:py:mod:`AFQ.recognition.roi`
=============================

.. py:module:: AFQ.recognition.roi


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


Functions
~~~~~~~~~

.. autoapisummary::

   AFQ.recognition.roi.check_sls_with_inclusion
   AFQ.recognition.roi.check_sl_with_inclusion
   AFQ.recognition.roi.check_sl_with_exclusion
   AFQ.recognition.roi.clean_by_endpoints



.. py:function:: check_sls_with_inclusion(sls, include_rois, include_roi_tols)


.. py:function:: check_sl_with_inclusion(sl, include_rois, include_roi_tols)

   
   Helper function to check that a streamline is close to a list of
   inclusion ROIS.
















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       !! processed by numpydoc !!

.. py:function:: check_sl_with_exclusion(sl, exclude_rois, exclude_roi_tols)

   
   Helper function to check that a streamline is not too close to a
   list of exclusion ROIs.
















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       !! processed by numpydoc !!

.. py:function:: clean_by_endpoints(streamlines, target, target_idx, tol=0, flip_sls=None, accepted_idxs=None)

   
   Clean a collection of streamlines based on an endpoint ROI.
   Filters down to only include items that have their start or end points
   close to the targets.
   Parameters
   ----------
   streamlines : sequence of N by 3 arrays
       Where N is number of nodes in the array, the collection of
       streamlines to filter down to.
   target: Nifti1Image
       Nifti1Image containing a boolean representation of the ROI.
   target_idx: int.
       Index within each streamline to check if within the target region.
       Typically 0 for startpoint ROIs or -1 for endpoint ROIs.
       If using flip_sls, this becomes (len(sl) - this_idx - 1) % len(sl)
   tol : int, optional
       A distance tolerance (in units that the coordinates
       of the streamlines are represented in). Default: 0, which means that
       the endpoint is exactly in the coordinate of the target ROI.
   flip_sls : 1d array, optional
       Length is len(streamlines), whether to flip the streamline.
   accepted_idxs : 1d array, optional
       Boolean array, where entries correspond to eachs streamline,
       and streamlines that pass cleaning will be set to 1.
   Yields
   -------
   boolean array of streamlines that survive cleaning.
















   ..
       !! processed by numpydoc !!