diff --git a/recipes/README.md b/recipes/README.md index e3d18289ef1aaf06bc9cae228e9a08fd81d0d365..79f87775c7d8bd6dadd0c3e3d9a8328ee17889a3 100644 --- a/recipes/README.md +++ b/recipes/README.md @@ -77,3 +77,70 @@ For example: ./larvatagger.sh train /path/to/data/repo my-tagger --backend MaggotUBA ./larvatagger.sh predict /path/to/data/file --backend MaggotUBA --model-instance models/my-tagger --skip-make-dataset ``` + +## Windows PowerShell example + +Using a few [sample files](https://gitlab.pasteur.fr/nyx/artefacts/-/tree/master/PlanarLarvae): +``` +PS D:\> ls | Select Name + +Name +---- +trx.mat +trx_small.mat + + +PS D:\> mkdir models +``` +We train a *test-tagger* model instance for the *MaggotUBA* backend shipped with image *flaur/larvatagger:latest*: +``` +PS D:\> docker run -v ${PWD}:/data --mount type=bind,src=D:/models,dst=/app/MaggotUBA/models flaur/larvatagger train /app/MaggotUBA /data/trx.mat test-tagger --labels run_large,cast_large,back_large,stop_large --layers 2 +┌ Info: Pushing file to backend +│ backend = "MaggotUBA" +│ instance = "test-tagger" +└ file = "/data/trx.mat" +WARNING: could not import HDF5.exists into MAT +INFO:main: running make_dataset.py +[ Info: Counting behavior labels in run: test-tagger +┌ Info: Sample sizes (observed, selected): +│ stop_large = (392, 392) +│ cast_large = (30339, 784) +│ run_large = (68764, 784) +└ back_large = (1818, 392) +[ Info: Sampling series of spines in run: test-tagger +INFO:main: running train_model.py +DEBUG:train_model: trailing arguments: {'layers': '2'} +PS D:\> ls models/test-tagger | Select Name + +Name +---- +autoencoder_config.json +best_validated_encoder.pt +clf_config.json +retrained_encoder.pt +trained_classifier.pt + +``` +This results in a new directory in *models*. + +We now tag a second data file using the *test-tagger* instance: +``` +PS D:\> docker run -v ${PWD}:/data --mount type=bind,src=D:/models,dst=/app/MaggotUBA/models flaur/larvatagger predict /app/MaggotUBA test-tagger /data/trx_small.mat --skip-make-dataset +┌ Info: Pushing file to backend +│ backend = "MaggotUBA" +│ instance = "test-tagger" +└ file = "/data/trx_small.mat" +WARNING: could not import HDF5.exists into MAT +INFO:main: running predict_model.py +PS D:\> ls | Select Name + +Name +---- +models +predicted.label +trx.mat +trx_small.mat + +``` +A *predicted.label* file was generated. +This file can be loaded in the LarvaTagger.jl viewer like any *table.csv*, *.mat* or *.outline* file.