From 1e8678128eaff2451b7b6379304c06bb52390c27 Mon Sep 17 00:00:00 2001
From: korbinian90 <korbinian90@gmail.com>
Date: Mon, 14 Oct 2024 17:29:06 +0200
Subject: [PATCH] add B0 weighting options; add B0_snr output

---
 ext/RomeoApp/argparse.jl       | 4 ++++
 ext/RomeoApp/caller.jl         | 6 ++++--
 test/RomeoApp/dataset_small.jl | 8 ++++++++
 3 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/ext/RomeoApp/argparse.jl b/ext/RomeoApp/argparse.jl
index aa4a065..76a3a1c 100644
--- a/ext/RomeoApp/argparse.jl
+++ b/ext/RomeoApp/argparse.jl
@@ -56,6 +56,10 @@ function getargs(args::AbstractVector, version)
             default = ""
             nargs = '?'
             constant = "B0"
+        "--B0-phase-weighting"
+            help = """phase_snr | average | TEs | mag | magTEs | simulated_mag
+                Set the weighting for the B0 calculation."""
+            default = "phase_snr"
         "--phase-offset-correction"
             help = """on | off | bipolar.
                 Applies the MCPC3Ds method to perform phase offset
diff --git a/ext/RomeoApp/caller.jl b/ext/RomeoApp/caller.jl
index 7174d5a..1906bb2 100644
--- a/ext/RomeoApp/caller.jl
+++ b/ext/RomeoApp/caller.jl
@@ -1,4 +1,4 @@
-function ROMEO.unwrapping_main(args; version="App 4.4")
+function ROMEO.unwrapping_main(args; version="App 4.5")
     settings = getargs(args, version)
     data = load_data_and_resolve_args!(settings)
 
@@ -242,8 +242,10 @@ function computeB0(settings, data)
         end
         data["mag"] = to_dim(exp.(-settings["TEs"]/20), 4) # T2*=20ms decay (low value to reduce noise contribution of later echoes)
     end
-    B0 = calculateB0_unwrapped(data["phase"], data["mag"], settings["TEs"])
+    B0 = calculateB0_unwrapped(data["phase"], data["mag"], settings["TEs"], Symbol(settings["B0-phase-weighting"]))
     save(B0, settings["compute-B0"], settings)
+    snr = get_B0_snr(data["mag"], settings["TEs"], Symbol(settings["B0-phase-weighting"]))
+    save(snr, settings["compute-B0"]*"_snr", settings)
 end
 
 function write_qualitymap(settings, data, keyargs)
diff --git a/test/RomeoApp/dataset_small.jl b/test/RomeoApp/dataset_small.jl
index 0597cf4..1281fc0 100644
--- a/test/RomeoApp/dataset_small.jl
+++ b/test/RomeoApp/dataset_small.jl
@@ -84,6 +84,12 @@ configurations_me(pm) = [
     [pm..., "--phase-offset-correction", "bipolar", "-t", "[2,4,6]"],
     [pm..., "--phase-offset-correction", "-t", "[2,4,6]", "--phase-offset-smoothing-sigma-mm", "[5,8,4]"],
     [pm..., "--phase-offset-correction", "-t", "[2,4,6]", "--write-phase-offsets"],
+    [pm..., "-t", "[2,4,6]", "-B", "--B0-phase-weighting", "phase_snr"],
+    [pm..., "-t", "[2,4,6]", "-B", "--B0-phase-weighting", "average"],
+    [pm..., "-t", "[2,4,6]", "-B", "--B0-phase-weighting", "TEs"],
+    [pm..., "-t", "[2,4,6]", "-B", "--B0-phase-weighting", "mag"],
+    [pm..., "-t", "[2,4,6]", "-B", "--B0-phase-weighting", "magTEs"],
+    [pm..., "-t", "[2,4,6]", "-B", "--B0-phase-weighting", "simulated_mag"],
 ]
 
 files = [(phasefile_1eco, magfile_1eco), (phasefile_1arreco, magfile_1arreco), (phasefile_1eco, magfile_1arreco), (phasefile_1arreco, magfile_1eco), (phasefile_2D, magfile_2D)]
@@ -192,11 +198,13 @@ unwrapping_main([phasefile_me, "-o", testpath, "-m", magfile_me, "-t", "[2,4,6]"
 testpath = joinpath(tmpdir, "testB0_1")
 unwrapping_main([phasefile_me, "-o", testpath, "-m", magfile_me, "-t", "[2,4,6]", "-B"])
 @test isfile(joinpath(testpath, "B0.nii"))
+@test isfile(joinpath(testpath, "B0_snr.nii"))
 
 testpath = joinpath(tmpdir, "testB0_2")
 name = "B0_output"
 unwrapping_main([phasefile_me, "-o", testpath, "-m", magfile_me, "-t", "[2,4,6]", "-B", name])
 @test isfile(joinpath(testpath, "$name.nii"))
+@test isfile(joinpath(testpath, "$(name)_snr.nii"))
 
 ## TODO add and test homogeneity corrected output