fix: argument parsing -> allow "qualitymask 0.5" as one argument

korbinian90 · Sep 9, 2024 · 2c7e116 · 2c7e116 · korbinian90 · Sep 9, 2024
1 parent 406a4da
commit 2c7e116
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Showing 3 changed files with 15 additions and 3 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "ROMEO"
 uuid = "1ea8258b-a15d-4adb-ad20-01632f467a84"
-authors = ["Korbinian Eckstein", "Barbara Dymerska"]
-version = "1.1.2"
+authors = ["Korbinian Eckstein", "Barbara Dymerska", "Simon Robinson"]
+version = "1.1.3"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"

diff --git a/ext/RomeoApp/caller.jl b/ext/RomeoApp/caller.jl
@@ -203,9 +203,11 @@ function set_mask!(data, settings)
         template_echo = min(settings["template"], size(data["mag"], 4))
         data["mask"] = robustmask(data["mag"][:,:,:,template_echo])
         save(data["mask"], "mask", settings)
-    elseif settings["mask"][1] == "qualitymask"
+    elseif contains(settings["mask"][1], "qualitymask")
         threshold = if length(settings["mask"]) > 1
             parse(Float32, settings["mask"][2])
+        elseif length(split(settings["mask"][1])) > 1
+            parse(Float32, split(settings["mask"][1])[2])
         else
             0.1 # default threshold
         end

diff --git a/romeo.jl b/romeo.jl
@@ -1,3 +1,13 @@
+#!/usr/bin/env -S julia --color=yes --startup-file=no --threads=auto
+
+## Usage
+
+# Call with: `<path-to-file>/romeo.jl ARGS`
+# On windows use: `julia --threads=auto <path-to-file>/romeo.jl ARGS`
+
+# Example call:
+# `./romeo.jl -p phase.nii.gz -m mag.nii.gz -t [0.025 0.05] -o output.nii.gz
+
 import Pkg
 Pkg.activate(@__DIR__)
 try