yzx9 / swcgeom

Neuron geometry library for swc format.

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• 🔭 I’m currently pursuing my master's degree at SHU and GDIIST
• 🌱 I’m actively working on improving my English language skills.
• ⚡ Fun fact: Software Engineering and Computational Neuroscience

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swcgeom's Issues

Detecting Cyclic Points

We have now provided a function named has_cyclic to detect if a SWC tree contains a cycle. Going further, we can offer a method to detect the cyclic points. Assuming this is a directed graph, and we start from a point (the root of the tree), then we can definitely find the points where paths overlap.

Support neurolucida ASC format

See Specification Neurolucida

L-Measure support

See http://cng.gmu.edu:8080/Lm/help/index.htm

`Tree.get_bifurcations` should rename to `Tree.get_furcations`

Preserve original annotation information when reading and writing swc

DO NOT throw out the annatation in SWC files.

Onion-ring `traverse` API

def traverse(next):
  enter = do_something() # same as the enter callback
  children = next(enter)
  leave = do_something_else(children) # same as leave the callback
  return leave

Tree.from_swc(...).traverse(traverse)

The advantage of this onion-ring API design is that users can hold a closure to easily retain some information. However, I am not quite sure if such a call would lead to a too deep call stack (in some extreme cases, a neuron may have hundreds of thousands of points).

Direction Indicator is wrong

draw.direction_indicator plot wrong directions, possibly swapping the two axes to get the correct answer

Improve Soma Support

1. Add more soma type support, now only supports single soma, see MorphIO
2. the soma does not need to be the first point.

Assemble `BranchTree` to `Tree`

How to asemble a BranchTree to Tree?

If available, we can resamble tree by: Tree -> BranchTree -> resamble branches -> assemble BranchTree to Tree

Stat brain region projection matrix

Not just geometry anymore since `images` module added

Maybe rename to neurolit?

`pycurl` requires `curl`

curl is not a required component, especially on windows

Calculate volume size

SWC is a representation of neurons composed of the radius of points and their connectivity, therefore there are various specific ways of representation. A typical method is to consider the nodes as spheres, and the connections between them as truncated cones with different radii at the top and bottom surfaces. We can at least support the volume calculation in this manner.

Remove deprecated typing alias

See also: PEP-585 and Deprecated aliases

Image foramt support for `v3dpbd` and `v3draw`

try:

pip install v3d-py-helper