allensdk.internal.pipeline_modules.run_ophys_time_sync module¶
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class
allensdk.internal.pipeline_modules.run_ophys_time_sync.
TimeSyncOutputs
[source]¶ Bases:
tuple
Schema for synchronization outputs
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behavior_alignment
¶ Alias for field number 12
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behavior_delta
¶ Alias for field number 5
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behavior_times
¶ Alias for field number 9
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experiment_id
¶ Alias for field number 0
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eye_alignment
¶ Alias for field number 11
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eye_delta
¶ Alias for field number 4
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eye_times
¶ Alias for field number 8
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ophys_delta
¶ Alias for field number 2
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ophys_times
¶ Alias for field number 6
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stimulus_alignment
¶ Alias for field number 10
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stimulus_delay
¶ Alias for field number 1
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stimulus_delta
¶ Alias for field number 3
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stimulus_times
¶ Alias for field number 7
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class
allensdk.internal.pipeline_modules.run_ophys_time_sync.
TimeSyncWriter
(output_h5_path: str, output_json_path: Optional[str] = None)[source]¶ Bases:
object
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validate_paths
(self)[source]¶ Determines whether we can actually write to the specified paths, allowing for creation of intermediate directories. It is a good idea to run this beore doing any heavy calculations!
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write
(self, outputs: allensdk.internal.pipeline_modules.run_ophys_time_sync.TimeSyncOutputs)[source]¶ Convenience for writing both an output h5 and (if applicable) an output json.
Parameters: - outputs : the data to be written
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allensdk.internal.pipeline_modules.run_ophys_time_sync.
check_stimulus_delay
(obt_delay: float, min_delay: float, max_delay: float)[source]¶ Raise an exception if the monitor delay is not within specified bounds
Parameters: - obt_delay : obtained monitor delay (s)
- min_delay : lower threshold (s)
- max_delay : upper threshold (s)
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allensdk.internal.pipeline_modules.run_ophys_time_sync.
run_ophys_time_sync
(aligner: allensdk.internal.brain_observatory.time_sync.OphysTimeAligner, experiment_id: int, min_stimulus_delay: float, max_stimulus_delay: float) → allensdk.internal.pipeline_modules.run_ophys_time_sync.TimeSyncOutputs[source]¶ Carry out synchronization of timestamps across the data streams of an ophys experiment.
Parameters: - aligner : drives alignment. See OphysTimeAligner for details of the
attributes and properties that must be implemented.
- experiment_id : unique identifier for the experiment being aligned
- min_stimulus_delay : reject alignment run (raise a ValueError) if the
calculated monitor delay is below this value (s).
- max_stimulus_delay : reject alignment run (raise a ValueError) if the
calculated monitor delay is above this value (s).
Returns: - A TimeSyncOutputs (see definintion for more information) of output
parameters and arrays of aligned timestamps.