Ibl exporter by jonahpearl · Pull Request #3522 · SpikeInterface/spikeinterface

jonahpearl · 2024-11-06T17:59:13Z

Function for #2843
Would be great if a few others could test on their data. Thanks!

Co-authored-by: Garcia Samuel <sam.garcia.die@gmail.com>

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zm711 · 2024-11-07T00:08:11Z

This looks like it is off of the bug fixes branch. @jonahpearl you want to switch this to main instead?

jonahpearl · 2024-11-07T02:44:40Z

I'm not 100% sure what you mean. Do you want me to cherry-pick / rebase my changes onto the main branch? I branched it a while ago so I've had to merge main in a few times.

alejoe91 · 2024-11-07T09:27:35Z

@jonahpearl thanks for this! Is it ok if I push to this PR?

I've been working on refining the export function so I'd be good to be in sync :)

alejoe91 · 2024-11-07T09:28:21Z

This looks like it is off of the bug fixes branch. @jonahpearl you want to switch this to main instead?

I think it's correctly using the SortingAnalyzer. Maybe the added branch in the actions yaml was confusing, so let's just remove it

alejoe91 · 2024-11-07T09:31:29Z

        templates_ind[unit_ind, : len(chan_inds)] = chan_inds

-    if not sorting_analyzer.has_extension("template_similarity"):
+    if sorting_analyzer.get_extension("template_similarity") is None:


You're suggesting we put this back to "has_extension"? Any reason this one and not the other ones? The ibl export relies on doing a Phy export, and as discussed elsewhere this "has_extension" pattern is no longer safe if the folder exists but without any data inside.

yes, all of them. I think it's much easier to read :)

I agree that it'd be easier to read, but I disagree that it's preferable, because it will break if the extension folder exists but doesn't have data. It's not unusual to end up in that kind of state — eg if you run analyzer.compute(["random_spikes", "spike_amplitudes"]) on a new analyzer, the spike_amplitudes folder will get made but nothing will be in it because the analyzer will need "templates" to be computed. There are various ways to fix that involving try/excepts / clean-ups, but in the current context, I don't think it makes sense to not catch this case.

That's a separate issue :) we should delay folder creation until dependencies are checked. Can you open another issue about it?

alejoe91 · 2024-11-07T09:31:49Z

+from spikeinterface.core import extract_waveforms
+from spikeinterface.extractors import toy_example
+from spikeinterface.comparison import compare_templates
+
+import numpy as np


this belongs to a different PR

Yes, not sure how this slipped in.

alejoe91 · 2024-11-07T14:55:49Z

+
+import numpy as np
+import numpy.typing as npt
+from scipy.signal import welch


import scipy should be done within the functions using it because it's not a mandatory requirement (see failing tests)

Co-authored-by: Alessio Buccino <alejoe9187@gmail.com>

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zm711

Just a docstring fix while you're at it. I believe we add this to the dev docs after this PR was started which is why this was missed.

zm711 · 2024-11-07T18:41:22Z

+    ----------
+    analyzer: SortingAnalyzer
+        The sorting analyzer object.
+    output_folder: str | Path
+        The output folder where the phy template-gui files are saved
+    rms_win_length_sec: float, default: 3
+        The window length in seconds for the RMS calculation.
+    welch_win_length_samples: int, default: 1024
+        The window length in samples for the Welch method.
+    total_secs: int, default: 100
+        The total number of seconds to use for the spectral density calculation.
+    only_ibl_specific_steps: bool, default: False
+        If True, only the IBL specific steps are run (i.e. skips calling `export_to_phy`)
+    compute_pc_features: bool, default: False
+        If True, pc features are computed
+    compute_amplitudes: bool, default: True
+        If True, waveforms amplitudes are computed
+    sparsity: ChannelSparsity or None, default: None
+        The sparsity object (currently only respected for phy part of the export)
+    copy_binary: bool, default: True
+        If True, the recording is copied and saved in the phy "output_folder"
+    remove_if_exists: bool, default: False
+        If True and "output_folder" exists, it is removed and overwritten
+    template_mode: str, default: "median"
+        Parameter "mode" to be given to WaveformExtractor.get_template()
+    dtype: dtype or None, default: None
+        Dtype to save binary data
+    verbose: bool, default: True
+        If True, output is verbose
+    use_relative_path : bool, default: False
+        If True and `copy_binary=True` saves the binary file `dat_path` in the `params.py` relative to `output_folder` (ie `dat_path=r"recording.dat"`). If `copy_binary=False`, then uses a path relative to the `output_folder`
+        If False, uses an absolute path in the `params.py` (ie `dat_path=r"path/to/the/recording.dat"`)


Suggested change

----------

analyzer: SortingAnalyzer

The sorting analyzer object.

output_folder: str | Path

The output folder where the phy template-gui files are saved

rms_win_length_sec: float, default: 3

The window length in seconds for the RMS calculation.

welch_win_length_samples: int, default: 1024

The window length in samples for the Welch method.

total_secs: int, default: 100

The total number of seconds to use for the spectral density calculation.

