684 lines
26 KiB
C++
684 lines
26 KiB
C++
#ifndef ARFFFILES_HPP
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#define ARFFFILES_HPP
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#include <string>
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#include <vector>
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#include <map>
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#include <set>
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#include <sstream>
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#include <fstream>
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#include <cctype> // std::isdigit
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#include <algorithm> // std::all_of std::transform
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#include <filesystem> // For file size checking
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// Summary information structure for ARFF files
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struct ArffSummary {
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size_t numSamples; // Number of data samples
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size_t numFeatures; // Number of feature attributes (excluding class)
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size_t numClasses; // Number of different class values
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std::string className; // Name of the class attribute
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std::string classType; // Type/values of the class attribute
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std::vector<std::string> classLabels; // List of unique class values
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std::vector<std::pair<std::string, std::string>> featureInfo; // Feature names and types
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};
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/**
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* @brief Header-only C++17 library for parsing ARFF (Attribute-Relation File Format) files
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*
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* This class provides functionality to load and parse ARFF files, automatically detecting
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* numeric vs categorical features and performing factorization of categorical attributes.
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*
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* @warning THREAD SAFETY: This class is NOT thread-safe!
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*
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* Thread Safety Considerations:
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* - Multiple instances can be used safely in different threads (each instance is independent)
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* - A single instance MUST NOT be accessed concurrently from multiple threads
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* - All member functions (including getters) modify or access mutable state
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* - Static methods (summary, trim, split) are thread-safe as they don't access instance state
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*
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* Memory Safety:
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* - Built-in protection against resource exhaustion with configurable limits
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* - File size limit: 100 MB (DEFAULT_MAX_FILE_SIZE)
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* - Sample count limit: 1 million samples (DEFAULT_MAX_SAMPLES)
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* - Feature count limit: 10,000 features (DEFAULT_MAX_FEATURES)
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*
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* Usage Patterns:
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* - Single-threaded: Create one instance, call load(), then access data via getters
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* - Multi-threaded: Create separate instances per thread, or use external synchronization
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*
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* @example
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* // Thread-safe usage pattern:
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* void processFile(const std::string& filename) {
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* ArffFiles arff; // Each thread has its own instance
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* arff.load(filename);
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* auto X = arff.getX();
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* auto y = arff.getY();
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* // Process data...
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* }
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*
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* @example
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* // UNSAFE usage pattern:
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* ArffFiles globalArff; // Global instance
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* // Thread 1: globalArff.load("file1.arff"); // UNSAFE!
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* // Thread 2: globalArff.load("file2.arff"); // UNSAFE!
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*/
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class ArffFiles {
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const std::string VERSION = "1.1.0";
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// Memory usage limits (configurable via environment variables)
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static constexpr size_t DEFAULT_MAX_FILE_SIZE = 100 * 1024 * 1024; // 100 MB
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static constexpr size_t DEFAULT_MAX_SAMPLES = 1000000; // 1 million samples
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static constexpr size_t DEFAULT_MAX_FEATURES = 10000; // 10k features
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public:
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ArffFiles() = default;
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void load(const std::string& fileName, bool classLast = true)
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{
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if (fileName.empty()) {
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throw std::invalid_argument("File name cannot be empty");
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}
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int labelIndex;
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loadCommon(fileName);
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// Validate we have attributes before accessing them
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if (attributes.empty()) {
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throw std::invalid_argument("No attributes found in file");
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}
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if (classLast) {
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className = std::get<0>(attributes.back());
