Merge branch 'master' into benchmark

JuliaHealth · Jul 3, 2024 · b4a5e88 · b4a5e88
2 parents 61fec64 + 17ef89d
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diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 
 <div align="center">
 
-![][julia-19] [![][gh-actions-komamri]][gh-actions-url] [![][buildkite-badge]][buildkite-url] [![][codecov-komamri]][codecov-url] [![][license]][license-url] [![][julia-blue]][julia-blue-url] [![][total-downloads-komamri]][downloads-komamri-url]
+![][julia-19] [![][gh-actions-komamri]][gh-actions-url] [![][buildkite-badge]][buildkite-url] [![][codecov-komamri]][codecov-url] [![][license]][license-url] [![][julia-blue]][julia-blue-url] [![][total-downloads-komamri]][downloads-komamri-url] ![](https://img.shields.io/github/stars/JuliaHealth/KomaMRI.jl?style=flat&label=Stars&color=blue&logo=data:image/svg%2bxml;base64,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)
 
 [![][docr-img]][docr-url] [![][docd-img]][docd-url] [![][paper-img]][paper-url]
 

diff --git a/examples/4.reproducible_notebooks/pluto-01-gradient-echo-spin-echo.jl b/examples/4.reproducible_notebooks/pluto-01-gradient-echo-spin-echo.jl
@@ -1,5 +1,5 @@
 ### A Pluto.jl notebook ###
-# v0.19.42
+# v0.19.43
 
 #> [frontmatter]
 #> title = "Understanding basic MRI sequences"
@@ -20,7 +20,7 @@ macro bind(def, element)
 end
 
 # ╔═╡ d6b1729a-874d-11ee-151a-9b0fcce2c4fd
-using KomaMRICore, KomaMRIPlots, PlutoPlotly, PlutoUI
+using KomaMRICore, KomaMRIPlots, FFTW, PlutoPlotly, PlutoUI
 
 # ╔═╡ 5df97874-f09c-4173-a2f6-893db322ccaf
 md"# Understanding basic MRI sequences"
@@ -179,7 +179,10 @@ raw_gre = simulate(obj, seq_gre, sys)
 
 # ╔═╡ 9a88a54b-bcc7-41ad-8e60-f4d450dccb2d
 # (2.7) Reconstruct the 1D image
-recon_gre = plot(abs.(KomaMRI.fftc(raw_gre.profiles[1].data)))
+begin
+    fftc(x; dims=[1,2]) = fftshift(fft(ifftshift(x, dims), dims), dims)/prod(size(x)[dims])
+    recon_gre = plot(abs.(fftc(raw_gre.profiles[1].data)))
+end
 
 # ╔═╡ 41d14dec-b852-4316-aefb-c3d08fa43216
 # (2.6) Plot the simulated signal
@@ -273,7 +276,7 @@ end
 
 # ╔═╡ 4a4a6bd3-b820-479c-89e3-f3ce79a316db
 # (3.6) Reconstruct the 1D image
-recon_t2_star_gre = plot(abs.(KomaMRI.fftc(raw_t2_star_gre.profiles[1].data)))
+recon_t2_star_gre = plot(abs.(fftc(raw_t2_star_gre.profiles[1].data)))
 
 # ╔═╡ 964404f6-7f46-4df9-ad98-921948c3be69
 begin
@@ -356,7 +359,7 @@ end
 
 # ╔═╡ 2e65ae31-f50a-462b-9744-80bf6cdb388e
 # (4.9) Reconstruct the 1D image
-recon_t2_star_se = plot(abs.(KomaMRI.fftc(raw_t2_star_se.profiles[1].data)))
+recon_t2_star_se = plot(abs.(fftc(raw_t2_star_se.profiles[1].data)))
 
 # ╔═╡ 34824db7-13c4-45e2-befa-f027b9b585c0
 begin
@@ -387,12 +390,14 @@ end
 # ╔═╡ 00000000-0000-0000-0000-000000000001
 PLUTO_PROJECT_TOML_CONTENTS = """
 [deps]
+FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 KomaMRICore = "4baa4f4d-2ae9-40db-8331-a7d1080e3f4e"
 KomaMRIPlots = "76db0263-63f3-4d26-bb9a-5dba378db904"
 PlutoPlotly = "8e989ff0-3d88-8e9f-f020-2b208a939ff0"
 PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
 
 [compat]
+FFTW = "~1.8.0"
 KomaMRICore = "~0.8.3"
 KomaMRIPlots = "~0.8.3"
 PlutoPlotly = "~0.4.6"
@@ -405,7 +410,7 @@ PLUTO_MANIFEST_TOML_CONTENTS = """
 
 julia_version = "1.10.4"
 manifest_format = "2.0"
-project_hash = "ac4a136318692ed9929d4df54938b984e4c67341"
+project_hash = "0f2e80720e96a9c2feec29eaa1a1b0b2acbb995f"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]