diff --git a/scripts/larvatagger.jl b/scripts/larvatagger.jl index 794bc59cb7bf32b3ee186706a45d57750e8bbbe7..fb9352a28da17f9ba0d476bc83053bcd7d1683c1 100755 --- a/scripts/larvatagger.jl +++ b/scripts/larvatagger.jl @@ -24,7 +24,7 @@ LarvaTagger.jl Usage: larvatagger.jl open <file-path> [--backends=<path>] [--port=<number>] [--quiet] [--viewer] [--browser] [--manual-label=<label>] - larvatagger.jl import <input-path> [<output-file>] [--id=<id>] [--framerate=<fps>] [--pixelsize=<μm>] [--overrides=<comma-separated-list>] [--default-label=<label>] [--manual-label=<label>] [--decode] + larvatagger.jl import <input-path> [<output-file>] [--id=<id>] [--framerate=<fps>] [--pixelsize=<μm>] [--overrides=<comma-separated-list>] [--default-label=<label>] [--manual-label=<label>] [--decode] [--copy-labels] larvatagger.jl train <backend-path> <data-path> <model-instance> [--pretrained-model=<instance>] [--labels=<comma-separated-list>] [--sample-size=<N>] [--balancing-strategy=<strategy>] [--class-weights=<csv>] [--manual-label=<label>] [--layers=<N>] [--iterations=<N>] [--seed=<seed>] larvatagger.jl predict <backend-path> <model-instance> <data-path> [--output=<filename>] [--make-dataset] [--skip-make-dataset] [--data-isolation] larvatagger.jl merge <input-path> <input-file> [<output-file>] [--manual-label=<label>] [--decode] @@ -50,6 +50,7 @@ Options: --iterations=<N> (MaggotUBA) Number of training iterations (can be two integers separated by a comma). --seed=<seed> Seed for the backend's random number generators. --decode Do not encode the labels into integer indices. + --copy-labels Replicate discrete behavior data from the input file. --default-label=<label> Label all untagged data as <label>. --manual-label=<label> Secondary label for manually labelled data [default: edited]. --labels=<comma-separated-list> Comma-separated list of behavior tags/labels. diff --git a/scripts/larvatagger.sh b/scripts/larvatagger.sh index faaea47be6714aec8c03c9f08c0c887289fec275..5f4b7fbe8308538731dde0bda4ba5287e5b49ded 100755 --- a/scripts/larvatagger.sh +++ b/scripts/larvatagger.sh @@ -174,6 +174,7 @@ mkdir -p "$external_models_dir" src=$(cd "$external_models_dir"; pwd -P) RUN_ARGS="$RUN_ARGS --mount type=bind,src=\"$src\",dst=/app/$backend/models" fi +RUN_ARGS="$RUN_ARGS --entrypoint=/app/scripts/larvatagger-toolkit.jl" DOCKER_RUN="$docker run $DOCKER_ARGS$RUN_ARGS \"$LARVATAGGER_IMAGE\" train \"/app/$backend\" \"/data/$data_repository\" \"$tagger\" $@" echo $DOCKER_RUN