AFQ.recognition.utils
=====================

.. py:module:: AFQ.recognition.utils


Attributes
----------

.. autoapisummary::

   AFQ.recognition.utils.axes_dict


Classes
-------

.. autoapisummary::

   AFQ.recognition.utils.SlsBeingRecognized


Functions
---------

.. autoapisummary::

   AFQ.recognition.utils.manual_orient_sls
   AFQ.recognition.utils.tolerance_mm_to_vox
   AFQ.recognition.utils.flip_sls
   AFQ.recognition.utils.cut_sls_by_closest
   AFQ.recognition.utils.orient_by_streamline
   AFQ.recognition.utils.resample_tg


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

.. py:data:: axes_dict

.. py:function:: manual_orient_sls(fgarray)

   
   Helper function to manually orient streamlines by their endpoints,
   according to LPI+ pyAFQ standard assuming streamlines are in RASMM
















   ..
       !! processed by numpydoc !!

.. py:function:: tolerance_mm_to_vox(img, dist_to_waypoint, input_dist_to_atlas)

.. py:function:: flip_sls(select_sl, idx_to_flip, in_place=False)

   
   Helper function to flip streamlines
















   ..
       !! processed by numpydoc !!

.. py:function:: cut_sls_by_closest(select_sl, roi_closest, roi_idxs, in_place=False)

   
   Helper function to cut streamlines according to which points
   are closest to certain rois.


   :Parameters:

       **select_sl**
           streamlines to cut

       **roi_closest**
           indices into given streamline of points nearest
           to inclusion rois

       **roi_idxs**
           two indices into the list of inclusion rois to use for the cut

       **in_place**
           whether to modify select_sl














   ..
       !! processed by numpydoc !!

.. py:function:: orient_by_streamline(sls, template_sl)

.. py:function:: resample_tg(tg, n_points)

.. py:class:: SlsBeingRecognized(sls, save_intermediates, b_name, ref, n_roi)

   .. py:attribute:: oriented_yet
      :value: False



   .. py:attribute:: selected_fiber_idxs


   .. py:attribute:: sls_flipped


   .. py:attribute:: start_time
      :value: -1



   .. py:attribute:: save_intermediates


   .. py:attribute:: b_name


   .. py:attribute:: ref_sls


   .. py:attribute:: ref


   .. py:attribute:: n_roi


   .. py:method:: initiate_selection(clean_name)


   .. py:method:: select(idx, clean_name, cut=False)


   .. py:method:: get_selected_sls(cut=False, flip=False)


   .. py:method:: reorient(idx)


   .. py:method:: __bool__()


   .. py:method:: __len__()


   .. py:method:: copy(new_name, n_roi)


   .. py:method:: export_selected(chunk_offset)


   .. py:method:: from_selected(survivor_dicts, full_streamlines, save_intermediates, b_name, ref, n_roi)
      :classmethod: