.. highlight:: rest

.. _makez:

Stage 3 - Observations, background and priors
==================================

The solution of :ref:`Equation 1 <equation1>` requires a prior estimate of s (called s\ :sub:`p` or sprior).  The user must create 
the *sprior* file with dimensions ntimesteps x nlandcells, so there is a value for each land cell at each time step. 


:ref:`Equation 1 <equation1>` also uses *z*, a vector of measurements for use in the term
:math:`(z-Hs_p)`.  This term is defined as

        :math:`(z-Hs_p)` = (observation - bg - Hs\ :sub:`p` - Hother )

The program **make_z.py** makes these calculations and creates one file used in the inversion, 

        * *zhsp.txt* - contains :math:`(z-Hs_p)`\ , dimensions (nobs)

and several additional files for information:

        * *obs-bg.txt* - Observation values minus the background values.
        * *hsprior.txt* - H convolved with sprior.

Prerequisites
-------------

        * observation list - File with observation values, one value per line for each receptor. 
        * background list - File with background values, one value per line for each receptor. 
        * sprior - contains s\ :sub:`p`\ . Can be either a numpy save file, dimensions (ntimesteps x ncells), or 
          a netcdf file, with a variable named 'sprior' and dimensions (ntimesteps x nlat x nlon)
        * H blocks created by :ref:`hsplit.py <hsplit>`.
        * (Optional) hother, one value per line for each receptor, with additional values to subtract from *z*.

Usage
-------------

        **make_z.py** is run with::

                Usage: make_z.py [--other=otherdata] [-c configfile] obsfile spriorfile backgroundfile

                where 

                  Reguired arguments
                        obsfile            : file with observation value, one line per receptor.
                        spriorfile         : file with sprior data. It can be either .npy or netcdf format.
                        backgroundfile     : file with background value, one line per receptor. Default is 'bg.txt'.

                  Optional arguments
                        -c configfile      : file with configuration data.  Default is 'config.ini'.
                        --other=otherdata  : file with other values to subtract from observations, one line per receptor.


                  Output:
                        zhsp.txt    - Observations minus background minus hsprior minus hother
                        hsprior.txt - H convolved with sprior
                        obs-bg.txt  - Observations minus background