Merge pull request #2 from korbinian90/development

Merge new developments

README.md

@@ -5,12 +5,12 @@
 [![Codecov](https://codecov.io/gh/korbinian90/MriResearchTools.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/korbinian90/MriResearchTools.jl)
 [![Coveralls](https://coveralls.io/repos/github/korbinian90/MriResearchTools.jl/badge.svg?branch=master)](https://coveralls.io/github/korbinian90/MriResearchTools.jl?branch=master)
 
-### Prerequisites
+## Prerequisites
 A Julia installation v1.x is required.
 
 Magnitude and Phase images in NIfTI fileformat (4D images with echoes in the 4th dimension)
 
-### Installing
+## Installing
 Open the Julia REPL and type
 
 ```julia
@@ -20,25 +20,62 @@ julia> ] # enter julia package manager
 julia>
 ```
 
-### Included Functionality
+## Quick Start
+Open multi-echo 4D NIfTI phase and magnitude files and perform ROMEO phase unwrapping.
 
-ROMEO 3D/4D Phase Unwrapping
+```julia
+using MriResearchTools
+# input images
+TEs = [4,8,12]
+nifti_folder = joinpath("test", "data", "small")
+magfile = joinpath(nifti_folder, "Mag.nii") # Path to the magnitude image in nifti format, must be .nii or .hdr
+phasefile = joinpath(nifti_folder, "Phase.nii") # Path to the phase image
+# load images
+mag = readmag(magfile)
+phase = readphase(phasefile)
+# unwrap
+unwrapped = romeo(phase; mag=mag, TEs=TEs)
+# save unwrapped image
+outputfolder = "outputFolder"
+mkpath(outputfolder)
+savenii(unwrapped, "unwrapped", outputfolder, header(phase))
+```
+
+## Included Functionality
+
+ROMEO 3D/4D Phase Unwrapping\
+`romeo` `unwrap` `unwrap_individual`
+
+Reading, writing and other functions for NIfTI files (adapted from JuliaIO/NIfTI)\
+`readphase` `readmag` `niread` `savenii` `header`
+
+Magnitude homogeneity correction ([example](https://github.com/korbinian90/Magnitude-Intensity-Correction/blob/master/Intensity%20Correction.ipynb))\
+`makehomogeneous`
+
+Simple robust masking (threshold)\
+`robustmask`
 
-Reading and writing NIfTI files (adapted from JuliaIO/NIfTI)
+Combine multiple echoes\
+`RSS`
 
-Magnitude homogeneity correction ([example](https://github.com/korbinian90/Magnitude-Intensity-Correction/blob/master/Intensity%20Correction.ipynb))
+Laplacian unwrapping\
+`laplacianunwrap`
 
-Simple robust masking (threshold)
+Unwarping of B0 dependent shifts\
+`getVSM` `thresholdforward` `unwarp`
 
-Combine multiple echoes
+Fast gaussian smoothing\
+`gaussiansmooth3d`
+  - standard
+  - weighted
+  - with missing values
 
-Laplacian unwrapping
+Other functions
+`robustrescale` `getHIP` `getsensitivity` `getscaledimage` `estimatequantile`
 
-Unwarping of B0 dependent shifts
+## License
+This project is licensed under the MIT License - see the [LICENSE](https://github.com/korbinian90/MriResearchTools.jl/blob/master/LICENSE) for details
 
-Fast gaussian smoothing
-- standard
-- weighted
-- with missing values
 
-TODO: Tests and Examples
+## TODO
+Tests, Examples and Documentation

src/MriResearchTools.jl

@@ -16,10 +16,11 @@ include("romeo.jl")
 
 export Data,
         readphase, readmag, niread,
+        header,
         savenii,
         robustmask, robustmask!,
         robustrescale,
-        combine_echoes,
+        #combine_echoes,
         getHIP,
         laplacianunwrap, laplacianunwrap!,
         getVSM,
@@ -31,7 +32,7 @@ export Data,
         getscaledimage,
         estimatequantile,
         RSS,
-        unwrap, unwrap!,
+        unwrap, unwrap!, romeo,
         unwrap_individual, unwrap_individual!
 
 end # module

src/romeo.jl

@@ -1,3 +1,4 @@
+romeo = unwrap # access unwrap function via alias romeo
 # multi echo unwrapping
 function ROMEO.unwrap!(
     wrapped::AbstractArray{T, 4}; TEs=1:size(wrapped, 4), template=2, p2ref=1, keyargs...

src/utility.jl

@@ -19,12 +19,14 @@ end
 Base.copy(x::NIfTI.NIfTI1Header) = NIfTI.NIfTI1Header([getfield(x, k) for k ∈ fieldnames(NIfTI.NIfTI1Header)]...)
 
 function Base.similar(header::NIfTI.NIfTI1Header)
-    hdr = NIfTI.copy(header)
+    hdr = copy(header)
     hdr.scl_inter = 0
     hdr.scl_slope = 1
-    hdr
+    return hdr
 end
 
+header(v::NIfTI.NIVolume) = similar(v.header)
+
 Base.minimum(I::Array{AbstractFloat}) = NaNMath.minimum(I)
 Base.maximum(I::Array{AbstractFloat}) = NaNMath.maximum(I)
 

test/utility_test.jl

@@ -27,7 +27,13 @@ GC.gc()
 
 @test estimatequantile(1:1000, 0.8) ≈ 800 atol=1
 
-hdr = similar(mag_nii.header)
-@test hdr.scl_inter == 0
-@test hdr.scl_slope == 1
-@test hdr.dim == mag_nii.header.dim
+function header_test(hdr, hdr2)
+    @test hdr.scl_inter == 0
+    @test hdr.scl_slope == 1
+    @test hdr.dim == hdr2.dim
+end
+# similar
+header_test(similar(mag_nii.header), mag_nii.header)
+# header
+header_test(header(mag_nii), mag_nii.header)
+header_test(header(phase_nii), phase_nii.header)