pyfast_adt.main.tracking.rigid_body_model

Attributes

model

Classes

MastronardeRigidBody

Module Contents

class pyfast_adt.main.tracking.rigid_body_model.MastronardeRigidBody(folder_path, fit_range, pixelsize_nm, delimiter='\t', plot_intermediate=False, theta_sim_deg=0)

folder_path

pixelsize_nm

pixelsize_um

delimiter = '\t'

plot_intermediate = False

theta_sim_deg = 0

results = []

datasets = []

_get_dataset(dataset_index=0)

static mastronarde_rot2D(alpha_rad, y0, z0, ys, theta_deg, y_mean)

mastronarde_point(alpha_rad, y0, z0, ys, theta_deg, y_mean=0.0): Return rotated (y, x) coordinates from Mastronarde model

zheng_point(alpha_rad, y0, z0, ys, theta_deg, y_mean=0.0)

fit_dataset(idx)

fit_single_dataset_from_gui(data_path=None, switch_axis=False)

load_tracking_data_pyfast(path)

plot_intermediate_dataset(alpha, x_ccd, y_ccd, alpha_rad, popt, fname)

run_fits()

compute_linear_fits()

plot_summary(save=True)

plot_trajectories_stacked(dy_offset=1.0, out_path=None, filename='trajectories_all_datasets_stacked.png'): Plot stacked rotated XY trajectories with Mastronarde model overlay. Theoretical model is split for positive and negative alpha values and plotted with a small offset to inspect symmetry.

plot_z_scan(alpha_range_deg=np.linspace(-60, 60, 300), out_path=None, filename='plot_z_scan.png'): Plot n–z arcs using Mastronarde rigid body model

plot_single_dataset_summary(dataset_index=0, save=False): Summary plots for a SINGLE dataset.

analyze_xy_dynamics(dataset_index=0, n_alpha=500, deg_step=5, out_path=None, scaling=1, original_range=False, deg_markers=False, pixels=True)

Analyze velocity and acceleration of projected CCD motion assuming linear relation between tilt angle and time (1 deg = 1 time unit).

Markers are placed EXACTLY every deg_step degrees.

analyze_xy_dynamics_multiple(deg_step=5, n_alpha=500, scaling=1, original_range=False, deg_markers=False, out_path=None, pixels=True)

Analyze XY dynamics for all datasets and compute max velocity & acceleration. Also plots max |v| and |a| vs Z stage (dataset index).

Includes the same style as analyze_xy_dynamics: - Optional deg markers with text - Velocity & acceleration twin y-axis - Component plots

pyfast_adt.main.tracking.rigid_body_model.model