:mod:`neuron_morphology.transforms.scale_correction.compute_scale_correction`
=============================================================================

.. py:module:: neuron_morphology.transforms.scale_correction.compute_scale_correction


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


Functions
~~~~~~~~~

.. autoapisummary::

   neuron_morphology.transforms.scale_correction.compute_scale_correction.estimate_scale_correction
   neuron_morphology.transforms.scale_correction.compute_scale_correction.get_soma_marker_from_marker_file
   neuron_morphology.transforms.scale_correction.compute_scale_correction.run_scale_correction
   neuron_morphology.transforms.scale_correction.compute_scale_correction.collect_inputs
   neuron_morphology.transforms.scale_correction.compute_scale_correction.main


.. function:: estimate_scale_correction(morphology: Morphology, soma_depth: float, soma_marker_z: float, cut_thickness: Optional[float] = 350)

   Estimate a scale factor to correct the reconstructed morphology
   for slice shrinkage

   Prior to reconstruction, the slice shrinks due to evaporation.
   This is most notable in the z axis, which is the slice thickness.

   To correct for shrinkage we compare soma depth within the slice
   obtained soon after cutting the slice to the fixed_soma_depth obtained
   during the reconstruction. Then the scale correction is estimated as:
   scale  = soma_depth / fixed_soma_depth.
   This is sensible as long as the z span of the corrected reconstruction
   is contained  within the slice thickness. Thus we also estimate
   the maximum scale correction as:
   scale_max  = cut_thickness / z_span,
   and take the smaller of scale and scale_max

   :Parameters:

       **morphology: Morphology object**
           ..

       **soma_depth: recorded depth of the soma when it was sliced**
           ..

       **soma_marker_z: soma marker z value from revised marker file**
           (z is on the slice surface for the marker file)

       **cut_thickness: thickness of the cut slice**
           ..

   :Returns:

       scale factor correction
           ..













   ..
       !! processed by numpydoc !!


.. function:: get_soma_marker_from_marker_file(marker_path: str)


.. function:: run_scale_correction(morphology: Morphology, soma_marker_z: float, soma_depth: float, cut_thickness: float)


.. function:: collect_inputs(args: Dict[str, Any]) -> Dict[str, Any]

   :Parameters:

       **args: dict of InputParameters**
           ..

   :Returns:

       dict with string keys:
           morphology: Morphology object
           soma_marker_z: z value from the marker file
           soma_depth: soma depth
           cut_thickness: slice thickness













   ..
       !! processed by numpydoc !!


.. function:: main()