Index: unk/FACT++/src/FitsLoader.cc
===================================================================
--- /trunk/FACT++/src/FitsLoader.cc	(revision 10793)
+++ 	(revision )
@@ -1,712 +1,0 @@
-//****************************************************************
-/** @class FitsLoader
-
-  @brief Load a given Fits file and table, and dump selected columns if requested.
-
-  It derives from StateMachineDim. the first parent is here to enforce
-  a state machine behaviour
-  The possible states and transitions of the machine are:
-  \dot
-  digraph FitsLoader {
-          node [shape=record, fontname=Helvetica, fontsize=10];
-      e [label="Error" color="red"];
-   r [label="Ready"]
-   d [label="FileLoaded"]
-
-  e -> r
-  r -> e
-  r -> d
-  d -> r
-   }
-  \enddot
- */
- //****************************************************************
-#include "FACT.h"
-#include "Event.h"
-#include "StateMachineDim.h"
-#include "WindowLog.h"
-#include "Configuration.h"
-#include "LocalControl.h"
-#include "Description.h"
-
-
-#include <boost/bind.hpp>
-#if BOOST_VERSION < 104400
-#if (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 4))
-#undef BOOST_HAS_RVALUE_REFS
-#endif
-#endif
-#include <boost/thread.hpp>
-
-#include <iostream>
-
-#include <CCfits/CCfits>
-
-class FitsLoader : public StateMachineDim
-{
-
-public:
-    enum
-    {
-        kSM_FileLoaded = 20,
-    } localstates_t;
-
-    FitsLoader(ostream& out);
-    ~FitsLoader();
-
-    ///Define command names
-    static const char* fLoadFits;
-    static const char* fUnloadFits;
-    static const char* fListColumns;
-    static const char* fDumpColumns;
-    static const char* fClearDumpList;
-    static const char* fDoDump;
-    static const char* fConfigFileName;
-    static const char* fConfigTableName;
-    static const char* fConfigPrecName;
-    static const char* fConfigFileOutName;
-
-private:
-    ///Name of the fits file to load
-    string fFileName;
-    ///Name of the table to load from the  file
-    string fTableName;
-    ///FITS pointer
-    CCfits::FITS* fFile;
-    ///Table pointer
-    CCfits::Table* fTable;
-    ///Precision of the ofstream. Used to output a given number of significant digits for floats or doubles
-    int fStreamPrecision;
-    ///Name of the output file
-    string fFileOut;
-    ///map between the column names and their CCfits objects
-    map<string, CCfits::Column*> fColMap;
-    ///List of the column names to be dumped
-    vector<string> fDumpList;
-    ///Transition from ready to fileLoaded.
-    int LoadPlease();
-    ///Transition from fileLoaded to ready
-    int UnloadPlease();
-    ///Lists the loaded column names
-    int ListColumnsPlease(const Event&);
-    ///Add a column name to the dump list
-    int AddDumpColumnsPlease(const Event&);
-    ///Clear the dump list
-    int ClearDumpListPlease(const Event&);
-    ///Perform the dumping, based on the current dump list
-    int DoDumpPlease(const Event&);
-    ///Set the name of the Fits file to be loaded
-    int ConfigFileNamePlease(const Event&);
-    ///Set the name of the table to be loaded
-    int ConfigTableNamePlease(const Event&);
-    ///Set the ofstream precision
-    int SetOFStreamPrecisionPlease(const Event&);
-    ///Set the name of the output file
-    int SetFileOutPlease(const Event&);
-    ///Calculate the buffer size required to read a row of the fits table, as well as the offsets to each column
-    vector<int> CalculateBufferSize();
-    ///Write a single row of the selected data
-    void writeValuesFromFits(vector<int>& offsets,ofstream& targetFile, unsigned char* fitsBuffer);
-
-public:
-    ///Configures the fitsLoader from the config file and/or command arguments.
