diff --git a/scripts/larvatagger-gui.jl b/scripts/larvatagger-gui.jl
new file mode 100755
index 0000000000000000000000000000000000000000..fed465faba452e064b60529d61e91de3615e08c2
--- /dev/null
+++ b/scripts/larvatagger-gui.jl
@@ -0,0 +1,24 @@
+#!/bin/bash
+#=
+if [ -z "$(which realpath)" ]; then
+macos_realpath=$( cd "$(dirname "${BASH_SOURCE[0]}")" ; pwd -P )
+PROJECT_DIR=$(dirname $macos_realpath)
+else
+PROJECT_DIR=$(dirname $(dirname $(realpath "${BASH_SOURCE[0]}")))
+fi
+FLAGS=
+if [ "$1" = "--sysimage" -o "$1" = "-J" ]; then FLAGS="--sysimage $2 "; shift 2; fi
+if [ "${1:0:2}" = "-J" ]; then FLAGS="$1 "; shift; fi
+if [ -n "$1" -a -e "$1" ]; then FLAGS="$FLAGS -iq "; fi
+if [ -z "$JULIA" ]; then JULIA=julia; fi
+ exec $JULIA --project="$PROJECT_DIR" --color=yes --startup-file=no $FLAGS\
+ "${BASH_SOURCE[0]}" "$@"
+=#
+
+projectdir = dirname(Base.active_project())
+
+include(joinpath(projectdir, "src/cli_open.jl")) # defines `main`
+
+using .GUI
+
+main();
diff --git a/scripts/larvatagger-toolkit.jl b/scripts/larvatagger-toolkit.jl
new file mode 100755
index 0000000000000000000000000000000000000000..08988999ad27cc2aba2da750f152c052887d12cc
--- /dev/null
+++ b/scripts/larvatagger-toolkit.jl
@@ -0,0 +1,23 @@
+#!/bin/bash
+#=
+if [ -z "$(which realpath)" ]; then
+macos_realpath=$( cd "$(dirname "${BASH_SOURCE[0]}")" ; pwd -P )
+PROJECT_DIR=$(dirname $macos_realpath)
+else
+PROJECT_DIR=$(dirname $(dirname $(realpath "${BASH_SOURCE[0]}")))
+fi
+FLAGS=
+if [ "$1" = "--sysimage" -o "$1" = "-J" ]; then FLAGS="--sysimage $2 "; shift 2; fi
+if [ "${1:0:2}" = "-J" ]; then FLAGS="$1"; shift; fi
+if [ -z "$JULIA" ]; then JULIA=julia; fi
+exec $JULIA --project="$PROJECT_DIR" --color=yes --startup-file=no $FLAGS\
+ "${BASH_SOURCE[0]}" "$@"
+=#
+
+projectdir = dirname(Base.active_project())
+
+include(joinpath(projectdir, "src/cli_toolkit.jl")) # defines `main`
+
+using .Toolkit
+
+main();
diff --git a/scripts/larvatagger.jl b/scripts/larvatagger.jl
index d053125de4a2a6b97e123712cc7a90a19de8f0c9..cb3898615029cc61a58dfdb5249c31ad1980c23c 100755
--- a/scripts/larvatagger.jl
+++ b/scripts/larvatagger.jl
@@ -1,3 +1,105 @@
+#!/bin/bash
+
+# This script is written in Bash and replaces a Julia script whose name (and extension)
+# is kept for backward compatibility.
+
+# Former scripts/larvatagger.jl and src/cli.jl have been split in distinct scripts and
+# source files in an attempt to fix issue https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/issues/61
+
+currentdir=$(dirname "${BASH_SOURCE[0]}")
+
+if [ -z "$1" -o "$1" = "-h" -o "$1" = "--help" ]; then
+cat << "EOT"
+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 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>]
+ larvatagger.jl predict <backend-path> <model-instance> <data-path> [--make-dataset] [--skip-make-dataset] [--data-isolation]
+ larvatagger.jl merge <input-path> <input-file> [<output-file>] [--manual-label=<label>] [--decode]
+ larvatagger.jl -V | --version
+ larvatagger.jl -h | --help
+
+Options:
+ -h --help Show this screen.
