.. _scanrowcolcorr:

Scanrowcolcorr
--------------

 
Program to evaluate the performance of scanner by correlating adjacent rows 
and lines with each other from a pure noise image.


        +--------------------------------------------------+--------------------------------------------------+
        | |scanrowcolcorr_input.png|                       | |scanrowcolcorr_output.png|                      |
        +--------------------------------------------------+--------------------------------------------------+
        | Input: Micrograph                                | Output: Diagnostic plot                          |
        +--------------------------------------------------+--------------------------------------------------+
        
        .. |scanrowcolcorr_input.png| image:: ../gallery_images/scanrowcolcorr_input.png
            :alt: tree
            :width: 4 cm
            :target: ../_images/scanrowcolcorr_input.png
            
        .. |scanrowcolcorr_output.png| image:: ../gallery_images/scanrowcolcorr_output.png
            :alt: tree
            :width: 4 cm
            :target: ../_images/scanrowcolcorr_output.png

        

.. _making_a_scanrowcolcorr_table_for_beginner:

Parameters
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}|

==============================================================================   ==============================================================================   ====================================================================================================
Parameter                                                                        Example (default)                                                                Description
==============================================================================   ==============================================================================   ====================================================================================================
Micrograph                                                                       cs_scan034.tif                                                                   Input micrograph: accepted file formats (tif, .mrc, .mrcs, .spi, .hdf, .img, .hed).
Diagnostic plot                                                                  scanrowcolcorr_diag.pdf                                                          Output diagnostic plot: accepted file formats (pdf, .png, .bmp, .emf, .eps, .gif, .jpeg, .jpg, .ps, .raw, .rgba, .svg, .svgz, .tif, .tiff).
==============================================================================   ==============================================================================   ====================================================================================================



.. _scanrowcolcorr_parameter_file_for_beginner:

Sample parameter file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  

You may run the program in the command line by providing the parameters via a text file::

    scanrowcolcorr --f parameterfile.txt

Where the format of the parameters is::

    Micrograph                               = cs_scan034.tif
    Diagnostic plot                          = scanrowcolcorr_diag.pdf


.. _making_a_scanrowcolcorr_table_for_intermediate:

Additional parameters (intermediate level)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}|

==============================================================================   ==============================================================================   ====================================================================================================
Parameter                                                                        Example (default)                                                                Description
==============================================================================   ==============================================================================   ====================================================================================================
==============================================================================   ==============================================================================   ====================================================================================================



.. _scanrowcolcorr_parameter_file_for_intermediate:

Sample parameter file (intermediate level)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  

You may run the program in the command line by providing the parameters via a text file::

    scanrowcolcorr --f parameterfile.txt

Where the format of the parameters is::

    Micrograph                               = cs_scan034.tif
    Diagnostic plot                          = scanrowcolcorr_diag.pdf


.. _making_a_scanrowcolcorr_table_for_expert:

Additional parameters (expert level)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}|

==============================================================================   ==============================================================================   ====================================================================================================
Parameter                                                                        Example (default)                                                                Description
==============================================================================   ==============================================================================   ====================================================================================================
Percentage of micrograph area to be analyzed                                     90                                                                               0-100 percent from the row and column dimensions of micrograph (accepted values min=0, max=100).
==============================================================================   ==============================================================================   ====================================================================================================



.. _scanrowcolcorr_parameter_file_for_expert:

Sample parameter file (expert level)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  

You may run the program in the command line by providing the parameters via a text file::

    scanrowcolcorr --f parameterfile.txt

Where the format of the parameters is::

    Micrograph                               = cs_scan034.tif
    Diagnostic plot                          = scanrowcolcorr_diag.pdf
    Percentage of micrograph area to be analyzed = 90

.. _using_scanrowcolcorr_on_cmdline:

Command line options
~~~~~~~~~~~~~~~~~~~~~~~

When invoking scanrowcolcorr, you may specify any of these options::

    usage: scanrowcolcorr [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [input_output [input_output ...]]
    
    Program to evaluate the performance of scanner by correlating adjacent rows and lines with each other from a pure noise image.
    
    positional arguments:
      input_output          Input and output files
    
    optional arguments:
      -h, --help            show this help message and exit
      --g, --GUI            GUI option: read input parameters from GUI
      --p, --promptuser     Prompt user option: read input parameters from prompt
      --f FILENAME, --parameterfile FILENAME
                            File option: read input parameters from FILENAME
      --c, --cmd            Command line parameter option: read only boolean input parameters from command line and all other parameters will be assigned
                            from other sources
      --l LOGFILENAME, --logfile LOGFILENAME
                            Output logfile name as specified
      --d DIRECTORY_NAME, --directory DIRECTORY_NAME
                            Output directory name as specified
      --version             show program's version number and exit


Program flow
~~~~~~~~~~~~~~~~~~~~
#. readmic: Read input micrograph
#. evalrowcc: Evaluate row-to-row cross-correlation
#. evalcolcc: Evaluate column-to-column cross-correlation
#. visrowcolcc: Visualize row-to-row and column-to-column correlation


Functions
~~~~~~~~~~~~~~~~~~~~

.. toctree::
   :maxdepth: 1

   scanrowcolcorr_functions