IMASggd.jl

interp(
    prop_values::Vector{T},
    kdtree::KDTree;
    use_nearest_n::Int=4,
    weighing::Function=(d) -> 1 / d,
) where {T <: Real}

Lowest level interpolation function. It takes a vector of property values and a KDTree defined over a 2D space with the same number of nodes as the property values. It returns a function that can be used to interpolate the property values at any point in the space.

interp(
    y::Vector{T},
    TPS_mats::Tuple{Matrix{U}, Matrix{U}, Matrix{U}, Vector{Tuple{U, U}}},
) where {T <: Real, U <: Real}

Lowest level function for Thin Plate Spline method

interp(y::Vector{T}, x::Vector{Tuple{U, U}}) where {T <: Real, U <: Real}

Thin plate smoothing interpolation function for a 2d space scalar function. The algorithm has been adopted from:

http://www.geometrictools.com/Documentation/ThinPlateSplines.pdf

This is an implementation of Euler-Lagrange equation for minimizing bending energy of a surface.

interp(
    prop_values::Vector{T},
    space::IMASdd.edge_profiles__grid_ggd___space
) where {T <: Real}

If the whole space is provided instead of a kdtree, calculate the kdtree for whole space. Again, here it is assumed that the property values are porvided for each node of the space.

interp(
    prop_values::Vector{Real},
    space::IMASdd.edge_profiles__grid_ggd___space,
    subset::IMASdd.edge_profiles__grid_ggd___grid_subset
)

If a subset of the space is provided, calculate the kdtree for the subset. In this case it is assumed that the property values are provided for each element of the subset.

interp(
    prop::edge_profiles__prop_on_subset,
    grid_ggd::IMASdd.edge_profiles__grid_ggd,
    value_field::Symbol=:values
)

Example:

grid_ggd = dd.edge_profiles.grid_ggd[1]
get_electron_density = interp(dd.edge_profiles.ggd[1].electrons.density[1], grid_ggd)
get_e_field_par = interp(dd.edge_profiles.ggd[1].e_field[1], grid_ggd, :parallel)

interp(
    prop_arr::AbstractVector{T},
    space::IMASdd.edge_profiles__grid_ggd___space,
    subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
    value_field::Symbol=:values
) where {T <: edge_profiles__prop_on_subset}

Example:

sol = get_grid_subset_with_index(dd.edge_profiles.grid_ggd[1], 23)
get_electron_density = interp(dd.edge_profiles.ggd[1].electrons.density, space, sol)

interp(
    prop_arr::AbstractVector{T},
    grid_ggd::IMASdd.edge_profiles__grid_ggd,
    grid_subset_index::Int,
    value_field::Symbol=:values
) where {T <: edge_profiles__prop_on_subset}

Example:

get_n_e_sep = interp(dd.edge_profiles.ggd[1].electrons.density, grid_ggd, 16)

interp(
    prop_arr::AbstractVector{T},
    TPS_mats::Tuple{Matrix{U}, Matrix{U}, Matrix{U}, Vector{Tuple{U, U}}},
    grid_subset_index::Int,
    value_field::Val{V}=Val(:values),
) where {T <: edge_profiles__prop_on_subset, U <: Real, V}

Same use case as above but allows one to reuse previously calculated TPS matrices.

Example:

TPS_mat = get_TPS_mats(dd.edge_profiles.grid_ggd[1], 5);

for it ∈ eachindex(dd.edge_profiles.ggd)
    get_n_e = interp(dd.edge_profiles.ggd[it].electrons.density, TPS_mat_sep, 5)
    println("This time step has n_e at (0, 0) = ", get_n_e(0, 0))
end

This will run faster as heavy matrix calculations will happen only once.

interp(eqt::IMASdd.equilibrium__time_slice)

For a given equilibrium time slice, return a function that can be used to interpolate from (r, z) space to rho (normalized toroidal flux coordinate)space.

Example:

rz2rho = interp(dd.equilibrium.time_slice[1])
rho = rz2rho.([(r, z) for r ∈ 3.0:0.01:9.0, z ∈ -5.0:0.01:5.0])

interp(
    prop::Vector{T},
    prof::IMASdd.core_profiles__profiles_1d,
) where {T <: Real}

Returns an inteprolation function for the core profile property values defined on normalized toroidal flux coordinate rho.

