From fa5f9b941d59dabd66692ba5baee63f0a45faded Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fran=C3=A7ois=20Laurent?= <francois.laurent@posteo.net>
Date: Wed, 22 Mar 2023 16:21:43 +0100
Subject: [PATCH] extra doc and bug fix for extra input arguments
---
recipes/README.md | 38 ++++++++++++++++++++++++++++++--------
scripts/larvatagger.bat | 1 +
scripts/larvatagger.ps1 | 12 +++++++++---
3 files changed, 40 insertions(+), 11 deletions(-)
create mode 100644 scripts/larvatagger.bat
diff --git a/recipes/README.md b/recipes/README.md
index 9457b7c..b0eb228 100644
--- a/recipes/README.md
+++ b/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
diff --git a/scripts/larvatagger.bat b/scripts/larvatagger.bat
new file mode 100644
index 0000000..553c213
--- /dev/null
+++ b/scripts/larvatagger.bat
@@ -0,0 +1 @@
+PowerShell.exe -ExecutionPolicy ByPass -File larvatagger.ps1 $*
diff --git a/scripts/larvatagger.ps1 b/scripts/larvatagger.ps1
index 54275af..79b8c86 100644
--- a/scripts/larvatagger.ps1
+++ b/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
}
--
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