-    void SetupConfig(Configuration& conf);
-};
-
-const char* FitsLoader::fLoadFits = "load";
-const char* FitsLoader::fUnloadFits = "unload";
-const char* FitsLoader::fListColumns = "list_columns";
-const char* FitsLoader::fDumpColumns = "add_dump";
-const char* FitsLoader::fClearDumpList = "clear_dump";
-const char* FitsLoader::fDoDump = "dump";
-const char* FitsLoader::fConfigFileName = "set_file";
-const char* FitsLoader::fConfigTableName = "set_table";
-const char* FitsLoader::fConfigPrecName = "set_prec";
-const char* FitsLoader::fConfigFileOutName = "set_outfile";
-
-// --------------------------------------------------------------------------
-//
-//! Set the name of the output file
-//! @param evt
-//!        the event transporting the file name
-//
-int FitsLoader::SetFileOutPlease(const Event& evt)
-{
-    fFileOut = string(evt.GetText());
-    stringstream str;
-    str << "Output file is now " << fFileOut;
-    Message(str.str());
-    return 0;
-}
-// --------------------------------------------------------------------------
-//
-//! Set the precision of the ofstream. So that an appropriate number of significant digits are outputted.
-//! @param evt
-//!        the event transporting the precision
-//
-int FitsLoader::SetOFStreamPrecisionPlease(const Event& evt)
-{
-    fStreamPrecision = evt.GetInt();
-    stringstream str;
-    str << "OFStream precision is now " << fStreamPrecision;
-    Message(str.str());
-    return 0;
-}
-// --------------------------------------------------------------------------
-//
-//! Writes a single row of the selected FITS data to the output file.
-//! @param offsets
-//!         a vector containing the offsets to the columns (in bytes)
-//! @param targetFile
-//!         the ofstream where to write to
-//! @param fitsBuffer
-//!         the memory were the row has been loaded by cfitsio
-//
-void FitsLoader::writeValuesFromFits(vector<int>& offsets,ofstream& targetFile, unsigned char* fitsBuffer)
-{
-    targetFile.precision(fStreamPrecision);
-    map<string, CCfits::Column*>::iterator it;
-   for (it=fColMap.begin(); it != fColMap.end(); it++)
-    {
-        bool found = false;
-        for (vector<string>::iterator jt=fDumpList.begin(); jt != fDumpList.end(); jt++)
-        {
-            if (it->first == *jt)
-            {
-                found = true;
-                break;
-            }
-        }
-        if (!found)
-            continue;
-       int offset = offsets[it->second->index()-1];
-       const char* charSrc = reinterpret_cast<char*>(&fitsBuffer[offset]);
-        unsigned char copyBuffer[30];//max size of a single variable
-        for (int width = 0; width<it->second->width(); width++)
-        {
-            switch (it->second->type())
-            {
-            case CCfits::Tbyte:
-                targetFile << *charSrc;
-                charSrc += sizeof(char);
-            break;
-            case CCfits::Tushort:
-                targetFile << *reinterpret_cast<const unsigned short*>(charSrc);
-                charSrc += sizeof(char);
-            break;
-            case CCfits::Tshort:
-                targetFile << *reinterpret_cast<const short*>(charSrc);
-                charSrc += sizeof(char);
-            break;
-            case CCfits::Tuint:
-                reverse_copy(charSrc, charSrc+sizeof(unsigned int), copyBuffer);
-                //warning suppressed in gcc4.0.2
-                targetFile << *reinterpret_cast<unsigned int*>(copyBuffer);
-                charSrc += sizeof(int);
-            break;
-            case CCfits::Tint:
-                reverse_copy(charSrc, charSrc+sizeof(int), copyBuffer);
-                targetFile << *reinterpret_cast<int*>(copyBuffer);
-                charSrc += sizeof(int);
-            break;
-            case CCfits::Tulong:
-                reverse_copy(charSrc, charSrc+sizeof(unsigned long), copyBuffer);
-                targetFile << *reinterpret_cast<unsigned long*>(copyBuffer);
-                charSrc += sizeof(int);
-            break;
-            case CCfits::Tlong:
-                reverse_copy(charSrc, charSrc+sizeof(long), copyBuffer);
-                targetFile << *reinterpret_cast<long*>(copyBuffer);
