macrobot.mb_pipeline

Main class for the Macrobot pathogen segmentation pipelines. Version 0.4

Module Contents

Classes

MacrobotPipeline

Macrobot pipeline main class.

Attributes

__author__

__copyright__

__license__

macrobot.mb_pipeline.__author__ = Stefanie Lueck
macrobot.mb_pipeline.__copyright__ = Stefanie Lueck
macrobot.mb_pipeline.__license__ = NonCommercial-ShareAlike 2.0 Generic (CC BY-NC-SA 2.0) License
class macrobot.mb_pipeline.MacrobotPipeline(image_list, path_source, destination_path, store_leaf_path, experiment, dai, file_results)

Bases: object

Macrobot pipeline main class.

Parameters

  • image_list (list) – A list of all images names per plate (green channel, blue channel, red channel, backlight image, UVS image.

  • path (str) – The path which contains the raw images coming from the macrobot image acquisition.

  • destination_path (str) – The path to store the final result images and csv file.

  • file_results (file object) – The CSV file for each experiments which contains the pathogen prediction per leaf.

  • experiment (str) – The experiment name.

  • dai (str) – Days after inoculation.

  • resize_scale (float) – Scale for resizing the images.

  • plate_id (str) – Plate ID without the barcode.

  • y_position (int) – Y Position for the leaves.

NAME = invalid
create_folder_structure(self)

Create all necessary folders.

read_images(self)

Reading and resizing the images.

merge_channels(self)

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

do_whitebalance(self)

Calling white balance function in helpers module.

get_lanes_rgb(self)

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

get_lanes_binary(self)

Create a binary image from the lanes.

get_leaves_binary(self)

Segment the single leaves.

get_features(self)

Features extraction. Different for each pathogen should be overridden

get_prediction_per_lane(self)

Predict pathogen. Different for each pathogen should be overridden

save_images_for_report(self)
create_report(self)
start_pipeline(self)

Starts the Macrobot analysis pipeline.