extra doc and bug fix for extra input arguments

recipes/README.md

@@ -4,24 +4,24 @@ Docker images can be used with the `docker` command.
 To make their usage easier, standalone scripts are available in the *scripts* directory.
 They can be used with no installation step other than setting up Docker.
 
-Windows users should use the [larvatagger.ps1 script](#the-larvataggerps1-script), while macOS and Linux users should use the [larvatagger.sh script](#the-larvataggersh-script) instead.
+Windows users should use the [larvatagger.bat script](#the-larvataggerbat-script), while macOS and Linux users should use the [larvatagger.sh script](#the-larvataggersh-script) instead.
 
 The first two sections describe how to use these scripts.
 The last section is dedicated to Singularity/Apptainer.
 
-## The *larvatagger.ps1* script
+## The *larvatagger.bat* script
 
 ### Getting the script
 
-The *larvatagger.ps1* script is available in the *scripts* directory of the project.
+The *larvatagger.bat* script is available in the *scripts* directory of the project.
 
-If you do not have a copy of the project, you can simply [download the script](https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/raw/main/scripts/larvatagger.ps1?inline=false).
+If you do not have a copy of the project, you can simply [download the script](https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/raw/main/scripts/larvatagger.bat?inline=false) and save it in your `C:\Users\<user>` directory.
 
 Note that Docker still has to be installed.
 
-In PowerShell, to check the script works properly, change directory to where the *larvatagger.ps1* script is located and try:
+In the command prompt (`cmd`), to check the script works properly, try:
 ```
-PowerShell.exe -ExecutionPolicy ByPass -File larvatagger.ps1 --version
+larvatagger.bat --version
 ```
 
 The first time the script runs, Docker downloads the latest image.
@@ -30,19 +30,41 @@ The first time the script runs, Docker downloads the latest image.
 
 To open a track data file, try:
 ```
-PowerShell.exe -ExecutionPolicy ByPass -File larvatagger.ps1 open Z:\path\to\datafile
+larvatagger.bat open Z:\path\to\datafile
 ```
 This turns the commandline into a Julia interpreter to serve the app as a webserver.
 
 As instructed, open `localhost:9284` in your webbrowser to access the app.
 
-Unlike instructed, you can stop the server in the commandline pressing Ctrl+C instead of Ctrl+D.
+You can stop the server in the commandline pressing Ctrl+C.
 The server can also be exited typing `exit()` and pressing Enter.
 
+The `--browser` argument mentioned elsewhere does not work with the *larvatagger.bat* script yet.
+
 A default tagger will be available in the app.
 
+### Automatic tagging
+
+To apply a tagger (e.g. `20230311`) to a track data file, type:
+```
+larvatagger.bat predict Z:\path\to\datafile 20230311
+```
+This will create a *predicted.label* in the same directory as the data file. If the file already exists, it is overwritten.
+
+To apply a custom tagger, named e.g. *mytagger* and stored in the `C:\Users\<user>\models\mytagger` directory, type instead:
+```
+larvatagger.bat predict Z:\path\to\datafile models\mytagger
+```
+Here, `models\mytagger` is the relative path of the directory of the tagger.
+This path has to include at least one `\` character so that it is identified as an external tagger.
+Otherwise, LarvaTagger.jl would look up for the tagger inside the Docker container, and fail to find it.
+
 ### More to come...
 
+The `train`, `merge` and `import` commands work similarly to the *larvatagger.sh* script. See the below section to know more about these commands.
+
+Not all arguments and options are available, though. See also `larvatagger.bat --help`.
+
 
 ## The *larvatagger.sh* script
 

scripts/larvatagger.bat

+PowerShell.exe -ExecutionPolicy ByPass -File larvatagger.ps1 $*

scripts/larvatagger.ps1

@@ -36,7 +36,9 @@ function Call1 {
     $args = $args -split ' '
     $cmd = $args[0]
     $path = Convert-Path $args[1]
-    $extraargs = $args[2..($args.count - 1)]
+    if ($args.count -gt 2) {
+        $extraargs = $args[2..($args.count - 1)]
+    }
     if ($cmd -eq 'open') {
         $runargs = '-p', '9284:9284', '-i'
     }
@@ -99,7 +101,9 @@ Switch ($args[0])
             New-Item -Path $modelsdir -ItemType 'directory'
         }
         $taggername = Split-Path -Leaf $taggerpath
-        $extraargs = $args[3..($args.count - 1)]
+        if ($args.count -gt 3) {
+            $extraargs = $args[3..($args.count - 1)]
+        }
         Write-Host "docker run --mount `"type=bind,src=$modelsdir,dst=/app/$TAGGING_BACKEND/models`" -v ${parentdir}:/data $LARVATAGGER_IMAGE train /app/$TAGGING_BACKEND /data/$dirname $taggername $extraargs"
         docker run --mount "type=bind,src=$modelsdir,dst=/app/$TAGGING_BACKEND/models" -v ${parentdir}:/data $LARVATAGGER_IMAGE train /app/$TAGGING_BACKEND /data/$dirname $taggername $extraargs
     }
@@ -116,7 +120,9 @@ Switch ($args[0])
         }
         $parentdir = Split-Path -Parent $path
         $filename = Split-Path -Leaf $path
-        $extraargs = $args[3..($args.count - 1)]
+        if ($args.count -gt 3) {
+            $extraargs = $args[3..($args.count - 1)]
+        }
         Write-Host "docker run $runargs -v ${parentdir}:/data $LARVATAGGER_IMAGE predict /app/$TAGGING_BACKEND $taggername /data/$filename $extraargs"
         docker run $runargs -v ${parentdir}:/data $LARVATAGGER_IMAGE predict /app/$TAGGING_BACKEND $taggername /data/$filename $extraargs
     }