program mia


  use orbit_mia
  use mia_plot
  use mia_input
  use mia_matrixops
  use mia_parse
  use mia_veto

  implicit none

  character* 1 char
  integer :: istat, i_set, narg, b
  logical :: good_input, more_files, first_run

  type(data_set), allocatable :: data(:)
  integer :: time(8)
  real :: startTime, endTime

  !Calls to date_and_time are for measuring MIA's run time
  call date_and_time(values=time)
  startTime = time(5) * 3600 + time(6) * 60 &
       + time(7) + 0.001 * time(8)

  more_files = .false.
  first_run = .true.

  !Whole program can be looped asking for more files.Code involving 
  !variable more_files can be uncommented to re-enable this.
  do while (more_files .or. first_run)
     nset = 2
     allocate (data(nset)) !MIA can run with only one file; however, allocate  for
                           !2 files by default for now

     !Check for and parse command line arguments:
     narg = IARGC()
     if (narg>0) call get_args(data)

     !nset is number of files to analyze. MIA wants one file with horizontal
     !shaking and one with vertical shaking, so this is normally 2.
     !Unless the user wants an FFT of a single file.
     if (fftOnly) nset = 1

     !Read data and perform SVD and FFT:
     do i_set = 1, nset            
        
        if(readOrbitData .and. i_set == 1) then
           call read_orbit_data(data(1),data(2))
        else if (.not. readOrbitData) then
           call read_data(data(i_set),i_set,nset)
        endif
        
        !Initialize data structures after reading number of
        !turns, BPMs, etc from first file (second file is expected
        !to match, or else MIA quits)
        if (i_set == 1) call initialize_struct(data(i_set), .false.)

        !Parse detector names, get S positions, etc:
        call bpm_ops(data,i_set, nset, first_run)

        call svd_fft(data(i_set))

    end do

!@@@@@@@@@@@    

    first_run = .false.
    call match_tau_column(nset,data)


871  continue
     if (NUM_BPMS > 20) then
        !call autoCut(data)
     end if
!     call autoVeto(data)
567  continue
     if (vetoBPM) then
        
        call clean(.false.)
        call initialize_struct(data(1), .true.)
        call findPair(nset,data)

        call svd_fft(data(1))
        call svd_fft(data(2))
        call match_tau_column(nset,data)
        vetoBPM = .false.

        goto 871

     end if



    !**For single-file SVD analysis:
    if (fftOnly) then
       call combineFFT(data(1))
       call plots(data, 1)
       call combinedfftOut(data)
       deallocate(data)
       call clean(.false.)
       STOP !Quit before analysis requiring second file
    end if


!     call getLatticeAndTune
     call tune(data)
     Print *, "A tune: ", data_struc%tune(1)
     Print *, "B tune: ", data_struc%tune(2)
     call convert_data_from_pi_matrix(data)
     call calculate_with_known_spacing(data)

     if (.not. silentMode) then
        call plots(data, 2)         !Use plot_it2
     end if
     !Check if user has vetoed a detector:
     if (vetoBPM) then
        !Parse user input and remove vetoed detector(s)
        call veto(data, inputPasser)
        goto 567

     end if

     if(readOrbitData) then
        call write_orbits(data)
        STOP
     end if

!Write the output files
     call whichVersion(data)
     call output (data)
     call rawfftOut(data)
!     call debOut(data)
!     call posOut(data)

     if (.not. noSPos) then
        call cesrv_out()
     end if

!Disabled to make batch analysis easier; can uncomment this
!to give the user the option of running MIA with a new set of files
!without exiting
!     if (.not. silentMode) then
!        call logic_get('Y', 'N', 'Repeat calculations with different files?',&
!             more_files)
!     else
!        more_files = .false.
!     endif
     if (.not. more_files) then
        deallocate (data)
     end if
     call clean (more_files)
  enddo


  call date_and_time(values=time)
  endTime = time(5) * 3600 + time(6) * 60 &
       + time(7) + 0.001 * time(8) - startTime
  Print *, "MIA ran in ", endTime, "seconds."

end program mia