source: trunk/FACT++/src/fixfits.cc@ 20037

//Compile with g++ -o FixFits fixFits.cpp -O2 -std=c++11
//This is a "FITS file fixer" program for FACT.
//It goes through the file, relying only on basic header data and compressed blocks headers
//It will reconstruct the catalog data too in the output file a strip all corrupt data
//The actual header keywords must be edited with the FTOOLS afterwards

#include <string>
#include <iostream>
#include <iomanip>
#include <fstream>
#include <cstring>
#include <vector>
#include <algorithm>
#include <sstream>

#include <boost/filesystem.hpp>

#include "FITS.h"
#include "Time.h"
#include "Configuration.h"

using namespace std;
using namespace FITS;
namespace fs = boost::filesystem;


template<size_t N>
    void revcpy(char *dest, const char *src, int num)
{
    const char *pend = src + num*N;
    for (const char *ptr = src; ptr<pend; ptr+=N, dest+=N)
        std::reverse_copy(ptr, ptr+N, dest);
}

bool update_header_key(char buffer[], const string& keyword, uint64_t value, const string& comment)
{
    ostringstream str;
    str << value;

    const auto num_length = str.str().size();
    str.str("");

    str << setfill(' ');
    str << left << setw(8) << keyword;

    str << "= ";

    str << right << setw(20) << value << " / " << comment;

    str << setw(80-str.str().size()) << ' ';

    cout << keyword.size() << ":" << num_length << ":" << str.str().size() << ":" << str.str() << '\n';

    if (str.str().size() != 80)
    {
        cerr << "Wrong " << keyword << " string size." << endl;
        return false;
    }

    memcpy(buffer, str.str().c_str(), 80);

    return true;
}

void SetupConfiguration(Configuration &conf)
{
    po::options_description control("Root to SQL");
    control.add_options()
        ("file",  var<string>()->required(),  "Input file name. Fits file to be repaired.")
        ("out,o", var<string>(),              "Output file name (+'.repaired' if empty), dry-run if not provided")
        ("no-progress", po_switch(),          "Suppress progress output")
        ("dry-run", po_switch(),              "Do not write any output")
        ;

    po::positional_options_description p;
    p.add("file", 1); // All positional options
    p.add("out",  1); // All positional options

    conf.AddOptions(control);
    conf.SetArgumentPositions(p);
}

void PrintUsage()
{
    cout <<
        "fixfits - Fix the header of a none closed raw-data file\n"
        "\n"
        "The goal of this tool is to touch the data as less as possible. "
        "This, however, might result in a few more bytes being lost than "
        "strictly necessary.\n"
        "\n"
        "Usage: fixfits input-file-name [output-file-name]\n"
        "\n"
        ;
    cout << endl;
}


int main(int argc, const char* argv[])
{
    Configuration conf(argv[0]);
    conf.SetPrintUsage(PrintUsage);
    SetupConfiguration(conf);

    if (!conf.DoParse(argc, argv))
        return 127;

    // ----------------------------- Evaluate options --------------------------
    const string input_name  = conf.Get<string>("file");
    const string output_name = conf.Has("out") ? conf.Get<string>("out") :
        (input_name+".repaired");

    const bool no_progress = conf.Get<bool>("no-progress");
    const bool dry_run = conf.Get<bool>("dry-run");

    cout << "\nReading: " << input_name << endl;

    Time start_read;

    ifstream input(input_name.c_str(), ios_base::binary);
    if (!input)
    {
        cerr << "Error opening file: " << strerror(errno) << endl;
        return 6;
    }

    cout << "Seeking beginning of data table." << endl;

    // ------------------------------------------------------------

    //first off, find the beginning of the data table
    char buffer[2048];
    buffer[80] = '\0';

    size_t counter = 0;
    size_t num_bytes = 80;
    input.read(buffer, 80);

    while (counter != 2)
    {
        if (!strcmp(buffer, "XTENSION= 'BINTABLE'           / binary table extension                         "))
            counter++;

        if (input.eof())
        {
            cerr << "Reached end-of-file but could not find start of data table." << endl;
            return 2;
        }

        input.read(buffer, 80);
        num_bytes+=80;

        if (!no_progress)
            cout << "\rByte " << num_bytes << "      ";
    }
    if (no_progress)
        cout << "Reached " << num_bytes << '\n';
    cout << "\nFound beginning of data table." << endl;

    // ------------------------------------------------------------

    //we just read the start of the data table. continue until the end of the table header
    while (strcmp(buffer, "END                                                                             "))
    {
        if (input.eof())
        {
            cerr << "Data table header was not closed properly. Aborting." << endl;
            return 3;
        }

        input.read(buffer, 80);
        num_bytes+=80;

        if (!no_progress)
            cout << "\rByte " << num_bytes << "       ";
    }
    if (no_progress)
        cout << "Reached " << num_bytes << '\n';

    cout << "\nReached end of data table header" << endl;

    // ------------------------------------------------------------

    //now skip the fits padding
    while (num_bytes % 2880 != 0)
    {
        input.read(buffer, 80);
        num_bytes+=80;

        if (!no_progress)
            cout << "\rByte " << num_bytes << "       ";
    }
    if (no_progress)
        cout << "Reached " << num_bytes << '\n';


    const size_t output_catalog_start = input.tellg();

