int main	(	int	argc,
		const char **	argv
	)

Definition at line 1505 of file fitsDecompressor.cc.

References ofits::AddColumn(), buffer, ofits::close(), count, Configuration::DoParse(), Configuration::Get(), ofits::GetChecksumData(), fits::GetColumns(), fits::GetKeys(), fits::GetNextRow(), zfits::GetNumRows(), fits::GetSortedColumns(), fits::GetStr(), fits::GetUInt(), Configuration::Has(), fits::HasKey(), i, fits::IsCompressedFITS(), zfits::IsFileOk(), ofits::open(), printHelp(), printUsage(), ofits::SetKeyComment(), Configuration::SetPrintUsage(), fits::SetPtrAddress(), setupConfiguration(), str, type, Configuration::Vec(), ofits::WriteRow(), and ofits::WriteTableHeader().

{
     Configuration conf(argv[0]);
     conf.SetPrintUsage(printUsage);
     setupConfiguration(conf);

     if (!conf.DoParse(argc, argv, printHelp))
         return -1;

     //initialize the file names to nothing.
     string fileNameIn = "";
     string fileNameOut = "";
     string drsFileName = "";
     uint32_t numRowsPerTile = 100;
     bool displayText=true;

    //parse configuration
    if (conf.Get<bool>("quiet")) displayText = false;
    const vector<string> inputFileNameVec = conf.Vec<string>("inputFile");
    if (inputFileNameVec.size() != 1)
    {
       cout << "Error: ";
       if (inputFileNameVec.size() == 0) cout << "no";
       else cout << inputFileNameVec.size();
       cout << " input file(s) given. Expected one. Aborting. Input:" << endl;;
       for (unsigned int i=0;i<inputFileNameVec.size(); i++)
           cout << inputFileNameVec[i] << endl;
       return -1;
    }

    //Assign the input filename
    fileNameIn = inputFileNameVec[0];

    //Check if we have a drs calib too
    if (conf.Has("drs")) drsFileName = conf.Get<string>("drs");

    //Should we verify the data ?
    bool verifyDataPlease = false;
    if (conf.Has("verify")) verifyDataPlease = conf.Get<bool>("verify");


    //should we use a specific output filename ?
    if (conf.Has("output"))
        fileNameOut = conf.Get<string>("output");
    else
    {
        size_t pos = fileNameIn.find(".fits.fz");
        if (pos == string::npos)
        {
            cout << "ERROR: input file does not seems ot be fits. Aborting." << endl;
            return -1;
        }
        fileNameOut = fileNameIn.substr(0, pos) + ".fits";
    }


    //should we use specific compression on some columns ?
    const vector<string> columnsCompression = conf.Vec<string>("compression");

    //split up values between column names and compression scheme
    vector<std::pair<string, string>> compressions;
        for (unsigned int i=0;i<columnsCompression.size();i++)
    {
        size_t pos = columnsCompression[i].find_first_of("=");
        if (pos == string::npos)
        {
            cout << "ERROR: Something wrong occured while parsing " << columnsCompression[i] << ". Aborting." << endl;
            return -1;
        }
        string comp = columnsCompression[i].substr(pos+1);
        if (comp != "UNCOMPRESSED" && comp != "AMPLITUDE" && comp != "HUFFMAN" &&
            comp != "SMOOTHMAN" && comp != "INT_WAVELET")
        {
            cout << "Unkown compression scheme requested (" << comp << "). Aborting." << endl;
            return -1;
        }
        compressions.push_back(make_pair(columnsCompression[i].substr(0, pos), comp));
    }

    //How many rows per tile should we use ?
    if (conf.Has("rowPerTile")) numRowsPerTile = conf.Get<unsigned int>("rowPerTile");

    //  Done reading configuration. Open relevant files


    //Open input's fits file
    factfits inFile(fileNameIn, "", "Events", false);

    if (!inFile.IsCompressedFITS())
    {
        cout << "ERROR: input file is NOT a compressed fits. Cannot be decompressed: Aborting." << endl;
        return -1;
    }

