version increment

Manifest.toml

 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.7.1"
+julia_version = "1.7.0"
 manifest_format = "2.0"
 
 [[deps.AbstractFFTs]]
@@ -864,11 +864,11 @@ version = "0.1.1"
 
 [[deps.PlanarLarvae]]
 deps = ["DelimitedFiles", "JSON3", "MAT", "Meshes", "OrderedCollections", "SHA", "StaticArrays", "StructTypes"]
-git-tree-sha1 = "20a9e95162e6226283a7024ab2352f9d08822d4a"
-repo-rev = "dev"
+git-tree-sha1 = "d231f3b1d82d26c4d4ce6077db95ddeb2e8236f0"
+repo-rev = "main"
 repo-url = "https://gitlab.pasteur.fr/nyx/planarlarvae.jl"
 uuid = "c2615984-ef14-4d40-b148-916c85b43307"
-version = "0.4.0"
+version = "0.5.0"
 
 [[deps.PlotUtils]]
 deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"]

Project.toml

 name = "LarvaTagger"
 uuid = "8b3b36f1-dfed-446e-8561-ea19fe966a4d"
 authors = ["François Laurent", "Institut Pasteur"]
-version = "0.3.0"
+version = "0.4.0"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"

README.md

@@ -9,43 +9,60 @@ To run `LarvaTagger.jl`, you will need [`julia>=1.6`](https://julialang.org/down
 An example install procedure can be found in `scripts/make_demontrator.sh`.
 
 ## Install
-In a fresh directory:
+
 ```
+git clone https://gitlab.pasteur.fr/nyx/larvatagger.jl LarvaTagger
+cd LarvaTagger
 julia --project=. -e 'using Pkg; Pkg.instantiate()'
 ```
 
 ## Run
-In the same directory as above, launch the Julia interpreter:
+
+### Using the Julia interpreter
+
+In the `LarvaTagger` directory created above, launch the Julia interpreter:
 ```
 julia --project=.
 ```
 In the interpreter, to launch the editor, type:
 ```
-julia> using LarvaTagger; larvaeditor("path/to/file")
+julia> using LarvaTagger; larvaeditor("path/to/data/file")
 ```
 
 The first time the editor is loaded, it may take a while for a window in your webbrowser to open, and the data to be plotted.
 
-The Firefox webbrowser showed better performance than Chrome-like webbrowsers.
+The Firefox web browser showed better performance than Chrome-like browsers.
+
+To exit the interpreter, type `exit()` or press Ctrl+D.
+
+### Using the `larvatagger.jl` script
 
-To exit the interpreter, type `exit()`.
+The `LarvaTagger/scripts` directory contains a `larvatagger.jl` executable file.
+To launch the editor, type:
+```
+scripts/larvatagger.jl open path/to/data/file
+```
 
 ## Automatic tagging
 
-To extend the editor with `MaggotUBA` automatic tagging, still in the same directory:
+To extend the editor with `MaggotUBA` automatic tagging:
 ```
 git clone https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA -b 20220418
 cd MaggotUBA
-poetry install
+poetry install -vvv
 cd ..
-julia --project=.
 ```
+To let *larvaeditor* know about MaggotUBA, in the Julia interpreter, type:
 The last command launches the Julia interpreter again. There, you can type:
 ```
-julia> using LarvaTagger; larvaeditor("path/to/file"; backend_directory=".")
+julia> using LarvaTagger; larvaeditor("path/to/data/file"; backend_directory="path/to/MaggotUBA's/parent/directory")
+```
+Similarly, to let *larvatagger.jl* know about MaggotUBA:
+```
+scripts/larvatagger.jl open "path/to/data/file" --backends="path/to/MaggotUBA's/parent/directory"
 ```
 
-Note however that [`MaggotUBA-adapter`](https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter) requires the actual [`MaggotUBA`](https://gitlab.pasteur.fr/les-larves/structured-temporal-convolution/-/tree/dev-branch) code that is not open access.
+Note however that [`MaggotUBA-adapter`](https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter) requires the actual [`MaggotUBA`](https://gitlab.pasteur.fr/les-larves/structured-temporal-convolution/-/tree/dev-branch) code that is not open access yet.
 As a consequence, it is likely the installation step fails.
-`MaggotUBA` and a supervised variant will be released in the near future.
+The `MaggotUBA` tagging core will be fully released in the near future.
 

scripts/larvatagger.jl

@@ -37,6 +37,10 @@ function main()
     parsed_args = docopt(usage)
     if parsed_args["import"]
         infile = parsed_args["<input-path>"]
+        if !isfile(infile)
+            @error "File not found" $infile
+            return
+        end
         outfile = parsed_args["<output-file>"]
         kwargs = Dict{Symbol, Any}()
         framerate = parsed_args["--framerate"]
@@ -52,11 +56,16 @@ function main()
         if isnothing(outfile)
             Datasets.write_json(stdout, run)
         else
+            outfile = joinpath(dirname(infile), outfile)
             Datasets.to_json_file(outfile, run)
         end
     elseif parsed_args["open"]
         verbose = !parsed_args["--quiet"]
         infile = parsed_args["<input-path>"]
+        if !isfile(infile)
+            @error "File not found" $infile
+            return
+        end
         if parsed_args["--viewer"]
             app = larvaviewer(infile)
         else
@@ -81,7 +90,7 @@ function main()
             @info "Press Ctrl+D to kill the server"
         end
     elseif parsed_args["train"]
-        @error "not implemented yet"
+        @error "Not implemented yet"
     end
 end
 

scripts/make_demonstrator.sh

@@ -16,42 +16,52 @@ fi
 # make the `julia` command available on the commandline
 export PATH=~/.local/bin:$PATH
 # get LarvaTagger.jl source
-git clone https://gitlab.pasteur.fr/nyx/larvatagger.jl LarvaTagger
+# (the dev branch is used here for testing before release)
+git clone https://gitlab.pasteur.fr/nyx/larvatagger.jl LarvaTagger -b dev
 cd LarvaTagger
 # install LarvaTagger.jl
 julia --project=. -e 'using Pkg; Pkg.instantiate()'
+if ! [ -x ~/.local/bin/larvatagger.jl ]; then
+pushd ~/.local/bin
+ln -s ~/LarvaTagger/scripts/larvatagger.jl .
+popd
+fi
 # get MaggotUBA source and trained models - open-source part
 git clone https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA -b 20220418
 cd MaggotUBA
 # install Poetry
 python3 -m pip install poetry
-# copy MaggotUBA source - "firmware" part
-cp -r /home/share/structured-temporal-convolution .
-# install MaggotUBA
-python3 -m poetry add ./structured-temporal-convolution
+# install MaggotUBA; this step requires access to a private repo;
+# for a new user with no ssh or gpg keys, this is done logging in with `ssh -A` instead of `su`
 python3 -m poetry install
-cd ..
+cd
 # copy sample data
 cp -r /home/share/t15 .
-# autolaunch `larvaeditor` on starting `julia`
-mkdir -p ~/.julia/config
-cat <<"EOT" > ~/.julia/config/startup.jl
-if endswith(pwd(), "LarvaTagger")
-using JSServe
-port = occursin("anzhou", pwd()) ? 9285 : 9286
-JSServe.configure_server!(listen_port=port)
-using LarvaTagger
-app = larvaeditor("t15/GMR_SS02113@UAS_Chrimson_Venus_X_0070/r_LED100_30s2x15s30s#n#n#n@100/20140918_170215/20140918_170215@GMR_SS02113@UAS_Chrimson_Venus_X_0070@t15@r_LED100_30s2x15s30s#n#n#n@100.spine"; backend_directory=".")
-println("As soon as the `julia>` prompt appears below, in your web browser")
-println("you can go to: http://127.0.0.1:$port/browser-display")
-display(app)
-end
-EOT
+example_file="$HOME/t15/GMR_SS02113@UAS_Chrimson_Venus_X_0070/r_LED100_30s2x15s30s#n#n#n@100/20140918_170215/20140918_170215@GMR_SS02113@UAS_Chrimson_Venus_X_0070@t15@r_LED100_30s2x15s30s#n#n#n@100.spine"
 # make a `larvatagger` command
-if [ -z "$(grep 'alias larvatagger=' ~/.bash_aliases)" ]; then
-echo "alias larvatagger='cd ~/LarvaTagger; julia --project=. --banner=no'" >> ~/.bash_aliases
+if [ $USER = anzhou ]; then
+# for user 1
+port=9285
+else
+# for user 2
+port=9286
+fi
+if ! [ -f ~/.bash_aliases ] || [ -z "$(grep 'alias larvatagger=' ~/.bash_aliases)" ]; then
+echo "alias larvatagger='$HOME/LarvaTagger/scripts/larvatagger.jl open \"${example_file}\" --port=${port} --backends=\"$HOME/LarvaTagger\"'" >> ~/.bash_aliases
 fi
 # let the user know about the latter command on every login
 if [ -z "$(grep 'echo start the Nyx' ~/.bashrc)" ]; then
-echo "echo start the Nyx tagging UI with command: larvatagger" >> ~/.bashrc
+cat <<EOT >> ~/.bashrc
+echo start the Nyx tagging UI with command: larvatagger
+echo or, for a richer interface, type: larvatagger.jl
+echo
+echo more changes with v0.4:
+echo \* no need to add \"/browser-display\" after http://localhost:$port
+echo \* step forward/backward with the right/left arrow keys on your keyboard
+echo \* simultaneously tag individual time steps with buttons at the bottom
+echo
+echo a few tips:
+echo \* pan the larva view holding the right mouse button
+echo \* to properly refresh the page, press Ctrl+F5 instead of F5 alone
+EOT
 fi