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Author: JoeZiminski

doc/how_to/handle_times.rst

@@ -4,15 +4,13 @@ How SpikeInterface handles time
 Extracellular electrophysiology commonly involves synchronisation of events
 across many timestreams. For example, an experiment may involve
 displaying a stimuli to an animal and recording the stimuli-evoked
-neuronal responses. It is critical that timings is represented in
-a clear way across data streams so they may be properly synchronised during
+neuronal responses. It is critical that timings are represented
+accurately so they may be properly synchronised during
 analysis.
 
-Below, we will explore the ways that SpikeInterface represents time
+Below, we will explore the ways that SpikeInterface stores time
 information and how you can use it in your analysis to ensure the timing
-of your spike events is represented faithfully. The ways that will
-be explored are **providing no times**, **providing start times**
-and **providing the full time array**.
+of your spike events are accurate.
 
 A familiarity with the terms used in digital sampling (e.g. sampling
 frequency) will be assumed below. If you are not familiar with these concepts,
@@ -56,22 +54,21 @@ An Overview of the possible Time representations in SpikeInterface
 
 When you load a recording into SpikeInterface, it will be automatically
 associated with a time array. Depending on your data format, this might
-be loaded from metadata on your raw recording.
+be loaded from metadata on your raw recording. If there is no time metadata
+on your raw recording, the times will be generated based on your sampling
+rate and number of samples.
 
-**[TODO: concrete example of this?]**
+**[TODO: concrete example of a datatype that loads time also on the neo side]**
 
-If there is no time metadata on your raw recording, the times will be
-generated based on your sampling rate and number of samples.
-
-You can use the `get_times()` method to inspect the time array associated
-with your recording.
+You can use the :meth:`get_times() <spikeinterface.core.BaseRecording.get_times>`
+method to inspect the time array associated with your recording.
 
 .. code-block:: python
 
     import spikeinterface.full as si
 
     # Generate a recording for this example
-    recording, _ = si.generate_ground_truth_recording(durations=[10])
+    recording, sorting = si.generate_ground_truth_recording(durations=[10])
 
     print(f"number of samples: {recording.get_num_samples()}")
     print(f"sampling frequency: {recording.get_sampling_frequency()}"
@@ -80,22 +77,25 @@ with your recording.
         recording.get_times()
     )
 
-Here, we see that as no time metadata was associated with the loaded recording,
-the time array starts at 0 seconds and continues until 10 seconds
-(`10 * sampling_frequency`) in steps of sampling step (`1 / sampling_frequency`).
+Here, we see that as no time metadata is associated with the loaded recording,
+a default time array is generated from the number of samples and sampling frequency.
+The times starts at :math:`0` seconds and continues until :math:`10` seconds
+(:math:`10 \cdot \text{sampling frequency}` samples) in steps of sampling step size,
+:math:`\frac{1}{\text{sampling frequency}}`.
 
-If timings were loaded from metadata, you may find that the first timepoint is
-not zero, or the times may not be separated by exactly `1/sampling_frequency` but
-may be irregular due to small drifts in sampling rate during acquisition.
+If timings are obtained from metadata during file loading, you may find that the first timepoint is
+not zero, or the times may not be separated by exactly :math:`\frac{1}{\text{sampling frequency}}`
+but may be irregular due to small drifts in sampling rate during acquisition (so called 'clock drift').
 
 ^^^^^^^^^^^^^^^^^^^^^^^
 Shifting the start time
 ^^^^^^^^^^^^^^^^^^^^^^^
 
 Having loaded your recording object and inspected the associated
-time vector, you may want to change the start time of your recording.
+times, you may want to change the start time of your recording.
+
 For example, your recording may not have metadata attached and you
-want to shift the default time vector (with zero start time) to the
+want to shift the default times to start at the
 true (real world) start time of the recording, or relative to some
 other event (e.g. behavioural trial start time).
 
@@ -117,19 +117,52 @@ the start time.
 
     print(recording.get_times())  # time now start at 50 seconds
 
+**TODO: link to new function and test when other PR is merged**
+
+
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Setting time vector changes spike times
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If we sort out recording, the spike times will reflect the times
+set on the recording. In our case, because we already have the
+sorting object based on the default times, we will set the new
+recording object on the sorting.
+
+.. code-block:: python
+
+    unit_id_to_show = sorting.unid_ids[0]
+
+    spike_times_orig = sorting.get_unit_spike_train(unit_id_to_show, return_times=True)
+
+    sorting.register_recording(recording)
+
+    spike_times_new = sorting.get_unit_spike_train(unit_id_to_show, return_times=True)
+
 
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 Manually setting a time vector
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Less commonly, you may want to manually set the time vector on a recording.
-For example, maybe you have a known time vector with non-regularly spaced
-samples due to sampling drift, and you want to associate it with your recording.
+It is also possible to manualyl set an entire time vector on your recording.
+This might be useful in case you have the true sample timestamps of your
+recording but these were not automatically loaded from metadata.
 
