recording.py
SortGroup
¶
Bases: SpyglassMixin
, Manual
Source code in src/spyglass/spikesorting/v1/recording.py
set_group_by_shank(nwb_file_name, references=None, omit_ref_electrode_group=False, omit_unitrode=True)
classmethod
¶
Divides electrodes into groups based on their shank position.
- Electrodes from probes with 1 shank (e.g. tetrodes) are placed in a single group
- Electrodes from probes with multiple shanks (e.g. polymer probes) are placed in one group per shank
- Bad channels are omitted
Parameters:
Name | Type | Description | Default |
---|---|---|---|
nwb_file_name
|
str
|
the name of the NWB file whose electrodes should be put into sorting groups |
required |
references
|
dict
|
If passed, used to set references. Otherwise, references set using original reference electrodes from config. Keys: electrode groups. Values: reference electrode. |
None
|
omit_ref_electrode_group
|
bool
|
Optional. If True, no sort group is defined for electrode group of reference. |
False
|
omit_unitrode
|
bool
|
Optional. If True, no sort groups are defined for unitrodes. |
True
|
Source code in src/spyglass/spikesorting/v1/recording.py
SpikeSortingPreprocessingParameters
¶
Bases: SpyglassMixin
, Lookup
Parameters for preprocessing a recording prior to spike sorting.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
preproc_param_name
|
str
|
Name of the preprocessing parameters |
required |
preproc_params
|
dict
|
Dictionary of preprocessing parameters frequency_min: float High pass filter value in Hz frequency_max: float Low pass filter value in Hz margin_ms: float Margin in ms on border to avoid border effect seed: int Random seed for whitening min_segment_length: float Minimum segment length in seconds |
required |
Source code in src/spyglass/spikesorting/v1/recording.py
SpikeSortingRecordingSelection
¶
Bases: SpyglassMixin
, Manual
Source code in src/spyglass/spikesorting/v1/recording.py
insert_selection(key)
classmethod
¶
Insert a row into SpikeSortingRecordingSelection with an automatically generated unique recording ID as the sole primary key.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
key
|
dict
|
primary key of Raw, SortGroup, IntervalList, SpikeSortingPreprocessingParameters, LabTeam tables |
required |
Returns:
Type | Description |
---|---|
primary key of SpikeSortingRecordingSelection table
|
|
Source code in src/spyglass/spikesorting/v1/recording.py
SpikeSortingRecording
¶
Bases: SpyglassMixin
, Computed
Source code in src/spyglass/spikesorting/v1/recording.py
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|
make(key)
¶
Populate SpikeSortingRecording.
- Get valid times for sort interval from IntervalList
- Use spikeinterface to preprocess recording
- Write processed recording to NWB file
- Insert resulting ...
- Interval to IntervalList
- NWB file to AnalysisNwbfile
- Recording ids to SpikeSortingRecording
Source code in src/spyglass/spikesorting/v1/recording.py
get_recording(key)
classmethod
¶
Get recording related to this curation as spikeinterface BaseRecording
Parameters:
Name | Type | Description | Default |
---|---|---|---|
key
|
dict
|
primary key of SpikeSorting table |
required |
Source code in src/spyglass/spikesorting/v1/recording.py
update_ids()
¶
Update electrodes_id, and hash in SpikeSortingRecording table.
Only used for transitioning to recompute NWB files, see #1093.
Source code in src/spyglass/spikesorting/v1/recording.py
recompute(key)
¶
Recompute the processed recording.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
key
|
dict
|
primary key of SpikeSortingRecording table |
required |
SpikeInterfaceRecordingDataChunkIterator
¶
Bases: GenericDataChunkIterator
DataChunkIterator specifically for use on RecordingExtractor objects.
Source code in src/spyglass/spikesorting/v1/recording.py
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|
__init__(recording, segment_index=0, return_scaled=False, buffer_gb=None, buffer_shape=None, chunk_mb=None, chunk_shape=None, display_progress=False, progress_bar_options=None)
¶
Initialize an Iterable object which returns DataChunks with data and their selections on each iteration.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
recording
|
BaseRecording
|
The SpikeInterfaceRecording object which handles the data access. |
required |
segment_index
|
int
|
The recording segment to iterate on. Defaults to 0. |
0
|
return_scaled
|
bool
|
Whether to return the trace data in scaled units (uV, if True) or in the raw data type (if False). Defaults to False. |
False
|
buffer_gb
|
float
|
The upper bound on size in gigabytes (GB) of each selection from the iteration.
The buffer_shape will be set implicitly by this argument.
Cannot be set if |
None
|
buffer_shape
|
tuple
|
Manual specification of buffer shape to return on each iteration.
Must be a multiple of chunk_shape along each axis.
Cannot be set if |
None
|
chunk_mb
|
float
|
The upper bound on size in megabytes (MB) of the internal chunk for the HDF5 dataset.
The chunk_shape will be set implicitly by this argument.
Cannot be set if |
None
|
chunk_shape
|
tuple
|
Manual specification of the internal chunk shape for the HDF5 dataset.
Cannot be set if |
None
|
display_progress
|
bool
|
Display a progress bar with iteration rate and estimated completion time. |
False
|
progress_bar_options
|
dict
|
Dictionary of keyword arguments to be passed directly to tqdm. See https://github.com/tqdm/tqdm#parameters for options. |
None
|
Source code in src/spyglass/spikesorting/v1/recording.py
TimestampsSegment
¶
Bases: BaseRecordingSegment
Source code in src/spyglass/spikesorting/v1/recording.py
TimestampsDataChunkIterator
¶
Bases: GenericDataChunkIterator
DataChunkIterator specifically for use on RecordingExtractor objects.
Source code in src/spyglass/spikesorting/v1/recording.py
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|
__init__(recording, segment_index=0, return_scaled=False, buffer_gb=None, buffer_shape=None, chunk_mb=None, chunk_shape=None, display_progress=False, progress_bar_options=None)
¶
Initialize an Iterable object which returns DataChunks with data and their selections on each iteration.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
recording
|
SpikeInterfaceRecording
|
The SpikeInterfaceRecording object (RecordingExtractor or BaseRecording) which handles the data access. |
required |
segment_index
|
int
|
The recording segment to iterate on. Defaults to 0. |
0
|
return_scaled
|
bool
|
Whether to return the trace data in scaled units (uV, if True) or in the raw data type (if False). Defaults to False. |
False
|
buffer_gb
|
float
|
The upper bound on size in gigabytes (GB) of each selection from the iteration.
The buffer_shape will be set implicitly by this argument.
Cannot be set if |
None
|
buffer_shape
|
tuple
|
Manual specification of buffer shape to return on each iteration.
Must be a multiple of chunk_shape along each axis.
Cannot be set if |
None
|
chunk_mb
|
float
|
The upper bound on size in megabytes (MB) of the internal chunk for the HDF5 dataset.
The chunk_shape will be set implicitly by this argument.
Cannot be set if |
None
|
chunk_shape
|
tuple
|
Manual specification of the internal chunk shape for the HDF5 dataset.
Cannot be set if |
None
|
display_progress
|
bool
|
Display a progress bar with iteration rate and estimated completion time. |
False
|
progress_bar_options
|
dict
|
Dictionary of keyword arguments to be passed directly to tqdm. See https://github.com/tqdm/tqdm#parameters for options. |
None
|