14.1.5. Event Partition and Segment

14.1.5.1. mosaic.partition.eventSegment module

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Partition a trajectory into individual events and pass each event to an implementation of eventProcessor

Created:

7/17/2012

Author:

Arvind Balijepalli <arvind.balijepalli@nist.gov>

License:

See LICENSE.TXT

ChangeLog:

10/28/18 AB Fix spurious shallow events as outlined in https://github.com/usnistgov/mosaic/issues/102

9/25/17 AB Save unfiltered event padding by default.

1/18/17 AB Fix pre event baseline.

6/17/16 AB Log function timing in developer mode.

5/17/14 AB Delete plotting support

5/17/14 AB Add metaMDIO support for meta-data and time-series storage

2/14/14 AB Pass absdatidx argument to event processing to track absolute time of

event start for capture rate estimation.

6/22/13 AB Use plotting hooks in metaEventPartition to plot blockade depth histogram in

real-time using matplotlib.

4/22/13 AB Rewrote this class as an implementation of the base class metaEventPartition.

Included event processing parallelization using ZMQ.

9/26/12 AB Allowed automatic open channel state calculation to be overridden.

To do this the settings “meanOpenCurr”,”sdOpenCurr” and “slopeOpenCurr”

must be set manually. If all three settings are absent or

set to 01, they are autuomatically estimated.

Added “writeEventTS” boolean setting to control whether raw

events are written to file. Default is ON (1)

8/24/12 AB Settings are now read from a settings file that

is located either with the data or in the working directory

that the program is run from. Each class that relies on the

settings file will fallback to default values if the file

is not found.

7/17/12 AB Initial version

class mosaic.partition.eventSegment.eventSegment(trajDataObj, eventProcHnd, eventPartitionSettings, eventProcSettings, settingsString, **kwargs)

Bases: metaEventPartition

Implement an event partitioning algorithm by sub-classing the metaEventPartition class

Settings:

In addition to the parameters described in metaEventPartition, the following parameters from are read from the settings file (.settings in the data path or current working directory):

• blockSizeSecFunctions that perform block processing use this value to set the size of

  their windows in seconds. For example, open channel conductance is processed for windows with a size specified by this parameter. (default: 1 second)

• eventPad : Number of points to include before and after a detected event. (default: 500)

• minEventLength : Minimum number points in the blocked state to qualify as an event (default: 5)

• eventThresholdThreshold, number of SD away from the open channel mean. If the abs(curr) is less

  than ‘abs(mean)-(eventThreshold*SD)’ a new event is registered (default: 6)

• meanOpenCurrExplicitly set mean open channel current. (pA) (default: -1, to

  calculate automatically)

• sdOpenCurrExplicitly set open channel current SD. (pA) (default: -1, to

  calculate automatically)

• slopeOpenCurrExplicitly set open channel current slope. (default: -1, to

  calculate automatically)

formatoutputfiles()

Important

Abstract method: This method must be implemented by a sub-class.

Return a formatted string of output files.

formatsettings()

Return a formatted string of settings for display in the output log.

formatstats()

Return a formatted string of statistics for display in the output log.