+ -V --version Show version.
+ -q --quiet Do not show instructions.
+ --id=<id> Run or assay ID, e.g. `date_time`.
+ --framerate=<fps> Camera frame rate, in frames per second.
+ --pixelsize=<μm> Camera pixel size, in micrometers.
+ --backends=<path> Path to backend repository.
+ --port=<number> Port number the server listens to.
+ --viewer Disable editing capabilities.
+ --browser Automatically open a browser tab at the served location.
+ --make-dataset Perform the make_dataset stage prior to proceeding to predict_model.
+ --skip-make-dataset Skip the make_dataset stage (default behavior since TaggingBackends==0.10).
+ --data-isolation Isolate the backend data directories for parallel tagging of multiple data files.
+ --sample-size=<N> Sample only N track segments from the data repository.
+ --layers=<N> (MaggotUBA) Number of layers of the classifier.
+ --iterations=<N> (MaggotUBA) Number of training iterations (can be two integers separated by a comma).
+ --decode Do not encode the labels into integer indices.
+ --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.
+ --class-weights=<csv> Comma-separated list of floats.
+ --pretrained-model=<instance> Name of the pretrained encoder (from `pretrained_models` registry).
+ --balancing-strategy=<strategy> Any of `auto`, `maggotuba`, `none` [default: auto].
+ --overrides=<comma-separated-list> Comma-separated list of key:value pairs.
+
+
+Commands:
+
+ open Launch the server-based GUI.
+
+ Backends defined in LarvaTagger project root directory are automatically found. Other
+ backend locations can be specified with the --backends argument.
+
+ import Generate a label file and store metadata.
+
+ This command is particularly useful to specify missing information such as the camera
+ framerate for FIMTrack v2 table.csv files. A label file is created with a pointer to the
+ original csv file, and a metadata section with the provided information.
+ A second usage applies to label files specifically, and consists in extending the tracks
+ and timesteps on basis of the associated data dependencies and assigning a default label
+ to the data points that are not already defined in the label file.
+ Note: label files should always come as siblings of their data dependencies (located in
+ the same directory).
+
+ merge Combine the content of label files.
+
+ <input-path> is the path to a manually edited label file whose content is to be augmented
+ with manual editions from a second (sibling) label file <input-file>. If no output file
+ is specified, the resulting content is dumped onto the standard output. All label files
+ must be siblings, i.e. located in the same directory.
+ If no editions are found in the second input file, all the defined labels are copied from
+ the second to the first file.
+
+ train Train a tagger.
+
+ <data-path> can be a path to a file or directory.
+ --class-weights requires --labels to be defined and the specified comma-separated values
+ should match those given by --labels.
+
+ predict Automatically label tracking data.
+
+ <data-path> can be a path to a file or directory.
+ <data-path> can also be a .txt file listing data files; one relative path per line.
+
+EOT
+
+elif [ "$1" = "open" ]; then
+ shift
+ $currentdir/larvatagger-gui.jl $@
+
+else
+ $currentdir/larvatagger-toolkit.jl $@
+fi
+
+exit 0
+
+# Equivalent Julia script (slower):
+
#!/bin/bash
#=
if [ -z "$(which realpath)" ]; then
@@ -9,7 +111,7 @@ fi
FLAGS=
if [ "$1" = "--sysimage" -o "$1" = "-J" ]; then FLAGS="--sysimage $2 "; shift 2; fi
if [ "${1:0:2}" = "-J" ]; then FLAGS="$1"; shift; fi
-if [ "$1" = "open" ]; then FLAGS="$FLAGS -iq "; fi
+if [ "$1" = "open" -a -n "$2" -a -e "$2" ]; then FLAGS="$FLAGS -iq "; fi
if [ -z "$JULIA" ]; then JULIA=julia; fi
exec $JULIA --project="$PROJECT_DIR" --color=yes --startup-file=no $FLAGS\
"${BASH_SOURCE[0]}" "$@"
diff --git a/src/cli.jl b/src/cli.jl
index 6fb3a1db0710fe6b8fbcd24da3bfdafc860e4aaa..9fdf28250fcc86fb906e1370f79181e432c66bb7 100644
--- a/src/cli.jl
+++ b/src/cli.jl
@@ -1,15 +1,16 @@
-using DocOpt
-using Pkg
-using OrderedCollections
-using PlanarLarvae.Datasets, PlanarLarvae.Formats
-using LarvaTagger, LarvaTagger.Taggers
-using JSServe: JSServe, Server
+
+projectdir = dirname(Base.active_project())
+include(joinpath(projectdir, "src", "cli_open.jl"))
+include(joinpath(projectdir, "src", "cli_toolkit.jl"))
+
+using .GUI
+using .Toolkit
usage = """Larva Tagger.
Usage:
- 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 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 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>]
larvatagger.jl predict <backend-path> <model-instance> <data-path> [--make-dataset] [--skip-make-dataset] [--data-isolation]
larvatagger.jl merge <input-path> <input-file> [<output-file>] [--manual-label=<label>] [--decode]
@@ -83,258 +84,15 @@ Commands:
"""
-function main(args=ARGS; exit_on_error=true)
- parsed_args = try
- docopt(usage, args isa String ? split(args) : args;
- help=false, exit_on_error=exit_on_error)
- catch # for exit_on_error==false only
- print("Parsing error -- ") # help message follows
- Dict{String, Any}()
+function main(args=ARGS; kwargs...)
+ if args isa String
+ args = split(args)
end
-
- if isempty(parsed_args) || parsed_args["--help"]
+ if isempty(args) || "-h" in args || "--help" in args
print(usage)
-
- elseif parsed_args["--version"]
- println(Pkg.project().version)
-
- elseif parsed_args["import"]
- infile = parsed_args["<input-path>"]
- if !isfile(infile)
- @error "File not found; did you specify a file path after \"import\"?" infile
- exit()
- end
- outfile = parsed_args["<output-file>"]
- kwargs = Dict{Symbol, Any}()
- framerate = parsed_args["--framerate"]
- if !isnothing(framerate)
- kwargs[:framerate] = parse(Float64, framerate)
- end
- pixelsize = parsed_args["--pixelsize"]
- if !isnothing(pixelsize)
- kwargs[:pixelsize] = parse(Float64, pixelsize)
- end
- file = load(infile; kwargs...)
- #
- metadata = file.run.attributes[:metadata]
- overrides = parsed_args["--overrides"]
- if !isnothing(overrides)
- metadata[:overrides] = overrides′= Dict{String, Any}()
- for override in split(overrides, ',')
- key, value = split(override, ':'; limit=2)
- try
- value = parse(Int, value)
- catch
- try
- value = parse(Float64, value)
- catch
- end
- end
- overrides′[key] = value
- end
- end
- #
- runid = parsed_args["--id"]
- run = Run(isnothing(runid) ? file.run.id : runid,
- file.run.attributes,
- isa(file, Formats.JSONLabels) ? file.run.tracks : OrderedDict{Datasets.TrackID, Track}())
- if !haskey(run.attributes, :labels)
- run.attributes[:labels] = String[]
- end
- if isa(file, Formats.JSONLabels)
- for dep in getdependencies(file)
- Datasets.pushdependency!(run, dep)
- end
- else
- Datasets.pushdependency!(run, infile)
- end
- defaultlabel = parsed_args["--default-label"]
- if !isnothing(defaultlabel)
- appendlabel!(run, "edited"; ignore=[defaultlabel], ifempty=false)
- setdefaultlabel!(run, defaultlabel; filepath=infile)
- end
- #
- decode = parsed_args["--decode"]
- if !decode
- encodelabels!(run)
- end
- if isnothing(outfile)
- Datasets.write_json(stdout, run)
- else
- if '/' in outfile || '\\' in outfile
- @error "Output file name contains slashes or backslashes (should not be a path)" outfile
- exit()
- end
- outfile = joinpath(dirname(infile), outfile)
- Datasets.to_json_file(outfile, run)
- Taggers.check_permissions(outfile)
- end
-
- elseif parsed_args["merge"]
- input_path = parsed_args["<input-path>"]
- if !isfile(input_path)
- @error "File not found; did you specify a file path after \"combine\"?" input_path
- exit()
- end
- input_file = parsed_args["<input-file>"]
- if '/' in input_file || '\\' in input_file
- @error "Second input file name contains slashes or backslashes (should not be a path)" input_file
- exit()
- end
- second_input = joinpath(dirname(input_path), input_file)
- if !isfile(second_input)
- @error "File not found" second_input
- exit()
- end
- #
- first_input = load(input_path)
- if !(first_input isa Formats.JSONLabels)
- @error "Not a JSON label file" first_input
- exit()
- end
- second_input = load(second_input)
- if !(second_input isa Formats.JSONLabels)
- @error "Not a JSON label file" second_input
- exit()
- end
- #
- run = first_input.run
- run2 = second_input.run
- if !shareddependencies(run, run2; extend=true)
- exit()
- end
- #
- attributes = run.attributes
- attributes2 = run2.attributes
- edited = parsed_args["--manual-label"]
- if !(haskey(attributes, :secondarylabels) && edited ∈ attributes[:secondarylabels])
- @debug "Cannot find manual editions" first_input=basename(first_input.source) edited_label=edited expected_among=get(attributes, :secondarylabels, String[])
- end
- if haskey(attributes2, :secondarylabels) && edited ∈ attributes2[:secondarylabels]
- mergelabels!(run, run2) do labels
- labels isa Vector && edited ∈ labels
- end
- else
- @warn "Cannot find manual editions" second_input=basename(second_input.source) edited_label=edited expected_among=get(attributes2, :secondarylabels, String[])
- mergelabels!(run, run2)
- end
- #
- output = run
- # in the case the first input file was automatically generated, remove the metadata
- # used elsewhere to distinguish between automatically- and manually-assigned labels
- metadata = output.attributes[:metadata]
- if haskey(metadata, :software)
- software = metadata[:software]
- tagger = Datasets.coerce(eltype(keys(software)), :tagger)
- if haskey(software, tagger)
- delete!(software, tagger)
- if isempty(software)
- delete!(metadata, :software)
- end
- end
- end
- #
- decode = parsed_args["--decode"]
- if !decode
- encodelabels!(output)
- end
- #
- outfile = parsed_args["<output-file>"]
- if isnothing(outfile)
- Datasets.write_json(stdout, output)
- else
- if '/' in outfile || '\\' in outfile
- @error "Output file name contains slashes or backslashes (should not be a path)" outfile
- exit()
- end
- outfile = joinpath(dirname(input_path), outfile)
- Datasets.to_json_file(outfile, output)
- Taggers.check_permissions(outfile)
- end
-
- elseif parsed_args["open"]
- verbose = !parsed_args["--quiet"]
- infile = parsed_args["<file-path>"]
- if !isfile(infile)
- @error "File not found; did you specify a file path after \"open\"?" infile
- exit()
- end
- if parsed_args["--viewer"]
- app = larvaviewer(infile)
- else
- kwargs = Dict{Symbol, Any}()
- backends = parsed_args["--backends"]
- if !isnothing(backends)
- kwargs[:backend_directory] = backends
- end
- kwargs[:manualtag] = string(parsed_args["--manual-label"])
- app = larvaeditor(infile; kwargs...)
- end
- #
- port = parsed_args["--port"]
- port = isnothing(port) ? 9284 : parse(Int, port)
- server = Server(app, "0.0.0.0", port)
- if parsed_args["--browser"]
- JSServe.openurl("http://127.0.0.1:$(port)")
- elseif verbose
- @info "The server is ready at http://127.0.0.1:$(port)"
- end
- if verbose
- @info "Press Ctrl+D to stop the server (or Ctrl+C if in PowerShell)"
- end
- return server
-
- elseif parsed_args["train"]
- backend_path = parsed_args["<backend-path>"]
- model_instance = parsed_args["<model-instance>"]
- data_path = parsed_args["<data-path>"]
- #
- tagger = Tagger(backend_path, model_instance)
- Taggers.reset(tagger)
- Taggers.push(tagger, data_path)
- kwargs = Dict{Symbol, Any}()
- layers = parsed_args["--layers"]
- isnothing(layers) || (kwargs[:layers] = layers)
- iterations = parsed_args["--iterations"]
- isnothing(iterations) || (kwargs[:iterations] = iterations)
- classweights = parsed_args["--class-weights"]
- isnothing(classweights) || (kwargs[:class_weights] = classweights)
- train(tagger;
- pretrained_instance=parsed_args["--pretrained-model"],
- labels=parsed_args["--labels"],
- sample_size=parsed_args["--sample-size"],
- balancing_strategy=parsed_args["--balancing-strategy"],
- include_all=parsed_args["--manual-label"],
- kwargs...)
