Fits.cc

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// **************************************************************************
// **************************************************************************
#include "Fits.h"

#include "Time.h"
#include "Converter.h"
#include "MessageImp.h"

#include <sys/stat.h> //for file stats
#include <cstdio> // for file rename
#include <cerrno>

#include <boost/algorithm/string/predicate.hpp>

using namespace std;
using namespace CCfits;

// --------------------------------------------------------------------------
//
//
void Fits::AddStandardColumn(const Description& desc, const string &dataFormat, void* dataPointer, long unsigned int numDataBytes)
{
    //check if entry already exist
    for (vector<Description>::const_iterator it=fStandardColDesc.begin(); it != fStandardColDesc.end(); it++)
        if (it->name == desc.name)
            return;

    fStandardColDesc.push_back(desc);
    fStandardFormats.push_back(dataFormat);
    fStandardPointers.push_back(dataPointer);
    fStandardNumBytes.push_back(numDataBytes);
}

// --------------------------------------------------------------------------
//
//      
void Fits::InitDataColumns(const vector<Description> &desc, const vector<string>& dataFormat, MessageImp* out)
{
    fDataFormats = dataFormat;

    if ((desc.size() == 0) && (dataFormat.size() == 0))
    {
        fDataColDesc.clear();
        return;
    }

    //we will copy this information here. It duplicates the data, which is not great,
    // but it is the easiest way of doing it right now
    if (
        (desc.size() == dataFormat.size()+1) || // regular service
        (desc.size() == dataFormat.size()+2)    // service with ending string. skipped in fits
       )
    {
        //services have one (or two) more description than columns. skip the first entry while copying as it describes the table itself.

        fDataColDesc.clear();

        fTableDesc = desc[0].comment;
        if (fTableDesc.size() > 68)
        {
            out->Warn("Table description '" + fTableDesc + "' exceeds 68 chars... truncated.");
            fTableDesc = fTableDesc.substr(0,68);
        }

        for (unsigned int i=0; i<dataFormat.size(); i++)
        {
            string name = desc[i+1].name;
            if (name.length() > 68)
            {
                out->Warn("Column name '" + name + "' exceeds 68 chars... truncated.");
                name = name.substr(0, 68);
            }

            string comment = desc[i+1].comment;
            if (comment.length() + name.length() > 71)
            {
                out->Warn("Column '" + name + " / " + comment + "' exceeds 68 chars... truncated.");
                comment = comment.substr(0,68);
            }

            string unit = desc[i+1].unit;
            if (unit.length() > 68)
            {
                out->Warn("Unit '" + name + "' exceeds 68 chars... truncated.");
                unit = comment.substr(0,68);
            }

            const size_t p = fDataFormats[i].find_last_of('B');
            if ((boost::iequals(unit, "text") || boost::iequals(unit, "string")) && p!=string::npos)
            {
                out->Info("Column '" + name + "' detected to be an ascii string (FITS format 'A').");
                fDataFormats[i].replace(p, 1, "A");
            }

            fDataColDesc.push_back(Description(name, comment, unit));
        }
        return;
    }

    {//if we arrived here, this means that the columns descriptions could not be parsed
        ostringstream str;
        str << "Expected " << dataFormat.size() << " descriptions of columns, got " << (int)(desc.size())-1 << " for service: ";
        if (desc.size() > 0)
            str << desc[0].name;
        else
            str << "<unknown>";

        out->Warn(str.str());
    }

    fDataColDesc.clear();
 //   fDataColDesc.push_back(Description("service", "comment", "unit"));
    for (unsigned int i=0;i<dataFormat.size();i++)
    {
        ostringstream stt;
        stt << "Data" << i;
        fDataColDesc.push_back(Description(stt.str(), "", ""));
    }
}

// --------------------------------------------------------------------------
//
//
bool Fits::Open(const string& fileName, const string& tableName, uint32_t* fitsCounter, MessageImp* out, int runNumber, FITS* file)
{
    fRunNumber = runNumber;
    fMess = out;
    fFileName = fileName;

    if (fFile)
    {
        fMess->Error("File already open...");
        return false;
    }

    fFile = new FitsFile(*fMess);

    if (file == NULL)
    {
        if (!fFile->OpenFile(fileName, true))
            return false;

        fNumOpenFitsFiles = fitsCounter;
        (*fNumOpenFitsFiles)++;
    }
    else
    {
        if (!fFile->SetFile(file))
            return false;
    }

