Standardize yml (#11)

* Standardize make.jl

* Standardize yml

* Add _typos

* Use github url

* Show k-space row sampling

* Fix comment

Author: JeffFessler

.github/workflows/Documentation.yml

@@ -2,7 +2,11 @@ name: Documentation
 
 on:
   pull_request:
+    paths-ignore:
+      - 'README.md'
   push:
+    paths-ignore:
+      - 'README.md'
     branches:
       - 'main'
       - 'release-'
@@ -12,12 +16,12 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1'
-      - name: Cache artifacts
-        uses: actions/cache@v3
+      - name: CacheArtifacts
+        uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -27,13 +31,13 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - name: Install dependencies
+      - name: InstallDependencies
         run: |
           julia --project=docs/ -e '
-          ENV["JULIA_PKG_SERVER"] = ""
-          using Pkg
-          Pkg.develop(PackageSpec(path=pwd()))
-          Pkg.instantiate()'
+            ENV["JULIA_PKG_SERVER"] = ""
+            using Pkg
+            Pkg.develop(PackageSpec(path=pwd()))
+            Pkg.instantiate()'
       - name: BuildAndDeploy
         env:
 # https://juliadocs.github.io/Documenter.jl/stable/man/hosting/#Authentication:-GITHUB_TOKEN

.github/workflows/SpellCheck.yml

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/typos@master

.github/workflows/clean.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
       - name: Delete preview and history + push changes

_typos.toml

@@ -0,0 +1,5 @@
+[default]
+extend-ignore-identifiers-re = [
+    "iy",
+    "pn",
+]

docs/lit/mri/5-l-plus-s.jl

@@ -27,7 +27,7 @@ please cite that paper.
 # Packages needed here.
 
 ## using Unitful: s
-using Plots; default(markerstrokecolor=:auto, label="")
+using Plots; cgrad, default(markerstrokecolor=:auto, label="")
 using MIRT: Afft, Asense, embed
 using MIRT: pogm_restart, poweriter
 using MIRTjim: jim, prompt
@@ -90,15 +90,16 @@ based on the
 
 # ## Read data
 if !@isdefined(data)
-    url = "https://web.eecs.umich.edu/~fessler/irt/reproduce/19/lin-19-edp/data/"
+#src url = "https://web.eecs.umich.edu/~fessler/irt/reproduce/19/lin-19-edp/data/"
+    url = "https://github.com/JeffFessler/MIRTdata/raw/main/mri/lin-19-edp/"
     dataurl = url * "cardiac_perf_R8.mat"
     data = matread(Downloads.download(dataurl))
     xinfurl = url * "Xinf.mat"
     Xinf = matread(Downloads.download(xinfurl))["Xinf"]["perf"] # (128,128,40)
 end;
 
 # Show converged image as a preview:
-jim(Xinf, L"\mathrm{Converged\ image\ } X_∞")
+pinf = jim(Xinf, L"\mathrm{Converged\ image\ sequence } X_∞")
 
 # Organize k-space data:
 if !@isdefined(ydata0)
@@ -117,9 +118,22 @@ if !@isdefined(samp)
     end
     kx = -(nx÷2):(nx÷2-1)
     ky = -(ny÷2):(ny÷2-1)
-    jim(kx, ky, samp, "Sampling patterns for $nt frames"; xlabel=L"k_x", ylabel=L"k_y")
+    psamp = jim(kx, ky, samp, "Sampling patterns for $nt frames";
+       xlabel=L"k_x", ylabel=L"k_y")
 end
 
+#=
+Are all k-space rows are sampled in one of the 40 frames?
+Sadly no.
+The 10 blue rows shown below are never sampled.
+A better sampling pattern design
+could have avoided this issue.
+=#
+samp_sum = sum(samp, dims=3)
+color = cgrad([:blue, :black, :white], [0, 1/2nt, 1])
+pssum = jim(kx, ky, samp_sum; xlabel="kx", ylabel="ky",
+    color, clim=(0,nt), title="Number of sampled frames out of $nt")
+
 # Prepare coil sensitivity maps
 if !@isdefined(smaps)
     smaps_raw = data["b1"] # raw coil sensitivity maps
@@ -130,7 +144,7 @@ if !@isdefined(smaps)
     smaps = smaps_raw ./ ssos_raw
     ssos = ssos_fun(smaps)
     @assert all(≈(1), ssos)
-    jim(smaps, "Normalized |coil maps| for $nc coils")
+    pmap = jim(smaps, "Normalized |coil maps| for $nc coils")
 end
 
 
@@ -156,7 +170,7 @@ because Xinf was reconstructed
 using this regularizer!
 =#
 tmp = TF * Xinf
-jim(tmp, "|Temporal FFT of Xinf|")
+ptfft = jim(tmp, "|Temporal FFT of Xinf|")
 
 
 #=
@@ -211,7 +225,7 @@ end
 
 # Check scale factor of Xinf. (It should be ≈1.)
 tmp = A * Xinf
-scale = dot(tmp, ydata) / norm(tmp)^2 # 1.009 ≈ 1
+scale0 = dot(tmp, ydata) / norm(tmp)^2 # 1.009 ≈ 1
 
 # Crude initial image
 L0 = A' * ydata # adjoint (zero-filled)
@@ -221,7 +235,7 @@ L0 = A' * ydata # adjoint (zero-filled)
 S0 = zeros(ComplexF32, nx, ny, nt)
 X0 = cat(L0, S0, dims=ndims(L0)+1) # (nx, ny, nt, 2) = (128, 128, 40, 2)
 M0 = AII * X0 # L0 + S0
-jim(M0, "|Initial L+S via zero-filled recon|")
+pm0 = jim(M0, "|Initial L+S via zero-filled recon|")
 
 
 #=

docs/make.jl

@@ -1,6 +1,7 @@
 execute = isempty(ARGS) || ARGS[1] == "run"
 
-org, reps = :JuliaImageRecon, "Examples"
+org, reps = :JuliaImageRecon, :Examples
+eval(:(using $reps))
 import Documenter
 import Literate
 
@@ -20,6 +21,7 @@ nbviewer_root_url =
 binder_root_url =
     "https://mybinder.org/v2/gh/$base/gh-pages?filepath=generated"
 
+repo = eval(:($reps))
 # preprocessing
 inc1 = "include(\"../../inc/reproduce.jl\")"
 
@@ -77,7 +79,6 @@ Documenter.makedocs(;
     authors = "Jeff Fessler and contributors",
     sitename = "Examples",
     format,
-    strict = true, # fail on "warnings"
     pages = [
         "Home" => "index.md",
         "MRI" => pages("mri"),
@@ -92,6 +93,7 @@ if isci
         versions = nothing,
         forcepush = true,
         push_preview = true,
+        # see https://$org.github.io/$repo.jl/previews/PR##
     )
 else
     @warn "may need to: rm -r src/generated/"