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Updates to algorithm

Alessio Buccino requested to merge classes into master

Main updates:

  • Changed strategy to start extracting paths:

    • now a path is extracted only if the node is a local maximum (wrt neighbors) in the node heuristics space. This speeds up the finding of paths and only finds "good" paths in the first place

    • when a path is added, all channels within a defined radius (neighbor_radius) of all selected nodes are excluded from future searches

    • these two changes remove the need of "cleaning" paths. We could still keep the cleaning part for safety, but it would add a few parameters.

  • Moved SimpleAxonTracking to class-based approach

  • Removed amplitude based tracking and cleaned up tracking functions

  • Updated generation notebooks to use n=10 points for each electrodes

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