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19 changes: 19 additions & 0 deletions doc/development/development.rst
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Expand Up @@ -213,6 +213,25 @@ We use Sphinx to build the documentation. To build the documentation locally, yo
This will build the documentation in the :code:`doc/_build/html` folder. You can open the :code:`index.html` file in your browser to see the documentation.

Adding new documentation
------------------------

Documentation can be added as a
`sphinx-gallery <https://sphinx-gallery.github.io/stable/index.html>`_
python file ('tutorials')
or a
`sphinx rst <https://sphinx-tutorial.readthedocs.io/step-1/>`_
file (all other sections).

To add a new tutorial, add your ``.py`` file to ``spikeinterface/examples``.
Then, update the ``spikeinterface/doc/tutorials_custom_index.rst`` file
to make a new card linking to the page and an optional image. See
``tutorials_custom_index.rst`` header for more information.

For other sections, write your documentation in ``.rst`` format and add
the page to the appropriate ``index.rst`` file found in the relevant
folder (e.g. ``how_to/index.rst``).

How to run code coverage locally
--------------------------------
To run code coverage locally, you can use the following command:
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2 changes: 1 addition & 1 deletion doc/index.rst
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Expand Up @@ -51,7 +51,7 @@ SpikeInterface is made of several modules to deal with different aspects of the

overview
get_started/index
tutorials/index
tutorials_custom_index
how_to/index
modules/index
api
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196 changes: 196 additions & 0 deletions doc/tutorials_custom_index.rst
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@@ -0,0 +1,196 @@
.. This page provides a custom index to the 'Tutorials' page, rather than the default sphinx-gallery
.. generated page. The benefits of this are flexibility in design and inclusion of non-sphinx files in the index.
..
.. To update this index with a new documentation page
.. 1) Copy the grid-item-card and associated ".. raw:: html" section.
.. 2) change :link: to a link to your page. If this is an `.rst` file, point to the rst file directly.
.. If it is a sphinx-gallery generated file, format the path as separated by underscore and prefix `sphx_glr`,
.. pointing to the .py file. e.g. `tutorials/my/page.py` -> `sphx_glr_tutorials_my_page.py
.. 3) Change :img-top: to point to the thumbnail image of your choosing. You can point to images generated
.. in the sphinx gallery page if you wish.
.. 4) In the `html` section, change the `default-title` to your pages title and `hover-content` to the subtitle.
:orphan:

Tutorials
============

Longer form tutorials about using SpikeInterface. Many of these are downloadable
as notebooks or Python scripts so that you can "code along" with the tutorials.

If you're new to SpikeInterface, we recommend trying out the
:ref:`get_started/quickstart:Quickstart tutorial` first.

Updating from legacy
--------------------

.. toctree::
:maxdepth: 1

tutorials/waveform_extractor_to_sorting_analyzer

Core tutorials
--------------

These tutorials focus on the :py:mod:`spikeinterface.core` module.

.. grid:: 1 2 2 3
:gutter: 2

.. grid-item-card:: Recording objects
:link-type: ref
:link: sphx_glr_tutorials_core_plot_1_recording_extractor.py
:img-top: /tutorials/core/images/thumb/sphx_glr_plot_1_recording_extractor_thumb.png
:img-alt: Recording objects
:class-card: gallery-card
:text-align: center

.. grid-item-card:: Sorting objects
:link-type: ref
:link: sphx_glr_tutorials_core_plot_2_sorting_extractor.py
:img-top: /tutorials/core/images/thumb/sphx_glr_plot_2_sorting_extractor_thumb.png
:img-alt: Sorting objects
:class-card: gallery-card
:text-align: center

.. grid-item-card:: Handling probe information
:link-type: ref
:link: sphx_glr_tutorials_core_plot_3_handle_probe_info.py
:img-top: /tutorials/core/images/thumb/sphx_glr_plot_3_handle_probe_info_thumb.png
:img-alt: Handling probe information
:class-card: gallery-card
:text-align: center

.. grid-item-card:: SortingAnalyzer
:link-type: ref
:link: sphx_glr_tutorials_core_plot_4_sorting_analyzer.py
:img-top: /tutorials/core/images/thumb/sphx_glr_plot_4_sorting_analyzer_thumb.png
:img-alt: SortingAnalyzer
:class-card: gallery-card
:text-align: center

.. grid-item-card:: Append and/or concatenate segments
:link-type: ref
:link: sphx_glr_tutorials_core_plot_5_append_concatenate_segments.py
:img-top: /tutorials/core/images/thumb/sphx_glr_plot_5_append_concatenate_segments_thumb.png
:img-alt: Append/Concatenate segments
:class-card: gallery-card
:text-align: center

.. grid-item-card:: Handle time information
:link-type: ref
:link: sphx_glr_tutorials_core_plot_6_handle_times.py
:img-top: /tutorials/core/images/thumb/sphx_glr_plot_6_handle_times_thumb.png
:img-alt: Handle time information
:class-card: gallery-card
:text-align: center

Extractors tutorials
--------------------

The :py:mod:`spikeinterface.extractors` module is designed to load and save recorded and sorted data, and to handle probe information.

