Update Docs

KomaMRIBase/src/datatypes/sequence/ADC.jl

@@ -94,31 +94,32 @@ function get_adc_sampling_times(seq)
 end
 
 """
-    phase = get_adc_phase_compensation(seq)
+    comp = get_adc_phase_compensation(seq)
 
-Returns the array of phases for every acquired sample in the sequence `seq`.
-
-!!! note
-    This function is useful to compensate the phase when the RF pulse has a phase too. Refer
-    to the end of the [`run_sim_time_iter`](@ref) function to see its usage.
+Returns an array of phase compensation factors, ``\\exp(-\\mathrm{i}\\varphi)``, which are
+used to compensate the acquired signal ``S`` by applying the operation
+``S_{\\mathrm{comp}} = S \\exp(-\\mathrm{i}\\varphi)`` after the simulation. This compensation
+is necessary because the signal typically exhibits a phase offset of ``\\varphi`` following
+RF excitation with a phase of ``\\varphi``. Such pulses are commonly employed in sequences
+involving RF spoiling.
 
 # Arguments
 - `seq`: (`::Sequence`) sequence struct
 
 # Returns
-- `phase`: (`::Vector{Complex{Int64}}`, `[rad]`) array of phases for every acquired sample
+- `comp`: (`::Vector{Complex}`, `[rad]`) array of phase compensations for every acquired sample
 """
 function get_adc_phase_compensation(seq)
-  phase = ComplexF32[]
-  for i = 1:length(seq)
-      if is_ADC_on(seq[i])
-          N = seq.ADC[i].N
-          ϕ = seq.ADC[i].ϕ
-          aux = ones(N) .* exp(-1im*ϕ)
-          append!(phase, aux)
-      end
-  end
-  return phase
+    phase = ComplexF32[]
+    for i = 1:length(seq)
+        if is_ADC_on(seq[i])
+            N = seq.ADC[i].N
+            ϕ = seq.ADC[i].ϕ
+            aux = ones(N) .* exp(-1im*ϕ)
+            append!(phase, aux)
+        end
+    end
+    return phase
 end
 
 dur(adc::ADC) = adc.delay + adc.T

KomaMRICore/Project.toml

@@ -1,7 +1,7 @@
 name = "KomaMRICore"
 uuid = "4baa4f4d-2ae9-40db-8331-a7d1080e3f4e"
 authors = ["Carlos Castillo Passi <[email protected]>"]
-version = "0.8.1"
+version = "0.8.2"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

KomaMRIPlots/src/ui/DisplayFunctions.jl

@@ -171,55 +171,102 @@ function plot_seq(
     usadc(x) = show_adc || isempty(x) ? x : [first(x); last(x)]
     # Get the samples of the events in the sequence
     seq_samples = (get_samples(seq, i; freq_in_phase) for i in 1:length(seq))
-    gx  = (A=reduce(vcat, [block.gx.A; Inf]        for block in seq_samples),
-           t=reduce(vcat, [block.gx.t; Inf]        for block in seq_samples))
-    gy  = (A=reduce(vcat, [block.gy.A; Inf]        for block in seq_samples),
-           t=reduce(vcat, [block.gy.t; Inf]        for block in seq_samples))
-    gz  = (A=reduce(vcat, [block.gz.A; Inf]        for block in seq_samples),
-           t=reduce(vcat, [block.gz.t; Inf]        for block in seq_samples))
-    rf  = (A=reduce(vcat, [usrf(block.rf.A); Inf]  for block in seq_samples),
-           t=reduce(vcat, [usrf(block.rf.t); Inf]  for block in seq_samples))
-    Δf  = (A=reduce(vcat, [usrf(block.Δf.A); Inf]  for block in seq_samples),
-           t=reduce(vcat, [usrf(block.Δf.t); Inf]  for block in seq_samples))
-    adc = (A=reduce(vcat, [usadc(block.adc.A); Inf]       for block in seq_samples),
-           t=reduce(vcat, [usadc(block.adc.t); Inf]       for block in seq_samples))
+    gx = (
+        A=reduce(vcat, [block.gx.A; Inf] for block in seq_samples),
+        t=reduce(vcat, [block.gx.t; Inf] for block in seq_samples),
+    )
+    gy = (
+        A=reduce(vcat, [block.gy.A; Inf] for block in seq_samples),
+        t=reduce(vcat, [block.gy.t; Inf] for block in seq_samples),
+    )
+    gz = (
+        A=reduce(vcat, [block.gz.A; Inf] for block in seq_samples),
+        t=reduce(vcat, [block.gz.t; Inf] for block in seq_samples),
+    )
+    rf = (
+        A=reduce(vcat, [usrf(block.rf.A); Inf] for block in seq_samples),
+        t=reduce(vcat, [usrf(block.rf.t); Inf] for block in seq_samples),
+    )
+    Δf = (
+        A=reduce(vcat, [usrf(block.Δf.A); Inf] for block in seq_samples),
+        t=reduce(vcat, [usrf(block.Δf.t); Inf] for block in seq_samples),
+    )
+    adc = (
+        A=reduce(vcat, [usadc(block.adc.A); Inf] for block in seq_samples),
+        t=reduce(vcat, [usadc(block.adc.t); Inf] for block in seq_samples),
+    )
 