    //concatenate the standard and data columns
    //do it the inneficient way first: its easier and faster to code.
    for (unsigned int i=0;i<fStandardColDesc.size();i++)
    {
        fFile->AddColumn(fStandardColDesc[i].name, fStandardFormats[i],
                         fStandardColDesc[i].unit);
    }

    for (unsigned int i=0; i<fDataColDesc.size(); i++)
    {
        string name = fDataColDesc[i].name;
        if (name.empty())
        {
            ostringstream stt;
            stt << "Data" << i;
            name = stt.str();
        }
//cout << endl << "#####adding column: " << name << " " << fDataFormats[i] << " " << fDataColDesc[i].unit << endl << endl;
        fFile->AddColumn(name, fDataFormats[i], fDataColDesc[i].unit);
    }

    try
    {
        if (!fFile->OpenNewTable(tableName, 100))
        {
            Close();
            //if the file already exist, then the column names must have changed
            //let's move the file and try to open it again.
            string fileNameWithoutFits = fFileName.substr(0, fileName.size()-4);
            int counter = 0;
            while (counter < 100)
            {
                ostringstream newFileName;
                newFileName << fileNameWithoutFits << counter << ".fits";
                ifstream testStream(newFileName.str().c_str());
                if (!testStream)
                {
                    if (rename(fFileName.c_str(), newFileName.str().c_str()))
                        return false;
                    break;
                }
                counter++;
            }
            if (counter == 100)
                return false;
            //now we open it again.
            fFile = new FitsFile(*fMess);
            if (file == NULL)
            {
                if (!fFile->OpenFile(fileName, true))
                    return false;
                fNumOpenFitsFiles = fitsCounter;
                (*fNumOpenFitsFiles)++;
            }
            else
            {
                if (!fFile->SetFile(file))
                    return false;
            }
            //YES, we must also redo that thing here...
            //concatenate the standard and data columns
            //do it the inneficient way first: its easier and faster to code.
            for (unsigned int i=0;i<fStandardColDesc.size();i++)
            {
                fFile->AddColumn(fStandardColDesc[i].name, fStandardFormats[i],
                                 fStandardColDesc[i].unit);
            }

            for (unsigned int i=0; i<fDataColDesc.size(); i++)
            {
                string name = fDataColDesc[i].name;
                if (name.empty())
                {
                    ostringstream stt;
                    stt << "Data" << i;
                    name = stt.str();
                }
        //cout << endl << "#####adding column: " << name << " " << fDataFormats[i] << " " << fDataColDesc[i].unit << endl << endl;
                fFile->AddColumn(name, fDataFormats[i], fDataColDesc[i].unit);
            }
            if (!fFile->OpenNewTable(tableName, 100))
            {
                Close();
                return false;
            }
        }

        fCopyBuffer.resize(fFile->GetDataSize());
//write header comments

        ostringstream str;
        for (unsigned int i=0;i<fStandardColDesc.size();i++)
        {
            str.str("");
            str << "TTYPE" << i+1;
            fFile->WriteKeyNT(str.str(), fStandardColDesc[i].name, fStandardColDesc[i].comment);
            str.str("");
            str << "TCOMM" << i+1;
            fFile->WriteKeyNT(str.str(), fStandardColDesc[i].comment, "");
        }

        for (unsigned int i=0; i<fDataColDesc.size(); i++)
        {
            string name = fDataColDesc[i].name;
            if (name.empty())
            {
                ostringstream stt;
                stt << "Data" << i;
                name = stt.str();
            }
            str.str("");
            str << "TTYPE" << i+fStandardColDesc.size()+1;
            fFile->WriteKeyNT(str.str(), name, fDataColDesc[i].comment);
            str.str("");
            str << "TCOMM" << i+fStandardColDesc.size()+1;
            fFile->WriteKeyNT(str.str(), fDataColDesc[i].comment, "");
        }

        fFile->WriteKeyNT("COMMENT", fTableDesc, "");

        if (fFile->GetNumRows() == 0)
        {//if new file, then write header keys -> reset fEndMjD used as flag
            fEndMjD = 0;
        }
        else
        {//file is beingn updated. Prevent from overriding header keys
            fEndMjD = Time().Mjd();
        }

        return fFile->GetNumRows()==0 ? WriteHeaderKeys() : true;
    }
    catch (const CCfits::FitsException &e)
    {
        cout << "Exception !" << endl;
        fMess->Error("Opening or creating table '"+tableName+"' in '"+fileName+"': "+e.message());

        fFile->fTable = NULL;
        Close();
        return false;
    }
}

// --------------------------------------------------------------------------
//
//
bool Fits::WriteHeaderKeys()
{
    if (!fFile->fTable)
        return false;

    if (!fFile->WriteDefaultKeys("datalogger"))
        return false;