Example:

core_profile_n_e = dd.core_profiles.profiles_1d[1].electrons.density
get_n_e = interp(core_profile_n_e, dd.core_profiles.profiles_1d[1])
get_n_e(1) # Returns electron density at rho = 1 (separatix)

interp(
    prop::Vector{T},
    prof::IMASdd.core_profiles__profiles_1d,
    rz2rho::Function,
)

Returns an inteprolation function in (R, Z) domain for the core profile property values defined on normalized toroidal flux coordinate rho and with a provided function to convert (R,Z) to rho.

Example:

rz2rho = interp(dd.equilibrium.time_slice[1])
core_profile_n_e = dd.core_profiles.profiles_1d[1].electrons.density
get_n_e = interp(core_profile_n_e, dd.core_profiles.profiles_1d[1], rz2rho)
get_n_e(5.0, 3.5) # Returns electron density at (R, Z) = (5.0, 3.5)

interp(
    prop::Vector{T},
    prof::IMASdd.core_profiles__profiles_1d,
    eqt::IMASdd.equilibrium__time_slice,
) where {T <: Real}

Returns an inteprolation function in (R, Z) domain for the core profile property values defined on normalized toroidal flux coordinate rho and with a provided equilibrium time slice to get (R, Z) to rho conversion.

Example:

eqt = dd.equilibrium.time_slice[1]
core_profile_n_e = dd.core_profiles.profiles_1d[1].electrons.density
get_n_e = interp(core_profile_n_e, dd.core_profiles.profiles_1d[1], eqt)
get_n_e(5.0, 3.5) # Returns electron density at (R, Z) = (5.0, 3.5)

get_TPS_mats(x::Vector{Tuple{U, U}}) where {U <: Real}

We can separate matrix operations of thin plate spline method to utilize the calculation for itnerpolating over same space. Similar to the idea of reusing KDTree like above.

get_kdtree(space::IMASdd.edge_profiles__grid_ggd___space)

Get a KDTree for all the cells in the space for search for nearest neighbours.

get_kdtree(
    space::IMASdd.edge_profiles__grid_ggd___space,
    subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
)

Get a KDTree for a subset of the space for search for nearest neighbours.

add_subset_element!(
    subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
    sn::Int,
    dim::Int,
    index::Int,
    in_subset=(x...) -> true;
    kwargs...,
)

Adds a new element to girdsubset with properties space number (sn), dimension (dim), and index (index). The element is added only if the function insubset returns true.

add_subset_element!(
    subset,
    sn,
    dim,
    index::Vector{Int},
    in_subset=(x...) -> true;
    kwargs...,
)

Overloaded to work differently (faster) with list of indices to be added.

get_subset_space(
    space::IMASdd.edge_profiles__grid_ggd___space,
    elements::AbstractVector{<:IMASdd.edge_profiles__grid_ggd___grid_subset___element}
)

Returns an array of space object indices corresponding to the correct objectsperdimension (nodes, edges or cells) for the subset elements.

get_grid_subset(
    grid_ggd::IMASdd.edge_profiles__grid_ggd,
    grid_subset_index::Int,
)

Returns the gridsubset in a gridggd with the matching gridsubsetindex

get_grid_subset(
    grid_ggd::IMASdd.edge_profiles__grid_ggd,
    grid_subset_name::String,
)

Returns the gridsubset in a gridggd with the matching gridsubsetname

get_subset_boundary_inds(
    space::IMASdd.edge_profiles__grid_ggd___space,
    subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
)

Returns an array of space object indices corresponding to the boundary of the subset. That means, it returns indices of nodes that are at the end of open edge subset or it returns the indices of edges that are the the boundary of a cell subset. Returns an empty array if the subset is 1D (nodes).

get_subset_boundary(
    space::IMASdd.edge_profiles__grid_ggd___space,
    subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
)

Returns an array of elements of grid_subset generated from the boundary of the subset provided. The dimension of these elments is reduced by 1.

