flowstab.scripts.run_cov_integrals
==================================

.. py:module:: flowstab.scripts.run_cov_integrals

.. autoapi-nested-parse::

   Computes the integral of the random walk covariance matrices.
   This is done on a coarser temporal grid than the grid used for the slices of the 1st step (run_laplacians_transmats.py).
   The grid step size is defined by `int_length` in units of slices. By default, the integral of the covariance
   will be computed starting and ending from all combinations of the grid steps. Using `--only_from_start_and_finish`
   will compute the forward integrals from the first time point until each following grid steps and
   the backward integrals from the last time point until each previous grid steps.
   The resolutions (waiting times) are read from the saved inter-event transition matrices.
   For efficiency, only the first term (the sparse part) of the autocovariance integral is computed and saved.
   The results are saved in files named
   {savedir}/{net_name}_tau_w{tau_w}_PT_{initial_grid_point}_to_{final_grid_point}.{ext}
   It will use sparse-dot-mkl to do multithreaded sparse matrix products, if it is installed.

   The file {initial_grid_point}_to_{final_grid_point} contains the autocovariance integral between
   t1 and t2, where t1 is the *start time* of int_start and t2 is also the *start time*
   of int_stop (also valid when int_start > int_stop).

   The value saved is the upper triangular part of:

       int_t1^t2 T(t_1,t) P(t)^{-1} T(t_1,t)^T dt




Attributes
----------

.. autoapisummary::

   flowstab.scripts.run_cov_integrals.all_files
   flowstab.scripts.run_cov_integrals.ap
   flowstab.scripts.run_cov_integrals.compression
   flowstab.scripts.run_cov_integrals.datadir
   flowstab.scripts.run_cov_integrals.i
   flowstab.scripts.run_cov_integrals.inargs
   flowstab.scripts.run_cov_integrals.int_length
   flowstab.scripts.run_cov_integrals.int_length
   flowstab.scripts.run_cov_integrals.int_list
   flowstab.scripts.run_cov_integrals.integral_rtol
   flowstab.scripts.run_cov_integrals.intervals
   flowstab.scripts.run_cov_integrals.intervals
   flowstab.scripts.run_cov_integrals.ncpu
   flowstab.scripts.run_cov_integrals.net_name
   flowstab.scripts.run_cov_integrals.num_nodes
   flowstab.scripts.run_cov_integrals.num_points
   flowstab.scripts.run_cov_integrals.num_small_grid_points
   flowstab.scripts.run_cov_integrals.only_expm_transmats
   flowstab.scripts.run_cov_integrals.only_from_finish
   flowstab.scripts.run_cov_integrals.only_from_start
   flowstab.scripts.run_cov_integrals.only_from_start_and_finish
   flowstab.scripts.run_cov_integrals.only_lin_transmats
   flowstab.scripts.run_cov_integrals.only_one_interval
   flowstab.scripts.run_cov_integrals.optional
   flowstab.scripts.run_cov_integrals.print_interval
   flowstab.scripts.run_cov_integrals.print_mem_usage
   flowstab.scripts.run_cov_integrals.required
   flowstab.scripts.run_cov_integrals.rev_time_list
   flowstab.scripts.run_cov_integrals.save_intermediate
   flowstab.scripts.run_cov_integrals.savedir
   flowstab.scripts.run_cov_integrals.t_s
   flowstab.scripts.run_cov_integrals.tau_ws
   flowstab.scripts.run_cov_integrals.tau_ws
   flowstab.scripts.run_cov_integrals.time_direction
   flowstab.scripts.run_cov_integrals.tol
   flowstab.scripts.run_cov_integrals.use_expm_transmats
   flowstab.scripts.run_cov_integrals.use_expm_transmats
   flowstab.scripts.run_cov_integrals.use_lin_transmats
   flowstab.scripts.run_cov_integrals.use_lin_transmats
   flowstab.scripts.run_cov_integrals.verbose
   flowstab.scripts.run_cov_integrals.verbose_sparse_matmul


Functions
---------

.. autoapisummary::

   flowstab.scripts.run_cov_integrals.load_trans_mat
   flowstab.scripts.run_cov_integrals.main
   flowstab.scripts.run_cov_integrals.worker


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

.. py:function:: load_trans_mat(k_range, tau_w, lin, reverse_time)

   loads, computes and returns the transition matrix computed from k_range[0]
   to k_range[-1] and the corresponding time duration.

   used to quickly start again an integral computation.


.. py:function:: main()

.. py:function:: worker(ind_start_tau_w)

.. py:data:: all_files

.. py:data:: ap

.. py:data:: compression
   :value: None


.. py:data:: datadir

.. py:data:: i
   :value: 0


.. py:data:: inargs

.. py:data:: int_length

.. py:data:: int_length

.. py:data:: int_list

.. py:data:: integral_rtol

.. py:data:: intervals

.. py:data:: intervals

.. py:data:: ncpu

.. py:data:: net_name

.. py:data:: num_nodes
   :value: None


.. py:data:: num_points

.. py:data:: num_small_grid_points

.. py:data:: only_expm_transmats

.. py:data:: only_from_finish

.. py:data:: only_from_start

.. py:data:: only_from_start_and_finish

.. py:data:: only_lin_transmats

.. py:data:: only_one_interval

.. py:data:: optional

.. py:data:: print_interval

.. py:data:: print_mem_usage

.. py:data:: required

.. py:data:: rev_time_list
   :value: [False, True]


.. py:data:: save_intermediate

.. py:data:: savedir

.. py:data:: t_s

.. py:data:: tau_ws

.. py:data:: tau_ws

.. py:data:: time_direction

.. py:data:: tol

.. py:data:: use_expm_transmats
   :value: True


.. py:data:: use_expm_transmats
   :value: False


.. py:data:: use_lin_transmats
   :value: True


.. py:data:: use_lin_transmats
   :value: False


.. py:data:: verbose

.. py:data:: verbose_sparse_matmul