bactoscoop.omni
===============

.. py:module:: bactoscoop.omni

Classes and public operations
-----------------------------

Omnipose
~~~~~~~~

.. py:class:: Omnipose(imgs, paths)

   Omnipose.

   :param imgs: Input ``imgs`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
   :param paths: Input ``paths`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.

   :returns: None (no explicit return statement).

   **Assigned state:** ``self.imgs``, ``self.files``, ``self.use_GPU``, ``self.masks``, ``self.flows``, ``self.selected_imgs``, ``self.selected_files``, ``self.model``.

   `View current source, line 14 <../source-code/omni.html#omni-14>`_.

Omnipose.load_models
~~~~~~~~~~~~~~~~~~~~

.. py:method:: Omnipose.load_models(model_name)

   Load the desired omnipose model.

   :param model_name: Omnipose model identifier; default collection model is bact_phase_omni.

   :returns: None (no explicit return statement).

   **Assigned state:** ``self.model``.

   `View current source, line 28 <../source-code/omni.html#omni-28>`_.

   .. raw:: html

      <details><summary>Original docstring (legacy wording may differ from the current signature)</summary>

   .. code-block:: text

      Load the desired omnipose model.

   .. raw:: html

      </details>

Omnipose.process
~~~~~~~~~~~~~~~~

.. py:method:: Omnipose.process(n=(0,), mask_thresh=1, minsize=300)

   Segment the raw images and get their masks.

   :param n: Selected image positions; wrapper accepts None for all. Indices must be nonempty, unique valid integers.
   :param mask_thresh: Threshold passed as Omnipose mask_threshold.
   :param minsize: Minimum accepted segmentation-mask size in pixels.

   :returns: None (no explicit return statement).

   **Assigned state:** ``self.masks``, ``self.flows``, ``self.selected_imgs``, ``self.selected_files``.

   **Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded.

   `View current source, line 36 <../source-code/omni.html#omni-36>`_.

   .. raw:: html

      <details><summary>Original docstring (legacy wording may differ from the current signature)</summary>

   .. code-block:: text

      Segment the raw images and get their masks.

   .. raw:: html

      </details>

Omnipose.save_masks
~~~~~~~~~~~~~~~~~~~

.. py:method:: Omnipose.save_masks()

   Save the segmentation masks.

   :returns: None (no explicit return statement).

   **Explicitly raised exceptions:** ``RuntimeError``, ``ValueError``. Errors from called functions can also propagate or be recorded.

   `View current source, line 91 <../source-code/omni.html#omni-91>`_.

   .. raw:: html

      <details><summary>Original docstring (legacy wording may differ from the current signature)</summary>

   .. code-block:: text

      Save the segmentation masks.

   .. raw:: html

      </details>

Omnipose.compiled_process
~~~~~~~~~~~~~~~~~~~~~~~~~

.. py:method:: Omnipose.compiled_process(n, mask_thresh, minsize)

   Sequentially process and save the masks in one method.

   :param n: Selected image positions; wrapper accepts None for all. Indices must be nonempty, unique valid integers.
   :param mask_thresh: Threshold passed as Omnipose mask_threshold.
   :param minsize: Minimum accepted segmentation-mask size in pixels.

   :returns: None (no explicit return statement).

   `View current source, line 116 <../source-code/omni.html#omni-116>`_.

   .. raw:: html

      <details><summary>Original docstring (legacy wording may differ from the current signature)</summary>

   .. code-block:: text

      Sequentially process and save the masks in one method.

   .. raw:: html

      </details>