.. SPDX-FileCopyrightText: 1992-2026 NWO-I/SRON Space Research Organisation Netherlands
..
.. SPDX-License-Identifier: CC-BY-4.0

Data related procedures
=======================

The commands in this section are all related to the data structures within SPEX. They deal with
spectral data and responses, simulation of data, etc.

.. _spexapi_data:

Data
----

Loading spectral data and responses in SPEX is done with the ``data`` command. Data can be added
by loading a .res and .spo file that contain the response and spectral information for an
instrument. The Fortran API procedure is::

    call spex%data(resfile,spofile,ier)

where ``resfile`` is the response file, ``spofile`` the spectrum file, and ``ier`` the output
error condition.

::

     module subroutine spex_io_data(this,resname,sponame,ier)
        class(sapi),  intent(inout)   :: this
        character*(*), intent(in)     :: resname   !! Input .res file name
        character*(*), intent(in)     :: sponame   !! Input .spo file name
        integer, intent(out)          :: ier       !! Error status
     end subroutine

Note that this command needs the full filename (and if necessary the path to the file) including
the extension. This is the only difference with the SPEX syntax. Example::

    call spex%data('xifu.res','xifu.spo',ier)

.. _spexapi_data_del:

Data delete
"""""""""""

Deleting a loaded spectrum and response is done in SPEX with the ``data delete instrument #i``
command. In the Fortran API, the procedure is::

    call spex%data_del(ins,ier)

where ``ins`` is the instrument number to be deleted and ``ier`` the output error condition.

::

    module subroutine spex_io_data_del(this, ins, status)
        class(sapi),  intent(inout) :: this
        integer, intent(in)        :: ins         !! Instrument number
        integer, intent(inout)     :: status      !! Error status
    end subroutine

Example::

    call spex%data_del(1,ier)

.. _spexapi_data_save:

Data save
"""""""""

Simulated spectra can be saved as a .spo file. In SPEX, this is done using the
``data save #i <spofile>`` command. In the Fortran API, the command is::

    call spex%data_save(ins,sponame,overwrite,ier)

where ``ins`` is the instrument number of the data to be saved, ``spofile`` is the name of
the output .spo file. Again note that you should give the full file name, including the .spo
extension. The ``overwrite`` logical overwrites an existing file if true.

::

    module subroutine spex_io_data_save_spo(this,ins,sponame,overwrite,status)
        class(sapi),  intent(inout)      :: this
        integer, intent(in)              :: ins        !! Instrument number
        character*(*), intent(in)        :: sponame    !! Output spectrum file name (.spo)
        logical, intent(in)              :: overwrite  !! Overwrite existing file (true/false)
        integer, intent(inout)           :: status     !! Error status
    end subroutine

For example::

    call spex%data_save(1,'sim.spo',.true.,ier)

.. _spexapi_bin:

Binning and data selection
--------------------------

Unlike some other fitting packages, SPEX rebins the spectra within the program. The easiest binning
method is to just rebin with a certain integer factor. This is the ``bin`` command in SPEX. In
addition, SPEX contains a binning method based on the bin statistics (``vbin``) and an optimal
binning algorithm (``obin``) which takes the instrument resolution into account.

**Binning with factor**

Binning with an integer factor is done with the bin command::

    call spex%bin(in,ir,r1reb,r2reb,freb,unit,status)

The ``in`` parameter is the instrument number, the ``ir`` parameter the
region number, ``r1reb`` and ``r2reb`` are the lower and upper boundary of the
energy interval to be rebinned, ``freb`` is the rebinning factor, ``unit``
the physical unit of the energy range, and ``status`` is the output error condition.