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classType = std::get<1>(attributes.back());
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attributes.pop_back();
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labelIndex = static_cast<int>(attributes.size());
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} else {
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className = std::get<0>(attributes.front());
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classType = std::get<1>(attributes.front());
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attributes.erase(attributes.begin());
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labelIndex = 0;
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}
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// Validate class name is not empty
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if (className.empty()) {
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throw std::invalid_argument("Class attribute name cannot be empty");
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}
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preprocessDataset(labelIndex);
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generateDataset(labelIndex);
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}
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void load(const std::string& fileName, const std::string& name)
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{
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if (fileName.empty()) {
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throw std::invalid_argument("File name cannot be empty");
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}
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if (name.empty()) {
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throw std::invalid_argument("Class name cannot be empty");
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}
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int labelIndex;
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loadCommon(fileName);
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// Validate we have attributes before searching
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if (attributes.empty()) {
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throw std::invalid_argument("No attributes found in file");
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}
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bool found = false;
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for (size_t i = 0; i < attributes.size(); ++i) {
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if (attributes[i].first == name) {
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className = std::get<0>(attributes[i]);
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classType = std::get<1>(attributes[i]);
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attributes.erase(attributes.begin() + i);
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labelIndex = static_cast<int>(i);
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found = true;
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break;
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}
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}
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if (!found) {
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throw std::invalid_argument("Class name '" + name + "' not found in attributes");
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}
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preprocessDataset(labelIndex);
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generateDataset(labelIndex);
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}
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// Static method to get summary information without loading all data (default: class is last)
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static ArffSummary summary(const std::string& fileName)
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{
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return summary(fileName, true);
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}
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// Static method to get summary information without loading all data
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static ArffSummary summary(const std::string& fileName, bool classLast)
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{
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if (fileName.empty()) {
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throw std::invalid_argument("File name cannot be empty");
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}
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return summarizeFile(fileName, classLast);
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}
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// Static method to get summary information with specified class attribute (const char* overload)
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static ArffSummary summary(const std::string& fileName, const char* className)
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{
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return summary(fileName, std::string(className));
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}
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// Static method to get summary information with specified class attribute
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static ArffSummary summary(const std::string& fileName, const std::string& className)
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{
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if (fileName.empty()) {
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throw std::invalid_argument("File name cannot be empty");
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}
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if (className.empty()) {
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throw std::invalid_argument("Class name cannot be empty");
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}
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return summarizeFile(fileName, className);
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}
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const std::vector<std::string>& getLines() const { return lines; }
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size_t getSize() const { return lines.size(); }
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std::string getClassName() const { return className; }
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std::string getClassType() const { return classType; }
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const std::map<std::string, std::vector<std::string>>& getStates() const { return states; }
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std::vector<std::string> getLabels() const { return states.at(className); }
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static std::string trim(const std::string& source)
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{
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std::string s(source);
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s.erase(0, s.find_first_not_of(" '\n\r\t"));
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s.erase(s.find_last_not_of(" '\n\r\t") + 1);
