Scanrowcolcorr¶
Program to evaluate the performance of scanner by correlating adjacent rows and lines with each other from a pure noise image.
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 |
scanrowcolcorr_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:
scanrowcolcorr --f parameterfile.txt
Where the format of the parameters is:
Micrograph = cs_scan034.tif
Diagnostic plot = scanrowcolcorr_diag.pdf
Additional parameters (intermediate level)¶
Parameter |
Example (default) |
Description |
|---|---|---|
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
Additional parameters (expert level)¶
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). |
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
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