    //decide how many tiles should be put in the compressed file
    uint32_t originalNumRows = inFile.GetNumRows();
    uint32_t numTiles = (originalNumRows%numRowsPerTile) ? (originalNumRows/numRowsPerTile)+1 : originalNumRows/numRowsPerTile;
//    CompressedFitsWriter outFile(numTiles, numRowsPerTile);

    //should we use a specific number of threads for compressing ?
    unsigned int numThreads = 1;
    if (conf.Has("threads"))
    {
        numThreads = conf.Get<unsigned int>("threads");
//        outFile.setNumWorkingThreads(numThreads);
    }



    //Because the file to open MUST be given by the constructor, I must use a pointer instead
    factfits* drsFile = NULL;
    //try to open the Drs file. If any.
    if (drsFileName != "")
    {
        try
        {
            drsFile = new factfits(drsFileName);
        }
        catch (...)
        {
            cout << "Error: could not open " << drsFileName << " for calibration" << endl;
            return -1;
        }
    }

    if (displayText)
    {
        cout << endl;
        cout << "**********************" << endl;
        cout << "Will decompress from    : " << fileNameIn << endl;
        cout << "to                    : " << fileNameOut << endl;
        cout << "**********************" << endl;
        cout << endl;
    }

    //  Done opening input files. Allocate memory and configure output file

    //allocate the buffer for temporary storage of each read/written row
    uint32_t rowWidth = inFile.GetUInt("ZNAXIS1");
    char* buffer = new char[rowWidth + 12];
    memset(buffer, 0, 4);
    buffer = buffer+4;

    //get the source columns
    const fits::Table::Columns& columns = inFile.GetColumns();
    const fits::Table::SortedColumns& sortedColumns = inFile.GetSortedColumns();
    if (displayText)
        cout << "Input file has " << columns.size() << " columns and " << inFile.GetNumRows() << " rows" << endl;


    //  Done configuring compression. Do the real job now !
    vector<void*>   readPointers;
    vector<int32_t> readOffsets;
    vector<int32_t> readElemSize;
    vector<int32_t> readNumElems;
    //Get table name for later use in case the compressed file is to be verified
    string tableName = inFile.GetStr("EXTNAME");


    //and the header of the compressed file
    const fits::Table::Keys& header2 = inFile.GetKeys();

    //get a non-compressed writer
    ofits reconstructedFile;

    //figure out its name: /dev/null unless otherwise specified
    string reconstructedName = fileNameOut;
    reconstructedFile.open(reconstructedName.c_str(), false);

    //reconstruct the original columns from the compressed file.
    string origChecksumStr;
    string origDatasum;

    //reset tablename value so that it is re-read from compressed table's header
    tableName = "";

    /************************************************************************************
     *  Reconstruction setup done. Rebuild original header
     ************************************************************************************/

    //re-tranlate the keys
    for (fits::Table::Keys::const_iterator it=header2.begin(); it!= header2.end(); it++)
    {
        string k = it->first;
        if (k == "XTENSION" || k == "BITPIX"  || k == "PCOUNT"   || k == "GCOUNT" ||
            k == "TFIELDS"  || k == "ZTABLE"  || k == "ZNAXIS1"  || k == "ZNAXIS2" ||
            k == "ZHEAPPTR" || k == "ZPCOUNT" || k == "ZTILELEN" || k == "THEAP" ||
            k == "CHECKSUM" || k == "DATASUM" || k == "FCTCPVER" || k == "ZHEAP")
        {
            continue;
        }

        if (k == "ZCHKSUM")
        {
            reconstructedFile.SetKeyComment("CHECKSUM", it->second.comment);
            origChecksumStr = it->second.value;
            continue;
        }
        if (k == "RAWSUM")
        {
            continue;
        }

        if (k == "ZDTASUM")
        {
            reconstructedFile.SetKeyComment("DATASUM",  it->second.comment);
            origDatasum = it->second.value;
            continue;
        }

        if (k == "EXTNAME")
        {
            tableName = it->second.value;
        }

