Documented functions with links to source

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

class scandotfit.ScanDotFitPar

Class to initiate default dictionary with input parameters including help and range values and status dictionary

Methods

define_parameters_and_their_properties
define_program_states
set_bottomleft_coordinates
set_integration_width
set_topleft_coordinates
set_topright_coordinates

define_parameters_and_their_properties()

define_program_states()

set_integration_width(feature_set)

set_topleft_coordinates(feature_set)

set_topright_coordinates(feature_set)

set_bottomleft_coordinates(feature_set)

class scandotfit.ScanDotFit(parset=None)

• Class that holds functions for automated distance measurements from regular dots on micrograph

• __init__ Function to read in the entered parameter dictionary and load micrograph

1. Usage: ScanDotFit(pardict)

2. Input: pardict = OrderedDict of program parameters

Methods

dotdistance([dots, stepsize, no_cols, no_rows])	Function to determine distances between adjacent dots
pttoline([ptone, pttwo])	Function that determines line equation from two given points
searchdots([boxwidth, topleft, topright, …])	Function to determine coordinates of dots by center of gravity measurements
visdots([dots, horidots, vertdots])	Function to visualize detected dots using matplotlib
vismic(nx, ny, subplot)	Function to prepare a micrograph in row and column dimension for matplotlib

perform_scandotfit

pttoline(ptone=None, pttwo=None)

• Function that determines line equation from two given points

1. Usage: slope, intercept = pttoline(ptone, pttwo)

2. Input: ptone = tuple of x,y coordinates, pttwo = tuple of x,y coordinates

3. Output: slope, intercept

searchdots(boxwidth=None, topleft=None, topright=None, bottomleft=None, stepsize=None)

• Function to determine coordinates of dots by center of gravity measurements

1. Usage: dotx, doty = (boxwidth, topleft, topright, bottomleft, stepsize)

2. Input: boxwidth width of integration, topleft/topright/bottomleft coordinate pair

3. Output: dotx and doty = list of X and Y coordinates of dots

dotdistance(dots=None, stepsize=None, no_cols=None, no_rows=None)

• Function to determine distances between adjacent dots

1. Usage: distances = dotdistance(dots, stepsize, no_cols, no_rows)

2. Input: dots = list of X and Y coordinates of dots, scanner stepsize, number of columns, number of rows

3. Output: list of horizontal and vertical distances from adjacent dots

vismic(nx, ny, subplot)

• Function to prepare a micrograph in row and column dimension for matplotlib

1. Usage: plot = vismic(nx, ny, subplot)

2. Input: nx = number of rows, ny = number of columns, subplot = idendity of subplot

3. Output: subplot to be returned

visdots(dots=None, horidots=None, vertdots=None)

• Function to visualize detected dots using matplotlib

1. Usage: output = visfit(dots, horidots, vertdots)

2. Input: dots = list of X and Y coordinates of dots, horidots, vertdots = list of distances

3. Output: output plot to saved to PDF, PNG format

perform_scandotfit()

scandotfit.main()