pept.tracking.Reorient

class pept.tracking.Reorient(dimensions='xyz', basis=None, origin=None)

Bases: Reducer

Rotate a dataset such that it is oriented according to its principal axes.

Reducer signature:

      PointData -> Reorient.fit -> PointData
list[PointData] -> Reorient.fit -> PointData
     np.ndarray -> Reorient.fit -> PointData

By default, this reducer reorients the points such that the axis along which it is most spread out (e.g. lengthwise in a pipe) becomes the X-axis. The input argument dimensions sets this - the default “xyz” can be changed to e.g. “zyx” so that the longest data axis becomes the Z-axis.

The reducer also sets three attributes on the returned PointData: - origin: the origin relative to which the initial data was rotated. - basis: the principal components - or change of basis 3x3 matrix. - eigenvalues: how spread out the data is in each initial dimension.

If you’d like to reorient a second dataset to the same basis as a first one, set the basis and origin arguments.

New in pept-0.5.0

Examples

Reorient a dataset by aligning the longest principal component (e.g. lengthwise in a pipe) to the X-axis:

>>> import pept.tracking as pt
>>> data = PointData(...)
>>> reoriented = pt.Reorient().fit(data)

Reorient it such that the longest principal component (e.g. vertical in a mixer) becomes the Z-axis:

>>> reoriented = pt.Reorient("zyx").fit(data)

Reorient a second dataset to the same orientation basis as the first one:

>>> reoriented2 = pt.Reorient(
>>>     basis = reoriented.attrs["basis"],
>>>     origin = reoriented.attrs["origin"],
>>> ).fit(other_data)

__init__(dimensions='xyz', basis=None, origin=None)

Methods

__init__([dimensions, basis, origin])
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.

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")