.. _scandotfit:

Scandotfit
----------

 
Program to evaluate performance of scanner by measuring dots spaced 2.5 mm apart. 


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

        

.. _making_a_scandotfit_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                                                                  scandotfit_diag.pdf                                                              Output diagnostic plot: accepted file formats (pdf, .png, .bmp, .emf, .eps, .gif, .jpeg, .jpg, .ps, .raw, .rgba, .svg, .svgz, .tif, .tiff).
==============================================================================   ==============================================================================   ====================================================================================================



.. _scandotfit_parameter_file_for_beginner:

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

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

    scandotfit --f parameterfile.txt

Where the format of the parameters is::

    Micrograph                               = cs_scan034.tif
    Diagnostic plot                          = scandotfit_diag.pdf


.. _making_a_scandotfit_table_for_intermediate:

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

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

==============================================================================   ==============================================================================   ====================================================================================================
Parameter                                                                        Example (default)                                                                Description
==============================================================================   ==============================================================================   ====================================================================================================
Scanner step size in micrometer                                                  7.0                                                                              Characteristic resolution or step size of scanner in micrometer (accepted values min=1, max=1000).
Topleft coordinates of dot grid                                                  (539, 2129)                                                                      Comma-separated integer pair of coordinates (x, y) (accepted values min=0, max=30000).
Topright coordinates of dot grid                                                 (1493, 2173)                                                                     Comma-separated integer pair of coordinates (x, y) (accepted values min=0, max=30000).
Bottomleft coordinates of dot grid                                               (638, 46)                                                                        Comma-separated integer pair of coordinates (x, y) (accepted values min=0, max=30000).
==============================================================================   ==============================================================================   ====================================================================================================



.. _scandotfit_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::

    scandotfit --f parameterfile.txt

Where the format of the parameters is::

    Micrograph                               = cs_scan034.tif
    Diagnostic plot                          = scandotfit_diag.pdf
    Scanner step size in micrometer          = 7.0
    Topleft coordinates of dot grid          = (539, 2129)
    Topright coordinates of dot grid         = (1493, 2173)
    Bottomleft coordinates of dot grid       = (638, 46)


.. _making_a_scandotfit_table_for_expert:

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

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

==============================================================================   ==============================================================================   ====================================================================================================
Parameter                                                                        Example (default)                                                                Description
==============================================================================   ==============================================================================   ====================================================================================================
Width of integration in pixels                                                   100                                                                              Use default value: width of box in pixels used for dot determination - otherwise use with caution (accepted values min=1, max=500).
==============================================================================   ==============================================================================   ====================================================================================================



.. _scandotfit_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::

    scandotfit --f parameterfile.txt

Where the format of the parameters is::

    Micrograph                               = cs_scan034.tif
    Diagnostic plot                          = scandotfit_diag.pdf
    Scanner step size in micrometer          = 7.0
    Width of integration in pixels           = 100
    Topleft coordinates of dot grid          = (539, 2129)
    Topright coordinates of dot grid         = (1493, 2173)
    Bottomleft coordinates of dot grid       = (638, 46)

.. _using_scandotfit_on_cmdline:

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

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

    usage: scandotfit [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [input_output [input_output ...]]
    
    Program to evaluate performance of scanner by measuring dots spaced 2.5 mm apart.
    
    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
#. searchdots: Determines positions of dots by center of gravity calculation
#. dotdistance: Calculates distance between dots
#. visdots: Visualization of dots


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

.. toctree::
   :maxdepth: 1

   scandotfit_functions