    //now we are in the catalog. skip it until we find the string 'TILE'
    buffer[4] = '\0';
    while (strcmp(buffer, "TILE"))
    {
        input.read(buffer, 4);
        num_bytes += 4;

        if (!no_progress)
            cout << "\rByte " << num_bytes << "      ";
    }
    if (no_progress)
        cout << "Reached " << num_bytes << '\n';

    input.seekg(num_bytes-4);
    cout << "\nFound start of first compressed tile." << endl;

    // ------------------------------------------------------------

    const size_t output_heap_start = input.tellg();

    size_t byte_where_tile_start = input.tellg();

    //now figure out how many blocks are in each tile
    TileHeader tile_head;
    BlockHeader block_head;

    input.read(reinterpret_cast<char*>(&tile_head), sizeof(TileHeader));

    cout << "First tile is " << tile_head.size << " bytes long." << endl;

    // ------------------------------------------------------------

    size_t block_bytes = 0;
    size_t num_blocks = 0;

    while (size_t(input.tellg()) < byte_where_tile_start+tile_head.size)
    {
        input.read(reinterpret_cast<char*>(&block_head), sizeof(BlockHeader));
        block_bytes += block_head.size;

        input.seekg(byte_where_tile_start + sizeof(TileHeader) + block_bytes);
        num_blocks ++;

        if (input.eof())
        {
            cerr << "First tile seems broken unable to recover anything." << endl;
            return 4;
        }
    }

    if (size_t(input.tellg()) != byte_where_tile_start+tile_head.size)
    {
        cerr << "Discrepancy between tile size and sum of blocks size." << endl;
        return 1;
    }

    cout << "There are " << num_blocks << " blocks in each tile.\nLooping over all tiles" << endl;

    // ------------------------------------------------------------

    size_t num_tiles = 0;
    input.seekg(output_heap_start);

    size_t output_heap_end = input.tellg();
    size_t previous_heap_end = input.tellg();

    vector<vector<pair<int64_t, int64_t> > > catalog;

    uint64_t offset_in_heap = 0;
    while (!input.eof())
    {
        previous_heap_end = output_heap_end;
        output_heap_end = input.tellg();

        byte_where_tile_start = input.tellg();
        block_bytes = 0;

        if (input.peek() == EOF)
        {
            cout << "Reached end-of-file." << endl;
            break;
        }

        input.read(reinterpret_cast<char*>(&tile_head), sizeof(TileHeader));
        if (memcmp(tile_head.id, "TILE", 4) || input.eof())
        {
            cout << "Reached end-of-table padding or end-of-file." << endl;
            break;
        }

        offset_in_heap += sizeof(TileHeader);
        catalog.emplace_back();

        for (size_t i=0; i<num_blocks; i++)
        {
            input.read((char*)(&block_head), sizeof(BlockHeader));
            if (input.eof())
            {
                cout << "Reached end-of-file." << endl;
                break;
            }
            block_bytes += block_head.size;
            input.seekg(byte_where_tile_start + sizeof(TileHeader) + block_bytes);
            if (input.eof())
            {
                cout << "Reached end-of-file." << endl;
                break;
            }
            catalog.back().emplace_back((int64_t)(block_head.size),offset_in_heap);
            offset_in_heap += block_head.size;
        }

        //one last catalog entry for the column that has no data
        catalog.back().emplace_back(0,0);

        if (!no_progress)
            cout << "\rByte " << input.tellg() << "      ";
        num_tiles++;
    }

    input.clear();

    // ------------------------------------------------------------

    //ignore last read tile as we have no idea if it looked ok or not
    num_tiles--;
    output_heap_end = previous_heap_end;

    cout << "Recovery finished!\n";

    const auto time_read = Time().UnixTime()-start_read.UnixTime();

    // ============================================================
    //Now we have everything that we need. Go again through the input file and write the output, fixed file

    cout << "\nWriting: " << output_name << endl;

    Time start_write;

    const uint64_t num_cols = num_blocks+1;//+1 because of not-used drs-time-marker column
    const uint64_t output_catalog_end = output_catalog_start + num_tiles*num_cols*16;

    const uint64_t zheapptr = output_heap_start - output_catalog_start;
    const uint64_t theap    = output_catalog_end - output_catalog_start;


    if (!dry_run)
    {
        ofstream output(output_name.c_str(), ios_base::binary);
        input.seekg(0);