 You can associate any time vector with your recording (as long as it contains
-as many samples as the recording itself) using `recording.set_times()`.
+as many samples as the recording itself) using
+:meth:`set_times() <spikeinterface.core.BaseRecording.set_times>`
 
-[TODO - an example?]
+.. code-block:: python
+
+    times = np.linspace(0, 10, recording.get_num_samples()))
+    offset = np.cumsum(
+        np.linspace(0, 0.1, recording.get_num_samples())
+    )
+    true_times = times + offset
+
+    recording.set_times(true_times)
+
+    recording.get_times()
 
 .. warning::
 
@@ -142,8 +175,12 @@ as many samples as the recording itself) using `recording.set_times()`.
 Retrieving timepoints from sample index
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-SpikeInterface provides two convenience methods for obtaining the timepoint in seconds
-given an index of the time array:
+SpikeInterface provides two convenience methods for obtaining the
+timepoint in seconds given an index of the time array.
+
+Use
+:meth:`time_to_sample_index() <spikeinterface.core.BaseRecording.time_to_sample_index>`
+to go from time to the sample index:
 
 .. code-block:: python
 
@@ -152,7 +189,9 @@ given an index of the time array:
     print(sample_index)
 
 
-Similarly, you can retrieve the time array index given a timepoint:
+and
+:meth:`sample_index_to_to_time() <spikeinterface.core.BaseRecording.sample_index_to_to_time>`
+to can retrieve the index given a timepoint:
 
 
 .. code-block:: python
@@ -166,9 +205,12 @@ Aligning events across timestreams
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The alignment of electrophysiology recording time to other data streams (e.g. behaviour)
-is an important step in ephys analysis. To acheive this,it is common to collect
-a synconrisation ('sync') pulse on an additional channel. At present SpikeInterface does not include
-features for time-alignment, but some useful articles can be found on the following pages,
-`SpikeGLX <https://github.com/billkarsh/SpikeGLX/blob/master/Markdown/UserManual.md#procedure-to-calibrate-sample-rates>`_,
-`OpenEphys <https://open-ephys.github.io/gui-docs/Tutorials/Data-Synchronization.html>`_,
-`NWB <https://neuroconv.readthedocs.io/en/main/user_guide/temporal_alignment.html>`_
+is an important step in electrophysiology analysis. To achieve this,it is common to acquire
+a synchronisation ('sync') pulse on an additional channel.
+
+At present SpikeInterface does not include features for time-alignment,
+but some useful articles on how to approach this can be found on the following pages:
+
+* `SpikeGLX <https://github.com/billkarsh/SpikeGLX/blob/master/Markdown/UserManual.md#procedure-to-calibrate-sample-rates>`_,
+* `OpenEphys <https://open-ephys.github.io/gui-docs/Tutorials/Data-Synchronization.html>`_,
+* `NWB <https://neuroconv.readthedocs.io/en/main/user_guide/temporal_alignment.html>`_

doc/sg_execution_times.rst

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:02.107** total execution time for 15 files **from all galleries**:
+**00:01.439** total execution time for 17 files **from all galleries**:
 
 .. container::
 
