save GE corrected phase with steps

korbinian90 · Sep 4, 2024 · f20c88e · f20c88e · korbinian90 · Sep 4, 2024
1 parent 488822e
commit f20c88e
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/ext/ClearswiApp/caller.jl b/ext/ClearswiApp/caller.jl
@@ -14,11 +14,14 @@ function CLEARSWI.clearswi_main(args; version="1.3.3")
     end
 
     mkpath(writedir)
+    if !isnothing(settings["writesteps"]) mkpath(settings["writesteps"]) end
+
     saveconfiguration(writedir, settings, args, version)
 
     mag = readmag(settings["magnitude"]; mmap=!settings["no-mmap"])
-    phase = readphase(settings["phase"]; mmap=(!settings["no-mmap"] && !settings["fix-ge-phase"]), rescale=!settings["no-phase-rescale"], fix_ge=settings["fix-ge-phase"])
     hdr = CLEARSWI.MriResearchTools.header(mag)
+    phase = readphase(settings["phase"]; mmap=(!settings["no-mmap"] && !settings["fix-ge-phase"]), rescale=!settings["no-phase-rescale"], fix_ge=settings["fix-ge-phase"])        
+    settings["fix-ge-phase"] && savenii(collect(phase), "corrected_GE_phase", settings["writesteps"], hdr)
     neco = size(mag, 4)
 
     ## Echoes for unwrapping

diff --git a/src/functions.jl b/src/functions.jl
@@ -21,7 +21,6 @@ julia> swi = calculateSWI(data, options);
 ```
 """
 function calculateSWI(data::Data, options::Options=Options())
-    if !isnothing(options.writesteps) mkpath(options.writesteps) end
     getswimag(data, options) .* getswiphase(data, options)
 end
-Original file line number
+Diff line change
@@ Expand Up / @@ -21,7 +21,6 @@ julia> swi = calculateSWI(data, options); @@
     ```
     """
     function calculateSWI(data::Data, options::Options=Options())
-        if !isnothing(options.writesteps) mkpath(options.writesteps) end
         getswimag(data, options) .* getswiphase(data, options)
     end
@@ Expand Down @@