        k = k.substr(0,5);

        if (k == "TTYPE")
        {//we have an original column name here.
         //manually deal with these in order to preserve the ordering (easier than re-constructing yet another list on the fly)
            continue;
        }

        if (k == "TFORM" || k == "NAXIS" || k == "ZCTYP" )
        {
            continue;
        }

        if (k == "ZFORM" || k == "ZTYPE")
        {
            string tmpKey = it->second.fitsString;
            tmpKey[0] = 'T';
            reconstructedFile.SetKeyFromFitsString(tmpKey);
            continue;
        }

        reconstructedFile.SetKeyFromFitsString(it->second.fitsString);
    }

    if (tableName == "")
    {
        cout << "Error: table name from file " << fileNameOut << " could not be found. Aborting" << endl;
        return -1;
    }

    //Restore the original columns
    for (uint32_t numCol=1; numCol<10000; numCol++)
    {
        ostringstream str;
        str << numCol;
        if (!inFile.HasKey("TTYPE"+str.str())) break;

        string ttype    = inFile.GetStr("TTYPE"+str.str());
        string tform    = inFile.GetStr("ZFORM"+str.str());
        char   type     = tform[tform.size()-1];
        string number   = tform.substr(0, tform.size()-1);
        int    numElems = atoi(number.c_str());

        if (number == "") numElems=1;

        reconstructedFile.AddColumn(numElems, type, ttype, "", "", false);
    }

    reconstructedFile.WriteTableHeader(tableName.c_str());

    /************************************************************************************
     *  Original header restored. Do the data
     ************************************************************************************/

    //set pointers to the readout data to later be able to gather it to "buffer".
    readPointers.clear();
    readOffsets.clear();
    readElemSize.clear();
    readNumElems.clear();
    for (fits::Table::Columns::const_iterator it=columns.begin(); it!= columns.end(); it++)
    {
        readPointers.push_back(inFile.SetPtrAddress(it->first));
        readOffsets.push_back(it->second.offset);
        readElemSize.push_back(it->second.size);
        readNumElems.push_back(it->second.num);
    }

    //do the actual reconstruction work
    uint32_t i=1;
    while (i<=inFile.GetNumRows() && inFile.GetNextRow())
    {
        int count=0;
        for (fits::Table::Columns::const_iterator it=columns.begin(); it!= columns.end();it++)
        {
            memcpy(&buffer[readOffsets[count]], readPointers[count], readElemSize[count]*readNumElems[count]);
            count++;
        }
        if (displayText) cout << "\r Row " << i << flush;
        reconstructedFile.WriteRow(buffer, rowWidth);
        if (!reconstructedFile.good())
        {
            cout << "ERROR: no space left on device (probably)" << endl;
            return -1;
        }
        i++;
    }

    if (displayText) cout << endl;

    //close reconstruction input and output
//    Do NOT close the verify file, otherwise data cannot be flushed to copy file
//    verifyFile.close();
    if (!inFile.IsFileOk())
        cout << "ERROR: file checksums seems wrong" << endl;

    if (!reconstructedFile.close())
    {
        cout << "ERROR: disk probably full..." <<endl;
        return -1;
    }

    //get original and reconstructed checksum and datasum
    std::pair<string, int> origChecksum = make_pair(origChecksumStr, atoi(origDatasum.c_str()));
    std::pair<string, int> newChecksum = reconstructedFile.GetChecksumData();

    //verify that no mistake was made
    if (origChecksum.second != newChecksum.second)
    {
        cout << "ERROR: datasums are NOT identical: " << (uint32_t)(origChecksum.second) << " vs " << (uint32_t)(newChecksum.second) << endl;
        return -1;
    }
    if (origChecksum.first != newChecksum.first)
    {
        cout << "WARNING: checksums are NOT Identical: " << origChecksum.first << " vs " << newChecksum.first << endl;
    }
    else
    {
        if (true) cout << "Ok" << endl;
    }

    buffer = buffer-4;
    delete[] buffer;
    return 0;
}

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