Add adiabatic RF pulse tutorial (#791)

* docs: support Plotly animation embeds

* docs: add adiabatic RF pulse tutorial

* docs: fix chemical shift phantom plot layout

* docs: clean up slice-selective recon plot

* docs: fix tutorial plot layout

* docs: resolve tutorial preview issues

Author: cncastillo

docs/EmbeddPlotlyJSSyncPlotLiterate.jl

@@ -21,13 +21,17 @@ function Base.show(io::IO, ::MIME"text/html", fig::PlotlyJS.SyncPlot)
     # Copy is required because we pop layout width/height for Plotly's inner JSON.
     # Mutating fig.plot directly would change size(fig) and user-visible behavior.
     plot = copy(fig.plot)
+    plot.frames = fig.plot.frames
+    plot.config = deepcopy(fig.plot.config)
+    plot.config.displayModeBar = false
     default_width = layout_to_html_default_size!(plot.layout.fields, :width, get(plot.layout.fields, :width, nothing))
     default_height = layout_to_html_default_size!(plot.layout.fields, :height, get(plot.layout.fields, :height, nothing))
 
     html_buffer = IOBuffer()
     PlotlyJS.PlotlyBase.to_html(
         html_buffer,
         plot;
+        autoplay=false,
         full_html=true,
         include_plotlyjs="cdn",
         default_width=default_width,

examples/3.tutorials/adiabatic_pulses/BIR4.mat

@@ -8,8 +8,22 @@ sys = Scanner(); #hide
 obj = brain_phantom2D() # a slice of a brain
 p1 = plot_phantom_map(obj, :T2 ; height=400, width=400, view_2d=true)
 p2 = plot_phantom_map(obj, :Δw ; height=400, width=400, view_2d=true)
-#md [p1 p2] #hide
-#jl display([p1 p2])
+p = [p1 p2] #hide
+p.plot.layout.fields[:xaxis2][:scaleanchor] = "y2" #hide
+p.plot.layout.fields[:xaxis1][:domain] = [0.0, 0.40] #hide
+p.plot.layout.fields[:xaxis2][:domain] = [0.58, 0.98] #hide
+for axis in (:xaxis1, :yaxis1, :xaxis2, :yaxis2) #hide
+    p.plot.layout.fields[axis][:title] = "" #hide
+    p.plot.layout.fields[axis][:ticks] = "" #hide
+    p.plot.layout.fields[axis][:showticklabels] = false #hide
+end #hide
+for (trace, x) in zip(p.plot.data, (0.43, 1.02)) #hide
+    trace.fields[:marker][:colorbar][:x] = x #hide
+    trace.fields[:marker][:colorbar][:len] = 0.55 #hide
+    trace.fields[:marker][:colorbar][:thickness] = 14 #hide
+end #hide
+#md p #hide
+#jl display(p)
 
 # At the left, you can see the ``T_2`` map of the phantom,
 # and at the right, the off-resonance ``\Delta\omega``.

examples/3.tutorials/adiabatic_pulses/BIR4InversionB0B1.jl

@@ -47,6 +47,7 @@ p3 = plot_signal(raw; slider=false, height=300)
 # Finally, we reconstruct the acquiered images.
 
 ## Get the acquisition data
+raw.params["trajectory"] = "other"
 acq = AcquisitionData(raw)
 
 ## Setting up the reconstruction parameters and perform reconstruction
@@ -58,5 +59,15 @@ image = reconstruction(acq, reconParams)
 p4 = plot_image(abs.(image[:, :, 1]); height=360, title="Slice 1")
 p5 = plot_image(abs.(image[:, :, 2]); height=360, title="Slice 2")
 p6 = plot_image(abs.(image[:, :, 3]); height=360, title="Slice 3")
-#md [p4 p5 p6] #hide
-#jl display([p4 p5 p6])
+p = [p4 p5 p6] #hide
+foreach(t -> t.fields[:showscale] = false, p.plot.data) #hide
+for (i, xref) in enumerate(("x", "x2", "x3")) #hide
+    xaxis = Symbol("xaxis", i) #hide
+    yaxis = Symbol("yaxis", i) #hide
+    p.plot.layout.fields[yaxis][:scaleanchor] = xref #hide
+    p.plot.layout.fields[yaxis][:constrain] = "domain" #hide
+    p.plot.layout.fields[xaxis][:range] = [-0.5, Nx - 0.5] #hide
+    p.plot.layout.fields[yaxis][:range] = [-0.5, Ny - 0.5] #hide
+end #hide
+#md p #hide
+#jl display(p)