-
- elseif parsed_args["predict"]
- backend_path = parsed_args["<backend-path>"]
- model_instance = parsed_args["<model-instance>"]
- data_path = parsed_args["<data-path>"]
- data_isolation = parsed_args["--data-isolation"]
- #
- datapath = abspath(data_path)
- destination = if isfile(datapath)
- if endswith(datapath, ".txt")
- # assume that the file lists paths to data files to be processed;
- # in this case, the path to the txt file is not relevant
- pwd()
- else
- dirname(datapath)
- end
- else
- datapath
- end
- #
- tagger = Tagger(backend_path, model_instance)
- if data_isolation
- tagger = Taggers.isolate(tagger)
- @info "Tagger isolated" sandbox=tagger.sandbox
- end
- resetdata(tagger)
- Taggers.push(tagger, datapath)
- predict(tagger; skip_make_dataset=parsed_args["--skip-make-dataset"],
- make_dataset=parsed_args["--make-dataset"])
- Taggers.pull(tagger, destination)
+ elseif args[1] == "open"
+ GUI.main(args[2:end]; kwargs...)
+ else
+ Toolkit.main(args; kwargs...)
end
end
diff --git a/src/cli_open.jl b/src/cli_open.jl
new file mode 100644
index 0000000000000000000000000000000000000000..023b432a6a9c20d9bfb4657c44b6cabcf268ee97
--- /dev/null
+++ b/src/cli_open.jl
@@ -0,0 +1,80 @@
+module GUI
+
+using DocOpt
+using LarvaTagger
+using JSServe: JSServe, Server
+
+export main
+
+usage = """LarvaTagger.jl - launch the server-based GUI.
+
+Usage:
+ larvatagger-gui.jl <file-path> [--backends=<path>] [--port=<number>] [--quiet] [--viewer] [--browser] [--manual-label=<label>]
+ larvatagger-gui.jl -h | --help
+
+Options:
+ -h --help Show this screen.
+ -q --quiet Do not show instructions.
+ --backends=<path> Path to backend repository.
+ --port=<number> Port number the server listens to.
+ --viewer Disable editing capabilities.
+ --browser Automatically open a browser tab at the served location.
+ --manual-label=<label> Secondary label for manually labelled data [default: edited].
+
+Backends defined in LarvaTagger project root directory are automatically found. Other
+backend locations can be specified with the --backends argument.
+"""
+
+function main(args=ARGS; exit_on_error=false)
+ if isempty(args)
+ print(usage)
+ exit()
+ end
+
+ parsed_args = try
+ docopt(usage, args isa String ? split(args) : args;
+ help=false, exit_on_error=exit_on_error)
+ catch # for exit_on_error==false only
+ print("Parsing error -- ") # help message follows
+ true # docopt returns true if no input arguments are passed
+ end
+
+ if parsed_args === true || parsed_args["--help"]
+ print(usage)
+ exit()
+ end
+
+ verbose = !parsed_args["--quiet"]
+ infile = parsed_args["<file-path>"]
+ if !isfile(infile)
+ @error "File not found; did you specify a file path?" infile
+ exit()
+ end
+ if parsed_args["--viewer"]
+ app = larvaviewer(infile)
+ else
+ kwargs = Dict{Symbol, Any}()
+ backends = parsed_args["--backends"]
+ if !isnothing(backends)
+ kwargs[:backend_directory] = backends
+ end
+ kwargs[:manualtag] = string(parsed_args["--manual-label"])
+ app = larvaeditor(infile; kwargs...)