     # Define general params and the vector of plots
     idx = ["Gx" "Gy" "Gz"]
-	O = size(seq.RF, 1)
-	p = [scatter_fun() for _ in 1:(3 + 3O + 1)]
+    O = size(seq.RF, 1)
+    p = [scatter_fun() for _ in 1:(3 + 3O + 1)]
 
     # For GRADs
-	p[1] = scatter(x=gx.t*1e3, y=gx.A*1e3, name=idx[1], hovertemplate="(%{x:.4f} ms, %{y:.2f} mT/m)",
+    fgx = is_Gy_on(seq) ? 1.0 : Inf
+    fgy = is_Gx_on(seq) ? 1.0 : Inf
+    fgz = is_Gz_on(seq) ? 1.0 : Inf
+	p[1] = scatter(x=gx.t*1e3, y=gx.A*1e3*fgx, name=idx[1], hovertemplate="(%{x:.4f} ms, %{y:.2f} mT/m)",
 		    xaxis=xaxis, yaxis=yaxis, legendgroup="Gx", showlegend=showlegend, marker=attr(color="#636EFA"))
-	p[2] = scatter(x=gy.t*1e3, y=gy.A*1e3, name=idx[2], hovertemplate="(%{x:.4f} ms, %{y:.2f} mT/m)",
+    p[2] = scatter(x=gy.t*1e3, y=gy.A*1e3*fgy, name=idx[2], hovertemplate="(%{x:.4f} ms, %{y:.2f} mT/m)",
 			xaxis=xaxis, yaxis=yaxis, legendgroup="Gy", showlegend=showlegend, marker=attr(color="#EF553B"))
-	p[3] = scatter(x=gz.t*1e3, y=gz.A*1e3, name=idx[3], hovertemplate="(%{x:.4f} ms, %{y:.2f} mT/m)",
+    p[3] = scatter(x=gz.t*1e3, y=gz.A*1e3*fgz, name=idx[3], hovertemplate="(%{x:.4f} ms, %{y:.2f} mT/m)",
 			xaxis=xaxis, yaxis=yaxis, legendgroup="Gz", showlegend=showlegend, marker=attr(color="#00CC96"))
 
 	# For RFs
-	for j in 1:O
-        rf_amp = abs.(rf.A[:,j])
-        rf_phase = angle.(rf.A[:,j])
+    frf = is_RF_on(seq) ? 1.0 : Inf
+    for j in 1:O
+        rf_amp = abs.(rf.A[:, j])
+        rf_phase = angle.(rf.A[:, j])
         rf_phase[rf_amp .== Inf] .= Inf # Avoid weird jumps
         # Plot RF
-		p[2j-1+3] = scatter_fun(x=rf.t*1e3, y=rf_amp*1e6, name="|B1|_AM", hovertemplate="(%{x:.4f} ms, %{y:.2f} μT)",
+		p[2j-1+3] = scatter_fun(x=rf.t*1e3, y=rf_amp*1e6*frf, name="|B1|_AM", hovertemplate="(%{x:.4f} ms, %{y:.2f} μT)",
 					xaxis=xaxis, yaxis=yaxis, legendgroup="|B1|_AM", showlegend=showlegend, marker=attr(color="#AB63FA"))
-		p[2j+3] = scatter_fun(x=rf.t*1e3, y=rf_phase, text=ones(size(rf.t)), name="∠B1_AM", hovertemplate="(%{x:.4f} ms, ∠B1: %{y:.4f} rad)", visible="legendonly",
+        p[2j+3] = scatter_fun(x=rf.t*1e3, y=rf_phase*frf, text=ones(size(rf.t)), name="∠B1_AM", hovertemplate="(%{x:.4f} ms, ∠B1: %{y:.4f} rad)", visible="legendonly",
 					xaxis=xaxis, yaxis=yaxis, legendgroup="∠B1_AM", showlegend=showlegend, marker=attr(color="#FFA15A"))
         if !freq_in_phase
-            p[2j+4] = scatter_fun(x=Δf.t*1e3, y=Δf.A[:,j]*1e-3, text=ones(size(Δf.t)), name="B1_FM", hovertemplate="(%{x:.4f} ms, B1_FM: %{y:.4f} kHz)", visible="legendonly",
-                    xaxis=xaxis, yaxis=yaxis, legendgroup="B1_FM", showlegend=showlegend, marker=attr(color="#AB63FA"), line=attr(dash="dot"))
+            p[2j + 4] = scatter_fun(;
+                x=Δf.t * 1e3,
+                y=Δf.A[:, j] * 1e-3 * frf,
+                text=ones(size(Δf.t)),
+                name="B1_FM",
+                hovertemplate="(%{x:.4f} ms, B1_FM: %{y:.4f} kHz)",
+                visible="legendonly",
+                xaxis=xaxis,
+                yaxis=yaxis,
+                legendgroup="B1_FM",
+                showlegend=showlegend,
+                marker=attr(; color="#AB63FA"),
+                line=attr(; dash="dot"),
+            )
         end
-	end
+    end
 
