Main Function Operation and Use
================================

.. automodule:: Main
    :members:
	
---------------	
Operation
---------------
This main function reads in the configuration options, sets up some lists to pass information between functions and iterates through each run as a group.

First, the object :obj:`Spec` is created from the :class:`~BasicProcessing.UnispecProcessing` class.  The Init function for the class also opens the config file specified and loads the values into class level variables.

.. code-block:: python

    >path = str(os.path.realpath('.'))
    >Spec = UnispecProcessing(path + r'\config.txt')

Then, file lists for runs, white plates and stops are generated.  These lists are also stored within the class.

.. code-block:: python

    >run_count, WP_count, stop_count = Spec.GetFileLists()

For each run (as determined by the poisitions of white plates between stops in chronological order), arrays are created for the "raw" imported data and saturation counts.

.. code-block:: python

    >for run in range(0,run_count):
    >    
	>	#There must be at least one white plate and one stop for a run to produce any useful data, otherwise skip it.
    >    if (WP_count[run] == 0) or (stop_count[run] == 0):
    >        continue
    >
    >    WP_data = [[[None], [None]] for item in range(0,WP_count[run])]
    >    Stop_data = [[[None], [None]] for item in range(0,stop_count[run])]
    >    sat = [[None], [None]]

These arrays are populated by :func:`~BasicProcessing.UnispecProcessing.ReadFiles` with the white plates and stops as two seperate groups.

.. code-block:: python

    >    WP_data = Spec.ReadFiles(Spec.WPs[run], Spec.HeaderLines)
    >    Stop_data = Spec.ReadFiles(Spec.Stops[run], Spec.HeaderLines)


Next, both data sets are checked for saturated values and a count of these are returned.  These counts could be used as a condition for whether or not to keep data from a specific stop/run.

.. code-block:: python

    >    sat_WP = Spec.CheckSaturation(WP_data)
    >    sat_stops = Spec.CheckSaturation(Stop_data)


The counts for each white plate/stop are also printed as a diagnostic.

.. code-block:: python

    >    print("Saturated Measurement Count\n\t\tCh_B\tCh_A")
    >    for idx, curfile in enumerate(sat_WP):
    >        print("WP " + str(idx) + ":\t\t" + str(curfile[1]) + "\t" + str(curfile[2])) 
    >    for idx, curfile in enumerate(sat_stops):
    >        print("Stop " + str(idx) + ":\t\t" + str(curfile[1]) + "\t" + str(curfile[2]))        
    >    print("\n" + str(len(sat_WP)) + " WPs and " + str(len(sat_stops)) + " stops saturated.")


Optionally, saturated stops are removed.

.. code-block:: python

    >    #Spec.RemoveSaturated(WP_data, sat_WP)
    >    #Spec.RemoveSaturated(Stop_data, sat_stops)


The "raw" data is then interpolated to 1 1nm.

.. code-block:: python

    >    intdata_WPs = Spec.Interp(WP_data)
    >    intdata_Stops = Spec.Interp(Stop_data)


All of the white plate values are averaged to a single data set.

.. code-block:: python

    >    avg_WP = Spec.AvgWPs(intdata_WPs)


Optionally, the white plate average can be plotted against all of the individual measurments as a diagnostic.

.. code-block:: python

    >    #Plot all WPs with average
    >    #Spec.plot_Averaging(intdata_WPs, avg_WP)


Next, the reflectance values are calculated.

.. code-block:: python

    >    R = Spec.Refl(intdata_Stops, avg_WP)


These can also be plotted for a particular stop as a diasgnostic.

.. code-block:: python

    >    #Spec.plot_R(R,20)


Finally, the CSV output is generated.  The date and tiem from the first white plate of a given run are used in the filename as a reference.

.. code-block:: python

    >    dt = Spec.GetDateTime(WP_data[0])       
    >    Spec.WriteOutput(R, "c:\\UniSpec\\Test", "test_R_" + dt[consts.date] + "__" + dt[consts.time].replace(':','_') + ".csv")



----------------------
Configuration File
----------------------

The configuration file is seperated into an Input and an Output section to help organize parameters, especially as future options are potentially added.

.. code-block:: text

	[Input]
	SourcePath = C:\Users\amcmahon\Documents\TEST\UnispecScripts\TestData\2015
	WP_Identifier = 000
	HeaderLines = 10

	[Output]
	OutputPath = C:\\UniSpec\\Test