Scandotfit¶
Program to evaluate performance of scanner by measuring dots spaced 2.5 mm apart.
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 |
scandotfit_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:
scandotfit --f parameterfile.txt
Where the format of the parameters is:
Micrograph = cs_scan034.tif
Diagnostic plot = scandotfit_diag.pdf
Additional parameters (intermediate level)¶
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). |
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)
Additional parameters (expert level)¶
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). |
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)
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