remove QSM dependency;

clearswiApp uses QSM.jl RTS, since it is a lighter dependency
korbinian90 · Dec 5, 2023 · 77ae479 · 77ae479
1 parent 8015c55
commit 77ae479
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Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,12 +1,11 @@
 name = "CLEARSWI"
 uuid = "06ae4d9b-ce5e-4813-a1b3-426e46312ec2"
 authors = ["Korbinian Eckstein"]
-version = "1.2.0"
+version = "1.3.0"
 
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 MriResearchTools = "557dad86-b9bd-4533-8525-1a39684d020f"
-QuantitativeSusceptibilityMappingTGV = "bd393529-335a-4aed-902f-5de61cc7ff49"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [weakdeps]
@@ -18,5 +17,4 @@ ClearswiApp = "ArgParse"
 [compat]
 ArgParse = "1"
 MriResearchTools = "3.1"
-QuantitativeSusceptibilityMappingTGV = "0.2"
 julia = "1.7"
diff --git a/README.md b/README.md
@@ -93,6 +93,7 @@ phase_hp_sigma=[4,4,0]
 phase_scaling_type=:tanh
 phase_scaling_strength=4
 writesteps=nothing
+qsm=false
 ```
 
 * `mag_combine` selects the echo combination for the magnitude. Options are 
@@ -118,6 +119,8 @@ writesteps=nothing
 
 * Set `writesteps` to the path, where intermediate steps should be saved, e.g. `writesteps="/tmp/clearswi_steps"`. If set to `nothing`, intermediate steps won't be saved.
 
+* [Experimental] Set `qsm` to true to use QSM processing for the phase contrast. This requires the additional use of a QSM package. Supported are either [`QSM`](https://github.com/kamesy/QSM.jl) or [`QuantitativeSusceptibilityMappingTGV`](https://github.com/korbinian90/QuantitativeSusceptibilityMappingTGV.jl). Before setting this option, you need load one of these packages with `using`.
+
 ### Calculating T2* and B0 maps on multi-echo datasets
 
 T2* and B0 maps can be calculated using the package [MriResearchTools](https://github.com/korbinian90/MriResearchTools.jl):
@@ -161,7 +164,7 @@ usage: <PROGRAM> [-m MAGNITUDE] [-p PHASE] [-o OUTPUT]
                  [-e ECHOES [ECHOES...]] [-N] [--no-phase-rescale]
                  [--writesteps WRITESTEPS] [-v] [--version] [-h]
 
-3.6.4
+4.0.4
 
 optional arguments:
   -m, --magnitude MAGNITUDE
@@ -173,7 +176,7 @@ optional arguments:
                         The echo times are required for multi-echo
                         datasets specified in array or range syntax
                         (eg. "[1.5,3.0]" or "3.5:3.5:14").
-  --qsm                 When activated uses TGV-QSM for phase weighting
+  --qsm                 When activated uses RTS QSM for phase weighting
   --mag-combine MAG-COMBINE [MAG-COMBINE...]
                         SNR | average | echo <n> | SE <te>. Magnitude
                         combination algorithm. echo <n> selects a

diff --git a/clearswi.jl b/clearswi.jl
@@ -1,10 +1,10 @@
 import Pkg
 Pkg.activate(@__DIR__)
 try
-    using CLEARSWI, ArgParse
+    using CLEARSWI, QSM, ArgParse
 catch
-    Pkg.add(["CLEARSWI", "ArgParse"])
-    using CLEARSWI, ArgParse
+    Pkg.add(["CLEARSWI", "QSM", "ArgParse"])
+    using CLEARSWI, QSM, ArgParse
 end
 
 @time msg = clearswi_main(ARGS)

diff --git a/ext/ClearswiApp/argparse.jl b/ext/ClearswiApp/argparse.jl
@@ -21,7 +21,7 @@ function getargs(args::AbstractVector, version)
                 "3.5:3.5:14")."""
             nargs = '+'
         "--qsm"
-            help = """When activated uses TGV-QSM for phase weighting
+            help = """When activated uses RTS QSM for phase weighting.
             """
             action = :store_true
         "--mag-combine"

diff --git a/src/CLEARSWI.jl b/src/CLEARSWI.jl
@@ -1,7 +1,6 @@
 module CLEARSWI
 
 using MriResearchTools
-using QuantitativeSusceptibilityMappingTGV
 using Statistics
 
 include("tissue.jl")