:py:mod:`macrobot.mb_pipeline`
==============================

.. py:module:: macrobot.mb_pipeline

.. autoapi-nested-parse::

   Main class for the Macrobot pathogen segmentation pipelines.
   Version 0.4



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

Classes
~~~~~~~

.. autoapisummary::

   macrobot.mb_pipeline.MacrobotPipeline




Attributes
~~~~~~~~~~

.. autoapisummary::

   macrobot.mb_pipeline.__author__
   macrobot.mb_pipeline.__copyright__
   macrobot.mb_pipeline.__license__


.. py:data:: __author__
   :annotation: = Stefanie Lueck

   

.. py:data:: __copyright__
   :annotation: = Stefanie Lueck

   

.. py:data:: __license__
   :annotation: = NonCommercial-ShareAlike 2.0 Generic (CC BY-NC-SA 2.0) License

   

.. py:class:: MacrobotPipeline(image_list, path_source, destination_path, store_leaf_path, experiment, dai, file_results)

   Bases: :py:obj:`object`

   Macrobot pipeline main class.

   :param image_list: A list of all images names per plate (green channel, blue channel, red channel, backlight image, UVS image.
   :type image_list: list
   :param path: The path which contains the raw images coming from the macrobot image acquisition.
   :type path: str
   :param destination_path: The path to store the final result images and csv file.
   :type destination_path: str
   :param file_results: The CSV file for each experiments which contains the pathogen prediction per leaf.
   :type file_results: file object
   :param experiment: The experiment name.
   :type experiment: str
   :param dai: Days after inoculation.
   :type dai: str
   :param resize_scale: Scale for resizing the images.
   :type resize_scale: float
   :param plate_id: Plate ID without the barcode.
   :type plate_id: str
   :param y_position: Y Position for the leaves.
   :type y_position: int

   .. py:attribute:: NAME
      :annotation: = invalid

      

   .. py:method:: create_folder_structure(self)

      Create all necessary folders.


   .. py:method:: read_images(self)

      Reading and resizing the images.


   .. py:method:: merge_channels(self)

      Merging blue, red and green image to create a true 3-channel RGB image.


   .. py:method:: do_whitebalance(self)

      Calling white balance function in helpers module.


   .. py:method:: get_lanes_rgb(self)

      Extracts the lanes of the RGB image. Different for each pathogen. Should be overwritten.


   .. py:method:: get_lanes_binary(self)

      Create a binary image from the lanes.


   .. py:method:: get_leaves_binary(self)

      Segment the single leaves.


   .. py:method:: get_features(self)

      Features extraction. Different for each pathogen should be overridden


   .. py:method:: get_prediction_per_lane(self)

      Predict pathogen. Different for each pathogen should be overridden


   .. py:method:: save_images_for_report(self)


   .. py:method:: create_report(self)


   .. py:method:: start_pipeline(self)

      Starts the Macrobot analysis pipeline.