pept.tracking.SamplesCondition

class pept.tracking.SamplesCondition(*conditions)

Bases: Reducer

Select only samples satisfying multiple conditions, given as a string, a function or list thereof; e.g. Condition("sample_size > 30") selects all samples with a sample size larger than 30.

Filter signature:

PointData -> SamplesCondition.fit_sample -> PointData
 LineData -> SamplesCondition.fit_sample -> LineData

This is different to a Condition, which selects individual points; for SamplesCondition, each sample will be passed through the conditions.

Conditions can be defined as Python code using the following variables:

• sample - this is the full PointData or LineData, e.g. only keep samples with more than 30 points with “len(sample.points) > 30”.

• data - this is the raw NumPy array of data wrapped by a PointData or LineData, e.g. only keep samples which have all X coordinates beyond 100 with SamplesCondition(“np.all(data[:, 1] > 100)”).

• sample_size - this is a shorthand for the number of data points, e.g. only keep samples with more than 30 points with “sample_size > 30”.

Conditions can also be Python functions:

>>> def high_velocity_filter(sample):
>>>     return np.all(sample["v"] > 5)

>>> from pept.tracking import SamplesCondition
>>> filtered = SamplesCondition(high_velocity_filter).fit(point_data)

__init__(*conditions)

Methods

__init__(*conditions)
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.

Attributes

conditions

property conditions

fit(samples)

copy(deep=True)

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

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")