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Add an option to flip the order by depth #2005

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merged 4 commits into from
Sep 19, 2023
Merged

Add an option to flip the order by depth #2005

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c57cfa7
Add an option to flip the order by depth
samuelgarcia Sep 18, 2023
ef165cb
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 18, 2023
e88b4b5
Update src/spikeinterface/preprocessing/depth_order.py
samuelgarcia Sep 19, 2023
b202c43
Update src/spikeinterface/core/recording_tools.py
samuelgarcia Sep 19, 2023
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7 changes: 6 additions & 1 deletion src/spikeinterface/core/recording_tools.py
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Expand Up @@ -302,7 +302,7 @@ def get_chunk_with_margin(
return traces_chunk, left_margin, right_margin


def order_channels_by_depth(recording, channel_ids=None, dimensions=("x", "y")):
def order_channels_by_depth(recording, channel_ids=None, dimensions=("x", "y"), flip=False):
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@h-mayorquin h-mayorquin Sep 18, 2023 •
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Maybe using the standard name reversed from the python API would be a good idea?

https://docs.python.org/3/library/functions.html#sorted

It is also supported by the list.sort

But maybe you think that flip describes it better?
Just throwing something that I thought.

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Ah, on the other hand we have:

https://numpy.org/doc/stable/reference/generated/numpy.flip.html

Which seems to be aligned withat what you are doing.

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I started with reversed and finally change it to flip at the very last moment. I think flip is ok

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Yep. I also think that your docstring is doing the heavy lifting there anyway.

"""
Order channels by depth, by first ordering the x-axis, and then the y-axis.
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Question out of curiosity, do we have a convention that x goes along the width or the recorder and that y goes in the height / depth (the direction where it is usualy moves) or is it the other way around?

I found myself realizing that I did not know what to expect after reading this.

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Hi @h-mayorquin

Yes the convention is that x is width and y is depth. The ('x', 'y') tuple is fed into lexsort, which sorts outer to innermost dimensions ;)

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Thanks, @alejoe91.


Expand All @@ -316,6 +316,9 @@ def order_channels_by_depth(recording, channel_ids=None, dimensions=("x", "y")):
If str, it needs to be 'x', 'y', 'z'.
If tuple or list, it sorts the locations in two dimensions using lexsort.
This approach is recommended since there is less ambiguity, by default ('x', 'y')
flip: bool, default False
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If flip is False then the order is bottom first (starting from tip of the probe).
If flip is True then the order is upper first.

Returns
-------
Expand All @@ -341,6 +344,8 @@ def order_channels_by_depth(recording, channel_ids=None, dimensions=("x", "y")):
assert dim < ndim, "Invalid dimensions!"
locations_to_sort += (locations[:, dim],)
order_f = np.lexsort(locations_to_sort)
if flip:
order_f = order_f[::-1]
order_r = np.argsort(order_f, kind="stable")

return order_f, order_r
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2 changes: 2 additions & 0 deletions src/spikeinterface/core/tests/test_recording_tools.py
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Expand Up @@ -138,11 +138,13 @@ def test_order_channels_by_depth():
order_1d, order_r1d = order_channels_by_depth(rec, dimensions="y")
order_2d, order_r2d = order_channels_by_depth(rec, dimensions=("x", "y"))
locations_rev = locations_copy[order_1d][order_r1d]
order_2d_fliped, order_r2d_fliped = order_channels_by_depth(rec, dimensions=("x", "y"), flip=True)

assert np.array_equal(locations[:, 1], locations_copy[order_1d][:, 1])
assert np.array_equal(locations_copy[order_1d][:, 1], locations_copy[order_2d][:, 1])
assert np.array_equal(locations, locations_copy[order_2d])
assert np.array_equal(locations_copy, locations_copy[order_2d][order_r2d])
assert np.array_equal(order_2d[::-1], order_2d_fliped)


if __name__ == "__main__":
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10 changes: 8 additions & 2 deletions src/spikeinterface/preprocessing/depth_order.py
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Expand Up @@ -18,13 +18,18 @@ class DepthOrderRecording(ChannelSliceRecording):
If str, it needs to be 'x', 'y', 'z'.
If tuple or list, it sorts the locations in two dimensions using lexsort.
This approach is recommended since there is less ambiguity, by default ('x', 'y')
flip: bool, default: False
If flip is False then the order is bottom first (starting from tip of the probe).
If flip is True then the order is upper first.
"""

name = "depth_order"
installed = True

def __init__(self, parent_recording, channel_ids=None, dimensions=("x", "y")):
order_f, order_r = order_channels_by_depth(parent_recording, channel_ids=channel_ids, dimensions=dimensions)
def __init__(self, parent_recording, channel_ids=None, dimensions=("x", "y"), flip=False):
order_f, order_r = order_channels_by_depth(
parent_recording, channel_ids=channel_ids, dimensions=dimensions, flip=flip
)
reordered_channel_ids = parent_recording.channel_ids[order_f]
ChannelSliceRecording.__init__(
self,
Expand All @@ -35,6 +40,7 @@ def __init__(self, parent_recording, channel_ids=None, dimensions=("x", "y")):
parent_recording=parent_recording,
channel_ids=channel_ids,
dimensions=dimensions,
flip=flip,
)


Expand Down
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