.. _scanlinefit: Scanlinefit ----------- Program to evaluate scanner performance of scanner by measuring deviation from 45 degree line to determine CCD curvature and pincushion parameter. +--------------------------------------------------+--------------------------------------------------+ | |scanlinefit_input.png| | |scanlinefit_output.png| | +--------------------------------------------------+--------------------------------------------------+ | Input: Micrograph | Output: Diagnostic plot | +--------------------------------------------------+--------------------------------------------------+ .. |scanlinefit_input.png| image:: ../gallery_images/scanlinefit_input.png :alt: tree :width: 4 cm :target: ../_images/scanlinefit_input.png .. |scanlinefit_output.png| image:: ../gallery_images/scanlinefit_output.png :alt: tree :width: 4 cm :target: ../_images/scanlinefit_output.png .. _making_a_scanlinefit_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 scanlinefit_diag.pdf Output diagnostic plot: accepted file formats (pdf, .png, .bmp, .emf, .eps, .gif, .jpeg, .jpg, .ps, .raw, .rgba, .svg, .svgz, .tif, .tiff). ============================================================================== ============================================================================== ==================================================================================================== .. _scanlinefit_parameter_file_for_beginner: Sample parameter file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ You may run the program in the command line by providing the parameters via a text file:: scanlinefit --f parameterfile.txt Where the format of the parameters is:: Micrograph = cs_scan034.tif Diagnostic plot = scanlinefit_diag.pdf .. _making_a_scanlinefit_table_for_intermediate: Additional parameters (intermediate level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Topleft coordinates of line (180, 2302) Integer pair of coordinates (x,y) (accepted values min=0, max=30000). Bottomright coordinates of line (1889, 215) Integer pair of coordinates (x,y) (accepted values min=0, max=30000). ============================================================================== ============================================================================== ==================================================================================================== .. _scanlinefit_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:: scanlinefit --f parameterfile.txt Where the format of the parameters is:: Micrograph = cs_scan034.tif Diagnostic plot = scanlinefit_diag.pdf Topleft coordinates of line = (180, 2302) Bottomright coordinates of line = (1889, 215) .. _making_a_scanlinefit_table_for_expert: Additional parameters (expert level) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. tabularcolumns:: |p{4cm}|p{2.5cm}|p{9cm}| ============================================================================== ============================================================================== ==================================================================================================== Parameter Example (default) Description ============================================================================== ============================================================================== ==================================================================================================== Width of integration in pixels 9 Use default value: number of pixels used for line determination - otherwise use with caution (accepted values min=1, max=500). ============================================================================== ============================================================================== ==================================================================================================== .. _scanlinefit_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:: scanlinefit --f parameterfile.txt Where the format of the parameters is:: Micrograph = cs_scan034.tif Diagnostic plot = scanlinefit_diag.pdf Width of integration in pixels = 9 Topleft coordinates of line = (180, 2302) Bottomright coordinates of line = (1889, 215) .. _using_scanlinefit_on_cmdline: Command line options ~~~~~~~~~~~~~~~~~~~~~~~ When invoking scanlinefit, you may specify any of these options:: usage: scanlinefit [-h] [--g] [--p] [--f FILENAME] [--c] [--l LOGFILENAME] [--d DIRECTORY_NAME] [--version] [input_output [input_output ...]] Program to evaluate scanner performance of scanner by measuring deviation from 45 degree line to determine CCD curvature and pincushion parameter. 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 #. getline: Get line coordinates from micrograph #. fitcube: Fit extracted coordinates to cubic function #. visfit: Visualize extracted line and fitted function Functions ~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 scanlinefit_functions