Trace#
Module to trace paths of minimal resitance between two points in a 3d array.
- trace(source, score, start, stop, costPerDistance=1.0, minimumCostPerDistance=0.016666666666666666, tubenessMultiplier=4.0, minimalTubeness=0.1, returnQuality=False, maxSteps=None, verbose=False)[source]#
Trace a path in the 3d source image from start to stop
Arguments
- sroucearray
Input source.
- scorearray
A measure at each point to score a path. The higher the more likely is it that the path will go through and thus the score is a reward like measure. The cost for the path is approximately 1/score.
- startarray
Start position.
- stoparray
Stop position.
- costPerDistancefloat
Cost used to when estimating remaining distance. Can be used to weigh the estimated distance measure.
- minimalCostperDistancefloat
Minimal cost per distance used when tubeness measure is below this value.
- tubenessMultiplerfloat
Multiply the tubeness measure by this value before estimating coadt via inverse. Can be used to weigh tubness vs. distiance measures.
- minimalTubenessfloat
Minimal tubness measure to use (note the inverse of the tubness measure is used to calculate the cost, this effectively limits the maximal cost).
- maxStepsint or None
Number of maximal iteration steps.
Returns
- path2-D array
The path a list of coordinates.
- trace_to_mask(source, tubeness, start, mask, costPerDistance=1.0, minimumCostPerDistance=0.016666666666666666, tubenessMultiplier=4.0, minimalTubeness=0.1, returnQuality=False, maxSteps=None, verbose=False)[source]#
Trace a path in the 3d source image from start to a point on the mask
- Parameters:
source (array) – Input source.
tubeness (array) – Tubness measure used to score path
start (array) – starting point for tracing
mask (3-D array) – distance array to mask (goal points on mask == 0).
costPerDistance (float) – Cost used to when estimating remaining distance. Can be used to weigh the estimated distance measure
minimalCostperDistance (float) – Minimal cost per distance used when tubeness measure is below this value.
tubenessMultipler (float) – Multiply the tubeness measure by this value before estimating coadt via inverse. Can be used to weigh tubness vs. distiance measures.
maxSteps (int or None) – Number of maximal iteration steps.
Returns
- path2-D array
the path a list of coordinates