Scanlinefit¶
Program to evaluate scanner performance of scanner by measuring deviation from 45 degree line to determine CCD curvature and pincushion parameter.
Input: Micrograph
Output: Diagnostic plot
Parameters¶
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). |
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
Additional parameters (intermediate level)¶
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). |
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)
Additional parameters (expert level)¶
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). |
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)
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