macrobot.mb_pipeline
¶
Main class for the Macrobot pathogen segmentation pipelines. Version 0.4
Module Contents¶
Classes¶
Macrobot pipeline main class. |
Attributes¶
- 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()¶
Create all necessary folders.
- read_images()¶
Reading and resizing the images.
- merge_channels()¶
Merging blue, red and green image to create a true 3-channel RGB image.
- do_whitebalance()¶
Calling white balance function in helpers module.
- get_lanes_rgb()¶
Extracts the lanes of the RGB image. Different for each pathogen. Should be overwritten.
- get_lanes_binary()¶
Create a binary image from the lanes.
- get_leaves_binary()¶
Segment the single leaves.
- get_features()¶
Features extraction. Different for each pathogen should be overridden
- get_prediction_per_lane()¶
Predict pathogen. Different for each pathogen should be overridden
- save_images_for_report()¶
- create_report()¶
- start_pipeline()¶
Starts the Macrobot analysis pipeline.