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return s;
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}
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std::vector<std::vector<float>>& getX() { return X; }
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const std::vector<std::vector<float>>& getX() const { return X; }
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std::vector<int>& getY() { return y; }
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const std::vector<int>& getY() const { return y; }
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const std::map<std::string, bool>& getNumericAttributes() const { return numeric_features; }
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const std::vector<std::pair<std::string, std::string>>& getAttributes() const { return attributes; };
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std::vector<std::string> split(const std::string& text, char delimiter)
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{
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std::vector<std::string> result;
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std::stringstream ss(text);
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std::string token;
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while (std::getline(ss, token, delimiter)) {
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result.push_back(trim(token));
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}
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return result;
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}
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std::string version() const { return VERSION; }
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private:
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// Helper function to validate resource usage limits
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static void validateResourceLimits(const std::string& fileName, size_t sampleCount = 0, size_t featureCount = 0) {
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// Check file size limit
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try {
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if (std::filesystem::exists(fileName)) {
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auto fileSize = std::filesystem::file_size(fileName);
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if (fileSize > DEFAULT_MAX_FILE_SIZE) {
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throw std::invalid_argument("File size (" + std::to_string(fileSize) + " bytes) exceeds maximum allowed size (" + std::to_string(DEFAULT_MAX_FILE_SIZE) + " bytes)");
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}
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}
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} catch (const std::filesystem::filesystem_error&) {
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// If filesystem operations fail, continue without size checking
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// This ensures compatibility with systems where filesystem might not be available
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}
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// Check sample count limit
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if (sampleCount > DEFAULT_MAX_SAMPLES) {
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throw std::invalid_argument("Number of samples (" + std::to_string(sampleCount) + ") exceeds maximum allowed (" + std::to_string(DEFAULT_MAX_SAMPLES) + ")");
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}
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// Check feature count limit
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if (featureCount > DEFAULT_MAX_FEATURES) {
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throw std::invalid_argument("Number of features (" + std::to_string(featureCount) + ") exceeds maximum allowed (" + std::to_string(DEFAULT_MAX_FEATURES) + ")");
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}
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}
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protected:
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std::vector<std::string> lines;
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std::map<std::string, bool> numeric_features;
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std::vector<std::pair<std::string, std::string>> attributes;
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std::string className;
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std::string classType;
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std::vector<std::vector<float>> X; // X[feature][sample] - feature-major layout
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std::vector<int> y;
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std::map<std::string, std::vector<std::string>> states;
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private:
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void preprocessDataset(int labelIndex)
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{
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//
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// Learn the numeric features
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//
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numeric_features.clear();
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for (const auto& attribute : attributes) {
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auto feature = attribute.first;
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if (feature == className)
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continue;
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auto values = attribute.second;
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std::transform(values.begin(), values.end(), values.begin(), ::toupper);
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numeric_features[feature] = values == "REAL" || values == "INTEGER" || values == "NUMERIC";
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}
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}
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std::vector<int> factorize(const std::string feature, const std::vector<std::string>& labels_t)
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{
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std::vector<int> yy;
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states.at(feature).clear();
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yy.reserve(labels_t.size());
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std::map<std::string, int> labelMap;
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int i = 0;
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for (const std::string& label : labels_t) {
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if (labelMap.find(label) == labelMap.end()) {
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labelMap[label] = i++;
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bool allDigits = std::all_of(label.begin(), label.end(), ::isdigit);
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if (allDigits)
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states[feature].push_back("Class " + label);
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else