subset_do(
    set_operator,
    itrs::Vararg{
        AbstractVector{<:IMASdd.edge_profiles__grid_ggd___grid_subset___element},
    };
    space::IMASdd.edge_profiles__grid_ggd___space=IMASdd.edge_profiles__grid_ggd___space(),
    use_nodes=false
)

Function to perform any set operation (intersect, union, setdiff etc.) on subset.element to generate a list of elements to go to subset object. If usenodes is true, the set operation will be applied on the set of nodes from subset.element, space argument is required for this. Note: that the arguments are subset.element (not the subset itself). Similarly, the return object is a list of IMASdd.edgeprofiles__gridggd___gridsubset___element.

get_subset_centers(
    space::IMASdd.edge_profiles__grid_ggd___space,
    subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
)

Returns an array of tuples corresponding to (r,z) coordinates of the center of cells or the center of edges in the subset space.

project_prop_on_subset!(
    prop_arr::AbstractVector{T},
    from_subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
    to_subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
    space::IMASdd.edge_profiles__grid_ggd___space,
    value_field::Symbol=:values;
    TPS_mats::Union{
        Nothing,
        Tuple{Matrix{U}, Matrix{U}, Matrix{U}, Vector{Tuple{U, U}}},
    }=nothing,
) where {T <: edge_profiles__prop_on_subset, U <: Real}

This function can be used to add another instance on a property vector representing the value in a new subset that can be taken as a projection from an existing larger subset.

Input Arguments:

• prop: A property like electrons.density that is a vector of objects with fields coefficients, gridindex, gridsubsetindex, and values. The different instances in the vector correspond to different gridsubset for which the property is provided.
• fromsubset: gridsubset object which is already represented in the property instance. grid subset with index 5 is populated in electrons.density already if the values for all cells are present.
• tosubset: gridsubset which is either a smaller part of fromsubset (core, sol, idr, odr) but has same dimensions as fromsubset OR is smaller in dimension that goes through the fromsubset (coreboundary, separatix etc.)
• space: (optional) space object in gridggd is required only when fromsubset is higher dimensional than to_subset.

Returns: NOTE: This function ends in ! which means it updates prop argument in place. But for the additional utility, this function also returns a tuple (tosubsetcenters, topropvalues) when fromsubset dimension is greater than tosubset dimension OR (tosubseteleobjinds, topropvalues) when fromsubset dimension is same as tosubset dimension)

Descriptions: tosubsetcenters: center of cells or center of edges of the tosubset where property values are defined and stored tosubseteleobjinds: Indices of the elements of tosubset where property values are defined and stored topropvalues: The projected values of the properties added to prop object in a new instance

project_prop_on_subset!(
    prop_arr::AbstractVector{T},
    from_subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
    to_subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
    value_field::Symbol=:values,
) where {T <: edge_profiles__prop_on_subset}

If the dimensions of fromsubset and tosubset are the same, this function can be used to add another instance on a property vector representing the value in tosubset without any interpolation or use of space object. The function returns a tuple of indices of elements of tosubset and the values of the property in to_subset.

deepcopy_subset(subset::IMASdd.edge_profiles__grid_ggd___grid_subset)

Faster deepcopy function for gridsubset object. This function is used to create a deep copy of a gridsubset object bypassing several checks performed by IMASdd.

Base.:∈(
    point::Tuple{Real, Real},
    subset_of_space::Tuple{
        IMASdd.edge_profiles__grid_ggd___grid_subset,
        IMASdd.edge_profiles__grid_ggd___space,
    },
)

Overloading ∈ operator to check if a point is inside a subset of space.

If the subset is 1-dimensional, all points are searched. If the subset is 2-dimensional, it is checked if the point is within the enclosed area. It is assumed that a 2-dimensional subset used in such a context will form a closed area. If the subset is 3-dimensional, its boundary is calculated on the fly. If used multiple times, it is recommended to calculate the boundary once and store it in a variable.

