
|
||||
* Make sure save as PGM is successful.
|
||||
*/
|
||||
BOOST_AUTO_TEST_CASE(SavePGMBinaryTest) {
|
||||
arma::mat test = "1 5;"
|
||||
"2 6;"
|
||||
"3 7;"
|
||||
"4 8;";
|
||||
|
||||
BOOST_REQUIRE(data::Save("test_file.pgm", test) == true);
|
||||
|
||||
// Now reload through our interface.
|
||||
BOOST_REQUIRE(data::Load("test_file.pgm", test) == true);
|
||||
|
||||
BOOST_REQUIRE_EQUAL(test.n_rows, 4);
|
||||
BOOST_REQUIRE_EQUAL(test.n_cols, 2);
|
||||
|
||||
for (int i = 0; i < 8; i++)
|
||||
BOOST_REQUIRE_CLOSE(test[i], (double) (i + 1), 1e-5);
|
||||
|
||||
// Remove the file.
|
||||
remove("test_file.pgm");
|
||||
}
|
||||
@@ -0,0 +1,52 @@
|
||||
/**
|
||||
* @file save.hpp
|
||||
* @author Ryan Curtin
|
||||
*
|
||||
* Save an Armadillo matrix to file. This is necessary because Armadillo does
|
||||
* not transpose matrices upon saving, and it allows us to give better error
|
||||
* output.
|
||||
*/
|
||||
#ifndef __MLPACK_CORE_DATA_SAVE_HPP
|
||||
#define __MLPACK_CORE_DATA_SAVE_HPP
|
||||
|
||||
#include <mlpack/core/io/log.hpp>
|
||||
#include <mlpack/core/arma_extend/arma_extend.h> // Includes Armadillo.
|
||||
#include <string>
|
||||
|
||||
namespace mlpack {
|
||||
namespace data /** Functions to load and save matrices. */ {
|
||||
|
||||
/**
|
||||
* Saves a matrix to file, guessing the filetype from the extension. This
|
||||
* will transpose the matrix at save time. If the filetype cannot be
|
||||
* determined, an error will be given.
|
||||
*
|
||||
* The supported types of files are the same as found in Armadillo:
|
||||
*
|
||||
* - CSV (csv_ascii), denoted by .csv, or optionally .txt
|
||||
* - ASCII (raw_ascii), denoted by .txt
|
||||
* - Armadillo ASCII (arma_ascii), also denoted by .txt
|
||||
* - PGM (pgm_binary), denoted by .pgm
|
||||
* - PPM (ppm_binary), denoted by .ppm
|
||||
* - Raw binary (raw_binary), denoted by .bin
|
||||
* - Armadillo binary (arma_binary), denoted by .bin
|
||||
*
|
||||
* If the file extension is not one of those types, an error will be given.
|
||||
*
|
||||
* @param filename Name of file to save to.
|
||||
* @param matrix Matrix to save into file.
|
||||
* @param fatal If an error should be reported as fatal (default false).
|
||||
* @return Boolean value indicating success or failure of save.
|
||||
*/
|
||||
template<typename eT>
|
||||
bool Save(const std::string& filename,
|
||||
const arma::Mat<eT>& matrix,
|
||||
bool fatal = false);
|
||||
|
||||
}; // namespace data
|
||||
}; // namespace mlpack
|
||||
|
||||
// Include implementation.
|
||||
#include "save_impl.hpp"
|
||||
|
||||
#endif
|
||||
@@ -0,0 +1,117 @@
|
||||
/**
|
||||
* @file save_impl.hpp
|
||||
* @author Ryan Curtin
|
||||
*
|
||||
* Implementation of save functionality.
|
||||
*/
|
||||
#ifndef __MLPACK_CORE_DATA_SAVE_HPP
|
||||
#error "Don't include this file directly; include mlpack/core/data/save.hpp."
|
||||
#endif
|
||||
|
||||
#ifndef __MLPACK_CORE_DATA_SAVE_IMPL_HPP
|
||||
#define __MLPACK_CORE_DATA_SAVE_IMPL_HPP
|
||||
|
||||
namespace mlpack {
|
||||
namespace data {
|
||||
|
||||
template<typename eT>
|
||||
bool Save(const std::string& filename, const arma::Mat<eT>& matrix, bool fatal)
|
||||
{
|
||||
// First we will try to discriminate by file extension.
|
||||
size_t ext = filename.rfind('.');
|
||||
if (ext == std::string::npos)
|
||||
{
|
||||
if (fatal)
|
||||
Log::Fatal << "No extension given with filename '" << filename << "'; "
|
||||
<< "type unknown. Save failed." << std::endl;
|
||||
else
|
||||
Log::Warn << "No extension given with filename '" << filename << "'; "
|
||||
<< "type unknown. Save failed." << std::endl;
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
// Get the actual extension.
|
||||
std::string extension = filename.substr(ext + 1);
|
||||
|
||||
// Catch errors opening the file.
|
||||
std::fstream stream;
|
||||
stream.open(filename.c_str(), std::fstream::out);
|
||||
|
||||
if (!stream.is_open())
|
||||
{
|
||||
if (fatal)
|
||||
Log::Fatal << "Cannot open file '" << filename << "' for writing. "
|
||||
<< "Save failed." << std::endl;
|
||||
else
|
||||
Log::Warn << "Cannot open file '" << filename << "' for writing; save "
|
||||
<< "failed." << std::endl;
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
bool unknown_type = false;
|
||||
arma::file_type save_type;
|
||||
std::string string_type;
|
||||
|
||||
if (extension == "csv")
|
||||
{
|
||||
save_type = arma::csv_ascii;
|
||||
string_type = "CSV data";
|
||||
}
|
||||
else if (extension == "txt")
|
||||
{
|
||||
save_type = arma::raw_ascii;
|
||||
string_type = "raw ASCII formatted data";
|
||||
}
|
||||
else if (extension == "bin")
|
||||
{
|
||||
save_type = arma::arma_binary;
|
||||
string_type = "Armadillo binary formatted data";
|
||||
}
|
||||
else if (extension == "pgm")
|
||||
{
|
||||
save_type = arma::pgm_binary;
|
||||
string_type = "PGM data";
|
||||
}
|
||||
else
|
||||
{
|
||||
unknown_type = true;
|
||||
}
|
||||
|
||||
// Provide error if we don't know the type.
|
||||
if (unknown_type)
|
||||
{
|
||||
if (fatal)
|
||||
Log::Fatal << "Unable to determine format to save to from filename '"
|
||||
<< filename << "'. Save failed." << std::endl;
|
||||
else
|
||||
Log::Warn << "Unable to determine format to save to from filename '"
|
||||
<< filename << "'. Save failed." << std::endl;
|
||||
}
|
||||
|
||||
// Try to save the file.
|
||||
Log::Info << "Saving " << string_type << " to '" << filename << "'."
|
||||
<< std::endl;
|
||||
|
||||
// Transpose the matrix.
|
||||
arma::Mat<eT> tmp = trans(matrix);
|
||||
|
||||
if (!tmp.quiet_save(stream, save_type))
|
||||
{
|
||||
if (fatal)
|
||||
Log::Fatal << "Save to '" << filename << "' failed." << std::endl;
|
||||
else
|
||||
Log::Warn << "Save to '" << filename << "' failed." << std::endl;
|
||||
|
||||
return false;
|
||||
}
|
||||
|
||||
// Finally return success.
|
||||
return true;
|
||||
}
|
||||
|
||||
}; // namespace data
|
||||
}; // namespace mlpack
|
||||
|
||||
#endif
|
||||
Reference in New Issue
Block a user