+ end
+ #
+ port = parsed_args["--port"]
+ port = isnothing(port) ? 9284 : parse(Int, port)
+ server = Server(app, "0.0.0.0", port)
+ if parsed_args["--browser"]
+ JSServe.openurl("http://127.0.0.1:$(port)")
+ elseif verbose
+ @info "The server is ready at http://127.0.0.1:$(port)"
+ end
+ if verbose
+ @info "Press Ctrl+D to stop the server (or Ctrl+C if in PowerShell)"
+ end
+ return server
+
+end
+
+end
diff --git a/src/cli_toolkit.jl b/src/cli_toolkit.jl
new file mode 100644
index 0000000000000000000000000000000000000000..62bd46e828f99c8d2399bcc0a090310cad536b7f
--- /dev/null
+++ b/src/cli_toolkit.jl
@@ -0,0 +1,304 @@
+module Toolkit
+
+using DocOpt
+using Pkg
+using OrderedCollections
+using PlanarLarvae.Datasets, PlanarLarvae.Formats
+
+include("Taggers.jl")
+using .Taggers
+
+export main
+
+usage = """Larva Tagger.
+
+Usage:
+ larvatagger-toolkit.jl import <input-path> [<output-file>] [--id=<id>] [--framerate=<fps>] [--pixelsize=<μm>] [--overrides=<comma-separated-list>] [--default-label=<label>] [--manual-label=<label>] [--decode]
+ larvatagger-toolkit.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>]
+ larvatagger-toolkit.jl predict <backend-path> <model-instance> <data-path> [--make-dataset] [--skip-make-dataset] [--data-isolation]
+ larvatagger-toolkit.jl merge <input-path> <input-file> [<output-file>] [--manual-label=<label>] [--decode]
+ larvatagger-toolkit.jl -V | --version
+ larvatagger-toolkit.jl -h | --help
+
+Options:
+ -h --help Show this screen.
+ -V --version Show version.
+ --id=<id> Run or assay ID, e.g. `date_time`.
+ --framerate=<fps> Camera frame rate, in frames per second.
+ --pixelsize=<μm> Camera pixel size, in micrometers.
+ --make-dataset Perform the make_dataset stage prior to proceeding to predict_model.
+ --skip-make-dataset Skip the make_dataset stage (default behavior since TaggingBackends==0.10).
+ --data-isolation Isolate the backend data directories for parallel tagging of multiple data files.
+ --sample-size=<N> Sample only N track segments from the data repository.
+ --layers=<N> (MaggotUBA) Number of layers of the classifier.
+ --iterations=<N> (MaggotUBA) Number of training iterations (can be two integers separated by a comma).
+ --decode Do not encode the labels into integer indices.
+ --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.
+ --class-weights=<csv> Comma-separated list of floats.
+ --pretrained-model=<instance> Name of the pretrained encoder (from `pretrained_models` registry).
+ --balancing-strategy=<strategy> Any of `auto`, `maggotuba`, `none` [default: auto].
+ --overrides=<comma-separated-list> Comma-separated list of key:value pairs.
+
+
+Commands:
+
+ import Generate a label file and store metadata.
+
+ This command is particularly useful to specify missing information such as the camera
+ framerate for FIMTrack v2 table.csv files. A label file is created with a pointer to the
+ original csv file, and a metadata section with the provided information.
+ A second usage applies to label files specifically, and consists in extending the tracks
+ and timesteps on basis of the associated data dependencies and assigning a default label
+ to the data points that are not already defined in the label file.
+ Note: label files should always come as siblings of their data dependencies (located in
+ the same directory).
+
+ merge Combine the content of label files.
+
+ <input-path> is the path to a manually edited label file whose content is to be augmented
+ with manual editions from a second (sibling) label file <input-file>. If no output file
+ is specified, the resulting content is dumped onto the standard output. All label files
+ must be siblings, i.e. located in the same directory.
+ If no editions are found in the second input file, all the defined labels are copied from
+ the second to the first file.
+
+ train Train a tagger.
+
+ <data-path> can be a path to a file or directory.
+ --class-weights requires --labels to be defined and the specified comma-separated values
+ should match those given by --labels.
+
+ predict Automatically label tracking data.
+
+ <data-path> can be a path to a file or directory.