    if (!fFile->WriteKeyNT("TSTARTI",  0, "Time when first event received (integral part)")   ||
        !fFile->WriteKeyNT("TSTARTF",  0, "Time when first event received (fractional part)") ||
        !fFile->WriteKeyNT("TSTOPI",   0, "Time when last event received (integral part)")    ||
        !fFile->WriteKeyNT("TSTOPF",   0, "Time when last event received (fractional part)")  ||
        !fFile->WriteKeyNT("DATE-OBS", 0, "Time when first event received") ||
        !fFile->WriteKeyNT("DATE-END", 0, "Time when last event received") ||
        !fFile->WriteKeyNT("RUNID", fRunNumber, "Run number. 0 means not run file"))
        return false;

    return true;
}
void Fits::MoveFileToCorruptedFile()
{
    ostringstream corruptName;
    struct stat st;
    int append = 0;
    corruptName << fFileName << "corrupt" << append;
    while (!stat(corruptName.str().c_str(), &st))
    {
        append++;
        corruptName.str("");
        corruptName << fFileName << "corrupt" << append;
    }
    if (rename(fFileName.c_str(), corruptName.str().c_str()) != 0)
    {
        ostringstream str;
        str << "rename() failed for '" << fFileName << "': " << strerror(errno) << " [errno=" << errno << "]";
        fMess->Error(str);
        return;
    }

    fMess->Message("Renamed file " + fFileName + " to " + corruptName.str());

}
// --------------------------------------------------------------------------
//
//
bool Fits::Write(const Converter &conv, const void* data)
{
    //first copy the standard variables to the copy buffer
    int shift = 0;
    for (unsigned int i=0;i<fStandardNumBytes.size();i++)
    {
        const char *charSrc = reinterpret_cast<char*>(fStandardPointers[i]);
        reverse_copy(charSrc, charSrc+fStandardNumBytes[i], fCopyBuffer.data()+shift);
        shift += fStandardNumBytes[i];
    }
    try
    {
        //now take care of the DIM data. The Converter is here for that purpose
        conv.ToFits(fCopyBuffer.data()+shift, data, fCopyBuffer.size()-shift);
    }
    catch (const runtime_error &e)
    {
        ostringstream str;
        str << fFile->GetName() << ": " << e.what();
        fMess->Error(str);
        return false;
    }

    // This is not necessary, is it?
    // fFile->fTable->makeThisCurrent();
    if (!fFile->AddRow())
    {
        Close();
        MoveFileToCorruptedFile();
        return false;
    }
    if (!fFile->WriteData(fCopyBuffer))
    {
        Close();
        return false;
    }
    const double tm = *reinterpret_cast<double*>(fStandardPointers[0]);

    //the first standard variable is the current MjD
    if (fEndMjD==0)
    {
        // FIXME: Check error?
        fFile->WriteKeyNT("TSTARTI", uint32_t(floor(tm)),      "Time when first event received (integral part)");
        fFile->WriteKeyNT("TSTARTF", fmod(tm, 1),              "Time when first event received (fractional part)");
        fFile->WriteKeyNT("TSTOPI",  uint32_t(floor(fEndMjD)), "Time when last event received (integral part)");
        fFile->WriteKeyNT("TSTOPF",  fmod(fEndMjD, 1),         "Time when last event received (fractional part)");

        fFile->WriteKeyNT("DATE-OBS", Time(tm+40587).Iso(),
                          "Time when first event received");

        fFile->WriteKeyNT("DATE-END", Time(fEndMjD+40587).Iso(),
                          "Time when last event received");
    }

    fEndMjD = tm;

    return true;
}

// --------------------------------------------------------------------------
//
//      
void Fits::Close() 
{
    if (!fFile)
        return;
    if (fFile->IsOpen() && fFile->IsOwner())
    {
        // FIMXE: Check for error? (It is allowed that fFile is NULL)
        fFile->WriteKeyNT("TSTOPI", uint32_t(floor(fEndMjD)), "Time when last event received (integral part)");
        fFile->WriteKeyNT("TSTOPF", fmod(fEndMjD, 1),         "Time when last event received (fractional part)");

        fFile->WriteKeyNT("DATE-END", Time(fEndMjD+40587).Iso(),
                          "Time when last event received");
    }
    if (fFile->IsOwner())
    {
        if (fNumOpenFitsFiles != NULL)
            (*fNumOpenFitsFiles)--;
    }
    const string name = fFile->GetName();
    delete fFile;
    fFile = NULL;
    fMess->Info("Closed: "+name);
//    fMess = NULL;
}

void Fits::Flush()
{
    if (!fFile)
        return;

    fFile->Flush();
}
// --------------------------------------------------------------------------
int Fits::GetWrittenSize() const
{
    if (!IsOpen())
        return 0;

    struct stat st;
    if (stat(fFile->GetName().c_str(), &st))
        return 0;

    return st.st_size;
}

/*
 To be done:
 - Check the check for column names in opennewtable
 - If Open return false we end in an infinite loop (at least if
   the dynamic cats to Bintable fails.

*/