Move features to nat from other packages

natverse / nat

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

https://natverse.org/nat/

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Move features to nat from other packages #423

Closed SridharJagannathan closed 4 years ago

SridharJagannathan commented 4 years ago

Move the following features from:

1) Basic neuron manipulations: https://github.com/natverse/elmr

[x] Simplify neurons -> https://github.com/natverse/elmr/blob/master/R/simplify_neuron.R
[x] Stitch neurons -> https://github.com/natverse/elmr/blob/master/R/stitch_neuron.R
[x] Distal to -> http://natverse.org/elmr/reference/distal_to.html
[x] prune_twigs http://natverse.org/elmr/reference/prune_twigs.html 2) From registrations: (tbc @jefferis )
[x] tpsreg -> http://natverse.org/elmr/reference/tpsreg.html Each feature must be accompanied by relevant test cases (either synthetic or from actual neuron data)

SridharJagannathan commented 4 years ago

@jefferis: So far I have finished updating simplify_neuron both your and my implementations. As well as stitch_neurons_mst, I have also cross-verified the implementation made by @schlegelp and found both the results to be similar. I will continue updating and moving your other stitch_neurons and other features as requested. I have made this PR so it is easier for your to review.

jefferis commented 4 years ago

Super!

Is there any difference in the simplify_neuron functionality at present between your version and mine? I didn’t get to review yet.
I would bring in the stitch_neuron(s) functions in their current implementations and then switch to your new MST one.
it would be ideal if we could have a version that works for multiple neurons and a version that stitches a single neuron that has multiple trees. Alternatively there may be a nice way to make a single function that will do either if these.

jefferis commented 4 years ago

Closed by #424 972f2db