Gregor-Mendel-Institute/aradeepopsis: v1.2

New Features

• added --ignore_label parameter to exclude a segmentation class for trait calculation.
• added --masks parameter to skip semantic segmentation and run trait extraction using user-supplied masks
• added --label_spec parameter to allow for mapping of segmentation classes to pixel values of user-supplied segmentation masks. This is a requirement for the --masks parameter now.
• added --model 'DPP' and --dpp_checkpoint to allow for custom segmentation models, trained using the Deep Plant Phenomics framework

Fixes and general changes

• fixed an issue where the pipeline would crash if the input image contains an alpha channel
• updated base.config to avoid out-of-memory issues when running with --multiscale
• added log message to show current parameter settings when starting a pipeline run
• added a more informative log message if pipeline fails on systems with insufficient memory
• updated configuration for CBE cluster
• factored out Shiny dependencies into separate container (should be easier to deploy as a hosted Shiny app now)
• added Dockerfile + Conda environment for DPP v2.1.0

Dependency updates

• new (optional) dependency Deep Plant Phenomics v2.1.0
• updated shiny dependency 1.4.0 > 1.5.0
• updated scikit-image 0.16.2 > 0.17.2
• updated imagemagick dependency 7.0.9_27 > 7.0.10_23