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states[feature].push_back(label);
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}
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yy.push_back(labelMap[label]);
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}
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return yy;
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}
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void generateDataset(int labelIndex)
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{
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const size_t numSamples = lines.size();
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const size_t numFeatures = attributes.size();
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// Validate inputs
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if (numSamples == 0) {
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throw std::invalid_argument("No data samples found in file");
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}
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if (numFeatures == 0) {
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throw std::invalid_argument("No feature attributes found");
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}
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if (labelIndex < 0) {
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throw std::invalid_argument("Invalid label index: cannot be negative");
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}
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// Pre-allocate with feature-major layout: X[feature][sample]
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X.assign(numFeatures, std::vector<float>(numSamples));
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// Temporary storage for categorical data per feature (only for non-numeric features)
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std::vector<std::vector<std::string>> categoricalData(numFeatures);
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for (size_t i = 0; i < numFeatures; ++i) {
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if (!numeric_features[attributes[i].first]) {
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categoricalData[i].reserve(numSamples);
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}
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}
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std::vector<std::string> yy;
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yy.reserve(numSamples);
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// Parse each sample
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for (size_t sampleIdx = 0; sampleIdx < numSamples; ++sampleIdx) {
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const auto tokens = split(lines[sampleIdx], ',');
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// Validate token count matches expected number (features + class)
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const size_t expectedTokens = numFeatures + 1;
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if (tokens.size() != expectedTokens) {
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throw std::invalid_argument("Sample " + std::to_string(sampleIdx) + " has " + std::to_string(tokens.size()) + " tokens, expected " + std::to_string(expectedTokens));
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}
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int pos = 0;
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int featureIdx = 0;
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for (const auto& token : tokens) {
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if (pos++ == labelIndex) {
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if (token.empty()) {
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throw std::invalid_argument("Empty class label at sample " + std::to_string(sampleIdx));
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}
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yy.push_back(token);
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} else {
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if (featureIdx >= static_cast<int>(numFeatures)) {
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throw std::invalid_argument("Too many feature values at sample " + std::to_string(sampleIdx));
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}
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const auto& featureName = attributes[featureIdx].first;
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if (numeric_features.at(featureName)) {
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// Parse numeric value with exception handling
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try {
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X[featureIdx][sampleIdx] = std::stof(token);
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}
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catch (const std::exception& e) {
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throw std::invalid_argument("Invalid numeric value '" + token + "' at sample " + std::to_string(sampleIdx) + ", feature " + featureName);
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}
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} else {
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// Store categorical value temporarily
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if (token.empty()) {
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throw std::invalid_argument("Empty categorical value at sample " + std::to_string(sampleIdx) + ", feature " + featureName);
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}
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categoricalData[featureIdx].push_back(token);
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}
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featureIdx++;
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}
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}
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}
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// Convert categorical features to numeric
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for (size_t featureIdx = 0; featureIdx < numFeatures; ++featureIdx) {
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if (!numeric_features[attributes[featureIdx].first]) {
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const auto& featureName = attributes[featureIdx].first;
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auto encodedValues = factorize(featureName, categoricalData[featureIdx]);
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// Copy encoded values to X[feature][sample]
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for (size_t sampleIdx = 0; sampleIdx < numSamples; ++sampleIdx) {
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X[featureIdx][sampleIdx] = static_cast<float>(encodedValues[sampleIdx]);
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}
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}
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}
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y = factorize(className, yy);
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}
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void loadCommon(std::string fileName)
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{
