pynwb.icephys module
- pynwb.icephys.ensure_unit(self, name, current_unit, unit, nwb_version)[source]
A helper to ensure correct unit used.
Issues a warning with details if current_unit is to be ignored, and unit to be used instead.
- class pynwb.icephys.IntracellularElectrode(name, device, description, slice=None, seal=None, location=None, resistance=None, filtering=None, initial_access_resistance=None, cell_id=None)[source]
Bases:
NWBContainer
Describes an intracellular electrode and associated metadata.
- Parameters:
name (
str
) – the name of this electrodedevice (
Device
) – the device that was used to record from this electrodedescription (
str
) – Recording description, description of electrode (e.g., whole-cell, sharp, etc).slice (
str
) – Information about slice used for recording.seal (
str
) – Information about seal used for recording.location (
str
) – Area, layer, comments on estimation, stereotaxis coordinates (if in vivo, etc).resistance (
str
) – Electrode resistance, unit - Ohm.filtering (
str
) – Electrode specific filtering.initial_access_resistance (
str
) – Initial access resistance.cell_id (
str
) – Unique ID of cell.
- property cell_id
Unique ID of cell.
- property description
Recording description, description of electrode (e.g., whole-cell, sharp, etc).
- property device
the device that was used to record from this electrode
- property filtering
Electrode specific filtering.
- property initial_access_resistance
Initial access resistance.
- property location
Area, layer, comments on estimation, stereotaxis coordinates (if in vivo, etc).
- namespace = 'core'
- neurodata_type = 'IntracellularElectrode'
- property resistance
Electrode resistance, unit - Ohm.
- property seal
Information about seal used for recording.
- property slice
Information about slice used for recording.
- class pynwb.icephys.PatchClampSeries(name, data, unit, electrode, gain=None, stimulus_description='N/A', resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, offset=0.0, sweep_number=None)[source]
Bases:
TimeSeries
Stores stimulus or response current or voltage. Superclass definition for patch-clamp data (this class should not be instantiated directly).
- Parameters:
name (
str
) – The name of this TimeSeries datasetdata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – The data values. The first dimension must be time.unit (
str
) – The base unit of measurement (should be SI unit)electrode (
IntracellularElectrode
) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.gain (
float
) – Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)stimulus_description (
str
) – the stimulus name/protocolresolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valueoffset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.sweep_number (
int
oruint32
oruint64
) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
- property electrode
IntracellularElectrode group that describes the electrode that was used to apply or record this data.
- property stimulus_description
the stimulus name/protocol
- property sweep_number
Sweep number, allows for grouping different PatchClampSeries together via the sweep_table
- namespace = 'core'
- neurodata_type = 'PatchClampSeries'
- class pynwb.icephys.CurrentClampSeries(name, data, electrode, gain=None, stimulus_description='N/A', bias_current=None, bridge_balance=None, capacitance_compensation=None, resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None, offset=0.0, unit='volts')[source]
Bases:
PatchClampSeries
Stores voltage data recorded from intracellular current-clamp recordings. A corresponding CurrentClampStimulusSeries (stored separately as a stimulus) is used to store the current injected.
- Parameters:
name (
str
) – The name of this TimeSeries datasetdata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – The data values. The first dimension must be time.electrode (
IntracellularElectrode
) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.gain (
float
) – Units - Volt/Voltstimulus_description (
str
) – the stimulus name/protocolbias_current (
float
) – Unit - Ampbridge_balance (
float
) – Unit - Ohmcapacitance_compensation (
float
) – Unit - Faradresolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valuesweep_number (
int
oruint32
oruint64
) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_tableoffset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.unit (
str
) – The base unit of measurement (must be ‘volts’)
- property bias_current
Unit - Amp
- property bridge_balance
Unit - Ohm
- property capacitance_compensation
Unit - Farad
- namespace = 'core'
- neurodata_type = 'CurrentClampSeries'
- class pynwb.icephys.IZeroClampSeries(name, data, electrode, gain=None, stimulus_description='N/A', resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None, offset=0.0, unit='volts')[source]
Bases:
CurrentClampSeries
Stores recorded voltage data from intracellular recordings when all current and amplifier settings are off (i.e., CurrentClampSeries fields will be zero). There is no CurrentClampStimulusSeries associated with an IZero series because the amplifier is disconnected and no stimulus can reach the cell.
