opatIO.h

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/* ***********************************************************************
//
//   Copyright (C) 2025 -- The 4D-STAR Collaboration
//   File Author: Emily Boudreaux
//   Last Modified: March 07, 2025
//
//   4DSSE is free software; you can use it and/or modify
//   it under the terms and restrictions the GNU General Library Public
//   License version 3 (GPLv3) as published by the Free Software Foundation.
//
//   4DSSE is distributed in the hope that it will be useful,
//   but WITHOUT ANY WARRANTY; without even the implied warranty of
//   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
//   See the GNU Library General Public License for more details.
//
//   You should have received a copy of the GNU Library General Public License
//   along with this software; if not, write to the Free Software
//   Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
// *********************************************************************** */

 
#ifndef OPATIO_H
#define OPATIO_H
 
#include <fstream>
#include <memory>
#include <string>
#include <sys/types.h>
#include <vector>
#include <utility>
#include <cstdint>
#include <unordered_map>
#include <limits>
 
#include "indexVector.h"
 
namespace opat {

#pragma pack(1)
struct Header {
    char magic[4];           
    uint16_t version;        
    uint32_t numTables;      
    uint32_t headerSize;     
    uint64_t indexOffset;    
    char creationDate[16];   
    char sourceInfo[64];     
    char comment[128];       
    uint16_t numIndex;       
    uint8_t hashPrecision;  
    char reserved[23];       

    friend std::ostream& operator<<(std::ostream& os, const Header& header);
 
    void print() const; 
};
#pragma pack()

#pragma pack(1)
struct CardHeader {
    char magic[4];           
    uint32_t numTables;      
    uint32_t headerSize;     
    uint64_t indexOffset;    
    uint64_t cardSize;       
    char comment[128];       
    char reserved[100];      

    friend std::ostream& operator<<(std::ostream& os, const CardHeader& header);
};
#pragma pack()

struct CardCatalogEntry {
    FloatIndexVector index;  
    uint64_t byteStart;      
    uint64_t byteEnd;        
    char sha256[32];         

    friend std::ostream& operator<<(std::ostream& os, const CardCatalogEntry& entry);
};

struct CardCatalog {
    std::unordered_map<FloatIndexVector, CardCatalogEntry> tableIndex; 

    friend std::ostream& operator<<(std::ostream& os, const CardCatalog& catalog);
};
 
#pragma pack(1)
struct TableIndexEntry {
    char tag[8];             
    uint64_t byteStart;      
    uint64_t byteEnd;        
    uint16_t numColumns;     
    uint16_t numRows;        
    char columnName[8];      
    char rowName[8];         
    uint64_t size;           
    char reserved[12];       

    friend std::ostream& operator<<(std::ostream& os, const TableIndexEntry& entry);
};
#pragma pack()

struct TableIndex {
    std::unordered_map<std::string, TableIndexEntry> tableIndex; 

    friend std::ostream& operator<<(std::ostream& os, const TableIndex& index);

    [[nodiscard]] const TableIndexEntry& get(const std::string& tag) const;

    const TableIndexEntry& operator[](const std::string& tag) const;
};

struct Slice {
    uint32_t start; 
    uint32_t end;   

    friend std::ostream& operator<<(std::ostream& os, const Slice& slice);
};
 

struct OPATTable {
    std::unique_ptr<double[]> rowValues; 
    std::unique_ptr<double[]> columnValues; 
    std::unique_ptr<double[]> data; 
 
    uint32_t N_R;   
    uint32_t N_C;   
    uint64_t m_vsize; 

    [[nodiscard]] std::pair<double, double> size() const { return std::make_pair(N_R, N_C); }

    [[nodiscard]] int vsize() const { return static_cast<int>(m_vsize); }

    const double& operator()() const;

    OPATTable operator()(uint32_t row, uint32_t column) const;

    double operator()(uint32_t row, uint32_t column, uint64_t zdepth) const;

    OPATTable operator()(const Slice& rowSlice, const Slice& colSlice) const;

    [[nodiscard]] OPATTable getData(uint32_t row, uint32_t column) const;

    [[nodiscard]] double getData(uint32_t row, uint32_t column, uint64_t zdepth) const;

    [[nodiscard]] OPATTable getRow(uint32_t row) const;

    [[nodiscard]] OPATTable getColumn(uint32_t column) const;

    [[nodiscard]] OPATTable getRowValues() const;

    [[nodiscard]] OPATTable getColumnValues() const;

    [[nodiscard]] const double* getRawData() const;

    [[nodiscard]] OPATTable slice(const Slice& rowSlice, const Slice& colSlice) const;

    [[nodiscard]] std::string ascii() const;

    void print() const;
 
    friend std::ostream& operator<<(std::ostream& os, const OPATTable& table);
};

struct DataCard {
    CardHeader header; 
    TableIndex tableIndex; 
    std::unordered_map<std::string, OPATTable> tableData; 

    friend std::ostream& operator<<(std::ostream& os, const DataCard& card);

    [[nodiscard]] const OPATTable& get(const std::string& tag) const;

    const OPATTable& operator[](const std::string& tag) const;

    const OPATTable& operator[](const char* tag) const;

    const OPATTable& operator[](std::string_view tag) const;

    [[nodiscard]] std::vector<std::string> getKeys() const;
};

struct Bounds {
    double min = std::numeric_limits<double>::max(); 
    double max = std::numeric_limits<double>::min(); 
    friend std::ostream& operator<<(std::ostream& os, const Bounds& bounds);
};

struct OPAT {
    Header header; 
    CardCatalog cardCatalog; 
    std::unordered_map<FloatIndexVector, DataCard> cards; 

    friend std::ostream& operator<<(std::ostream& os, const OPAT& opat);

    [[nodiscard]] const DataCard& get(const FloatIndexVector& index) const;

    [[nodiscard]] const DataCard& get(const std::vector<double>& index) const {
        return get(FloatIndexVector(index));
    }

    const DataCard& operator[](const FloatIndexVector& index) const;

    const DataCard& operator[](const std::vector<double>& index) const {
        return get(FloatIndexVector(index));
    }

    [[nodiscard]] std::vector<Bounds> getBounds() const;
};

OPAT readOPAT(const std::string& filename);

Header readHeader(std::ifstream &file);

CardCatalogEntry readCardCatalogEntry(std::ifstream &file, uint64_t offset, uint16_t numIndex, uint8_t hashPrecision);

CardCatalog readCardCatalog(std::ifstream &file, const Header &header);

std::unordered_map<FloatIndexVector, DataCard> readDataCards(std::ifstream &file, const Header &header, const CardCatalog &cardCatalog);

DataCard readDataCard(std::ifstream &file, const CardCatalogEntry &entry);

CardHeader readDataCardHeader(std::ifstream &file, const CardCatalogEntry &entry);

TableIndex readTableIndex(std::ifstream &file, const CardCatalogEntry &entry, const CardHeader &header);

OPATTable readOPATTable(std::ifstream &file, const CardCatalogEntry &cardEntry, const TableIndexEntry &tableEntry);

bool hasMagic(const std::string& filename);

bool is_big_endian();

template <typename T>
T swap_bytes(T value) {
    static_assert(std::is_trivially_copyable_v<T>, "swap_bytes only supports trivial types.");
    T result;
    auto src = reinterpret_cast<uint8_t*>(&value);
    auto* dest = reinterpret_cast<uint8_t*>(&result);
    for (size_t i = 0; i < sizeof(T); i++) {
        dest[i] = src[sizeof(T) - 1 - i];
    }
    return result;
}
 
} // namespace opat
 
#endif