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1: the check of non constant type has a wrong message, it compares with root, not parent section
2: the remove zero lenght should have a hidden warning if it does it, and a strong warning if it removes a root section, as the whole tree will be removed. It removes if only one point is left.

The new version of nptyping breaks NeuroR.

@mariarv wants to sanitize dendrites for some morphologies, but does not care about soma. Some of her morphs don't have soma, so an option in sanitize such as ignore_soma=False could be of some use.

In https://github.com/BlueBrain/NeuroR/blob/master/neuror/sanitize.py#L39
it says no soma, but there can be a non valid soma, with for example this morph: https://github.com/BlueBrain/MorphIO/blob/master/tests/data/soma_single_frustum.swc

Maybe write 'no valid soma` instead?

In https://github.com/BlueBrain/NeuroR/blob/master/neuror/main.py#L243

Should be something like axons: Optional[List] = None, instead of axons: Optional[Path] = None,.

I found the PR which made sanitize crash: #52
See BlueBrain/NeuroM#977 (comment)

Hi, @Stannislav noticed that during sanitize of a neuron, if a section has zero length subsequent sections are deleted as well. This is probably coming from here:

This should not be the expected behavior for sanitize (imo). Instead when a zero length section is removed subsequent sections should be stitched back to its parent.

Could you please look into this issue? Thanks a lot!

This is a continuation of #99
Running neuror sanitize file simple1.asc out.asc on

("CellBody"
  (Color Red)
  (CellBody)
  (0.001000000 0.001000000 0.000000000 0.010000000)
  (-0.001000000 0.001000000 0.000000000 0.010000000)
  (-0.001000000 -0.001000000 0.000000000 0.010000000)
  (0.001000000 -0.001000000 0.000000000 0.010000000)
)

( (Color Cyan)
  (Axon)
  (0.000000000 0.000000000 0.000000000 2.000000000)
  (0.000000000 -4.000000000 0.000000000 2.000000000)
  (
    (0.000000000 -4.000000000 0.000000000 4.000000000)
    (0.000000000 -4.000000000 0.000000000 4.000000000)
    (0.000000000 -4.000000000 0.000000000 4.000000000)
    (
        (6.000000000 -4.000000000 0.000000000 4.000000000)
        (7.000000000 -5.000000000 0.000000000 4.000000000)
    |
        (6.000000000 -4.000000000 0.000000000 4.000000000)
        (8.000000000 -4.000000000 0.000000000 4.000000000)
    )
  |
    (0.000000000 -4.000000000 0.000000000 4.000000000)
    (-5.000000000 -4.000000000 0.000000000 4.000000000)
  )
)

[...snip cellbody]
( (Color Cyan)
  (Axon)
  (0.000000000 0.000000000 0.000000000 2.000000000)
  (0.000000000 -4.000000000 0.000000000 2.000000000)
  (
    (0.000000000 -4.000000000 0.000000000 4.000000000)
    (-5.000000000 -4.000000000 0.000000000 4.000000000)
  )
)

I tried to unravel the morphology of L23_PC_cADpyr_229_2 from the Blue Brain-database but the sections seem to get scattered in the x-direction.

import matplotlib.pyplot as plt

from morphio import Morphology
from neuror.unravel import unravel


def display(morph, color):
    for sec in morph.sections:
        x = sec.points.T
        plt.plot(x[0], x[1], x[2], c=color)


u, _ = unravel('data/morph_7.h5')
u.write('data/morph_7_unr.h5')

plt.subplot(projection='3d')
display(Morphology('data/morph_7.h5'), 'k')
display(Morphology('data/morph_7_unr.h5'), 'tab:blue')
plt.show()

This is related to #105.

Context

Currently, if a 0-length section is found at the soma, sanitize will drop the entire neurite that is attached to it.

This behavior is not what a normal user could expect, especially because there is no Warning or Error when this dropping takes place during sanitization and the user cannot know that this has happened.

Action

After discussions (@lidakanari @adrien-berchet @mgeplf @eleftherioszisis) we agreed that the solution would be to raise an informative Error (e.g. ValueError("Zero-length section found at the soma ...") and terminate the execution of sanitize.

This change is beyond the scope of #65 and will be treated in a future PR.
The rational is similar to synthesis, where all dendrites of all morphologies of same mtypes are used to synthesize a morphology, to avoid biases from specific features of morphologies. With this improvement, the repaired branches would be more varied, and not be almost a copy of other branches of the current morphology.

numpy==1.25 introduced simd vectorized version of quicksort with: numpy/numpy#23707

That change affects the behavior of the sort and argsort functions when using quicksort (default) based on the existence of the avx-512 instruction set.

In NeuroR, one of the functions that are affected is scipy.optimize.minimize:

which uses internally numpy's argsort in:
https://github.com/scipy/scipy/blob/cfe80116aaa145061246b8aec0e98248fbefb835/scipy/optimize/_optimize.py#L907

See also:
numpy/numpy#24064

Github hosted runners for ubuntu-latest seem to have enabled the aforementioned instruction set as they output different values than the expected ones in the past: https://github.com/BlueBrain/NeuroR/actions/runs/5484236591/jobs/9991722132

Just noticed it is outdated. Also, we need to add the .remove_unifurcations in the code once morphio is updated.

z-range is the thickness of the morpho in the z-direction, corresponding to slice thickness. A small range can be understood as an error from reconstruction

see: BlueBrain/morph-tool#59

When using neuror.zero_diameter_fixer.fix_zero_diameters on the attached morphology, I get a segmentation fault.
After some investigation with @arnaudon , it appeared that it happens when the Python recursion limit is updated in the function with sys.setrecursionlimit and is set to a value greater than the actual stack size (which can be updated using ulimit -s <new_size>). When increasing the stack size with ulimit the problem disappears.

Here is a MWE:
First update the stack size in bash then run Python:

    ulimit -s 8192
    python

    import morphio
    from neuror.zero_diameter_fixer import fix_zero_diameters
    morph = morphio.mut.Morphology("AA0319.asc")
    fix_zero_diameters(morph)