:mod:`neuron_morphology.layered_point_depths.__main__`
======================================================

.. py:module:: neuron_morphology.layered_point_depths.__main__


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


Functions
~~~~~~~~~

.. autoapisummary::

   neuron_morphology.layered_point_depths.__main__.translate_field
   neuron_morphology.layered_point_depths.__main__.setup_interpolator
   neuron_morphology.layered_point_depths.__main__.containing_layer
   neuron_morphology.layered_point_depths.__main__.tuplize
   neuron_morphology.layered_point_depths.__main__.step_from_node
   neuron_morphology.layered_point_depths.__main__.get_node_intersections
   neuron_morphology.layered_point_depths.__main__.setup_layers
   neuron_morphology.layered_point_depths.__main__.run_layered_point_depths
   neuron_morphology.layered_point_depths.__main__.main


.. function:: translate_field(field: xr.DataArray, by_x: float, by_y: float, inplace: bool = False)

   Translate a spatial xarray dataset


   :Parameters:

       **field** : to be translated
           ..

       **by_x** : =the translation along x
           ..

       **by_y** : the translation along y
           ..

       **inplace** : If True, modify this dataarray, otherwise modify a copy
           ..

   :Returns:

       translated dataarray, potentiall the same as the input
           ..













   ..
       !! processed by numpydoc !!


.. function:: setup_interpolator(field: xr.DataArray, dim: Optional[str], **kwargs) -> RegularGridInterpolator

   Build a regular grid interpolator from a dataarray


   :Parameters:

       **field** : Must have dimensions "x" and "y". May have dimension "dim"
           ..

       **dim** : base the interpolator on values from this dim slice. If None, ignore
           dim

       **\*\*kwargs** : passed to interpolator constructor
           ..

   :Returns:

       a callable interpolator
           ..













   ..
       !! processed by numpydoc !!


.. function:: containing_layer(pos: Tuple[float, float], layers: List[Dict]) -> Optional[str]

   Find the layer in which a point is contained


   :Parameters:

       **pos** : the coordinate of the point
           ..

       **layers** : Each has "name" - a string and "bounds" - a Polygon
           ..

   :Returns:

       The name of the containing layer or None if no containing layer was found
           ..













   ..
       !! processed by numpydoc !!


.. function:: tuplize(arr: np.array) -> Tuple

   Convert an array to a tuple
















   ..
       !! processed by numpydoc !!


.. function:: step_from_node(pos: Tuple[float, float], depth_interp: RegularGridInterpolator, dx_interp: RegularGridInterpolator, dy_interp: RegularGridInterpolator, surface: LineString, step_size: float, max_iter: int, adaptive_scale: int = 32) -> Optional[float]

   Walk through a gradient field, until a defined surface is passed.


   :Parameters:

       **pos** : the start position
           ..

       **depth_interp** : callable mapping positions to scalar depth values
           ..

       **dx_interp** : callable mapping positions to the x component of the gradient
           ..

       **dy_interp** : callable mapping positions to the y component of the gradient
           ..

       **surface** : Check for the intersection of the path with this surface
           ..

       **step_size** : Each step proceeds in the direction of the local gradient,
           scaled to this step size

       **max_iter** : give up (return None) if the surface is not intersected in this
           many steps

   :Returns:

       The depth of the intersection between the path walked and the given surface
           ..













   ..
       !! processed by numpydoc !!


.. function:: get_node_intersections(node: Dict, depth_interp: RegularGridInterpolator, dx_interp: RegularGridInterpolator, dy_interp: RegularGridInterpolator, layers: List[Dict], step_size: float, max_iter: int) -> Dict

   Given a node, find its layer and intersection depths. Then return a row
   of LayeredPointDepths for this node.


   :Parameters:

       **node** : Of a Morphology. must have:
           "id" - unique identifier
           "type" - which kind of node is this?
           "x", "y" - positions in x and y of this node

       **depth_interp** : callable mapping positions to scalar depth values
           ..

       **dx_interp** : callable mapping positions to the x component of the gradient
           ..

       **dy_interp** : callable mapping positions to the y component of the gradient
           ..

       **layers** : Each has
           "name" - an identifier
           "bounds" - a Polygon describing the entire boundary
           "pia_surface" - a LineString describing the piaward surface of this
               layer
           "wm_surface" - a LineString describing the white matter-wise surface of
               this layer

       **step_size** : Each step proceeds in the direction of the local gradient,
           scaled to this step size

       **max_iter** : give up (return None) if the surface is not intersected in this
           many steps

   :Returns:

       A dictionary representing a single row of LayeredPointDepths. Has Keys:
           "ids" - the identifier of this node
           "layer_name" - the layer containing this node
           "depth" - the depth of this node
           "local_layer_pia_side_depth" - the depth of the intersection between
               this node's steepest ascent path and the piaward surface of its
               containing layer
           "local_layer_wm_side_depth" - the depth of the intersection between
               this node's steepest ascent path and the white matterward surface
               of its containing layer
           "point_type": The type of this node













   ..
       !! processed by numpydoc !!


.. function:: setup_layers(layers: List[Dict])

   Convert layer bounds, pia, and white matter surfaces to shapely objects


   :Parameters:

       **layers** : Mutated inplace. Has keys:
           "bounds" - a Polygon describing the entire boundary
           "pia_surface" - a LineString describing the piaward surface of this
               layer
           "wm_surface" - a LineString describing the white matter-wise surface of
               this layer














   ..
       !! processed by numpydoc !!


.. function:: run_layered_point_depths(swc_path: str, depth: Dict, layers: List[Dict], step_size: float, max_iter: int, output_path: str)


.. function:: main()