-                charSrc += sizeof(int);
-            break;
-            case CCfits::Tlonglong:
-                reverse_copy(charSrc, charSrc+sizeof(long long), copyBuffer);
-                targetFile << *reinterpret_cast<long long*>(copyBuffer);
-                charSrc += sizeof(long long);
-            break;
-            case CCfits::Tfloat:
-                reverse_copy(charSrc, charSrc+sizeof(float), copyBuffer);
-                targetFile << *reinterpret_cast<float*>(copyBuffer);
-                charSrc += sizeof(float);
-            break;
-            case CCfits::Tdouble:
-                reverse_copy(charSrc, charSrc+sizeof(double), copyBuffer);
-                targetFile << *reinterpret_cast<double*>(copyBuffer);
-                charSrc += sizeof(double);
-            break;
-            case CCfits::Tnull:
-            case CCfits::Tbit:
-            case CCfits::Tlogical:
-            case CCfits::Tstring:
-            case CCfits::Tcomplex:
-            case CCfits::Tdblcomplex:
-            case CCfits::VTbit:
-            case CCfits::VTbyte:
-            case CCfits::VTlogical:
-            case CCfits::VTushort:
-            case CCfits::VTshort:
-            case CCfits::VTuint:
-            case CCfits::VTint:
-            case CCfits::VTulong:
-            case CCfits::VTlong:
-            case CCfits::VTlonglong:
-            case CCfits::VTfloat:
-            case CCfits::VTdouble:
-            case CCfits::VTcomplex:
-            case CCfits::VTdblcomplex:
-                Error("Data type not implemented yet.");
-                return;
-            break;
-            default:
-                Error("THIS SHOULD NEVER BE REACHED");
-                return;
-            }//switch
-            targetFile << " ";
-        }//width loop
-    }//iterator over the columns
-    targetFile << endl;
-}
-
-// --------------------------------------------------------------------------
-//
-//! Calculates the required buffer size for reading one row of the current table.
-//! Also calculates the offsets to all the columns
-//
-vector<int> FitsLoader::CalculateBufferSize()
-{
-    vector<int> result;
-    map<int,int> sizes;
-    int size = 0;
-
-    for (map<string, CCfits::Column*>::iterator it=fColMap.begin(); it != fColMap.end(); it++)
-    {
-        int width = it->second->width();
-        switch (it->second->type())
-        {
-        case CCfits::Tbyte:
-        case CCfits::Tushort:
-        case CCfits::Tshort:
-            Message("short");
-            sizes[it->second->index()] =  sizeof(char)*width;
-        break;
-        case CCfits::Tuint:
-        case CCfits::Tint:
-            Message("int");
-            sizes[it->second->index()] =  sizeof(int)*width;
-        break;
-        case CCfits::Tulong:
-        case CCfits::Tlong:
-            Message("long");
-            sizes[it->second->index()] = sizeof(int)*width;
-        break;
-        case CCfits::Tlonglong:
-            Message("longlong");
-            sizes[it->second->index()] =  sizeof(long long)*width;
-        break;
-        case CCfits::Tfloat:
-            Message("float");
-            sizes[it->second->index()] =  sizeof(float)*width;
-        break;
-        case CCfits::Tdouble:
-            Message("double");
-            sizes[it->second->index()] =  sizeof(double)*width;
-        break;
-        case CCfits::Tnull:
-        case CCfits::Tbit:
-        case CCfits::Tlogical:
-        case CCfits::Tstring:
-        case CCfits::Tcomplex:
-        case CCfits::Tdblcomplex:
-        case CCfits::VTbit:
-        case CCfits::VTbyte:
-        case CCfits::VTlogical:
-        case CCfits::VTushort:
-        case CCfits::VTshort:
-        case CCfits::VTuint:
-        case CCfits::VTint:
-        case CCfits::VTulong:
-        case CCfits::VTlong:
-        case CCfits::VTlonglong:
-        case CCfits::VTfloat:
-        case CCfits::VTdouble:
-        case CCfits::VTcomplex:
-        case CCfits::VTdblcomplex:
-            Error("Data type not implemented yet.");
-            return vector<int>();
-        break;
-        default:
-            Error("THIS SHOULD NEVER BE REACHED");
-            return vector<int>();
-        }
-    }
-    //calculate the offsets in the vector.
