:py:mod:`grouping`
==================

.. py:module:: grouping

.. autoapi-nested-parse::

   Module for handling performing Agglomerative Hierarchical Clustering Algorithm.

   Based on 'Detection of Intensity Change Points in Time-Resolved Single-Molecule Measurements'
   from Watkins nad Yang, J. Phys. Chem. B 2005, 109, 617-628 (http://pubs.acs.org/doi/abs/10.1021/jp0467548)

   Joshua Botha
   University of Pretoria
   2018



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

Classes
~~~~~~~

.. autoapisummary::

   grouping.Group
   grouping.ClusteringStep
   grouping.AHCA
   grouping.GlobalLevel



Functions
~~~~~~~~~

.. autoapisummary::

   grouping.max_jm



Attributes
~~~~~~~~~~

.. autoapisummary::

   grouping.logger


.. py:data:: logger
   :value: "'grouping'"

   

.. py:function:: max_jm(array: numpy.ndarray)

   Finds the j and m index for the max value.


.. py:class:: Group(lvls_inds: List[int_p_s] = None, particle: smsh5.Particle = None, group_ind: int = None)


   .. py:property:: num_photons
      :type: int_p_s


   .. py:property:: dwell_time_s
      :type: float


   .. py:property:: int_p_s
      :type: float


   .. py:property:: group_times_ns


   .. py:property:: group_microtimes


   .. py:attribute:: lvls_inds
      :value: 'None'

      

   .. py:attribute:: group_ind
      :value: 'None'

      

   .. py:attribute:: lvls
      :value: 'None'

      

   .. py:attribute:: histogram
      :value: 'None'

      


.. py:class:: ClusteringStep(particle: smsh5.Particle, first: bool = False, seed_groups: List[Group] = None, single_level: bool = False)


   .. py:property:: group_ints
      :type: List[float]


   .. py:property:: group_level_dwelltimes


   .. py:property:: group_total_dwelltime


   .. py:property:: group_num_levels


   .. py:property:: group_level_ints


   .. py:attribute:: _particle
      :type: smsh5.Particle

      

   .. py:attribute:: first
      :value: 'False'

      

   .. py:attribute:: single_level
      :value: 'False'

      

   .. py:attribute:: last
      :value: 'False'

      

   .. py:attribute:: _log_l_em
      :value: 'None'

      

   .. py:attribute:: _em_p_mj
      :value: 'None'

      

   .. py:attribute:: _em_log_l
      :value: 'None'

      

   .. py:attribute:: _ahc_p_mj
      :value: 'None'

      

   .. py:attribute:: _ahc_groups
      :value: 'None'

      

   .. py:attribute:: groups
      :value: 'None'

      

   .. py:attribute:: bic
      :value: 'None'

      

   .. py:attribute:: num_groups
      :value: 'None'

      

   .. py:attribute:: level_group_ind
      :value: 'None'

      

   .. py:attribute:: group_levels
      :value: 'None'

      

   .. py:attribute:: _num_prev_groups

      

   .. py:attribute:: groups_have_hists
      :value: 'False'

      

   .. py:method:: calc_int_bounds(order: str = 'descending') -> List[Tuple[float, float]]

      Calculates the bounds between the groups.

      :param order: Option are 'descending' and 'ascending'
      :type order: str


   .. py:method:: ahc()

      Agglomerative Hierarchical Clustering


   .. py:method:: emc()

      Expectation Maximisation clustering


   .. py:method:: calc_bic()


   .. py:method:: group_2_levels()


   .. py:method:: setup_next_step() -> ClusteringStep



.. py:class:: AHCA(particle)


   Class for executing Agglomerative Hierarchical Clustering Algorithm and storing the results.

   .. py:property:: selected_step
      :type: ClusteringStep


   .. py:property:: best_step
      :type: ClusteringStep


   .. py:property:: steps_num_groups
      :type: List[int]


   .. py:attribute:: backup
      :value: 'None'

      

   .. py:attribute:: has_groups
      :value: 'False'

      

   .. py:attribute:: _particle

      

   .. py:attribute:: uuid

      

   .. py:attribute:: steps
      :value: 'None'

      

   .. py:attribute:: best_step_ind
      :value: 'None'

      

   .. py:attribute:: bics
      :value: 'None'

      

   .. py:attribute:: selected_step_ind
      :value: 'None'

      

   .. py:attribute:: num_steps
      :value: 'None'

      

   .. py:attribute:: plots_need_to_be_updated
      :value: 'False'

      

   .. py:attribute:: use_roi_for_grouping
      :value: 'True'

      

   .. py:attribute:: grouped_with_roi
      :value: 'False'

      

   .. py:method:: clear_and_backup_results() -> None


   .. py:method:: restore_and_delete_backup() -> None


   .. py:method:: run_grouping(feedback_queue: multiprocessing.JoinableQueue = None)

      Run grouping


   .. py:method:: set_selected_step(step_ind: int)


   .. py:method:: reset_selected_step()



.. py:class:: GlobalLevel(global_particle: Union[smsh5.Particle, smsh5.GlobalParticle], parent_particle_dataset_ind: int, particle_levels: List[Union[change_point.Level, GlobalLevel]], int_p_s: float, group_ind: int, start_time_offset_ns: int, dwell_time_ns: float, num_photons: int)


   .. py:property:: times_s


   .. py:property:: dwell_time_s


   .. py:attribute:: is_global_level
      :value: 'True'

      

   .. py:attribute:: particle

      

   .. py:attribute:: parent_particle_dataset_ind

      

   .. py:attribute:: start_time_offset_ns

      

   .. py:attribute:: times_ns

      

   .. py:attribute:: int_p_s

      

   .. py:attribute:: group_ind

      

   .. py:attribute:: dwell_time_ns

      

   .. py:attribute:: num_photons

      

   .. py:attribute:: microtimes_particle_inds_pairs
      :value: '()'