quickstart-template.yaml

# phenopype quickstart template
# -----------------------------
# This template is intended to go with the phenopype quickstart materials 
# - for details see https://www.phenopype.org/docs/quickstart/ and refer to
# Figure 2 in Luerig 2021 (https://doi.org/10.1111/2041-210X.13771) or 
# phenopype tutorial 3 (https://www.phenopype.org/docs/tutorials/tutorial_3).
# Also check https://www.phenopype.org/gallery/projects/stickleback-landmarks/

processing_steps:
    - preprocessing:
        - create_mask:
            ANNOTATION: {type: mask, id: a, edit: false}
            tool: polygon
            label: plates
        - blur:
            kernel_size: 9
    - segmentation:
        - threshold:
            method: adaptive
            blocksize: 99
            constant: 5
        - detect_contour:
            ANNOTATION: {type: contour, id: a, edit: overwrite}
            retrieval: ext
            min_area: 150
    - measurement:
        - compute_shape_features:
            ANNOTATION: {type: shape_features, id: a, edit: overwrite}
    - visualization:
        - select_canvas:
            canvas: raw
        - draw_contour
        - draw_mask:
            label: true
    - export:
        - save_canvas
        - save_annotation:
            overwrite: true