-    int checkIndex = 1;
-    for (map<int,int>::iterator it=sizes.begin(); it != sizes.end(); it++)
-    {
-        result.push_back(size);
-        size += it->second;
-        if (it->first != checkIndex)
-        {
-            stringstream str;
-            str << "Expected index " << checkIndex << " found " << it->first;
-            Error(str.str());
-        }
-        checkIndex++;
-    }
-    result.push_back(size);
-    return result;
-}
-// --------------------------------------------------------------------------
-//
-//! Constructor
-//! @param out
-//!        the ostream where to redirect the outputs
-//
-FitsLoader::FitsLoader(ostream& out) : StateMachineDim(out, "FITS_LOADER")
-{
-    //Add the existing states
-    AddStateName(kSM_FileLoaded,  "FileLoaded", "A Fits file has been loaded");
-
-    //Add the possible transitions
-    AddEvent(kSM_FileLoaded, fLoadFits, kSM_Ready)
-            (boost::bind(&FitsLoader::LoadPlease, this))
-            ("Loads the given Fits file");
-    AddEvent(kSM_Ready, fUnloadFits, kSM_FileLoaded)
-            (boost::bind(&FitsLoader::UnloadPlease, this))
-            ("Unloads the given Fits file");
-
-    //Add the possible configurations
-    AddEvent(fListColumns, "", kSM_FileLoaded)
-            (boost::bind(&FitsLoader::ListColumnsPlease, this, _1))
-            ("List the columns that were loaded from that file");
-    AddEvent(fDumpColumns, "C", kSM_FileLoaded)
-            (boost::bind(&FitsLoader::AddDumpColumnsPlease, this, _1))
-            ("Add a given column to the dumping list");
-    AddEvent(fClearDumpList, "", kSM_FileLoaded)
-            (boost::bind(&FitsLoader::ClearDumpListPlease, this, _1))
-            ("Clear the dumping list");
-    AddEvent(fDoDump, "", kSM_FileLoaded)
-            (boost::bind(&FitsLoader::DoDumpPlease, this, _1))
-            ("Perform the dump of columns data, based on the to dump list");
-    AddEvent(fConfigFileName, "C", kSM_Ready, kSM_FileLoaded)
-            (boost::bind(&FitsLoader::ConfigFileNamePlease, this, _1))
-            ("Gives the name of the Fits file to be loaded");
-    AddEvent(fConfigTableName, "C", kSM_Ready, kSM_FileLoaded)
-            (boost::bind(&FitsLoader::ConfigTableNamePlease, this, _1))
-            ("Gives the name of the Table to be loaded");
-    AddEvent(fConfigPrecName, "I", kSM_Ready, kSM_FileLoaded)
-            (boost::bind(&FitsLoader::SetOFStreamPrecisionPlease, this, _1))
-            ("Set the precision of the ofstream, i.e. the number of significant digits being outputted");
-    AddEvent(fConfigFileOutName, "C", kSM_Ready, kSM_FileLoaded)
-            (boost::bind(&FitsLoader::SetFileOutPlease, this, _1))
-            ("Set the name of the outputted file.");
-
-    fFile = NULL;
-    fStreamPrecision = 20;
-
-}
-// --------------------------------------------------------------------------
-//
-//! Destructor
-//
-FitsLoader::~FitsLoader()
-{
-    if (fFile)
-        delete fFile;
-    fFile = NULL;
-}
-// --------------------------------------------------------------------------
-//
-//! Loads the fits file based on the current parameters
-//
-int FitsLoader::LoadPlease()
-{
-    stringstream str;
-    try
-    {
-        fFile = new CCfits::FITS(fFileName);
-    }
-    catch (CCfits::FitsException e)
-     {
-         str << "Could not open FITS file " << fFileName << " reason: " << e.message();
-         Error(str);
-         return kSM_Ready;
-     }
-    str.str("");
-    const multimap< string, CCfits::ExtHDU * > extMap = fFile->extension();
-    if (extMap.find(fTableName) == extMap.end())
-    {
-        str.str("");
-        str << "Could not open table " << fTableName << ". Tables in file are: ";
-        for (std::multimap<string, CCfits::ExtHDU*>::const_iterator it=extMap.begin(); it != extMap.end(); it++)
-            str << it->first << " ";
-        Error(str.str());
-        return kSM_Ready;
