neuro_morpho.model.simple_baseline
==================================

.. py:module:: neuro_morpho.model.simple_baseline

.. autoapi-nested-parse::

   A simple baseline model for testing.



Classes
-------

.. autoapisummary::

   neuro_morpho.model.simple_baseline.SimpleBaseLine


Functions
---------

.. autoapisummary::

   neuro_morpho.model.simple_baseline.make_binary


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

.. py:function:: make_binary(x: numpy.ndarray, percentile: int) -> numpy.ndarray

   Binarize an image based on a percentile threshold.

   This function thresholds the input image `x` at the given `percentile`
   and then skeletonizes the result.

   :param x: The input image. Should be of shape (n_samples, width, height).
   :type x: np.ndarray
   :param percentile: The percentile to use as the threshold.
   :type percentile: int

   :returns: The binarized and skeletonized image.
   :rtype: np.ndarray


.. py:class:: SimpleBaseLine(percentile: int = 95, name: str | None = None)

   Bases: :py:obj:`neuro_morpho.model.base.BaseModel`


   A simple baseline model for image segmentation.

   This model binarizes the input image based on a percentile threshold and
   then skeletonizes the result.


   .. py:attribute:: percentile
      :value: 95



   .. py:attribute:: name
      :value: 'simple_base_line'



   .. py:method:: fit(training_x_dir: pathlib.Path | str, training_y_dir: pathlib.Path | str, testing_x_dir: pathlib.Path | str, testing_y_dir: pathlib.Path | str) -> SimpleBaseLine

      This model does not require fitting, so this method just returns self.



   .. py:method:: predict(x: numpy.ndarray) -> numpy.ndarray

      Predict the segmentation for the input image.



   .. py:method:: predict_dir(in_dir: str | pathlib.Path, out_dir: str | pathlib.Path, tile_size: int = 512, tile_assembly: str = 'mean') -> None

      Predict the segmentation for all images in a directory.



   .. py:method:: save(path: pathlib.Path | str) -> None

      Save the model's percentile threshold to a file.



   .. py:method:: load(path: pathlib.Path | str) -> None

      Load the model's percentile threshold from a file.