.. grid:: 1 2 2 3
:gutter: 2

.. grid-item-card:: Read various formats
:link-type: ref
:link: sphx_glr_tutorials_extractors_plot_1_read_various_formats.py
:img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_1_read_various_formats_thumb.png
:img-alt: Read various formats
:class-card: gallery-card
:text-align: center

.. grid-item-card:: Working with unscaled traces
:link-type: ref
:link: sphx_glr_tutorials_extractors_plot_2_working_with_unscaled_traces.py
:img-top: /tutorials/extractors/images/thumb/sphx_glr_plot_2_working_with_unscaled_traces_thumb.png
:img-alt: Unscaled traces
:class-card: gallery-card
:text-align: center

Quality metrics tutorial
------------------------

The :code:`spikeinterface.qualitymetrics` module allows users to compute various quality metrics to assess the goodness of a spike sorting output.

.. grid:: 1 2 2 3
:gutter: 2

.. grid-item-card:: Quality Metrics
:link-type: ref
:link: sphx_glr_tutorials_qualitymetrics_plot_3_quality_mertics.py
:img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_3_quality_mertics_thumb.png
:img-alt: Quality Metrics
:class-card: gallery-card
:text-align: center

.. grid-item-card:: Curation Tutorial
:link-type: ref
:link: sphx_glr_tutorials_qualitymetrics_plot_4_curation.py
:img-top: /tutorials/qualitymetrics/images/thumb/sphx_glr_plot_4_curation_thumb.png
:img-alt: Curation Tutorial
:class-card: gallery-card
:text-align: center

Comparison tutorial
-------------------

The :code:`spikeinterface.comparison` module allows you to compare sorter outputs or benchmark against ground truth.

.. grid:: 1 2 2 3
:gutter: 2

.. grid-item-card:: Sorter Comparison
:link-type: ref
:link: sphx_glr_tutorials_comparison_plot_5_comparison_sorter_weaknesses.py
:img-top: /tutorials/comparison/images/thumb/sphx_glr_plot_5_comparison_sorter_weaknesses_thumb.png
:img-alt: Sorter Comparison
:class-card: gallery-card
:text-align: center

Widgets tutorials
-----------------

The :code:`widgets` module contains several plotting routines (widgets) for visualizing recordings, sorting data, probe layout, and more.

.. grid:: 1 2 2 3
:gutter: 2

.. grid-item-card:: RecordingExtractor Widgets
:link-type: ref
:link: sphx_glr_tutorials_widgets_plot_1_rec_gallery.py
:img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_1_rec_gallery_thumb.png
:img-alt: Recording Widgets
:class-card: gallery-card
:text-align: center

.. grid-item-card:: SortingExtractor Widgets
:link-type: ref
:link: sphx_glr_tutorials_widgets_plot_2_sort_gallery.py
:img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_2_sort_gallery_thumb.png
:img-alt: Sorting Widgets
:class-card: gallery-card
:text-align: center

.. grid-item-card:: Waveforms Widgets
:link-type: ref
:link: sphx_glr_tutorials_widgets_plot_3_waveforms_gallery.py
:img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_3_waveforms_gallery_thumb.png
:img-alt: Waveforms Widgets
:class-card: gallery-card
:text-align: center

.. grid-item-card:: Peaks Widgets
:link-type: ref
:link: sphx_glr_tutorials_widgets_plot_4_peaks_gallery.py
:img-top: /tutorials/widgets/images/thumb/sphx_glr_plot_4_peaks_gallery_thumb.png
:img-alt: Peaks Widgets
:class-card: gallery-card
:text-align: center

Download All Examples
---------------------

- :download:`Download all examples in Python source code </tutorials/tutorials_python.zip>`
- :download:`Download all examples in Jupyter notebooks </tutorials/tutorials_jupyter.zip>`
43 changes: 34 additions & 9 deletions src/spikeinterface/core/baserecording.py
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
from __future__ import annotations

import warnings
from pathlib import Path

Expand All @@ -7,14 +8,9 @@

from .base import BaseSegment
from .baserecordingsnippets import BaseRecordingSnippets
from .core_tools import (
convert_bytes_to_str,
convert_seconds_to_str,
)
from .recording_tools import write_binary_recording


from .core_tools import convert_bytes_to_str, convert_seconds_to_str
from .job_tools import split_job_kwargs
from .recording_tools import write_binary_recording


class BaseRecording(BaseRecordingSnippets):
Expand Down Expand Up @@ -509,6 +505,35 @@ def reset_times(self):
rs.t_start = None
rs.sampling_frequency = self.sampling_frequency

def shift_times(self, shift: int | float, segment_index: int | None = None) -> None:
"""
Shift all times by a scalar value.
Parameters
----------
shift : int | float
The shift to apply. If positive, times will be increased by `shift`.
e.g. shifting by 1 will be like the recording started 1 second later.
If negative, the start time will be decreased i.e. as if the recording
started earlier.
segment_index : int | None
The segment on which to shift the times.
If `None`, all segments will be shifted.
"""
if segment_index is None:
segments_to_shift = range(self.get_num_segments())
else:
segments_to_shift = (segment_index,)

for idx in segments_to_shift:
rs = self._recording_segments[idx]

if self.has_time_vector(segment_index=idx):
rs.time_vector += shift
else:
rs.t_start += shift

def sample_index_to_time(self, sample_ind, segment_index=None):
"""
Transform sample index into time in seconds
Expand Down Expand Up @@ -921,11 +946,11 @@ def time_to_sample_index(self, time_s):
sample_index = time_s * self.sampling_frequency
else:
sample_index = (time_s - self.t_start) * self.sampling_frequency
sample_index = round(sample_index)
sample_index = np.round(sample_index).astype(int)
else:
sample_index = np.searchsorted(self.time_vector, time_s, side="right") - 1

return int(sample_index)
return sample_index

def get_num_samples(self) -> int:
"""Returns the number of samples in this signal segment
Expand Down
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