+ <data-path> can also be a .txt file listing data files; one relative path per line.
+
+"""
+
+function main(args=ARGS; exit_on_error=true)
+ parsed_args = try
+ docopt(usage, args isa String ? split(args) : args;
+ help=false, exit_on_error=exit_on_error)
+ catch # for exit_on_error==false only
+ print("Parsing error -- ") # help message follows
+ Dict{String, Any}()
+ end
+
+ if isempty(parsed_args) || parsed_args["--help"]
+ print(usage)
+
+ elseif parsed_args["--version"]
+ println(Pkg.project().version)
+
+ elseif parsed_args["import"]
+ infile = parsed_args["<input-path>"]
+ if !isfile(infile)
+ @error "File not found; did you specify a file path after \"import\"?" infile
+ exit()
+ end
+ outfile = parsed_args["<output-file>"]
+ kwargs = Dict{Symbol, Any}()
+ framerate = parsed_args["--framerate"]
+ if !isnothing(framerate)
+ kwargs[:framerate] = parse(Float64, framerate)
+ end
+ pixelsize = parsed_args["--pixelsize"]
+ if !isnothing(pixelsize)
+ kwargs[:pixelsize] = parse(Float64, pixelsize)
+ end
+ file = load(infile; kwargs...)
+ #
+ metadata = file.run.attributes[:metadata]
+ overrides = parsed_args["--overrides"]
+ if !isnothing(overrides)
+ metadata[:overrides] = overrides′= Dict{String, Any}()
+ for override in split(overrides, ',')
+ key, value = split(override, ':'; limit=2)
+ try
+ value = parse(Int, value)
+ catch
+ try
+ value = parse(Float64, value)
+ catch
+ end
+ end
+ overrides′[key] = value
+ end
+ end
+ #
+ runid = parsed_args["--id"]
+ run = Run(isnothing(runid) ? file.run.id : runid,
+ file.run.attributes,
+ isa(file, Formats.JSONLabels) ? file.run.tracks : OrderedDict{Datasets.TrackID, Track}())
+ if !haskey(run.attributes, :labels)
+ run.attributes[:labels] = String[]
+ end
+ if isa(file, Formats.JSONLabels)
+ for dep in getdependencies(file)
+ Datasets.pushdependency!(run, dep)
+ end
+ else
+ Datasets.pushdependency!(run, infile)
+ end
+ defaultlabel = parsed_args["--default-label"]
+ if !isnothing(defaultlabel)
+ appendlabel!(run, "edited"; ignore=[defaultlabel], ifempty=false)
+ setdefaultlabel!(run, defaultlabel; filepath=infile)
+ end
+ #
+ decode = parsed_args["--decode"]
+ if !decode
+ encodelabels!(run)
+ end
+ if isnothing(outfile)
+ Datasets.write_json(stdout, run)
+ else
+ if '/' in outfile || '\\' in outfile
+ @error "Output file name contains slashes or backslashes (should not be a path)" outfile
+ exit()
+ end
+ outfile = joinpath(dirname(infile), outfile)
+ Datasets.to_json_file(outfile, run)
+ Taggers.check_permissions(outfile)
+ end
+
+ elseif parsed_args["merge"]
+ input_path = parsed_args["<input-path>"]
+ if !isfile(input_path)
+ @error "File not found; did you specify a file path after \"combine\"?" input_path
+ exit()
+ end
+ input_file = parsed_args["<input-file>"]
+ if '/' in input_file || '\\' in input_file
+ @error "Second input file name contains slashes or backslashes (should not be a path)" input_file
+ exit()
+ end
+ second_input = joinpath(dirname(input_path), input_file)
+ if !isfile(second_input)
+ @error "File not found" second_input
+ exit()
+ end
+ #
+ first_input = load(input_path)
+ if !(first_input isa Formats.JSONLabels)
+ @error "Not a JSON label file" first_input
+ exit()
+ end
+ second_input = load(second_input)
+ if !(second_input isa Formats.JSONLabels)
+ @error "Not a JSON label file" second_input
+ exit()
+ end
+ #
+ run = first_input.run
+ run2 = second_input.run
+ if !shareddependencies(run, run2; extend=true)
+ exit()
+ end
+ #