-	# For ADCs
-	p[3O+3+1] = scatter_fun(x=adc.t*1e3, y=adc.A*0, name="ADC", hovertemplate="(%{x:.4f} ms, %{y:i})",
-				xaxis=xaxis, yaxis=yaxis, legendgroup="ADC", showlegend=showlegend, mode=(show_adc ? "markers" : "line"), marker=attr(color="#19D3F3"))
+    # For ADCs
+    fa = is_ADC_on(seq) ? 0.0 : Inf
+    p[3O + 3 + 1] = scatter_fun(;
+        x=adc.t * 1e3,
+        y=adc.A * fa,
+        name="ADC",
+        hovertemplate="(%{x:.4f} ms, %{y:i})",
+        xaxis=xaxis,
+        yaxis=yaxis,
+        legendgroup="ADC",
+        showlegend=showlegend,
+        mode=(show_adc ? "markers" : "line"),
+        marker=attr(; color="#19D3F3"),
+    )
 
     # Return the plot
-	l, config = generate_seq_time_layout_config(title, width, height, range, slider, show_seq_blocks, darkmode; T0=get_block_start_times(seq))
-	return plot_koma(p, l; config)
+    l, config = generate_seq_time_layout_config(
+        title,
+        width,
+        height,
+        range,
+        slider,
+        show_seq_blocks,
+        darkmode;
+        T0=get_block_start_times(seq))
+    return plot_koma(p, l; config)
 end
 
 """

Project.toml

@@ -1,7 +1,7 @@
 name = "KomaMRI"
 uuid = "6a340f8b-2cdf-4c04-99be-4953d9b66d0a"
 authors = ["Carlos Castillo Passi <[email protected]>"]
-version = "0.8.0"
+version = "0.8.1"
 
 [deps]
 AssetRegistry = "bf4720bc-e11a-5d0c-854e-bdca1663c893"

docs/Project.toml

@@ -5,4 +5,4 @@ Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
 
 [compat]
-Documenter = "0.27"
+Documenter = "1"

docs/src/api.md

@@ -76,6 +76,7 @@ Scanner
 Phantom
 brain_phantom2D
 brain_phantom3D
+pelvis_phantom2D
 ```
 
 ### `Sequence`
@@ -127,11 +128,21 @@ roty
 rotz
 ```
 
+### `get_Mk`
+```@docs
+get_Mk
+```
+
 ### `get_kspace`
 ```@docs
 get_kspace
 ```
 
+### `get_M0`
+```@docs
+get_M0
+```
+
 ### `get_M1`
 ```@docs
 get_M1
@@ -157,11 +168,85 @@ is_RF_on
 is_GR_on
 ```
 
+### `is_Gx_on`
+```@docs
+is_Gx_on
+```
+
+### `is_Gy_on`
+```@docs
+is_Gy_on
+```
+
+### `is_Gz_on`
+```@docs
+is_Gz_on
+```
+
 ### `is_ADC_on`
 ```@docs
 is_ADC_on
 ```
 
+## Sampling-related Functions
+
+### `get_samples`
+```@docs
+get_samples
+```
+
+### `get_adc_sampling_times`
+```@docs
+get_adc_sampling_times
+```
+
+### `get_adc_phase_compensation`
+```@docs
+get_adc_phase_compensation
+```
+
+### `get_block_start_times`
+```@docs
+get_block_start_times
+```
+
+### `DiscreteSequence`
+```@docs
+DiscreteSequence
+```
+
+### `discretize`
+```@docs
+discretize
+```
+
+## Sampling Miscellaneous
+
+### `trapz`
+```@docs
+trapz
+```
+
+### `cumtrapz`
+```@docs
+cumtrapz
+```
+
+### `kfoldperm`
+```@docs
+kfoldperm
+```
+
+### `ampl`
+```@docs
+ampl
+```
+
+### `time`
+```@docs
+time
+```
+
 
 ## Prebuilt Sequence Building Blocks
 
@@ -281,6 +366,38 @@ signal_to_raw_data
 Mag
 ```
 
+## Simulation Miscellaneous
+
+### `Spinor`
+```@docs
+Spinor
+```
+
+### `Q`
+```@docs
+Q
+```
+
+### `Un`
+```@docs
+Un
+```
+
+### `Rx`
+```@docs
+Rx
+```
+
+### `Ry`
+```@docs
+Ry
+```
+
+### `Rz`
+```@docs
+Rz
+```
+
 
 ## Plots