Configuration

Configuration for TopoStats is done using a YAML configuration that is specified on the command line when invoking. A default configuration file is provided in the TopoStats repository at topostats/default_config.yaml. The file contains comments indicating valid values for many of the fields. If no configuration file is provided this default configuration is loaded automatically and used.

You can make a copy of the default_config.yaml and modify it for your own use. Once saved you can run TopoStats with this configuration file as shown below.

run_topostats --config my_config.yaml

On completion a copy of the configuration that was used is written to the output directory.

Fields

Aside from the comments in YAML file itself the fields are described below.

Section	Sub-Section	Data Type	Default	Description
base_dir		string	./	Directory to recursively search for files within.
output_dir		string	./output	Directory that output should be saved to.
warnings		string	ignore	Turns off warnings being shown.
cores		integer	4	Number of cores to run parallel processes on.
quiet		false
file_ext		string	.spm	File extensions to search for.
loading	channel	string	Height	The channel of data to be processed, what this is will depend on the file-format you are processing and the channel you wish to process.
filter	run	boolean	true	Whether to run the filtering stage, without this other stages won't run so leave as true.
	threshold_method	str	std_dev	Threshold method for filtering, options are ostu, std_dev or absolute.
	otsu_threshold_multiplier	float	1.0
	threshold_std_dev	float	1.0
	threshold_absolute_lower	float	-1.0
	threshold_absolute_upper	float	1.0
	gaussian_size	float	0.5	The number of standard deviations to build the Gaussian kernel and thus affects the degree of blurring. See skimage.filters.gaussian and sigma for more information
	gaussian_mode	string	nearest
grains	run	boolean	true	Whether to run grain finding. Options true, false
	absolute_smallest_grain_size	int	100	The smallest size of grains to be included (in pixels), anything smaller than this is considered noise and removed.
	threshold_method	float	std_dev	Threshold method for grain finding. Options : otsu, std_dev, absolute
	otsu_threshold_multiplier		1.0	Factor by which the derived Otsu Threshold should be scaled.
	threshold_std_dev		1.0
	threshold_absolute_lower		1.0
	threshold_absolute_upper		1.0
	absolute_area_threshold	dictionary
	...upper	list	[500,800]	Height above surface [Low, High] in nm^2 (also takes null)
	...lower		[null, null]	Height below surface [Low, High] in nm^2 (also takes null)
	direction		upper	Defines whether to look for grains above or below thresholds or both. Options: upper, lower, both
	background	float	0.0
grainstats	run	boolean	true	Whether to calculate grain statistics. Options : true, false
	cropped_size	float	40.0	Force cropping of grains to this length (in nm) of square cropped images (can take -1 for grain-sized box)
	save_cropped_grains	boolean	true	Options : true, false
dnatracing	run	boolean	true	Whether to run DNA Tracing. Options : true, false
plotting	run	boolean	true	Whether to run plotting. Options : true, false
	save_format	string	png	Format to save images in, see matplotlib.pyplot.savefig
	image_set	string	all	Which images to plot. Options : all, core
	zrange	list	[0, 3]	Low and high height range for core images (can take [null, null])
	colorbar	boolean	true	Whether to include the colorbar scale in plots. Options true, false
	axes	boolean	true	Wether to include the axes in the produced plots.
	cmap	string	nanoscope	Colormap to use in plotting. Options : nanoscope, afmhot
	histogram_log_axis	bbolean	false	Whether to plot hisograms using a logarithmic scale or not. Options: true, false.

Validation

Configuration files are validated against a schema to check that the values in the configuration file are within the expected ranges or valid parameters. This helps capture problems early and should provide informative messages as to what needs correcting if there are errors.