pept.processing.VectorField3D#

class pept.processing.VectorField3D(diameter, columns=['vx', 'vy', 'vz'], dimensions='xyz', resolution=(50, 50, 50), xlim=None, ylim=None, zlim=None, max_workers=None, verbose=True)[source]#

Bases: Reducer

Compute a 3D vector field - effectively three 3D grids computed from three columns, for example X, Y and Z velocities.

Reducer signature:

      PointData -> VectorField3D.fit -> VectorGrid3D
list[PointData] -> VectorField3D.fit -> VectorGrid3D
  numpy.ndarray -> VectorField3D.fit -> VectorGrid3D

Examples

Compute a 3D velocity vector field (velocities were first calculated using pept.tracking.Velocity):

>>> from pept.processing import *
>>> trajectories = pept.PointData(...)
>>> field = VectorField3D(0.6).fit(trajectories)
>>> field
VectorGrid3D(xvoxels, yvoxels, zvoxels)

Create a 3D vector field (needs PyVista):

>>> scaling = 16
>>> fig = field.vectors(scaling)
>>> fig.plot(cmap = "magma")

__init__(diameter, columns=['vx', 'vy', 'vz'], dimensions='xyz', resolution=(50, 50, 50), xlim=None, ylim=None, zlim=None, max_workers=None, verbose=True)[source]#

Methods

`__init__`(diameter[, columns, dimensions, ...])
`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)[source]#

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")