//Filename:       readabf.cxx
//Author:         Pamela Y. C. Fong
//Maintainer:     Qi Huang
//PI:             Henry A. Lester
//Organization:   California Institute of Technology
//
//                Reformulated and adapted from API copyrighted
//                by Axon Instruments, Inc.
//
//Created:        February 12, 2004
//Last Modified:  Tue Mar  2 02:02:57 PST 2004
//
 
 
//Centralize include files in readabf.h
#include "xx-abfheadr.h"
 
 
int main(int argc, char *argv[])
{
  if(argc != 2) {
    //Incorrect number of commandline arguments;
    //Invoke program followed by single filename
    cout << "usage:  readabf filename" << endl;
    return 1;
  }
 
  //Open the file specified by the commandline argument for binary input
  ifstream fin(argv[1], ios_base::in | ios_base::binary);
  if(!fin.is_open()) {
    //File cannot be opened for binary input
    cout << "error:  cannot open " << argv[1] << " for read";
    //Reset failbit
    fin.clear();
    cout << endl; 
    return 1;
  }
 
  //Declare ABFFileHeader structure to hold header information
  ABFFileHeader *myFH = new ABFFileHeader;
 
  //Prepare to read file header into myFH, by positioning the random-access
  //index to point to the beginning of the file
  fin.seekg(0, ios_base::beg);
 
  //Read the file header into myFH byte-by-byte
  fin.read((char *) myFH, sizeof *myFH);
 
  //Set fHeaderVersion to agree with current version specified by ABFHEADR.H 
  myFH->fHeaderVersionNumber = ABF_CURRENTVERSION;
 
 
  //To format floating point values as fixed decimals, uncomment the next line
  //cout.setf(ios_base::fixed);
 
 
  //Print out a few parameters
  cout << "fFileVersionNumber = "        <<  myFH->fFileVersionNumber        << "\n";
  cout << "nOperationMode = "            <<  myFH->nOperationMode            << "\n";
  cout << "lActualAcqLength = "          <<  myFH->lActualAcqLength          << "\n";
  cout << "nNumPointsIgnored = "         <<  myFH->nNumPointsIgnored         << "\n";
  cout << "lActualEpisodes = "           <<  myFH->lActualEpisodes           << "\n";
  cout << "lFileStartDate = "            <<  myFH->lFileStartDate            << "\n";
  cout << "lFileStartTime = "            <<  myFH->lFileStartTime            << "\n";
  cout << "lStopwatchTime = "            <<  myFH->lStopwatchTime            << "\n";
  cout << "fHeaderVersionNumber = "      <<  myFH->fHeaderVersionNumber      << "\n";
  cout << "nFileType = "                 <<  myFH->nFileType                 << "\n";
  cout << "nMSBinFormat = "              <<  myFH->nMSBinFormat              << "\n";
  cout << "lDataSectionPtr = "           <<  myFH->lDataSectionPtr           << "\n";
  cout << "lTagSectionPtr = "            <<  myFH->lTagSectionPtr            << "\n";
  cout << "lNumTagEntries = "            <<  myFH->lNumTagEntries            << "\n";
  cout << "lSynchArrayPtr = "            <<  myFH->lSynchArrayPtr            << "\n";
  cout << "lSynchArraySize = "           <<  myFH->lSynchArraySize           << "\n";
  cout << "nDataFormat = "               <<  myFH->nDataFormat               << "\n";
  cout << "nADCNumChannels = "           <<  myFH->nADCNumChannels           << "\n";
  cout << "fADCSampleInterval = "        <<  myFH->fADCSampleInterval        << "\n";
  cout << "fADCSecondSampleInterval = "  <<  myFH->fADCSecondSampleInterval  << "\n";
  cout << "lClockChange = "              <<  myFH->lClockChange              << "\n";
  cout << "fADCRange = "                 <<  myFH->fADCRange                 << "\n";
  cout << "lADCResolution = "            <<  myFH->lADCResolution            << "\n";
  cout << "fADCProgrammableGain[0] = "   <<  myFH->fADCProgrammableGain[0]   << "\n";
  cout << "fInstrumentScaleFactor[0] = " <<  myFH->fInstrumentScaleFactor[0] << "\n";
  cout << "fInstrumentOffset[0] = "      <<  myFH->fInstrumentOffset[0]      << "\n";
  cout << "fSignalGain[0] = "            <<  myFH->fSignalGain[0]            << "\n";
  cout << "fSignalOffset[0] = "          <<  myFH->fSignalOffset[0]          << "\n";
  cout << "nSignalType = "               <<  myFH->nSignalType               << "\n";
  cout << "nTelegraphEnable[0] = "       <<  myFH->nTelegraphEnable[0]       << "\n";
  cout << "fTelegraphAdditGain[0] = "    <<  myFH->fTelegraphAdditGain[0]    << "\n";
  cout << "lHeaderSize = "               <<  myFH->lHeaderSize               << "\n";
 
 
 

//Extract channel 0 signal assuming multiplexed two channel gap-free data

  //Extract parameters to convert ADC values to User Units
  float fADCToUUFactor;
  float fADCToUUShift;
  ABFH_GetADCtoUUFactors(myFH, 0, &fADCToUUFactor, &fADCToUUShift);
  cout << "pfADCToUUFactor = " << fADCToUUFactor << "\n";
  cout << "pfADCToUUShift = " << fADCToUUShift << "\n";

  //Print column headers
  cout.width(10);
  cout << "Sample";
  cout.width(15);
  cout << "Amplitude" << endl;

  //Prepare to extract data buffer by buffer
  long maxSampleBuf = 8192;                   //Maximum buffer size
  long lread = 0;                             //Multiplexed Sample number
  long lremain = myFH->lActualAcqLength;      //Number of unread samples
  short *ADCbuf = new short[8192];            //Buffer to hold two-byte ADC values
  float fUUValue;                             //ADC value converted to User Units
  long lbuf = (maxSampleBuf < lremain) ? maxSampleBuf : lremain;

  //Position random-access index at beginning of channel 0 data
  fin.seekg(myFH->lDataSectionPtr * 512, ios_base::beg);
  while (lbuf != 0) {
    //While there is a buffer full of unread points
    //Fetch two-bytes, lbuf times
    fin.read((char * ) ADCbuf, 2 * lbuf);
    
    //Process the buffer
    for (int i = 0 ; i < lbuf; i++) {
      if (lread % 2 == 0) {
        //But only if the two-channel multiplexed value belongs to channel 0

        //Convert ADC values to User Units
        fUUValue = ADCbuf[i] * fADCToUUFactor + fADCToUUShift;

        //Print data
        cout.width(10);
        cout << lread;
        cout.width(15);
        cout << fUUValue << "\n";
      }
      lread++;
    }
    lremain = myFH->lActualAcqLength - lread;
    lbuf = (maxSampleBuf < lremain) ? maxSampleBuf : lremain;
  }


  delete [] ADCbuf;
  delete myFH; 
  //Close file
  fin.close();
 
  return 0;
}