-    }
-    else
-        fTable = dynamic_cast<CCfits::Table*>(extMap.find(fTableName)->second);
-    int numRows = fTable->rows();
-    str.str("");
-    str << "Loaded table has " << numRows << " rows";
-    Message(str.str());
-
-    fColMap = fTable->column();
-    if (fDumpList.size() != 0)
-    {
-        bool should_clear = false;
-        for (vector<string>::iterator it=fDumpList.begin(); it!= fDumpList.end(); it++)
-        {
-            if (fColMap.find(*it) == fColMap.end())
-            {
-                should_clear = true;
-                Error("Config-given dump list contains invalid entry " + *it + " clearing the list");
-            }
-        }
-        if (should_clear)
-            fDumpList.clear();
-    }
-    return kSM_FileLoaded;
-}
-// --------------------------------------------------------------------------
-//
-//! Unloads the Fits file
-//
-int FitsLoader::UnloadPlease()
-{
-    if (fFile)
-        delete fFile;
-    else
-        Error("Error: Fits file is  NULL while it should not have been");
-    fFile = NULL;
-    return kSM_Ready;
-}
-// --------------------------------------------------------------------------
-//
-//! List the columns that are in the loaded Fits table
-//
-int FitsLoader::ListColumnsPlease(const Event&)
-{
-    Message("Columns in the loaded table are:");
-    map<string, CCfits::Column*>::iterator it;
-    for (it=fColMap.begin(); it != fColMap.end(); it++)
-        Message(it->first);
-    return GetCurrentState();
-}
-// --------------------------------------------------------------------------
-//
-//! Add a given column name  to the list of columns to dump
-//! @param evt
-//!        the event transporting the column name
-//
-int FitsLoader::AddDumpColumnsPlease(const Event& evt)
-{
-    string evtText(evt.GetText());
-    //TODO check that this column indeed exist in the file
-    if (fColMap.find(evtText) != fColMap.end())
-        fDumpList.push_back(evtText);
-    else
-        Error("Could not find column " + evtText + " int table");
-    Message("New dump list:");
-    for (vector<string>::iterator it=fDumpList.begin(); it != fDumpList.end(); it++)
-        Message(*it);
-    return GetCurrentState();
-}
-// --------------------------------------------------------------------------
-//
-//! Clear the list of columns to dump
-//
-int FitsLoader::ClearDumpListPlease(const Event&)
-{
-    fDumpList.clear();
-    Message("Dump list is now empty");
-    return GetCurrentState();
-}
-// --------------------------------------------------------------------------
-//
-//! Perform the actual dump, based on the current parameters
-//
-int FitsLoader::DoDumpPlease(const Event&)
-{
-    fTable->makeThisCurrent();
-    vector<int> offsets = CalculateBufferSize();
-    int size = offsets[offsets.size()-1];
-    offsets.pop_back();
-    unsigned char* fitsBuffer = new unsigned char[size];
-
-    ofstream targetFile(fFileOut);
-    int status = 0;
-
-    for (int i=1;i<=fTable->rows(); i++)
-    {
-        fits_read_tblbytes(fFile->fitsPointer(), i, 1, size, fitsBuffer, &status);
-        if (status)
-        {
-            stringstream str;
-            str << "An error occurred while reading fits row #" << i << " error code: " << status;
-            Error(str.str());
-            str.str("");
-            for (unsigned int j=0;j<offsets.size(); j++)
-                str << offsets[j] << " ";
-            Error(str.str());
-        }
-        writeValuesFromFits(offsets, targetFile, fitsBuffer);
-    }
-    delete[] fitsBuffer;
-    return GetCurrentState();
-}
-// --------------------------------------------------------------------------
-//
-//! Set the name of the intput Fits file
-//! @param evt
-//!        the event transporting the file name
-//
-int FitsLoader::ConfigFileNamePlease(const Event& evt)
-{
-    fFileName = string(evt.GetText());
-    Message("New Fits file: " + fFileName);
