pyfast_adt.main.tracking.rigid_body_model
=========================================

.. py:module:: pyfast_adt.main.tracking.rigid_body_model


Attributes
----------

.. autoapisummary::

   pyfast_adt.main.tracking.rigid_body_model.model


Classes
-------

.. autoapisummary::

   pyfast_adt.main.tracking.rigid_body_model.MastronardeRigidBody


Module Contents
---------------

.. py:class:: MastronardeRigidBody(folder_path, fit_range, pixelsize_nm, delimiter='\t', plot_intermediate=False, theta_sim_deg=0)

   .. py:attribute:: folder_path


   .. py:attribute:: pixelsize_nm


   .. py:attribute:: pixelsize_um


   .. py:attribute:: delimiter
      :value: '\t'



   .. py:attribute:: plot_intermediate
      :value: False



   .. py:attribute:: theta_sim_deg
      :value: 0



   .. py:attribute:: results
      :value: []



   .. py:attribute:: datasets
      :value: []



   .. py:method:: _get_dataset(dataset_index=0)


   .. py:method:: mastronarde_rot2D(alpha_rad, y0, z0, ys, theta_deg, y_mean)
      :staticmethod:



   .. py:method:: mastronarde_point(alpha_rad, y0, z0, ys, theta_deg, y_mean=0.0)

      Return rotated (y, x) coordinates from Mastronarde model



   .. py:method:: zheng_point(alpha_rad, y0, z0, ys, theta_deg, y_mean=0.0)


   .. py:method:: fit_dataset(idx)


   .. py:method:: fit_single_dataset_from_gui(data_path=None, switch_axis=False)


   .. py:method:: load_tracking_data_pyfast(path)


   .. py:method:: plot_intermediate_dataset(alpha, x_ccd, y_ccd, alpha_rad, popt, fname)


   .. py:method:: run_fits()


   .. py:method:: compute_linear_fits()


   .. py:method:: plot_summary(save=True)


   .. py:method:: 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.



   .. py:method:: 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



   .. py:method:: plot_single_dataset_summary(dataset_index=0, save=False)

      Summary plots for a SINGLE dataset.



   .. py:method:: 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.



   .. py:method:: 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



.. py:data:: model