only_ibl_specific_steps: bool, default: False

If True, only the IBL specific steps are run (i.e. skips calling `export_to_phy`)

compute_pc_features: bool, default: False

If True, pc features are computed

compute_amplitudes: bool, default: True

If True, waveforms amplitudes are computed

sparsity: ChannelSparsity or None, default: None

The sparsity object (currently only respected for phy part of the export)

copy_binary: bool, default: True

If True, the recording is copied and saved in the phy "output_folder"

remove_if_exists: bool, default: False

If True and "output_folder" exists, it is removed and overwritten

template_mode: str, default: "median"

Parameter "mode" to be given to WaveformExtractor.get_template()

dtype: dtype or None, default: None

Dtype to save binary data

verbose: bool, default: True

If True, output is verbose

use_relative_path : bool, default: False

If True and `copy_binary=True` saves the binary file `dat_path` in the `params.py` relative to `output_folder` (ie `dat_path=r"recording.dat"`). If `copy_binary=False`, then uses a path relative to the `output_folder`

If False, uses an absolute path in the `params.py` (ie `dat_path=r"path/to/the/recording.dat"`)

----------

analyzer : SortingAnalyzer

The sorting analyzer object.

output_folder : str | Path

The output folder where the phy template-gui files are saved

rms_win_length_sec : float, default: 3

The window length in seconds for the RMS calculation.

welch_win_length_samples : int, default: 1024

The window length in samples for the Welch method.

total_secs : int, default: 100

The total number of seconds to use for the spectral density calculation.

only_ibl_specific_steps : bool, default: False

If True, only the IBL specific steps are run (i.e. skips calling `export_to_phy`)

compute_pc_features : bool, default: False

If True, pc features are computed

compute_amplitudes : bool, default: True

If True, waveforms amplitudes are computed

sparsity : ChannelSparsity or None, default: None

The sparsity object (currently only respected for phy part of the export)

copy_binary : bool, default: True

If True, the recording is copied and saved in the phy "output_folder"

remove_if_exists : bool, default: False

If True and "output_folder" exists, it is removed and overwritten

template_mode : str, default: "median"

Parameter "mode" to be given to WaveformExtractor.get_template()

dtype : dtype or None, default: None

Dtype to save binary data

verbose : bool, default: True

If True, output is verbose

use_relative_path : bool, default: False

If True and `copy_binary=True` saves the binary file `dat_path` in the `params.py` relative to `output_folder` (ie `dat_path=r"recording.dat"`). If `copy_binary=False`, then uses a path relative to the `output_folder`

If False, uses an absolute path in the `params.py` (ie `dat_path=r"path/to/the/recording.dat"`)

We are working on implementing numpydoc linting in the future and it requires there to be a space after the parameter.

zm711 · 2024-11-07T18:41:49Z

+    try:
+        from scipy.signal import welch
+    except ImportError as e:
+        raise ImportError("Please install scipy to use the export_to_ibl function.") from e


I've never seen this before. How does this raise error from e work?

I would just import it in the function. The problem is that core tests will look in all files for tests, and script is not installed in core tests

samuelgarcia · 2024-11-08T09:17:43Z

+        "fscale": fscale(welch_win_length_samples, 1 / fs_ap, one_sided=True),
+        "tscale": wingen.tscale(fs=fs_ap),
+    }
+    win["spectral_density"] = np.zeros((len(win["fscale"]), analyzer.recording.get_num_channels()))


I think we should have a proper function to compute the spectrum if you need it.
So we could have proper tests for this.

samuelgarcia · 2024-11-08T09:18:20Z

+    total_samples_ap = int(np.min([fs_ap * total_secs, analyzer.recording.get_num_samples()]))
+
+    # the window generator will generates window indices
+    wingen = WindowGenerator(ns=total_samples_ap, nswin=rms_win_length_samples_ap, overlap=0)


we have already some function to generate window in spikeinterface.

samuelgarcia · 2024-11-08T09:25:24Z

Hi @jonahpearl
thanks for this contribution to spikeinetrface and making a bridge to ibl tools.

About to_ibl_utils.py I would identify function by function what the need and if there is an equivalent function in spikeinterface for it. Then I would implement then at the good place (core, preprocessing, postprocessing, ...) and also would make some tests function per function.

About the spectrum, I would implement it in a speparate file using the spikeinterface machinery on chunk parralelisation.

jonahpearl · 2024-11-08T13:53:00Z

Fair enough -- I don't have time to refactor this right now but I can work on it in the coming months.

jonahpearl · 2025-04-03T15:15:54Z

Closing in favor of newer version

jonahpearl · 2025-04-11T13:15:02Z

Closing in favor of newer version

#3857

alejoe91 and others added 30 commits March 8, 2024 18:01

release notes

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Co-authored-by: Garcia Samuel <sam.garcia.die@gmail.com>

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Co-authored-by: Alessio Buccino <alejoe9187@gmail.com>

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alejoe91 added the exporters Related to exporters module label Nov 13, 2024

jonahpearl closed this Apr 3, 2025

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