- Parameters:
name (
str
) – The name of this TimeSeries datasetdata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – The data values. The first dimension must be time.electrode (
IntracellularElectrode
) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.gain (
float
) – Units: Volt/Voltstimulus_description (
str
) – The stimulus name/protocol. Setting this to a value other than “N/A” is deprecated as of NWB 2.3.0.resolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valuesweep_number (
int
oruint32
oruint64
) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_tableoffset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.unit (
str
) – The base unit of measurement (must be ‘volts’)
- namespace = 'core'
- neurodata_type = 'IZeroClampSeries'
- class pynwb.icephys.CurrentClampStimulusSeries(name, data, electrode, gain=None, stimulus_description='N/A', resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None, offset=0.0, unit='amperes')[source]
Bases:
PatchClampSeries
Alias to standard PatchClampSeries. Its functionality is to better tag PatchClampSeries for machine (and human) readability of the file.
- Parameters:
name (
str
) – The name of this TimeSeries datasetdata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – The data values. The first dimension must be time.electrode (
IntracellularElectrode
) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.gain (
float
) – Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)stimulus_description (
str
) – the stimulus name/protocolresolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valuesweep_number (
int
oruint32
oruint64
) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_tableoffset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.unit (
str
) – The base unit of measurement (must be ‘amperes’)
- namespace = 'core'
- neurodata_type = 'CurrentClampStimulusSeries'
- class pynwb.icephys.VoltageClampSeries(name, data, electrode, gain=None, stimulus_description='N/A', capacitance_fast=None, capacitance_slow=None, resistance_comp_bandwidth=None, resistance_comp_correction=None, resistance_comp_prediction=None, whole_cell_capacitance_comp=None, whole_cell_series_resistance_comp=None, resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None, offset=0.0, unit='amperes')[source]
Bases:
PatchClampSeries
Stores current data recorded from intracellular voltage-clamp recordings. A corresponding VoltageClampStimulusSeries (stored separately as a stimulus) is used to store the voltage injected.
- Parameters:
name (
str
) – The name of this TimeSeries datasetdata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – The data values. The first dimension must be time.electrode (
IntracellularElectrode
) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.gain (
float
) – Units - Volt/Ampstimulus_description (
str
) – the stimulus name/protocolcapacitance_fast (
float
) – Unit - Faradcapacitance_slow (
float
) – Unit - Faradresistance_comp_bandwidth (
float
) – Unit - Hzresistance_comp_correction (
float
) – Unit - percentresistance_comp_prediction (
float
) – Unit - percentwhole_cell_capacitance_comp (
float
) – Unit - Faradwhole_cell_series_resistance_comp (
float
) – Unit - Ohmresolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valuesweep_number (
int
oruint32
oruint64
) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_tableoffset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.unit (
str
) – The base unit of measurement (must be ‘amperes’)
- property capacitance_fast
Unit - Farad
- property capacitance_slow
Unit - Farad
- property resistance_comp_bandwidth
Unit - Hz
- property resistance_comp_correction
Unit - percent
- property resistance_comp_prediction
Unit - percent
- property whole_cell_capacitance_comp
Unit - Farad
- property whole_cell_series_resistance_comp
Unit - Ohm
- namespace = 'core'
- neurodata_type = 'VoltageClampSeries'
- class pynwb.icephys.VoltageClampStimulusSeries(name, data, electrode, gain=None, stimulus_description='N/A', resolution=-1.0, conversion=1.0, timestamps=None, starting_time=None, rate=None, comments='no comments', description='no description', control=None, control_description=None, sweep_number=None, offset=0.0, unit='volts')[source]
Bases:
PatchClampSeries
Alias to standard PatchClampSeries. Its functionality is to better tag PatchClampSeries for machine (and human) readability of the file.
- Parameters:
name (
str
) – The name of this TimeSeries datasetdata (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – The data values. The first dimension must be time.electrode (
IntracellularElectrode
) – IntracellularElectrode group that describes the electrode that was used to apply or record this data.gain (
float
) – Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)stimulus_description (
str
) – the stimulus name/protocolresolution (
float
) – The smallest meaningful difference (in specified unit) between values in dataconversion (
float
) – Scalar to multiply each element in data to convert it to the specified unittimestamps (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orTimeSeries
) – Timestamps for samples stored in datastarting_time (
float
) – The timestamp of the first samplerate (
float
) – Sampling rate in Hzcomments (
str
) – Human-readable comments about this TimeSeries datasetdescription (
str
) – Description of this TimeSeries datasetcontrol (
Iterable
) – Numerical labels that apply to each element in datacontrol_description (
Iterable
) – Description of each control valuesweep_number (
int
oruint32
oruint64
) – Sweep number, allows for grouping different PatchClampSeries together via the sweep_tableoffset (
float
) – Scalar to add to each element in the data scaled by ‘conversion’ to finish converting it to the specified unit.unit (
str
) – The base unit of measurement (must be ‘volts’)
- namespace = 'core'
- neurodata_type = 'VoltageClampStimulusSeries'
- class pynwb.icephys.SweepTable(name='sweep_table', description='A sweep table groups different PatchClampSeries together.', id=None, columns=None, colnames=None)[source]
Bases:
DynamicTable
A SweepTable allows to group PatchClampSeries together which stem from the same sweep. A sweep is a group of PatchClampSeries which have the same starting point in time.
