SimpleBreathingMotionModule

class SimpleBreathingMotionModule(sub_trajectory, breathing_curve, breathing_cycle_duration)

Trajectory module wrapping another trajectory module with a global pure translational breathing motion. Arbitrary 3D breathing curves can be specified on a regular time grid. This curve is linearly interpolated on calling the module.

The wrapped trajectory module is assumed to gracefully handle potential out-of bound time-points (e.g. by assuming periodicity)

Parameters:

• sub_trajectory (BaseTrajectoryModule) – Instance of a BaseTrajectoryModule-subclass

• breathing_curve (Tensor) – (t, 3) Tensor containing the 3D points of the breathing trajectory assumed to be on a uniform temporal grid

• breathing_cycle_duration (Tensor) – Duration of the given breathing trajectory in milliseconds

Methods:

__call__(initial_positions, timing, **kwargs)	Evaluates the positions for particles at given initial positions for all times specified in the timing argument.
current_offset()	Returns the positional breathing offset for the current time
from_sinosoidal_motion(sub_trajectory, ...)	Instantiates a SimpleBreathingMotionModule from a sinusodial breathing curve
increment_particles(particle_positions, dt, ...)	Evaluates the new position of particles at given locations r for a temporal step width dt.

Attributes:

breathing_curve	(t, 3) Tensor containing the 3D points of the breathing trajectory assumed to be on a uniform temporal grid
breathing_cycle_duration	Duration of the given breathing trajectory in milliseconds
current_time_ms	Keeps track of the current timing when increment_particles is called.
sub_trajectory	Reference to the wrapped trajectory module

__call__(initial_positions, timing, **kwargs)

Evaluates the positions for particles at given initial positions for all times specified in the timing argument. For implementations using the increment_particles function in a loop the maximal time-delta must be specified.

Parameters:

• initial_positions (Tensor) – (N, 3)

• timing (Tensor) – (T, )

• kwargs – Can vary in concrete implementation

Return type:

(Tensor, Dict)

Returns:

• r_new [tf.Tensor, (T, N, 3)]

• additional_fields [dict] containing the lookup values for each step

current_offset()

Returns the positional breathing offset for the current time

classmethod from_sinosoidal_motion(sub_trajectory, breathing_period, breathing_direction, breathing_amplitude)

Instantiates a SimpleBreathingMotionModule from a sinusodial breathing curve

Parameters:

• sub_trajectory (BaseTrajectoryModule) –

• breathing_period (Quantity) –

• breathing_direction (ndarray) –

• breathing_amplitude (Quantity) –

increment_particles(particle_positions, dt, **kwargs)

Evaluates the new position of particles at given locations r for a temporal step width dt. If the concrete implementation involves a look up (e.g. velocity fields) the values at the old location is also returned as dictionary.

Note

concrete implementations must be compatible with tf.function decoration

Parameters:

• particle_positions (Tensor) – (N, 3) Current particle positions.

• dt (Tensor) – (,) Temporal step width in milliseconds to evaluate the next positions

• kwargs – Can vary in concrete implementation

Return type:

(Tensor, Dict)

Returns:

r_new [tf.Tensor, (N, 3)], additional_fields [dict] containing the lookup values

breathing_curve: Tensor

(t, 3) Tensor containing the 3D points of the breathing trajectory assumed to be on a uniform temporal grid

breathing_cycle_duration: Tensor

Duration of the given breathing trajectory in milliseconds

current_time_ms: Variable

Keeps track of the current timing when increment_particles is called.

sub_trajectory: BaseTrajectoryModule

Reference to the wrapped trajectory module