14.1.8. Miscellaneous

14.1.8.1. mosaic.settings module

Load analysis settings from a JSON file.

Created:

8/24/2012

Author:

Arvind Balijepalli <arvind.balijepalli@nist.gov>

License:

See LICENSE.TXT

ChangeLog:

3/20/23 AB Add support for pyabf

5/13/21 AB Include chimeraTrajio in default settings.

4/19/19 AB Added an option (trackBaseline) to continuously track the opent channel baseline current during an analysis.

9/22/17 AB Removed the filterEventPadding option to eventSegment.

7/15/17 AB Add the filterEventPadding option to eventSegment.

3/16/16 AB Replaced InitThreshold with StepSize in default settings for ADEPT and warn users when InitThreshold is used.

8/24/15 AB Updated algorithm names.

6/24/15 AB Added an option to unlink the RC constants in stepResponseAnalysis.

3/20/15 AB Added MaxEventLength to multiStateAnalysis settings

3/6/15 JF Corrected formatting on cusumLevelAnalysis and multiStateAnalysis dictionary file

3/6/15 AB Added MinStateLength parameter for multiStateAnalysis to dictionary

2/14/15 AB Added default settings for cusumLevelAnalysis.

8/20/14 AB Changed precedence of settings file search to datpath/.settings,

datpath/settings, coderoot/.settings and coderoot/settings

8/6/14 AB Add a function to parse a settings string.

9/5/13 AB Check for either .settings or settings in data directory

and code root. Warn when using default settings

8/24/12 AB Initial version

class mosaic.settings.settings(datpath, defaultwarn=True)

Bases: object

Initialize a settings object.

Args:

• datpath : Specify the location of the settings file. If a settings file is not found, return default settings.

• defaultwarn : If True warn the user if a settings file was not found in the path specified by datpath.

getSettings(section)

Return settings for a specified section as a Python dict.

Args:

• section : specifies the section for which settings are requested. Returns an empty dictionary if the settings file doesn’t exist the section is not found.

14.1.8.2. mosaic.utilities.ionic_current_stats module

Created:

10/30/2014

Author:

Arvind Balijepalli <arvind.balijepalli@nist.gov>

License:

See LICENSE.TXT

ChangeLog:

5/24/19 AB Python 3.7 port

7/29/16 KB Added weights to histogram fitting

15/12/15 KB Added error checking and limits to baseline calculations

10/30/14 AB Initial version

mosaic.utilities.ionic_current_stats.OpenCurrentDist(dat, limit, minBaseline=-1, maxBaseline=-1)

Calculate the mean and standard deviation of a time-series.

Args:

• dat : time-series data

• limit : limit the calculation to the top 50% (+0.5) of the range, bottom 50% (-0.5) or the entire range (0). Any other value of limit will cause it to be reset to 0 (i.e. full range).

14.1.8.3. mosaic.utilities.util module

A collection of utility functions

mosaic.utilities.util.avg(dat)

Calculate the average of a list of reals

mosaic.utilities.util.commonest(dat)

Return the most common element in a list.

mosaic.utilities.util.decimate(dat, size)

Decimate dat for a specified window size.

mosaic.utilities.util.filter(dat, windowSz)

Filter the data using a convolution. Returns an array of size len(dat)-windowSz+1 if dat is longer than windowSz. If len(dat) < windowSz, raise WindowSizeError

mosaic.utilities.util.flat2(dat)

Flatten a 2D array to a list

mosaic.utilities.util.partition(dat, size)

Partition a list into sub-lists, each of length size. If the number of elements in dat does not partition evenly, the last sub-list will have fewer elements.

mosaic.utilities.util.sd(dat)

Wrapper for numpy std

mosaic.utilities.util.selectS(dat, nSigma, mu, sd)

Select and return data from a list that lie within nSigma * SD of the mean.

14.1.8.4. mosaic.utilities.mosaicLogFormat module

An object that allows arbitrary formatting of log text.

Created:

09/12/2015

Author:

Arvind Balijepalli <arvind.balijepalli@nist.gov>

License:

See LICENSE.TXT

ChangeLog:

06/14/16 AB Added a new Python property class mimic to add log property set, get and del.

06/13/16 AB Remove mosaicLogFormat class

09/12/15 AB Initial version

mosaic.utilities.mosaicLogFormat._d(msg, *args)

Format a debug log message. This function will automatically append calling function name and file/line number.

Parameters:

• msg : Log message formatted using the Python formatter class.

• args : Message arguments.

