allensdk.brain_observatory.sync_dataset module

dataset.py

Dataset object for loading and unpacking an HDF5 dataset generated by

sync.py

@author: derricw

Allen Institute for Brain Science

Dependencies

numpy http://www.numpy.org/ h5py http://www.h5py.org/

class allensdk.brain_observatory.sync_dataset.Dataset(path)

Bases: object

A sync dataset. Contains methods for loading

and parsing the binary data.

Parameters:

pathstr

Path to HDF5 file.

Examples

>>> dset = Dataset('my_h5_file.h5')
>>> logger.info(dset.meta_data)
>>> dset.stats()
>>> dset.close()

>>> with Dataset('my_h5_file.h5') as d:
...     logger.info(dset.meta_data)
...     dset.stats()

The sync file documentation from MPE can be found at sharepoint > Instrumentation > Shared Documents > Sync_line_labels_discussion_2020-01-27-.xlsx # NOQA E501 Direct link: https://alleninstitute.sharepoint.com/:x:/s/Instrumentation/ES2bi1xJ3E9NupX-zQeXTlYBS2mVVySycfbCQhsD_jPMUw?e=Z9jCwH

BEHAVIOR_TRACKING_KEYS = ('beh_frame_received', 'cam1_exposure', 'behavior_monitoring')

DEPRECATED_KEYS = {}

EYE_TRACKING_KEYS = ('eye_frame_received', 'cam2_exposure', 'eyetracking', 'eye_cam_exposing', 'eye_tracking')

FRAME_KEYS = ('frames', 'stim_vsync', 'vsync_stim')

OPTOGENETIC_STIMULATION_KEYS = ('LED_sync', 'opto_trial')

PHOTODIODE_KEYS = ('photodiode', 'stim_photodiode')

property analog_meta_data

close()

Closes the dataset.

duty_cycle(line)

Doesn’t work right now. Freezes python for some reason.

Returns the duty cycle of a line.

frequency(line, edge='rising')

Returns the average frequency of a line.

get_all_bits()

Returns the data for all bits.

get_all_events()

Returns all counter values and their cooresponding IO state.

get_all_times(units='samples')

Returns all counter values.

Parameters:

unitsstr

Return times in ‘samples’ or ‘seconds’

get_analog_channel(channel, start_time=0.0, stop_time=None, downsample=1)

Returns the data from the specified analog channel between the

timepoints.

Args:

channel (int, str): desired channel index or label start_time (Optional[float]): start time in seconds stop_time (Optional[float]): stop time in seconds downsample (Optional[int]): downsample factor

Returns:

ndarray: slice of data for specified channel

Raises:

KeyError: no analog data present

get_analog_meta()

Returns the metadata for the analog data.

get_bit(bit)

Returns the values for a specific bit.

Parameters:

bitint

Bit to return.

get_bit_changes(bit)

Returns the first derivative of a specific bit.

Data points are 1 on rising edges and 255 on falling edges.

Parameters:

bitint

Bit for which to return changes.

get_edges(kind: str, keys: str | Sequence[str], units: str = 'seconds', permissive: bool = False) → ndarray | None

Utility function for extracting edge times from a line

Parameters:

kindOne of “rising”, “falling”, or “all”. Should this method return

timestamps for rising, falling or both edges on the appropriate line

keysThese will be checked in sequence. Timestamps will be returned

for the first which is present in the line labels

unitsone of “seconds”, “samples”, or “indices”. The returned

“time”stamps will be given in these units.

raise_missingIf True and no matching line is found, a KeyError will

be raised

Returns:

An array of edge times. If raise_missing is False and none of the keys

were found, returns None.

Raises:

KeyErrornone of the provided keys were found among this dataset’s

line labels

get_events_by_bit(bit, units='samples')

Returns all counter values for transitions (both rising and falling)

for a specific bit.

Parameters:

bitint

Bit for which to return events.

get_events_by_line(line, units='samples')

Returns all counter values for transitions (both rising and falling)

for a specific line.

Parameters:

linestr

Line for which to return events.

get_falling_edges(line, units='samples')

Returns the counter values for the falling edges for a specific bit

or line.

Parameters:

linestr

Line for which to return edges.

get_line(line)

Returns the values for a specific line.

Parameters:

linestr

Line to return.

get_line_changes(line)

Returns the first derivative of a specific line.

Data points are 1 on rising edges and 255 on falling edges.

Parameters:

line(str)

Line name for which to return changes.

get_nearest(source, target, source_edge='rising', target_edge='rising', direction='previous', units='indices')

For all values of the source line, finds the nearest edge from the

target line.

By default, returns the indices of the target edges.

Args:

source (str, int): desired source line target (str, int): desired target line source_edge [Optional(str)]: “rising” or “falling” source edges target_edge [Optional(str): “rising” or “falling” target edges direction (str): “previous” or “next”. Whether to prefer the

previous edge or the following edge.

units (str): “indices”

get_rising_edges(line, units='samples')

Returns the counter values for the rizing edges for a specific bit or

line.

Parameters:

linestr

Line for which to return edges.

line_stats(line, print_results=True)

Quick-and-dirty analysis of a bit.

##TODO: Split this up into smaller functions.

load(path)

Loads an hdf5 sync dataset.

Parameters:

pathstr

Path to hdf5 file.

period(line, edge='rising')

Returns a dictionary with avg, min, max, and st of period for a line.

plot_all(start_time, stop_time, auto_show=True)

Plot all active bits.

Yikes. Come up with a better way to show this.

plot_bit(bit, start_time=0.0, end_time=None, auto_show=True, axes=None, name='')

Plots a specific bit at a specific time period.

plot_bits(bits, start_time=0.0, end_time=None, auto_show=True)

Plots a list of bits.

plot_line(line, start_time=0.0, end_time=None, auto_show=True)

Plots a specific line at a specific time period.

plot_lines(lines, start_time=0.0, end_time=None, auto_show=True)

Plots specific lines at a specific time period.

property sample_freq

stats()

Quick-and-dirty analysis of all bits. Prints a few things about each

bit where events are found.

allensdk.brain_observatory.sync_dataset.get_bit(uint_array, bit)

Returns a bool array for a specific bit in a uint ndarray.

Parameters:

uint_array(numpy.ndarray)

The array to extract bits from.

bit(int)

The bit to extract.

allensdk.brain_observatory.sync_dataset.unpack_uint32(uint32_array, endian='L')

Unpacks an array of 32-bit unsigned integers into bits.

Default is least significant bit first.

*Not currently used by sync dataset because get_bit is better and does

basically the same thing. I’m just leaving it in because it could potentially account for endianness and possibly have other uses in the future.