pept.tracking.Debug#

class pept.tracking.Debug(verbose=5, max_samples=10)[source]#

Bases: Reducer

Print types and statistics about the objects being processed in a pept.Pipeline.

Reducer signature:

      PointData -> Debug.fit -> PointData
       LineData -> Debug.fit -> LineData
list[PointData] -> Debug.fit -> list[PointData]
 list[LineData] -> Debug.fit -> list[LineData]
     np.ndarray -> Debug.fit -> np.ndarray
            Any -> Debug.fit -> Any

This is a reducer, so it will collect all samples processed up to the point of use, print them, and return them unchanged.

New in pept-0.5.1

Examples

A Debug is normally added in a Pipeline:

>>> import pept
>>> import pept.tracking as pt
>>>
>>> pept.Pipeline([
>>>     # First pass of clustering
>>>     pt.Cutpoints(max_distance = 0.2),
>>>     pt.HDBSCAN(true_fraction = 0.15),
>>>     pt.SplitLabels() + pt.Centroids(cluster_size = True, error = True),
>>>
>>>     pt.Debug(),
>>>     pt.Stack(),
>>> ])

__init__(verbose=5, max_samples=10)[source]#

Methods

`__init__`([verbose, max_samples])
`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.

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")

fit(samples)[source]#