@@ -32,48 +32,54 @@ Computation times
    * - Example
      - Time
      - Mem (MB)
-   * - :ref:`sphx_glr_tutorials_core_plot_4_sorting_analyzer.py` (``../examples/tutorials/core/plot_4_sorting_analyzer.py``)
-     - 00:02.107
+   * - :ref:`sphx_glr_tutorials_core_plot_4_sorting_analyzer.py` (``..\examples\tutorials\core\plot_4_sorting_analyzer.py``)
+     - 00:01.425
      - 0.0
-   * - :ref:`sphx_glr_tutorials_comparison_plot_5_comparison_sorter_weaknesses.py` (``../examples/tutorials/comparison/plot_5_comparison_sorter_weaknesses.py``)
+   * - :ref:`sphx_glr_tutorials_core_plot_7_handle_times_new.py` (``..\examples\tutorials\core\plot_7_handle_times_new.py``)
+     - 00:00.013
+     - 0.0
+   * - :ref:`sphx_glr_tutorials_comparison_generate_erroneous_sorting.py` (``..\examples\tutorials\comparison\generate_erroneous_sorting.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_tutorials_comparison_plot_5_comparison_sorter_weaknesses.py` (``..\examples\tutorials\comparison\plot_5_comparison_sorter_weaknesses.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_core_plot_1_recording_extractor.py` (``../examples/tutorials/core/plot_1_recording_extractor.py``)
+   * - :ref:`sphx_glr_tutorials_core_plot_1_recording_extractor.py` (``..\examples\tutorials\core\plot_1_recording_extractor.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_core_plot_2_sorting_extractor.py` (``../examples/tutorials/core/plot_2_sorting_extractor.py``)
+   * - :ref:`sphx_glr_tutorials_core_plot_2_sorting_extractor.py` (``..\examples\tutorials\core\plot_2_sorting_extractor.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_core_plot_3_handle_probe_info.py` (``../examples/tutorials/core/plot_3_handle_probe_info.py``)
+   * - :ref:`sphx_glr_tutorials_core_plot_3_handle_probe_info.py` (``..\examples\tutorials\core\plot_3_handle_probe_info.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_core_plot_5_append_concatenate_segments.py` (``../examples/tutorials/core/plot_5_append_concatenate_segments.py``)
+   * - :ref:`sphx_glr_tutorials_core_plot_5_append_concatenate_segments.py` (``..\examples\tutorials\core\plot_5_append_concatenate_segments.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_core_plot_6_handle_times.py` (``../examples/tutorials/core/plot_6_handle_times.py``)
+   * - :ref:`sphx_glr_tutorials_core_plot_6_handle_times.py` (``..\examples\tutorials\core\plot_6_handle_times.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_extractors_plot_1_read_various_formats.py` (``../examples/tutorials/extractors/plot_1_read_various_formats.py``)
+   * - :ref:`sphx_glr_tutorials_extractors_plot_1_read_various_formats.py` (``..\examples\tutorials\extractors\plot_1_read_various_formats.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_extractors_plot_2_working_with_unscaled_traces.py` (``../examples/tutorials/extractors/plot_2_working_with_unscaled_traces.py``)
+   * - :ref:`sphx_glr_tutorials_extractors_plot_2_working_with_unscaled_traces.py` (``..\examples\tutorials\extractors\plot_2_working_with_unscaled_traces.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_qualitymetrics_plot_3_quality_mertics.py` (``../examples/tutorials/qualitymetrics/plot_3_quality_mertics.py``)
+   * - :ref:`sphx_glr_tutorials_qualitymetrics_plot_3_quality_mertics.py` (``..\examples\tutorials\qualitymetrics\plot_3_quality_mertics.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_qualitymetrics_plot_4_curation.py` (``../examples/tutorials/qualitymetrics/plot_4_curation.py``)
+   * - :ref:`sphx_glr_tutorials_qualitymetrics_plot_4_curation.py` (``..\examples\tutorials\qualitymetrics\plot_4_curation.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_widgets_plot_1_rec_gallery.py` (``../examples/tutorials/widgets/plot_1_rec_gallery.py``)
+   * - :ref:`sphx_glr_tutorials_widgets_plot_1_rec_gallery.py` (``..\examples\tutorials\widgets\plot_1_rec_gallery.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_widgets_plot_2_sort_gallery.py` (``../examples/tutorials/widgets/plot_2_sort_gallery.py``)
+   * - :ref:`sphx_glr_tutorials_widgets_plot_2_sort_gallery.py` (``..\examples\tutorials\widgets\plot_2_sort_gallery.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_widgets_plot_3_waveforms_gallery.py` (``../examples/tutorials/widgets/plot_3_waveforms_gallery.py``)
+   * - :ref:`sphx_glr_tutorials_widgets_plot_3_waveforms_gallery.py` (``..\examples\tutorials\widgets\plot_3_waveforms_gallery.py``)
      - 00:00.000
      - 0.0
-   * - :ref:`sphx_glr_tutorials_widgets_plot_4_peaks_gallery.py` (``../examples/tutorials/widgets/plot_4_peaks_gallery.py``)
+   * - :ref:`sphx_glr_tutorials_widgets_plot_4_peaks_gallery.py` (``..\examples\tutorials\widgets\plot_4_peaks_gallery.py``)
      - 00:00.000
      - 0.0