::

    module subroutine spex_io_bin(this,in,ir,r1reb,r2reb,freb,unit,status)
        class(sapi),  intent(inout)      :: this
        integer, intent(in)              :: in     !! Instrument number
        integer, intent(in)              :: ir     !! Region number
        real(dp), intent(in)             :: r1reb  !! Lower rebinning boundary
        real(dp), intent(in)             :: r2reb  !! Upper rebinning boundary
        integer, intent(in)              :: freb   !! Factor binning
        character*(*), intent(in)        :: unit   !! Unit of provided boundaries
        integer, intent(out)             :: status !! Error status
    end subroutine

In this example, we bin the spectrum with a factor of 5 between 0.3 and 10 keV::

    call spex%bin(1,1,0.3,10.,5,'kev',status)

**Variable binning**

Variable binning is done with the vbin command::

    call spex%vbin(in,ir,r1,r2,unit,ivarbin,snlim,status)

The ``in`` parameter is the instrument number, the ``ir`` parameter the
region number, ``r1`` and ``r2`` are the lower and upper boundary of the
energy interval to be rebinned, ``unit`` the physical unit of the energy range,
``ivarbin`` is the minimum number of bins to be added, ``snlim`` is the
minimum signal to noise and ``status`` is the output error condition.

::

    module subroutine spex_io_vbin(this,in,ir,r1,r2,unit,ivarbin,snlim,status)
        class(sapi),  intent(inout)      :: this
        integer, intent(in)              :: in      !! Instrument number
        integer, intent(in)              :: ir      !! Region number
        real(dp), intent(in)             :: r1      !! Lower rebinning boundary
        real(dp), intent(in)             :: r2      !! Upper rebinning boundary
        character*(*), intent(in)        :: unit    !! Unit of provided boundaries
        integer, intent(in)              :: ivarbin !! Minimum number of bins to be added
        real(dp), intent(in)             :: snlim   !! Minimum S/N ratio to be achieved
        integer, intent(out)             :: status  !! Error status
    end subroutine

In this example, we bin the spectrum with a minimum factor of 3 and a minimum signal-to-noise
ratio of 25 between 0.3 and 10 keV::

    call spex%vbin(1,1,0.3,10.,3,25.,'kev',status)

**Optimal binning**

The optimal binning algorithm bins based on the instrument resolution and statistics::

    call spex%obin(in,ir,r1reb,r2reb,unit,status)

The ``in`` parameter is the instrument number, the ``ir`` parameter the
region number, ``r1reb`` and ``r2reb`` are the lower and upper boundary of the
energy interval to be rebinned, ``unit`` the physical unit of the energy range,
and ``status`` is the output error condition.

::

    module subroutine spex_io_obin(this,in,ir,r1reb,r2reb,unit,status)
        class(sapi),  intent(inout)      :: this
        integer, intent(in)              :: in      !! Instrument number
        integer, intent(in)              :: ir      !! Region number
        real(dp), intent(in)             :: r1reb   !! Lower rebinning boundary
        real(dp), intent(in)             :: r2reb   !! Upper rebinning boundary
        character*(*), intent(in)        :: unit    !! Unit of provided boundaries
        integer, intent(out)             :: status  !! Error status
    end subroutine

In this example, we optimally bin the spectrum between 0.3 and 10 keV::

    call spex%obin(1,1,0.3,10.,'kev',status)

.. _spexapi_use:

Data selection
""""""""""""""

Selecting data is done using the ``use`` and ``ignore`` commands. By default, the bin selection
in the ``.spo`` file is loaded, which should use all the good bins.

**Use function**

::

    call spex%use(in,ir,r1,r2,unit,status)

The ``in`` parameter is the instrument number, the ``ir`` parameter the
region number, ``r1`` and ``r2`` are the lower and upper boundary of the
energy interval to be used, ``unit`` the physical unit of the energy range,
and ``status`` is the output error condition.