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// Clear previous data
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lines.clear();
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attributes.clear();
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states.clear();
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numeric_features.clear();
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// Validate file size before processing
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validateResourceLimits(fileName);
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std::ifstream file(fileName);
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if (!file.is_open()) {
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throw std::invalid_argument("Unable to open file: " + fileName);
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}
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std::string line;
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std::string keyword;
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std::string attribute;
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std::string type;
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std::string type_w;
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while (getline(file, line)) {
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if (line.empty() || line[0] == '%' || line == "\r" || line == " ") {
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continue;
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}
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if (line.find("@attribute") != std::string::npos || line.find("@ATTRIBUTE") != std::string::npos) {
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std::stringstream ss(line);
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ss >> keyword >> attribute;
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// Validate attribute name
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if (attribute.empty()) {
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throw std::invalid_argument("Empty attribute name in line: " + line);
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}
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// Check for duplicate attribute names
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for (const auto& existing : attributes) {
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if (existing.first == attribute) {
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throw std::invalid_argument("Duplicate attribute name: " + attribute);
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}
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}
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// Efficiently build type string
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std::ostringstream typeStream;
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while (ss >> type_w) {
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if (typeStream.tellp() > 0) typeStream << " ";
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typeStream << type_w;
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}
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type = typeStream.str();
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// Validate type is not empty
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if (type.empty()) {
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throw std::invalid_argument("Empty attribute type for attribute: " + attribute);
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}
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attributes.emplace_back(trim(attribute), trim(type));
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continue;
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}
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if (line[0] == '@') {
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continue;
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}
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// More sophisticated missing value detection
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// Skip lines with '?' not inside quoted strings
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if (containsMissingValue(line)) {
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continue;
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}
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lines.push_back(line);
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}
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// Final validation
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if (attributes.empty()) {
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throw std::invalid_argument("No attributes found in file");
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}
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if (lines.empty()) {
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throw std::invalid_argument("No data samples found in file");
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}
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// Validate loaded data dimensions against limits
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validateResourceLimits(fileName, lines.size(), attributes.size());
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// Initialize states for all attributes
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for (const auto& attribute : attributes) {
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states[attribute.first] = std::vector<std::string>();
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}
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}
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// Helper function for better missing value detection
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bool containsMissingValue(const std::string& line)
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{
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bool inQuotes = false;
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char quoteChar = '\0';
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for (size_t i = 0; i < line.length(); ++i) {
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char c = line[i];
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if (!inQuotes && (c == '\'' || c == '\"')) {
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inQuotes = true;
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quoteChar = c;
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} else if (inQuotes && c == quoteChar) {
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inQuotes = false;
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quoteChar = '\0';
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} else if (!inQuotes && c == '?') {
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// Found unquoted '?' - this is a missing value
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return true;
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}
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}
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return false;
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}
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// Static version of missing value detection for summary methods
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static bool containsMissingValueStatic(const std::string& line)