- Parameters:
name (
str
) – name of this SweepTabledescription (
str
) – Description of this SweepTableid (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this tablecolnames (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the ordered names of the columns in this table. columns must also be provided.
- add_entry(pcs)[source]
Add the passed PatchClampSeries to the sweep table.
- Parameters:
pcs (
PatchClampSeries
) – PatchClampSeries to add to the table must have a valid sweep_number
- namespace = 'core'
- neurodata_type = 'SweepTable'
- class pynwb.icephys.IntracellularElectrodesTable(id=None, columns=None, colnames=None)[source]
Bases:
DynamicTable
Table for storing intracellular electrode related metadata’
- Parameters:
id (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this tablecolnames (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the ordered names of the columns in this table. columns must also be provided.
- namespace = 'core'
- neurodata_type = 'IntracellularElectrodesTable'
- class pynwb.icephys.IntracellularStimuliTable(id=None, columns=None, colnames=None)[source]
Bases:
DynamicTable
Table for storing intracellular electrode related metadata’
- Parameters:
id (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this tablecolnames (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the ordered names of the columns in this table. columns must also be provided.
- namespace = 'core'
- neurodata_type = 'IntracellularStimuliTable'
- class pynwb.icephys.IntracellularResponsesTable(id=None, columns=None, colnames=None)[source]
Bases:
DynamicTable
Table for storing intracellular electrode related metadata’
- Parameters:
id (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this tablecolnames (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the ordered names of the columns in this table. columns must also be provided.
- namespace = 'core'
- neurodata_type = 'IntracellularResponsesTable'
- class pynwb.icephys.IntracellularRecordingsTable(id=None, columns=None, colnames=None, category_tables=None, categories=None)[source]
Bases:
AlignedDynamicTable
A table to group together a stimulus and response from a single electrode and a single simultaneous_recording. Each row in the table represents a single recording consisting typically of a stimulus and a corresponding response.
- Parameters:
id (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this tablecolnames (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the ordered names of the columns in this table. columns must also be provided.category_tables (
list
) – List of DynamicTables to be added to the container. NOTE - Only regular DynamicTables are allowed. Using AlignedDynamicTable as a category for AlignedDynamicTable is currently not supported.categories (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – List of names with the ordering of category tables
- add_recording(electrode=None, stimulus_start_index=None, stimulus_index_count=None, stimulus=None, stimulus_template_start_index=None, stimulus_template_index_count=None, stimulus_template=None, response_start_index=None, response_index_count=None, response=None, electrode_metadata=None, stimulus_metadata=None, response_metadata=None)[source]
Add a single recording to the IntracellularRecordingsTable table.
Typically, both stimulus and response are expected. However, in some cases only a stimulus or a response may be recodred as part of a recording. In this case, None may be given for either stimulus or response, but not both. Internally, this results in both stimulus and response pointing to the same TimeSeries, while the start_index and index_count for the invalid series will both be set to -1.
- Parameters:
electrode (
IntracellularElectrode
) – The intracellular electrode usedstimulus_start_index (
int
) – Start index of the stimulusstimulus_index_count (
int
) – Stop index of the stimulusstimulus (
TimeSeries
) – The TimeSeries (usually a PatchClampSeries) with the stimulusstimulus_template_start_index (
int
) – Start index of the stimulus templatestimulus_template_index_count (
int
) – Stop index of the stimulus templatestimulus_template (
TimeSeries
) – The TimeSeries (usually a PatchClampSeries) with the stimulus template waveformsresponse_start_index (
int
) – Start index of the responseresponse_index_count (
int
) – Stop index of the responseresponse (
TimeSeries
) – The TimeSeries (usually a PatchClampSeries) with the responseelectrode_metadata (
dict
) – Additional electrode metadata to be stored in the electrodes tablestimulus_metadata (
dict
) – Additional stimulus metadata to be stored in the stimuli tableresponse_metadata (
dict
) – Additional resposnse metadata to be stored in the responses table
- Returns:
Integer index of the row that was added to this table
- Return type:
- to_dataframe(ignore_category_ids=False, electrode_refs_as_objectids=False, stimulus_refs_as_objectids=False, response_refs_as_objectids=False)[source]
Convert the collection of tables to a single pandas DataFrame
- Parameters:
ignore_category_ids (
bool
) – Ignore id columns of sub-category tableselectrode_refs_as_objectids (
bool
) – replace object references in the electrode column with object_idsstimulus_refs_as_objectids (
bool
) – replace object references in the stimulus column with object_idsresponse_refs_as_objectids (
bool
) – replace object references in the response column with object_ids
- namespace = 'core'
- neurodata_type = 'IntracellularRecordingsTable'
- class pynwb.icephys.SimultaneousRecordingsTable(intracellular_recordings_table=None, id=None, columns=None, colnames=None)[source]
Bases:
DynamicTable
A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes.