        //copy everything until the catalog start and update header values on our way
        counter = 0;
        for (uint64_t i=0; i<output_catalog_start; i+=80)
        {
            input.read(buffer, 80);

            if (!strcmp(buffer, "XTENSION= 'BINTABLE'           / binary table extension                         "))
                counter++;

            if (counter == 2)
            {
                bool rc = true;

                if (!memcmp(buffer, "NAXIS2", 6))
                    rc &= update_header_key(buffer, "NAXIS2", num_tiles, "number of rows in table");
                if (!memcmp(buffer, "ZNAXIS2", 7))
                    rc &= update_header_key(buffer, "ZNAXIS2", num_tiles, "Number of uncompressed rows");
                if (!memcmp(buffer, "PCOUNT", 6))
                    rc &= update_header_key(buffer, "PCOUNT", output_heap_end - output_catalog_end, "size of special data area");
                if (!memcmp(buffer, "THEAP", 5))
                    rc &= update_header_key(buffer, "THEAP", theap, "Pointer to heap");
                if (!memcmp(buffer, "ZHEAPPTR", 8))
                    rc &= update_header_key(buffer, "ZHEAPPTR", zheapptr, "Pointer to data");

                if (!rc)
                    return 5;
            }

            output.write(buffer, 80);

            if (!no_progress)
                cout << "\rByte " << input.tellg() << "       ";
        }

        if (no_progress)
            cout << "Reached " << input.tellg() << '\n';

        // ------------------------------------------------------------

        // now write the updated catalog
        const uint64_t reserved_num_tiles   = zheapptr / (num_cols*16);
        const uint32_t one_catalog_row_size = num_cols*16;
        const uint32_t total_catalog_size   = reserved_num_tiles*one_catalog_row_size;

        vector<char> swapped_catalog(total_catalog_size);

        uint32_t shift = 0;
        for (auto it=catalog.cbegin(); it!=catalog.cend(); it++)
        {
            revcpy<sizeof(int64_t)>(swapped_catalog.data() + shift, (char*)(it->data()), num_cols*2);
            shift += one_catalog_row_size;
        }

        if (num_tiles < reserved_num_tiles)
            memset(swapped_catalog.data()+shift, 0, total_catalog_size - shift);

        output.write(swapped_catalog.data(), total_catalog_size);

        // ------------------------------------------------------------

        // we are now at the beginning of the heap in the output file. Move there in the input file
        input.seekg(output_heap_start);

        uint64_t num_heap_bytes_written = 0;
        uint64_t total_heap_bytes_to_write = output_heap_end - output_heap_start;

        cout << "\nCatalog updated.\nCopying " << total_heap_bytes_to_write << " of data now." << endl;

        while (num_heap_bytes_written != total_heap_bytes_to_write)
        {
            uint64_t bytes_to_write = 2048;
            if (total_heap_bytes_to_write - num_heap_bytes_written < 2048)
                bytes_to_write = total_heap_bytes_to_write - num_heap_bytes_written;

            input.read(buffer, bytes_to_write);
            output.write(buffer, bytes_to_write);
            num_heap_bytes_written += bytes_to_write;

            if (!no_progress)
                cout << "\rByte " << input.tellg() << "           ";
        }
        if (no_progress)
            cout << "Reached " << input.tellg() << '\n';

        cout << "\nData written. Adding FITS padding. " << endl;

        // ------------------------------------------------------------

        //now add the FITS padding at the end
        while (output.tellp() % 2880 != 0)
            output.write("\0", 1);
    }
    else
        cout << " ... skipped ...\n";

    const auto time_write = Time().UnixTime()-start_write.UnixTime();

    cout << "File recovered!\n";

    // ------------------------------------------------------------

    cout << "\nValid num tiles  : " << setw(12) << num_tiles;
    cout << "\nNAXIS2           : " << setw(12) << num_tiles;
    cout << "\nZNAXIS2          : " << setw(12) << num_tiles;
    cout << "\nCatalog start    : " << setw(12) << output_catalog_start;
    cout << "\nCatalog end      : " << setw(12) << output_catalog_end;
    cout << "\nZHEAPPTR         : " << setw(12) << zheapptr;
    cout << "\nTHEAP            : " << setw(12) << theap;
    cout << "\nHeap start       : " << setw(12) << output_heap_start;
    cout << "\nHeap end         : " << setw(12) << output_heap_end;
    cout << "\nPCOUNT           : " << setw(12) << output_heap_end - output_catalog_end;
    cout << '\n';
    cout << "\nInput  file size : " << setw(12) << fs::file_size(input_name);
    if (!dry_run)
    {
        cout << "\nOutput file size : " << setw(12) << fs::file_size(output_name);
        cout << "\nLost bytes       : " << setw(12) << fs::file_size(input_name)-fs::file_size(output_name);
        cout << "\nLost fraction    : " << setw(12) << 1-double(fs::file_size(output_name))/fs::file_size(input_name);
    }
    cout << "\n";

    cout << "\nExecution [read]  : " << time_read  << "s, " << fs::file_size(input_name)/1024./1024/time_read << "Mb/s";
    cout << "\nExecution [write] : " << time_write << "s, " << fs::file_size(output_name)/1024./1024/time_write << "Mb/s";

    cout << "\n\nYou should now:\n";
    cout << "- update TSTOPI and TSTOPF using \"fitsdump -c UnixTimeUTC --minmax --nozero\" and then fv\n";
    cout << "- update DATE-END using TSTOP given to the MjDtoISO program in ~fact_arc/ingestScripts and then fv again\n";
    cout << "- update the checksum of the file with \"fchecksum update+ <filename>\"\n" << endl;

    return 0;

}