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Merged
merged 5 commits into from
Oct 20, 2025
Merged

Improve invalid escape character on neuropixel tools #369

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6c2fdff
remove invalid escpae character in neuropixels
h-mayorquin Oct 14, 2025
2a4bcbd
imprve docs
h-mayorquin Oct 14, 2025
9443ab8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 14, 2025
f19b9f1
Apply suggestion from @chrishalcrow
h-mayorquin Oct 15, 2025
1409e1e
Apply suggestion from @chrishalcrow
h-mayorquin Oct 15, 2025
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48 changes: 31 additions & 17 deletions src/probeinterface/neuropixels_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -145,21 +145,29 @@ def make_mux_table_array(mux_information) -> np.array:

def get_probe_contour_vertices(shank_width, tip_length, probe_length) -> list:
"""
Function to get the vertices of the probe contour from probe properties. The probe contour can be constructed
from five points. These are the vertices shown in the following figure:

A | | E
| |
.
.
.
| |
B | | D
\\ /
\\/
C

This function returns the points indicated in the diagram above in a list [A,B,C,D,E].
Function to get the vertices of the probe contour from probe properties.
The probe contour can be constructed from five points.

These are the vertices shown in the following figure:

Top of probe (y = probe_length)
A +-------------------------------+ E
| |
| |
| Shank body |
| (shank_width) |
| |
| |
B +-------------------------------+ D (y = 0)
\ /
\ Tip region /
\ (tip_length) /
\ /
\ /
\ /
+-----------------+ C (y = -tip_length)

This function returns the vertices in the order [A, B, C, D, E] as a list of (x, y) coordinates.

Parameters
----------
Expand All @@ -172,8 +180,14 @@ def get_probe_contour_vertices(shank_width, tip_length, probe_length) -> list:

Returns
-------
polygon_vertices : list
List of five points which make up the probe contour.
polygon_vertices : tuple of tuple
Five vertices as (x, y) coordinate pairs in micrometers, returned in the
order [A, B, C, D, E] corresponding to the diagram above:
A = (0, probe_length) - top-left corner
B = (0, 0) - bottom-left corner at shank base
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This is not exactly tru. This 0, 0 is the bottom, left contact center no ?

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@chrishalcrow chrishalcrow Oct 23, 2025 •
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We shift the entire probe after we run this function (I can't remember why - probably to make it easier to figure out the probe contour?). See code here:

probeinterface/src/probeinterface/neuropixels_tools.py

Line 288 in de4fb10

polygon = np.array(

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Thanks @chrishalcrow, maybe we should use a unified frame of reference (x and y axis center) across our code so don't confuse ourselves?

Or ... maybe we should use random generator for the center in every different function and correct on the spot to remind ourselves that everything is relative. Food for thought.

C = (shank_width/2, -tip_length) - tip point (center bottom)
D = (shank_width, 0) - bottom-right corner at shank base
E = (shank_width, probe_length) - top-right corner
"""

# this dict define the contour for one shank (duplicated when several shanks so)
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