Scandotfit

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

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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

  1. readmic: Read input micrograph

  2. searchdots: Determines positions of dots by center of gravity calculation

  3. dotdistance: Calculates distance between dots

  4. visdots: Visualization of dots