Usage:

Log an integer or a float variable.

_d("Var x has value {0}", x)

_d("Var y is a float with value {0:0.2f} to 2 decimal places.", y)

mosaic.utilities.mosaicLogFormat._dprop(msg, *args)

Format a debug log message for a class property. This function will automatically append calling function name and file/line number.

Parameters:

• msg : Log message formatted using the Python formatter class.

• args : Message arguments.

Usage:

Log a property that returns an integer or a float.

_dprop("Var x has value {0}", x)

_dprop("Var y is a float with value {0:0.2f} to 2 decimal places.", y)

class mosaic.utilities.mosaicLogFormat.mosaic_property(fget=None, fset=None, fdel=None, doc=None)

Bases: object

Emulate Python property. Add support to the getter and setter methods to automatically log properties in debug mode. The new class can be used exactly as the built-in Python property class, for example as a decorator

class foo:
        def __init__(self):
                self.x=100

        @mosaic_property
        def x(self):
                return self.x

        @x.setter
        def x(self, val):
                self.x=val

Adapted from: https://docs.python.org/2/howto/descriptor.html#properties.

14.1.8.5. mosaic.utilities.mosaicLogging module

An implementation of Python logging heavily adapted from http://stackoverflow.com/questions/15727420/using-python-logging-in-multiple-modules.

Created:

5/29/2016

Author:

Arvind Balijepalli <arvind.balijepalli@nist.gov>

License:

See LICENSE.TXT

ChangeLog:

5/30/16 AB Strip whitespace from rotating file handler messages.

5/29/16 AB Initial version

class mosaic.utilities.mosaicLogging.MessageFormatter(fmt=None, datefmt=None, style='%', validate=True, *, defaults=None)

Bases: Formatter

format(record)

Format the specified record as text.

The record’s attribute dictionary is used as the operand to a string formatting operation which yields the returned string. Before formatting the dictionary, a couple of preparatory steps are carried out. The message attribute of the record is computed using LogRecord.getMessage(). If the formatting string uses the time (as determined by a call to usesTime(), formatTime() is called to format the event time. If there is exception information, it is formatted using formatException() and appended to the message.

class mosaic.utilities.mosaicLogging.mosaicLogging(*args, **kwargs)

Bases: object

A custom logging class that uses the Python logging facility. Logs are automatically saved to a metaMDIO instance, and to a file log when DeveloperMode is active.

static getLogger(name=None, dbHnd=None)

Get a logger instance.

Parameters:

• name : Logger name

• dbHnd : MetaMDIO handle to allow logs to be saved to the database.

Usage:

In this example, we get an instance of a logger with the module name and log a debug message.

logger=mosaicLogging().getLogger(__name__)

logger.debug("Test debug message")

14.1.8.6. mosaic.utilities.mosaicTiming module

A class that provides platform independent timing and function profiling utilities.

Created:

4/10/2016

Author:

Arvind Balijepalli <arvind.balijepalli@nist.gov>

License:

See LICENSE.TXT

ChangeLog:

4/14/21 AB Windows fixes

6/17/16 AB Only profile functions in DeveloperMode. Log timing output.

4/10/16 AB Initial version

class mosaic.utilities.mosaicTiming.mosaicTiming

Bases: object

Profile code by attaching an instance of this class to any function. All the methods in this class are valid for the function being profiled.

FunctionTiming(func)

Pass the function to be profiled as an argument. Alternatively with python 2.4+, attach a decorator to the function being profiled.

Parameters:

• func : function to be profiled

Usage:

funcTimer=mosaicTiming.mosaicTiming()

@funcTimer.FunctionTiming
def someFunc():
                print 'doing something'

# summarize the profiling results for someFunc
funcTimer.PrintStatistics()

PrintCurrentTime()

Print timing results of the most recent function call

PrintStatistics()

Print average timing results of the function call

Reset(funcname=None)

Reset all profiling data collected for a specified function or all stored functions.

time()

A platform independent timing function.

14.1.8.7. mosaic.utilities.fit_funcs module

Fit functions used in processing algorithms.

Created:

10/30/2014

Author:

Arvind Balijepalli <arvind.balijepalli@nist.gov>

License:

See LICENSE.TXT

ChangeLog:

12/09/15 KB Added a wrapper for multiStateFunc

6/24/15 AB Relaxed stepResponseFunc to include different RC constants

for up and down states.

12/31/14 AB Changed multi-state function to include a separate tau for

each state following Balijepalli et al, ACS Nano 2014.

11/19/14 AB Initial version