KomaMRIPlots

p = plot_phantom_map(obj::Phantom, key::Symbol; kwargs...)

Plots a phantom map for a specific spin parameter given by key.

Arguments

• obj: (::Phantom) Phantom struct
• key: (::Symbol, opts: [:ρ, :T1, :T2, :T2s, :x, :y, :z]) symbol for displaying different parameters of the phantom spins

Keywords

• height: (::Integer, =600) plot height
• width: (::Integer, =nothing) plot width
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style
• view_2d: (::Bool, =false) boolean to indicate whether to use a 2D scatter plot
• colorbar: (::Bool, =true) boolean to indicate whether to display a colorbar
• max_spins:(::Int, =100_000) maximum number of displayed spins
• time_samples:(::Int, =0) intermediate time samples between motion t_start and t_end
• max_time_samples:(::Int, =100) maximum number of time samples
• frame_duration_ms:(::Int, =250) time in miliseconds between two frames

Returns

• p: (::PlotlyJS.SyncPlot) plot of the phantom map for a specific spin parameter

References

Colormaps from https://github.com/markgriswold/MRFColormaps Towards Unified Colormaps for Quantitative MRF Data, Mark Griswold, et al. (2018).

Examples

julia> obj2D, obj3D = brain_phantom2D(), brain_phantom3D();

julia> plot_phantom_map(obj2D, :ρ)

julia> plot_phantom_map(obj3D, :ρ)

p = plot_seq(seq::Sequence; kwargs...)

Plots a sequence struct.

Arguments

• seq: (::Sequence) Sequence struct

Keywords

• width: (::Integer, =nothing) plot width
• height: (::Integer, =nothing) plot height
• slider: (::Bool, =true) boolean to indicate whether to display a slider
• show_seq_blocks: (::Bool, =false) boolean to indicate whether to display sequence blocks
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style
• range: (::Vector{Real}, =[]) time range to be displayed initially
• title: (::String, ="") plot title
• freq_in_phase: (::Bool, =true) Include FM modulation in RF phase
• gl: (::Bool, =false) use PlotlyJS.scattergl backend (faster)
• max_rf_samples: (::Integer, =100) maximum number of RF samples
• show_adc: (::Bool, =false) plot ADC samples with markers

Returns

• p: (::PlotlyJS.SyncPlot) plot of the Sequence struct

Examples

julia> seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/1.sequences/spiral.seq")

julia> seq = read_seq(seq_file)

julia> plot_seq(seq)

p = plot_kspace(seq::Sequence; width=nothing, height=nothing, darkmode=false)

Plots the k-space of a Sequence struct.

Arguments

• seq: (::Sequence) Sequence struct

Keywords

• width: (::Integer, =nothing) plot width
• height: (::Integer, =nothing) plot height
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style

Returns

• p: (::PlotlyJS.SyncPlot) plot of the k-space of the Sequence struct

Examples

julia> seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/1.sequences/spiral.seq")

julia> seq = read_seq(seq_file)

julia> plot_kspace(seq)

p = plot_M0(seq::Sequence; kwargs...)

Plots the zero order moment (M0) of a Sequence struct.

Arguments

• seq: (::Sequence) Sequence struct

Keywords

• width: (::Integer, =nothing) plot width
• height: (::Integer, =nothing) plot height
• slider: (::Bool, =true) boolean to indicate whether to display a slider
• show_seq_blocks: (::Bool, =false) boolean to indicate whether to display sequence blocks
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style
• range: (::Vector{Real}, =[]) time range to be displayed initially
• title: (::String, ="") plot title

Returns

• p: (::PlotlyJS.SyncPlot) plot of the moment M0 of the Sequence struct

Examples

julia> seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/1.sequences/spiral.seq")

julia> seq = read_seq(seq_file)

julia> plot_M0(seq)

p = plot_M1(seq::Sequence; kwargs...)

Plots the first order moment (M1) of a Sequence struct.

Arguments

• seq: (::Sequence) Sequence struct

Keywords

• width: (::Integer, =nothing) plot width
• height: (::Integer, =nothing) plot height
• slider: (::Bool, =true) boolean to indicate whether to display a slider
• show_seq_blocks: (::Bool, =false) boolean to indicate whether to display sequence blocks
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style
• range: (::Vector{Real}, =[]) time range to be displayed initially
• title: (::String, ="") plot title

Returns

• p: (::PlotlyJS.SyncPlot) plot of the moment M1 of the Sequence struct

Examples

julia> seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/1.sequences/spiral.seq")

julia> seq = read_seq(seq_file)

julia> plot_M1(seq)

p = plot_M2(seq::Sequence; kwargs...)

Plots the second order moment (M2) of a Sequence struct.