-    return GetCurrentState();
-}
-// --------------------------------------------------------------------------
-//
-//! Set the name of the input table
-//! @param evt
-//!        the event transporting the table name
-//
-int FitsLoader::ConfigTableNamePlease(const Event& evt)
-{
-    fTableName = string(evt.GetText());
-    Message("New Fits table: " + fTableName);
-    return GetCurrentState();
-}
-// --------------------------------------------------------------------------
-//
-//! Retrieves the configuration parameters
-//! @param conf
-//!             the configuration object
-//
-void FitsLoader::SetupConfig(Configuration& conf)
-{
-    if (conf.Has("outfile"))
-    {
-        this->fFileOut = conf.Get<string>("outfile");
-        Message("Output file is: " + fFileOut);
-    }
-    if (conf.Has("fitsfile"))
-    {
-        this->fFileName = conf.Get<string>("fitsfile");
-        Message("Input fits is: " + fFileName);
-    }
-    if (conf.Has("tablename"))
-    {
-        this->fTableName = conf.Get<string>("tablename");
-        Message("Input Table is: " + fTableName);
-    }
-    if (conf.Has("dump"))
-    {
-        this->fDumpList = conf.Get<vector<string>>("dump");
-        Message("Dump list is:");
-        for (vector<string>::iterator it=fDumpList.begin(); it != fDumpList.end(); it++)
-            Message(*it);
-    }
-    if (conf.Has("precision"))
-    {
-        this->fStreamPrecision = conf.Get<int>("precision");
-        stringstream str;
-        str << "OFStream precision is: " << fStreamPrecision;
-        Message(str.str());
-    }
-}
-void RunThread(FitsLoader* loader)
-{
-    loader->Run(true);
-    Readline::Stop();
-}
-template<class T>
-int RunShell(Configuration& conf)
-{
-    static T shell(conf.GetName().c_str(), conf.Get<int>("console")!=1);
-
-    WindowLog& wout = shell.GetStreamOut();
-
-    FitsLoader loader(wout);
-    loader.SetupConfig(conf);
-    shell.SetReceiver(loader);
-
-    boost::thread t(boost::bind(RunThread, &loader));
-
-    shell.Run();
-
-    loader.Stop();
-
-    t.join();
-
-    return 0;
-}
-void PrintUsage()
-{
-    cout << "This is a usage. to be completed" << endl;
-}
-void PrintHelp()
-{
-    cout << "This is the help. I know, not so helpfull at the moment..." << endl;
-}
-void SetupConfiguration(Configuration& conf)
-{
-    po::options_description configp("Programm options");
-    configp.add_options()
-            ("console,c", var<int>(), "Use console (0=shell, 1=simple buffered, X=simple unbuffered)");
-
-    po::options_description configs("Fits Loader options");
-    configs.add_options()
-            ("outfile,o", var<string>(), "Output file")
-            ("fitsfile,f", var<string>(), "Input Fits file")
-            ("tablename,t", var<string>(), "Input Table")
-            ("dump,d", vars<string>(), "List of columns to dump")
-            ("precision,p", var<int>(), "Precision of ofstream")
-            ;
-//    conf.AddEnv("dns", "DIM_DNS_NODE");
-
-    conf.AddOptions(configp);
-    conf.AddOptions(configs);
-}
-int main(int argc, const char** argv)
-{
-    Configuration conf(argv[0]);
-    conf.SetPrintUsage(PrintUsage);
-    SetupConfiguration(conf);
-
-    po::variables_map vm;
-    try
-    {
-        vm = conf.Parse(argc, argv);
-    }
-    catch (exception& e)
-    {
-        cout << "Sorry, could not properly parse the program's arguments. returning" << endl;
-        cout << e.what() << endl;
-        return -1;
-    }
-
-    if (conf.HasPrint())
-            return -1;
-    if (conf.HasVersion())
-    {
-        FACT::PrintVersion(argv[0]);
-        return -1;
-    }
-
-    if (conf.HasHelp())
-    {
-        PrintHelp();
-        return -1;
-    }
-
-//    if (!conf.Has("console"))
-//        return Run(conf);
-    if (conf.Get<int>("console")==0)
-        return RunShell<LocalShell>(conf);
-    else
-        return RunShell<LocalConsole>(conf);
-
-    return 0;
-}