Example:

if (5.5, 0.0) ∈ (subset_sol, space)
    println("Point (5.5, 0.0) is inside the SOL subset.")
else
    println("Point (5.5, 0.0) is outside the SOL subset.")
end

get_prop_with_grid_subset_index(
    prop::AbstractVector{T},
    grid_subset_index::Int,
) where {T <: edge_profiles__prop_on_subset}

Find the edgeprofiles property instance in an array of properties that corresponds to the gridsubset_index provided.

get_types_with(parent::Type, field::Symbol)

A type creation utility meant for searching types in IMAS database. This function returns a list of types that are fields at any level below the parent data type which have a particular field present in it.

Example:

get_types_with(IMASdd.edge_profiles, :grid_subset_index)

returns all edgeprofiles types that have a subfield named gridsubset_index.

plot(space::IMASdd.edge_profiles__grid_ggd___space)

Plot the grid_ggd space object. Defaults to size of [600, 900] and linecolor of :black, linewidth of 0.2, and no legend.

plot(
    space::IMASdd.edge_profiles__grid_ggd___space,
    subset::IMASdd.edge_profiles__grid_ggd___grid_subset,
)

Plot the a subset of a space. Defaults to size of [600, 900] and linecolor of :black, linewidth of 0.2, and no legend.

plot(
    grid_ggd::IMASdd.edge_profiles__grid_ggd,
    prop::IMASdd.IDSvectorElement,
)

Plot 2D heatmap of edgeprofilesggd property on a gridggd space object. Defaults to size of [635, 900], xaxis of "R / m", yaxis of "Z / m", and no legend. If :seriescolor is not provided, :inferno color scheme is used. If :colorbartitle is not provided, the property name is used. This function creates a plot with layout [a{0.95w} b] where a is the heatmap and b is the colorbar.

plot(
    grid_ggd_arr::AbstractVector{<:IMASdd.edge_profiles__grid_ggd},
    prop::IMASdd.IDSvectorElement,
)

Plot 2D heatmap of edgeprofilesggd property on a gridggd space object. Defaults to size of [635, 900], xaxis of "R / m", yaxis of "Z / m", and no legend. If :seriescolor is not provided, :inferno color scheme is used. If :colorbartitle is not provided, the property name is used. This function creates a plot with layout [a{0.95w} b] where a is the heatmap and b is the colorbar.

plot(
    ifo::IMASdd.interferometer,
)

Plot all the channels of interferometer object. Optional keywords:

• :plottype: :los(default), :ne, or :neaverage. :los plots the line of sight of the channel in a 2D plot, :ne plots the integrated ne along the line of sight vs time, and :neaverage plots the average n_e vs time.
• :mirror: true(default) or false.
• :mirror_length: 0.5(default).
• :mirror_thickness: 0.1(default).

plot(
    ifo_ch::IMASdd.interferometer__channel,
)

Plot individual channel of interferometer. Optional keywords:

• :plottype: :los(default), :ne, or :neaverage. :los plots the line of sight of the channel in a 2D plot, :ne plots the integrated ne along the line of sight vs time, and :neaverage plots the average n_e vs time.
• :mirror: true(default) or false.
• :mirror_length: 0.5(default).
• :mirror_thickness: 0.1(default).

plot(
    ifo_ch_los::IMASdd.interferometer__channel___line_of_sight,
)

Plot line of sight of a channel of interferometer.

Default plot settings:

• subplot: 1
• size: [600, 900]
• xaxis: "R / m"
• yaxis: "Z / m"

Optional keywords:

• :mirror: true(default) or false.
• :mirror_length: 0.5(default).
• :mirror_thickness: 0.1(default).

plot(
    ifo_ch_n_e_line::IMASdd.interferometer__channel___n_e_line,
)

Plot line integrated electron density of a channel of interferometer.

Default plot settings:

• subplot: 1
• xaxis: "time / s"
• yaxis: "Integerated n_e / m^-2"

Optional keywords:

• :average: true or false(default). If true, plot the average n_e vs time.

plot(
    ifo_ch_n_e_line_average::IMASdd.interferometer__channel___n_e_line_average,
)

Plot average electron density of a channel of interferometer.

Default plot settings:

• subplot: 1
• xaxis: "time / s"
• yaxis: "Average n_e / m^-3"