Merge branch 'dev'

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.

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