output_initialise Subroutine

  subroutine output_initialise(hydrotope_id, hydrotope_area, hydrotope_subbasin, &
    subbasin_id, subbasin_nhydrotopes, subbasin_catchment, catchment_id, &
    hydrotope_input_fid, subbasin_input_fid)
    ! Process user input before variables are registered
    use utilities, only: string_index
    integer, dimension(:), intent(in) :: &
      ! Hydrotope IDs and subbasin mapping (must be same length)
      hydrotope_id, hydrotope_subbasin, &
      ! Subbasin IDs and catchment mapping (must be same length)
      subbasin_id, subbasin_nhydrotopes, subbasin_catchment, &
      !Catchment IDs
      catchment_id
    ! Hydrotope area for weighted averages
    real, dimension(:), intent(in) :: hydrotope_area
    ! File ids to read output labels
    integer, intent(in) :: hydrotope_input_fid
    integer, intent(in) :: subbasin_input_fid
    integer s

    ! Hydrotope arrays
    output_nhydrotopes = size(hydrotope_id)
    allocate(output_hydrotope_id(output_nhydrotopes))
    allocate(output_hydrotope_subbasin_ix(output_nhydrotopes))
    allocate(output_hydrotope_subbasin_share(output_nhydrotopes))
    output_hydrotope_id = hydrotope_id

    ! Subbasin arrays
    output_nsubbasins = size(subbasin_id)
    allocate(output_subbasin_id(output_nsubbasins))
    allocate(output_subbasin_catchment_ix(output_nsubbasins))
    ! initialised with 2 because if catchment ids not read with subcatch = False
    ! 2 is the index of the default catchment ID, 1 being the total catchment
    output_subbasin_catchment_ix = 2
    allocate(output_subbasin_catchment_share(output_nsubbasins))
    output_subbasin_id = subbasin_id
    allocate(output_subbasin_nhydrotopes(output_nsubbasins))
    output_subbasin_nhydrotopes = subbasin_nhydrotopes
    allocate(output_subbasin_hydrotope_stix(output_nsubbasins))
    output_subbasin_hydrotope_stix = 0
    ! Make cumsum out of sparse hydrotope numbers for quick start index
    do s = 1, output_nsubbasins-1
      output_subbasin_hydrotope_stix(s+1) = &
        output_subbasin_hydrotope_stix(s) + subbasin_nhydrotopes(s)
    end do

    ! Catchment arrays
    output_ncatchments = size(catchment_id) + 1  ! one extra for catchment total
    allocate(output_catchment_id(output_ncatchments))
    allocate(output_catchment_basin_share(output_ncatchments))
    output_catchment_id(1) = 0
    output_catchment_id(2:output_ncatchments) = catchment_id

    allocate(output_storage_index(output_nfiles, output_nvars))
    output_storage_index = 0

    call output_initialise_unit_shares(hydrotope_subbasin, subbasin_catchment, hydrotope_area)
    call output_initialise_time
    ! Fill convenience matrix
    call output_initialise_is_requested
    call output_initialise_storage(hydrotope_input_fid, subbasin_input_fid)

    call output_allocate(output_nsubbasins, output_nsubbasins)

  end subroutine output_initialise