load_sorting_analyzer not defined

[mtehrani-code]

Hi,

Working with the November 2023 tutorial, I created and saved the SortingAnalyzer:

SortingAnalyzer: 49 channels - 120 units - 1 segments - binary_folder - has recording Loaded 0 extensions:

But when I try to load it, I get the error:

sorting_analyzer=load_sorting_analyzer(folder="sorting_analyzer") NameError: name 'load_sorting_analyzer' is not defined

Also, I can still calculate the extensions, but when I run:

pc0 = pc.get_projections(unit_id=0) print(f"PC scores shape: {pc0.shape}") all_labels, all_pcs = pc.get_all_projections() print(f"All PC scores shape: {all_pcs.shape}")

I get:

AttributeError: 'ComputePrincipalComponents' object has no attribute 'get_projections'

Would appreciate your help trying to figure out the errors...

M

[zm711]

How did you import load_sorting_analyzer?

You probably need to do

sorting_analyzer = si.load_sorting_analyzer(folder='sorting_analyzer')

Also what is your script for getting the pcs?

[mtehrani-code]

I imported spikeinterface at the beginning:

import spikeinterface.full as si

Isn't load_sorting_analyzer within the spikeinterface.full module? Didn't know I was supposed to import it separately.

This is the script for the pc:

pc = sorting_analyzer.compute(input="principal_components", n_components=3, mode="by_channel_local")

M

[zm711]

You imported the module with the alias of si. So whenever you want to use any code you have to start that code with the alias si. We explain how this works here and here is a random article about namespaces in python article. Basically in python if you import something with an alias you have to use that alias. This helps prevent polluting the name space. :) For example I could also do

import spikeinterface.full as the_coolest_package_ever
analyzer = the_coolest_package_ever.load_sorting_analyzer()

We probably changed the name of that function (sorry during some code updates probably). See here.

Basically it should be

pc = sorting_analyzer.compute(xx)
pc0 = pc.get_projections_one_unit(0)

[mtehrani-code]

That all worked. Thank you!

Now when I want to look at data associated with the extensions using get_data( ), nothing is returned. Eg.:

unit_locations = sorting_analyzer.get_extension (extension_name="unit_locations") unit_locations_data = unit_locations.get_data()

I computed (or think I did) unit_locations earlier:

unit_locations=sorting_analyzer.compute("unit_locations", method="monopolar_triangulation")

I tried this on a couple of other extensions (templates and waveforms) and I get the same thing, i.e. no output.

What am I missing?

[mtehrani-code]

...I am able to plot the unit locations however.

[zm711]

I just tried that on my computer and it worked fine. If you just type:

sorting_analyzer

into your console which extensions show up?

[mtehrani-code]

When I type sorting_analyzer, I get:

SortingAnalyzer: 49 channels - 120 units - 1 segments - binary_folder - has recording Loaded 6 extensions: random_spikes, waveforms, templates, noise_levels, principal_components, unit_locations

[zm711]

What if you just type

sorting_analyzer.get_extension('unit_locations')

[mtehrani-code]

Then I get:

<spikeinterface.postprocessing.unit_localization.ComputeUnitLocations at 0x1bfb0b41e50>

[zm711]

Well that didn't return None. Cool. So now do

unit_locations = sorting_analyzer.get_extension('unit_locations')
unit_locations.get_data()

[mtehrani-code]

That worked! Got a long array of numbers.

Hmm, I tried this version earlier, but it didn't return anything:

unit_locations = sorting_analyzer.get_extension(extension_name="unit_locations") unit_locations_data = unit_locations.get_data()

Anyway, thanks for your help!!

[zm711]

I see what happened!

unit_locations = sorting_analyzer.get_extension (extension_name="unit_locations")

You have an extra space between extension and (.

You need to type sorting_analyzer.get_extension(extension_name="unit_locations").

We can close this, but as always just open a new issue if something comes up.

[mtehrani-code]

Ah, I see. Thank you!