Filters¶

This module defines the structure for filters objects (see FilterGeneral).

Various filters are then defined in submodules, by subclassing.

The subclass needs to define at least two things:

the attribute _label (string or unicode) which defines filter operation
the func method, that performs and outputs the boolean test

Some useful functions are defined here as well.

class tunacell.filters.main.FilterAND(*filters)¶

Defines boolean AND operation between same type filters.

Parameters:	filters (sequence of `FilterGeneral` instances) –
Returns:	will perform AND boolean operation between the various filters passed as arguments.
Return type:	`FilterGeneral` instance

Notes

Defines a FilterTrue

func(target)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

exception tunacell.filters.main.FilterArgError¶: Exception raised when Argument format is not suitable.

class tunacell.filters.main.FilterBoolean¶

General class to implement Boolean operations between filters

label¶: Get label of applied filter(s)

exception tunacell.filters.main.FilterError¶: Superclass for errors while filtering

class tunacell.filters.main.FilterGeneral¶

General class for filtering cell (i.e. tunacell.base.cell.Cell) instances.

Important property is to make the instance callable, and define with a human readable label the action of filter.

func(*args)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

label¶: Get label of applied filter(s)

obs¶: Provides the list of hidden observables

exception tunacell.filters.main.FilterLabelError¶: Exception when label is not (properly) set.

class tunacell.filters.main.FilterNOT(filt)¶

Defines boolean NOT operation on filter.

Parameters:	filter (`FilterGeneral` instance) –

func(target)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.main.FilterOR(*filters)¶

Defines boolean OR operation between same type filters.

Parameters:	filters (sequence of `FilterGeneral` instances) –

func(target)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

exception tunacell.filters.main.FilterParamsError¶: Exception when parameters are not set for a given test.

class tunacell.filters.main.FilterSet(label=None, filtercell=FilterTRUE(), filterlineage=FilterTRUE(), filtertree=FilterTRUE(), filtercontainer=FilterTRUE())¶

Collects filters of each type in a single object

obs¶: Provides the list of hidden observables

class tunacell.filters.main.FilterTRUE¶

Returns True for argument of any type, can be used in Boolean filters

We need this artificial Filter to plug in defaults FilterSets.

func(*args)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

exception tunacell.filters.main.FilterTypeError¶: Error raised when one tries to combine different types of filters

tunacell.filters.main.bounded(arg, lower_bound=None, upper_bound=None)¶

Function that test whether argument is bounded.

By convention, lower bound is included, upper bound is excluded. Thus it tests whether lower_bound <= arg < upper_bound. If arg is an iterable, the test must be satisfied for every element (hence the minimal value must be greater or equal to lower_bound and the maximal value must be lower than the upper bound).

Parameters:	arg (int or float) – quantity to be tested for bounds lower_bound (int or float (default None)) – upper_bound (int or float (default None)) –
Returns:
Return type:	Boolean

This module defines filters for Cell instances

class tunacell.filters.cells.FilterCell¶: General class for filtering cell objects (reader.Cell instances)

class tunacell.filters.cells.FilterCellAny¶

Class that does not filter anything.

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterCellIDbound(lower_bound=None, upper_bound=None)¶

Test class

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterCellIDparity(parity='even')¶

Test whether identifier is odd or even

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterCompleteCycle(daughter_min=1)¶

Test whether a cell has a given parent and at least one daughter.

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterCycleFrames(lower_bound=None, upper_bound=None)¶

Check whether cell has got a minimal number of datapoints.

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterCycleSpanIncluded(lower_bound=None, upper_bound=None)¶

Check that cell cycle time interval is within valid bounds.

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterData¶

Default filter test only if cell exists and cell.data non empty.

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterDaughters(daughter_min=1, daughter_max=2)¶

Test whether a given cell as at least one daughter cell

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterHasParent¶

Test whether a cell has an identified parent cell

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterLengthIncrement(lower_bound=None, upper_bound=None)¶

Check increments are bounded.

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterObservableBound(obs=Observable(name='undefined', raw='undefined', scale='linear', differentiate=False, local_fit=False, time_window=0.0, join_points=3, mode='dynamics', timing='t', tref=None, ), tref=None, lower_bound=None, upper_bound=None)¶

Check that a given observable is bounded.

Parameters:	obs (Observable instance) – observable that will be tested for bounds works only for continuous observable (mode=’dynamics’) tref (float (default None)) – Time of reference at which to test dynamics observable value lower_bound (float (default None)) – upper_bound (float (default None)) –

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterSymmetricDivision(raw='area', lower_bound=0.4, upper_bound=0.6)¶

Check that cell division is (roughly) symmetric.

Parameters:	raw (str) – column label of raw observable to test for symmetric division (usually one of ‘length’, ‘area’). This quantity will be approximated

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.

class tunacell.filters.cells.FilterTimeInCycle(tref=0.0)¶

Check that tref is within cell birth and division time

func(cell)¶

This is the boolean operation to define in specific Filter instances

Default operation returns True.