- Parameters:
intracellular_recordings_table (
IntracellularRecordingsTable
) – the IntracellularRecordingsTable table that the recordings column indexes. May be None when reading the Container from file as the table attribute is already populated in this case but otherwise this is required.id (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this tablecolnames (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the ordered names of the columns in this table. columns must also be provided.
- add_simultaneous_recording(recordings)[source]
- Add a single simultaneous recording (i.e., one sweep, or one row) consisting of one or more
recordings and associated custom simultaneous recording metadata to the table.
- Parameters:
recordings (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the indices of the recordings belonging to this simultaneous recording- Returns:
Integer index of the row that was added to this table
- Return type:
- namespace = 'core'
- neurodata_type = 'SimultaneousRecordingsTable'
- class pynwb.icephys.SequentialRecordingsTable(simultaneous_recordings_table=None, id=None, columns=None, colnames=None)[source]
Bases:
DynamicTable
A table for grouping different intracellular recording simultaneous_recordings from the SimultaneousRecordingsTable table together. This is typically used to group together simultaneous_recordings where the a sequence of stimuli of the same type with varying parameters have been presented in a sequence.
- Parameters:
simultaneous_recordings_table (
SimultaneousRecordingsTable
) – the SimultaneousRecordingsTable table that the simultaneous_recordings column indexes. May be None when reading the Container from file as the table attribute is already populated in this case but otherwise this is required.id (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this tablecolnames (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the ordered names of the columns in this table. columns must also be provided.
- add_sequential_recording(stimulus_type, simultaneous_recordings)[source]
- Add a sequential recording (i.e., one row) consisting of one or more simultaneous recordings
and associated custom sequential recording metadata to the table.
- Parameters:
stimulus_type (
str
) – the type of stimulus used for the sequential recordingsimultaneous_recordings (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the indices of the simultaneous_recordings belonging to this sequential recording
- Returns:
Integer index of the row that was added to this table
- Return type:
- namespace = 'core'
- neurodata_type = 'SequentialRecordingsTable'
- class pynwb.icephys.RepetitionsTable(sequential_recordings_table=None, id=None, columns=None, colnames=None)[source]
Bases:
DynamicTable
A table for grouping different intracellular recording sequential recordings together. With each SweepSequence typically representing a particular type of stimulus, the RepetitionsTable table is typically used to group sets of stimuli applied in sequence.
- Parameters:
sequential_recordings_table (
SequentialRecordingsTable
) – the SequentialRecordingsTable table that the sequential_recordings column indexes. May be None when reading the Container from file as the table attribute is already populated in this case but otherwise this is required.id (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this tablecolnames (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the ordered names of the columns in this table. columns must also be provided.
- add_repetition(sequential_recordings=None)[source]
- Add a repetition (i.e., one row) consisting of one or more sequential recordings
and associated custom repetition metadata to the table.
- Parameters:
sequential_recordings (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the indices of the sequential recordings belonging to this repetition- Returns:
Integer index of the row that was added to this table
- Return type:
- namespace = 'core'
- neurodata_type = 'RepetitionsTable'
- class pynwb.icephys.ExperimentalConditionsTable(repetitions_table=None, id=None, columns=None, colnames=None)[source]
Bases:
DynamicTable
A table for grouping different intracellular recording repetitions together that belong to the same experimental conditions.
- Parameters:
repetitions_table (
RepetitionsTable
) – the RepetitionsTable table that the repetitions column indexesid (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
orDataIO
orElementIdentifiers
) – the identifiers for this tablecolnames (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the ordered names of the columns in this table. columns must also be provided.
- add_experimental_condition(repetitions=None)[source]
- Add a condition (i.e., one row) consisting of one or more repetitions of sequential recordings
and associated custom experimental_conditions metadata to the table.
- Parameters:
repetitions (
ndarray
orlist
ortuple
orDataset
orArray
orStrDataset
orHDMFDataset
orAbstractDataChunkIterator
) – the indices of the repetitions belonging to this condition- Returns:
Integer index of the row that was added to this table
- Return type:
- namespace = 'core'
- neurodata_type = 'ExperimentalConditionsTable'