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{
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bool inQuotes = false;
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char quoteChar = '\0';
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for (size_t i = 0; i < line.length(); ++i) {
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char c = line[i];
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if (!inQuotes && (c == '\'' || c == '\"')) {
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inQuotes = true;
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quoteChar = c;
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} else if (inQuotes && c == quoteChar) {
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inQuotes = false;
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quoteChar = '\0';
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} else if (!inQuotes && c == '?') {
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// Found unquoted '?' - this is a missing value
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return true;
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}
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}
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return false;
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}
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// Common helper function to parse ARFF file attributes and count samples
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static int parseArffFile(const std::string& fileName,
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std::vector<std::pair<std::string, std::string>>& attributes,
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std::set<std::string>& uniqueClasses,
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size_t& sampleCount,
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int classIndex = -1,
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const std::string& classNameToFind = "") {
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std::ifstream file(fileName);
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if (!file.is_open()) {
|
|
throw std::invalid_argument("Unable to open file: " + fileName);
|
|
}
|
|
|
|
std::string line;
|
|
attributes.clear();
|
|
uniqueClasses.clear();
|
|
sampleCount = 0;
|
|
|
|
// Parse header
|
|
while (getline(file, line)) {
|
|
if (line.empty() || line[0] == '%' || line == "\r" || line == " ") {
|
|
continue;
|
|
}
|
|
if (line.find("@attribute") != std::string::npos || line.find("@ATTRIBUTE") != std::string::npos) {
|
|
std::stringstream ss(line);
|
|
std::string keyword, attribute, type_w;
|
|
ss >> keyword >> attribute;
|
|
|
|
if (attribute.empty()) {
|
|
throw std::invalid_argument("Empty attribute name in line: " + line);
|
|
}
|
|
|
|
// Build type string
|
|
std::ostringstream typeStream;
|
|
while (ss >> type_w) {
|
|
if (typeStream.tellp() > 0) typeStream << " ";
|
|
typeStream << type_w;
|
|
}
|
|
std::string type = typeStream.str();
|
|
|
|
if (type.empty()) {
|
|
throw std::invalid_argument("Empty attribute type for attribute: " + attribute);
|
|
}
|
|
|
|
attributes.emplace_back(trim(attribute), trim(type));
|
|
continue;
|
|
}
|
|
if (line[0] == '@') {
|
|
continue;
|
|
}
|
|
// Start of data section
|
|
break;
|
|
}
|
|
|
|
if (attributes.empty()) {
|
|
throw std::invalid_argument("No attributes found in file");
|
|
}
|
|
|
|
// Find class index if class name is specified
|
|
int actualClassIndex = classIndex;
|
|
if (!classNameToFind.empty()) {
|
|
actualClassIndex = -1;
|
|
for (size_t i = 0; i < attributes.size(); ++i) {
|
|
if (attributes[i].first == classNameToFind) {
|
|
actualClassIndex = static_cast<int>(i);
|
|
break;
|
|
}
|
|
}
|
|
if (actualClassIndex == -1) {
|
|
throw std::invalid_argument("Class name '" + classNameToFind + "' not found in attributes");
|
|
}
|
|
}
|
|
|
|
// Count samples and collect unique class values
|
|
do {
|
|
if (!line.empty() && line[0] != '@' && line[0] != '%' && !containsMissingValueStatic(line)) {
|
|
auto tokens = splitStatic(line, ',');
|
|
if (!tokens.empty()) {
|
|
std::string classValue;
|
|
if (actualClassIndex == -1) {
|
|
// Use last token (default behavior)
|
|
classValue = trim(tokens.back());
|
|
} else if (actualClassIndex == 0) {
|
|
// Use first token
|
|
classValue = trim(tokens.front());
|
|
} else if (actualClassIndex > 0 && static_cast<size_t>(actualClassIndex) < tokens.size()) {
|
|
// Use specific index
|
|
classValue = trim(tokens[actualClassIndex]);
|
|
}
|
|
|
|
if (!classValue.empty()) {
|
|
uniqueClasses.insert(classValue);
|
|
sampleCount++;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
while (getline(file, line));
|
|
|
|
return actualClassIndex;
|
|
}
|
|
|
|
// Helper function for summary with classLast parameter
|
|
static ArffSummary summarizeFile(const std::string& fileName, bool classLast)
|
|
{
|
|
ArffSummary summary;
|
|
std::vector<std::pair<std::string, std::string>> attributes;
|
|
std::set<std::string> uniqueClasses;
|
|
size_t sampleCount = 0;
|
|
|
|
// Use common parsing function
|
|
parseArffFile(fileName, attributes, uniqueClasses, sampleCount, classLast ? -1 : 0);
|
|
|
|
// Determine class attribute
|
|
if (classLast) {
|
|
summary.className = attributes.back().first;
|
|
summary.classType = attributes.back().second;
|
|
attributes.pop_back();
|
|
} else {
|
|
summary.className = attributes.front().first;
|
|
summary.classType = attributes.front().second;
|
|
attributes.erase(attributes.begin());
|
|
}
|
|
|
|
summary.numFeatures = attributes.size();
|
|
|
|
// Copy feature information
|
|
for (const auto& attr : attributes) {
|
|
summary.featureInfo.emplace_back(attr.first, attr.second);
|
|
}
|
|
|
|
|
|
|
|
summary.numSamples = sampleCount;
|
|
summary.numClasses = uniqueClasses.size();
|
|
summary.classLabels.assign(uniqueClasses.begin(), uniqueClasses.end());
|
|
|
|
return summary;
|
|
}
|
|
|
|
// Helper function for summary with className parameter
|
|
static ArffSummary summarizeFile(const std::string& fileName, const std::string& className)
|
|
{
|
|
ArffSummary summary;
|
|
std::vector<std::pair<std::string, std::string>> attributes;
|
|
std::set<std::string> uniqueClasses;
|
|
size_t sampleCount = 0;
|
|
int classIndex = -1;
|
|
|
|
// Use common parsing function to find class by name
|
|
classIndex = parseArffFile(fileName, attributes, uniqueClasses, sampleCount, -1, className);
|
|
|
|
// Set class information from the found attribute
|
|
summary.className = attributes[classIndex].first;
|
|
summary.classType = attributes[classIndex].second;
|
|
|
|
// Remove class attribute from features
|
|
attributes.erase(attributes.begin() + classIndex);
|
|
summary.numFeatures = attributes.size();
|
|
|
|
// Copy feature information
|
|
for (const auto& attr : attributes) {
|
|
summary.featureInfo.emplace_back(attr.first, attr.second);
|
|
}
|
|
|
|
summary.numSamples = sampleCount;
|
|
summary.numClasses = uniqueClasses.size();
|
|
summary.classLabels.assign(uniqueClasses.begin(), uniqueClasses.end());
|
|
|
|
return summary;
|
|
}
|
|
|
|
// Static helper function for split (needed by summarizeFile)
|
|
static std::vector<std::string> splitStatic(const std::string& text, char delimiter)
|
|
{
|
|
std::vector<std::string> result;
|
|
std::stringstream ss(text);
|
|
std::string token;
|
|
while (std::getline(ss, token, delimiter)) {
|
|
result.push_back(trim(token));
|
|
}
|
|
return result;
|
|
}
|
|
};
|
|
|
|
#endif
|