Data Dictionary

Output from TopoStats includes two sets of statistics in ASCII text .csv files. The tables below detail the columns of these files, the data types, a description and their units where appropriate.

all_statistics.csv

The all_statistics.csv file contains details on each grain that has been detected and traced and has the following fields.

Column / field / feature	Description	Type	Units
image	Filename (minus extension) of scan.	str	N/A
threshold	Whether grain is above or below a threshold.	str	N/A
grain_number	Number of found grain (starts at 0)	int	N/A
centre_x	x coordinate of grain centre.	float	m
centre_y	y coordinate of grain centre.	float	m
radius_min	minimum distance from the centroid to edge of the grain.	float	m
radius_max	maximum distance from the centroid to edge of the grain.	float	m
radius_mean	mean distance from the centroid to the edge of the grain.	float	m
radius_median	median distance from the centroid to the edge of the grain.	float	m
height_min	Minimum height of grain.	float	m
height_max	Maximum height of grain.	float	m
height_median	Median height of grain.	float	m
height_mean	Mean height of grain.	float	m
volume	Volume of the grain calculated as the number of pixels multiplied by each height and scaled to metres.	float	m^3
area	Area of the grain itself calculated as the number of pixels scaled to metres.	float	m^2
area_cartesian_bbox	Area of the bounding box for the grain along the cartesian axes. (Not the smallest bounding box).	float	m^2
smallest_bounding_width	Width of the smallest bounding box for the grain (not along cartesian axes).	float	m
smallest_bounding_length	Length of the smallest bounding box for the grain (not along cartesian axes).	float	m
smallest_bounding_area	Area of the smallest bounding box for the grain (not along cartesian axes).	float	m^2
aspect_ratio	Aspect ratio of the grain (length / width), always >= 1.	float	N/A
max_feret	Longest length of the grain (see Feret diameter).	float	m
min_feret	Shortest width of the grain (see Feret diameter).	float	m
basename	Directory in which images was found.	str	N/A
grain_endpoints	The number of pixels designated as endpoints (only 1 neighbour) in the pruned skeleton. NB molecules with zero end-points are circular/closed loops.	integer	N/A
grain_junctions	The number of pixels designated as junctions (>2 neighbours) in the pruned skeleton.	integer	N/A
total_branch_length	The sum of all branch lengths in the pruned skeleton.	float	m
grain_width_mean	The mean width of the grain.	float	m
num_crossings	The number of crossing regions found in the grain. Note: this will be equal to or lower than the number of junctions explained in the previous section.	integer	N/A
avg_crossing_confidence	The average of all pseudo crossing confidences. Used to estimate quality of predictions.	float	N/A
min_crossing_confidence	The minimum of all pseudo crossing confidences. Used to estimate quality of predictions.	float	N/A
num_molecules	The number of molecules found by following the tracing paths. Note: This will always be 1 for the TopoStats method.	integer	N/A
writhe_string	The writhe sign (+/-) which describes the crossing directionality. If a crossing contains > 2 crossing branches, the single crossing region is split into pairs and the writhe calculated in brackets i.e. "+(-++)".	str	N/A
total_contour_length	The total length along the splined trace of all identified molecules.	float	m
average_end_to_end_distance	The average distance from two endpoints of the spline of all identified linear molecules.	float	m

image_stats.csv

The image_stats.csv summarises the metrics

Column / field / feature	Description	Type	Units
image	Filename of image statistics pertain to.	str	N/A
image_size_x_m	Width of image.	float	m
image_size_y_m	Height of image.	float	m
image_area_m2	Area of image (width x height).	float	m^2
image_size_x_px	Width of image in pixels.	int	N/A
image_size_y_px	Height of image in pixels.	int	N/A
image_area_px2	Area of image in pixels squared.	int	N/A
grains_number_above	Number of grains found above threshold.	int	N/A
grains_per_m2_above	Density of grains above upper threshold.	int	N/A
grains_number_below	Number of grains found below threshold.	int	N/A
grains_per_m2_below	Density of grains below lower threshold.	int	N/A
rms_roughness	Root Mean Square Roughness, the square root of the mean squared heights across the surface (Surface Roughness; Surface roughness (Wikipedia))	float	N/A

all_disordered_segment_statistics.csv

Please refer to the specific sections on output from running Disordered Segment Statistics Tracing section of the Disordered Tracing page for the data dictionary of the all_disordered_segment_statistics.csv output.