::

    module subroutine spex_io_use(this,in,ir,r1,r2,unit,status)
        class(sapi),  intent(inout)       :: this
        integer, intent(in)              :: in     !! Instrument number
        integer, intent(in)              :: ir     !! Region number
        real(dp), intent(in)             :: r1     !! Lower range boundary
        real(dp), intent(in)             :: r2     !! Upper range boundary
        character*(*), intent(in)        :: unit   !! Unit of provided boundaries
        integer, intent(out)             :: status !! Status error
    end subroutine

Example::

    call spex%use(1,1,0.3,10.,'kev')

**Ignore function**

::

    call spex%ignore(in,ir,r1,r2,unit,status)

The ``in`` parameter is the instrument number, the ``ir`` parameter the
region number, ``r1`` and ``r2`` are the lower and upper boundary of the
energy interval to be ignored, ``unit`` the physical unit of the energy range,
and ``status`` is the output error condition.

Example::

    call spex%ignore(1,1,0.0,0.3,'kev')
    call spex%ignore(1,1,10.,100.,'kev')

.. _spexapi_syserr:

Systematic errors
-----------------

If needed, the error bars on the source and background spectrum can be enlarged by the ``syserr``
command::

    call spex%syserr(in,ir,r1,r2,unit,serr,berr,status)

The ``in`` parameter is the instrument number, the ``ir`` parameter the
region number, ``r1`` and ``r2`` are the lower and upper boundary of the
energy interval to be changed, ``unit`` the physical unit of the energy range,
``serr`` is the systematic error on the source to be added, ``berr`` is the
systematic error on the background, and ``status`` is the output error condition.

::

    module subroutine spex_io_syserr(this,in,ir,r1,r2,unit,serr,berr,status)
        class(sapi),  intent(inout)       :: this
        integer, intent(in)              :: in     !! Instrument number
        integer, intent(in)              :: ir     !! Region number
        real(dp), intent(in)             :: r1     !! Lower range boundary
        real(dp), intent(in)             :: r2     !! Upper range boundary
        character*(*), intent(in)        :: unit   !! Unit of provided boundaries
        real(dp), intent(in)             :: serr   !! Systematic error source spectrum
        real(dp), intent(in)             :: berr   !! Systematic error background spectrum
        integer, intent(out)             :: status !! Error status
    end subroutine

Example::

    call spex%syserr(1,1,0.1,10.,'kev',0.1,0.1,status)


.. warning::

    To use this function, you need to know what you are doing statistically. In many cases, this
    function would produce wrong results.

Other commands
--------------

Setting instrument normalisations
"""""""""""""""""""""""""""""""""

During spectral fitting, instrument normalisations can be set
and freed to account for cross-calibration issues between instruments::

    call spex%set_inst_norm(is,ir,norm,ier)

Where ``is`` is the instrument number, ``ir`` the region number,
``norm`` the instrument normalisation, and ``ier`` the error code.

The Fortran interface::

      module subroutine spex_io_set_inst_norm(this, is, ir, norm, ier)
        class(sapi), intent(inout) :: this
        integer, intent(in)       :: is     !instrument number
        integer, intent(in)       :: ir     !region number
        real, intent(in)          :: norm   !instrument normalisation
        integer, intent(out)      :: ier    !error status
      end subroutine

The normalisation can also be fixed or freed::

    call spex%set_inst_free(is,ir,free,ier)

Where ``is`` is the instrument number, ``ir`` the region number,
``free`` is a logical (.true. is free), and ``ier`` is the error code.

The Fortran interface::

    module subroutine spex_io_set_inst_norm_free(this, is, ir, free, ier)
      class(sapi), intent(inout) :: this
      integer, intent(in)       :: is     !instrument number
      integer, intent(in)       :: ir     !region number
      logical, intent(in)       :: free   !instrument normalisation free=.true./frozen=.false.
      integer, intent(out)      :: ier    !error status
    end subroutine

Delete all instruments (reset)
""""""""""""""""""""""""""""""

Example::

    call spex%reset_data()

The Fortran interface::

    module subroutine spex_io_reset(this)
      class(sapi), intent(inout) :: this
    end subroutine