Arguments

• seq: (::Sequence) Sequence struct

Keywords

• width: (::Integer, =nothing) plot width
• height: (::Integer, =nothing) plot height
• slider: (::Bool, =true) boolean to indicate whether to display a slider
• show_seq_blocks: (::Bool, =false) boolean to indicate whether to display sequence blocks
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style
• range: (::Vector{Real}, =[]) time range to be displayed initially
• title: (::String, ="") plot title

Returns

• p: (::PlotlyJS.SyncPlot) plot of the moment M2 of the Sequence struct

Examples

julia> seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/1.sequences/spiral.seq")

julia> seq = read_seq(seq_file)

julia> plot_M2(seq)

p = plot_eddy_currents(seq::Sequence, λ; kwargs...)

Plots the eddy currents of a Sequence struct.

Arguments

• seq: (::Sequence) Sequence struct
• λ: (::Real, [s]) time constant for the decay of Eddy currents

Keywords

• α: (::Vector{Real}, =ones(size(λ))) eddy currents factors
• width: (::Integer, =nothing) plot width
• height: (::Integer, =nothing) plot height
• slider: (::Bool, =true) boolean to indicate whether to display a slider
• show_seq_blocks: (::Bool, =false) boolean to indicate whether to display sequence blocks
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style
• range: (::Vector{Real}, =[]) time range to be displayed initially
• title: (::String, ="") plot title

Returns

• p: (::PlotlyJS.SyncPlot) plot of the Eddy currents of the Sequence struct

Examples

julia> seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/1.sequences/spiral.seq")

julia> seq = read_seq(seq_file)

julia> plot_eddy_currents(seq, 80e-3)

p = plot_slew_rate(seq::Sequence; kwargs...)

Plots the slew rate currents of a Sequence struct.

Arguments

• seq: (::Sequence) Sequence struct

Keywords

• width: (::Integer, =nothing) plot width
• height: (::Integer, =nothing) plot height
• slider: (::Bool, =true) boolean to indicate whether to display a slider
• show_seq_blocks: (::Bool, =false) boolean to indicate whether to display sequence blocks
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style
• range: (::Vector{Real}, =[]) time range to be displayed initially
• title: (::String, ="") plot title

Returns

• p: (::PlotlyJS.SyncPlot) plot of the slew rate currents of the Sequence struct

Examples

julia> seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/1.sequences/spiral.seq")

julia> seq = read_seq(seq_file)

julia> plot_slew_rate(seq)

p = plot_seqd(seq::Sequence; sampling_params=KomaMRIBase.default_sampling_params())

Plots a sampled sequence struct.

Arguments

• seq: (::Sequence) Sequence struct

Keywords

• sampling_params: (::Dict{String,Any}(), =KomaMRIBase.default_sampling_params()) dictionary of sampling parameters

Returns

• p: (::PlotlyJS.SyncPlot) plot of the sampled Sequence struct

Examples

julia> seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/1.sequences/spiral.seq")

julia> seq = read_seq(seq_file)

julia> plot_seqd(seq)

p = plot_signal(raw::RawAcquisitionData; kwargs...)

Plots a raw signal in ISMRMRD format.

Arguments

• raw: (::RawAcquisitionData) RawAcquisitionData struct (raw signal in ISMRMRD format)

Keywords

• width: (::Integer, =nothing) plot width
• height: (::Integer, =nothing) plot height
• slider: (::Bool, =true) boolean to indicate whether to display a slider
• show_sim_blocks: (::Bool, =false) boolean to indicate whether to display sequence blocks
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style
• range: (::Vector{Real}, =[]) time range to be displayed initially

Returns

• p: (::PlotlyJS.SyncPlot) plot of the raw signal

Examples

julia> seq_file = joinpath(dirname(pathof(KomaMRI)), "../examples/5.koma_paper/comparison_accuracy/sequences/EPI/epi_100x100_TE100_FOV230.seq");

julia> sys, obj, seq = Scanner(), brain_phantom2D(), read_seq(seq_file)

julia> raw = simulate(obj, seq, sys)

julia> plot_signal(raw)

p = plot_image(image; height, width, zmin, zmax, darkmode, title)

Plots an image matrix.

Arguments

• image: (::Matrix{Number}) image matrix

Keywords

• width: (::Integer, =nothing) plot width
• height: (::Integer, =nothing) plot height
• zmin: (::Real, =minimum(abs.(image[:]))) reference value for minimum color
• zmax: (::Real, =maximum(abs.(image[:]))) reference value for maximum color
• darkmode: (::Bool, =false) boolean to indicate whether to display darkmode style
• title: (::String, ="") plot title

Returns

• p: (::PlotlyJS.SyncPlot) plot of the image matrix

str = plot_dict(dict::Dict)

Generates an HTML table based on the dictionary dict.

Arguments

• dict: (::Dict) dictionary

Returns

• str: (::String) dictionary as an HTML table