Configuration

The config module can be used to alter and ColiCoords’ default configuration values. These are mostly default values in relation to the generation of graphs via the plot module and they do not affect coordinate transformations. These default values for plot generation can be overruled by giving explicit keyword arguments to plot functions.

Name	Type	Default value	Units	Description
IMG_PIXELSIZE	float	80	Nanometers	Pixel size of the acquired images.
ENDCAP_RANGE	float	20.0	Pixels	Default bounds for positions of cell’s poles used in bounded optimization.
R_DIST_STOP	float	20.0	Pixels	Upper limit for generation of radial distribution curves.
R_DIST_STEP	float	0.5	Pixels	Step size between datapoints for generation of radial distribution curves
R_DIST_SIGMA	float	0.3	Pixels	Size of the sigma parameter of gaussian used for convolution to generate radial distribution curves.
L_DIST_NBINS	int	100	-	Number of bins to generate the longitudinal distribution curves.
L_DIST_SIGMA	float	0.5	Pixels	Size of the sigma parameter of gaussian used for convolution to generate longitudinal distribution curves.
PHI_DIST_STEP	float	1.0	Degrees	Step size between datapoints for generation of angular distribution curves.
PHI_DIST_SIGMA	float	5.0	Degrees	Size of the sigma parameter of gaussian used for convolution to generate longitudinal distribution curves.
CACHE_DIR	str		-	Path to the chache dir directory.
DEBUG	bool	False	-	Set to True to print numpy division warnings.