+ attributes = run.attributes
+ attributes2 = run2.attributes
+ edited = parsed_args["--manual-label"]
+ if !(haskey(attributes, :secondarylabels) && edited ∈ attributes[:secondarylabels])
+ @debug "Cannot find manual editions" first_input=basename(first_input.source) edited_label=edited expected_among=get(attributes, :secondarylabels, String[])
+ end
+ if haskey(attributes2, :secondarylabels) && edited ∈ attributes2[:secondarylabels]
+ mergelabels!(run, run2) do labels
+ labels isa Vector && edited ∈ labels
+ end
+ else
+ @warn "Cannot find manual editions" second_input=basename(second_input.source) edited_label=edited expected_among=get(attributes2, :secondarylabels, String[])
+ mergelabels!(run, run2)
+ end
+ #
+ output = run
+ # in the case the first input file was automatically generated, remove the metadata
+ # used elsewhere to distinguish between automatically- and manually-assigned labels
+ metadata = output.attributes[:metadata]
+ if haskey(metadata, :software)
+ software = metadata[:software]
+ tagger = Datasets.coerce(eltype(keys(software)), :tagger)
+ if haskey(software, tagger)
+ delete!(software, tagger)
+ if isempty(software)
+ delete!(metadata, :software)
+ end
+ end
+ end
+ #
+ decode = parsed_args["--decode"]
+ if !decode
+ encodelabels!(output)
+ end
+ #
+ outfile = parsed_args["<output-file>"]
+ if isnothing(outfile)
+ Datasets.write_json(stdout, output)
+ else
+ if '/' in outfile || '\\' in outfile
+ @error "Output file name contains slashes or backslashes (should not be a path)" outfile
+ exit()
+ end
+ outfile = joinpath(dirname(input_path), outfile)
+ Datasets.to_json_file(outfile, output)
+ Taggers.check_permissions(outfile)
+ end
+
+ elseif parsed_args["train"]
+ backend_path = parsed_args["<backend-path>"]
+ model_instance = parsed_args["<model-instance>"]
+ data_path = parsed_args["<data-path>"]
+ #
+ tagger = Tagger(backend_path, model_instance)
+ Taggers.reset(tagger)
+ Taggers.push(tagger, data_path)
+ kwargs = Dict{Symbol, Any}()
+ layers = parsed_args["--layers"]
+ isnothing(layers) || (kwargs[:layers] = layers)
+ iterations = parsed_args["--iterations"]
+ isnothing(iterations) || (kwargs[:iterations] = iterations)
+ classweights = parsed_args["--class-weights"]
+ isnothing(classweights) || (kwargs[:class_weights] = classweights)
+ train(tagger;
+ pretrained_instance=parsed_args["--pretrained-model"],
+ labels=parsed_args["--labels"],
+ sample_size=parsed_args["--sample-size"],
+ balancing_strategy=parsed_args["--balancing-strategy"],
+ include_all=parsed_args["--manual-label"],
+ kwargs...)
+
+ elseif parsed_args["predict"]
+ backend_path = parsed_args["<backend-path>"]
+ model_instance = parsed_args["<model-instance>"]
+ data_path = parsed_args["<data-path>"]
+ data_isolation = parsed_args["--data-isolation"]
+ #
+ datapath = abspath(data_path)
+ destination = if isfile(datapath)
+ if endswith(datapath, ".txt")
+ # assume that the file lists paths to data files to be processed;
+ # in this case, the path to the txt file is not relevant
+ pwd()
+ else
+ dirname(datapath)
+ end
+ else
+ datapath
+ end
+ #
+ tagger = Tagger(backend_path, model_instance)
+ if data_isolation
+ tagger = Taggers.isolate(tagger)
+ @info "Tagger isolated" sandbox=tagger.sandbox
+ end
+ resetdata(tagger)
+ Taggers.push(tagger, datapath)
+ predict(tagger; skip_make_dataset=parsed_args["--skip-make-dataset"],
+ make_dataset=parsed_args["--make-dataset"])
+ Taggers.pull(tagger, destination)
+ end
+end
+
+end