pept.tracking.RemoveStatic

class pept.tracking.RemoveStatic(time_window, max_distance, quantile=0.9)

Bases: Reducer

Remove parts of a PointData where the tracer remains static.

Reducer signature:

      PointData -> OutOfViewFilter.fit -> PointData
list[PointData] -> OutOfViewFilter.fit -> PointData
  numpy.ndarray -> OutOfViewFilter.fit -> PointData

If there is a time_window in which the tracer does not move more than max_distance, it is removed.

The distances moved are computed relative to the average position within each time window; to make the reducer more robust to noise, the given distance quantile is compared to max_distance.

New in pept-0.5.2

Examples

Given some trajectories from e.g. a long experiment where the particle may have got stuck at some points, we can remove the static windows with:

import pept
import pept.tracking as pt

trajectories = ...

# Remove positions that spent more than 2 seconds without moving more
# than 20 mm
trajectories_nonstatic = RemoveStatic(
    time_window = 2000,
    max_distance = 20,
).fit(trajectories)

This reducer, like the rest in pept.tracking, can be chained into a pipeline, for example:

import pept
import pept.tracking as pt

pipeline = pept.Pipeline([
    # Remove positions with high errors
    pt.Condition("error < 20"),

    # Remove tracers that got stuck
    pt.RemoveStatic(time_window = 2000, max_distance = 20),

    # Trajectory separation
    pt.Segregate(window = 20, cut_distance = 15),

    # Group each trajectory into its own sample, then stack them
    pt.GroupBy("label"),
    pt.Stack(),
])

__init__(time_window, max_distance, quantile=0.9)

Methods

__init__(time_window, max_distance[, quantile])
copy([deep])	Create a deep copy of an instance of this class, including all inner attributes.
fit(samples)
load(filepath)	Load a saved / pickled PEPTObject object from filepath.
save(filepath)	Save a PEPTObject instance as a binary pickle object.

copy(deep=True)

Create a deep copy of an instance of this class, including all inner attributes.

fit(samples)

static load(filepath)

Load a saved / pickled PEPTObject object from filepath.

Most often the full object state was saved using the .save method.

Parameters

filepathfilename or file handle

If filepath is a path (rather than file handle), it is relative to where python is called.

Returns

pept.PEPTObject subclass instance

The loaded object.

Examples

Save a LineData instance, then load it back:

>>> lines = pept.LineData([[1, 2, 3, 4, 5, 6, 7]])
>>> lines.save("lines.pickle")

>>> lines_reloaded = pept.LineData.load("lines.pickle")

save(filepath)

Save a PEPTObject instance as a binary pickle object.

Saves the full object state, including inner attributes, in a portable binary format. Load back the object using the load method.

Parameters

filepathfilename or file handle

If filepath is a path (rather than file handle), it is relative to where python is called.

Examples

Save a LineData instance, then load it back:

>>> lines = pept.LineData([[1, 2, 3, 4, 5, 6, 7]])
>>> lines.save("lines.pickle")

>>> lines_reloaded = pept.LineData.load("lines.pickle")