-
Notifications
You must be signed in to change notification settings - Fork 13
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #50 from kahaaga/kah/plotrecipes
Plot recipes
- Loading branch information
Showing
20 changed files
with
771 additions
and
371 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| if VERSION >= v"0.7.0-" | ||
| # Adding Pkg in test/REQUIRE would be an error in 0.6. Using | ||
| # Project.toml still has some gotchas. So: | ||
| Pkg = Base.require(Base.PkgId(Base.UUID(0x44cfe95a1eb252eab672e2afdf69b78f), "Pkg")) | ||
| end | ||
|
|
||
| # Let PyCall.jl use Python interpreter from Conda.jl | ||
| # See: https://github.com/JuliaPy/PyCall.jl | ||
| ENV["PYTHON"] = "" | ||
| Pkg.build("PyCall") | ||
|
|
||
| using Conda | ||
| Conda.add("scipy") |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| if lowercase(get(ENV, "CI", "false")) == "true" | ||
| include("install_dependencies.jl") | ||
| end | ||
|
|
||
| using TransferEntropy | ||
| using Test | ||
| using Distances | ||
|
|
||
|
|
||
| n_realizations = 50 | ||
|
|
||
| @testset "Visitation frequency estimator" begin | ||
| include("transferentropy/test_transferentropy_visitfreq.jl") | ||
| end | ||
|
|
||
| @testset "kNN (Kraskov) estimator" begin | ||
| include("transferentropy/test_transferentropy_kraskov.jl") | ||
| end | ||
|
|
||
| @testset "Transfer operator grid estimator" begin | ||
| include("transferentropy/test_transferentropy_transferoperator_grid.jl") | ||
| end |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,112 @@ | ||
| ######################################################### | ||
| # Helper functions to plot 3D rectangles. | ||
| ######################################################### | ||
| """ | ||
| rectangle3dpts(x, y, z, ϵx, ϵy, ϵz) | ||
| Compute the coordinates of the vertices of a 3D rectangle, given the | ||
| coordinates of the origin (`x`, `y`, and `z`) and the corresponding edge lengths | ||
| (`ϵx`, `ϵy`, `ϵz`). | ||
| """ | ||
| function rectangle3dpts(x, y, z, ϵx, ϵy, ϵz) | ||
| v1b = [x, y, z] | ||
| v2b = [x+ϵx, y, z] | ||
| v3b = [x+ϵx, y+ϵy, z] | ||
| v4b = [x, y+ϵy, z] | ||
| v1t = [x, y, z+ϵz] | ||
| v2t = [x+ϵx, y, z+ϵz] | ||
| v3t = [x+ϵx, y+ϵy, z+ϵz] | ||
| v4t = [x, y+ϵy, z+ϵz] | ||
| (v1b, v2b, v3b, v4b, v1t, v2t, v3t, v4t) | ||
| end | ||
|
|
||
| """ | ||
| rectangle3dpts(o, ϵ) | ||
| Given the origin `o` (3-element vector) and edge lengths `ϵ` (also a | ||
| 3-element vector) of a 3D rectangle, return the coordinates of its | ||
| vertices. | ||
| """ | ||
| function rectangle3dpts(o, ϵ) | ||
| x, y, z = (o...,) | ||
| ϵx, ϵy, ϵz = (ϵ...,) | ||
| rectangle3dpts(x, y, z, ϵx, ϵy, ϵz) | ||
| end | ||
|
|
||
| """ | ||
| connectvertices(o, ϵ) | ||
| Given the origin `o` (3-element vector) and edge lengths `ϵ` (also a | ||
| 3-element vector) of a 3D rectangle, return a vector of line segments | ||
| (each a dim-by-n_vertices array) that when plotted together yields | ||
| the entire rectangle. | ||
| """ | ||
| function connectvertices(o, ϵ) | ||
| # Get the vertices | ||
| v1b, v2b, v3b, v4b, v1t, v2t, v3t, v4t = rectangle3dpts(o, ϵ) | ||
|
|
||
| # Connect vertices in top and bottom planes | ||
| connect_top = zeros(3, 5) | ||
| connect_bottom = zeros(3, 5) | ||
|
|
||
| # Connect corners of the top and bottom planes | ||
| corner1 = zeros(3, 2) | ||
| corner2 = zeros(3, 2) | ||
| corner3 = zeros(3, 2) | ||
| corner4 = zeros(3, 2) | ||
| connect_bottom[:, 1:5] = [v1b v2b v3b v4b v1b] | ||
| connect_top[:, 1:5] = [v1t v2t v3t v4t v1t] | ||
| corner1[:, 1:2] = [v1b v1t] | ||
| corner2[:, 1:2] = [v2b v2t] | ||
| corner3[:, 1:2] = [v3b v3t] | ||
| corner4[:, 1:2] = [v4b v4t] | ||
|
|
||
| return [connect_top, connect_bottom, | ||
| corner1, corner2, corner3, corner4] | ||
| end | ||
|
|
||
| """ | ||
| splitaxes(x) | ||
| Return a vector of the individual components of an array of points | ||
| provided as an array where each point is a column. | ||
| """ | ||
| splitaxes(x) = ([x[k, :] for k = 1:size(x, 1)]...,) | ||
|
|
||
| """ | ||
| plot_3D_rect!(p, origin, edgelengths; | ||
| lc = :black, lw = 1.0, ls = :solid) | ||
| Append a a 3D rectangle to an existing plot `p`, given the | ||
| origin `o` (3-element vector) and edge lengths | ||
| `ϵ` (3-element vector) of the rectangle. | ||
| """ | ||
| function plot_3D_rect!(p, o, ϵ; | ||
| lc = :black, lw = 1.0, ls = :solid, lα = 0.7) | ||
|
|
||
| linesegments = connectvertices(o, ϵ) | ||
| for segment in linesegments | ||
| plot!(p, splitaxes(segment), | ||
| lc = lc, lw = lw, ls = ls, lα = lα) | ||
| end | ||
| end | ||
|
|
||
| """ | ||
| Given the `origin` of a hyperrectangle and the `stepsizes` along each | ||
| coordinate axis, divide each axis into `N` stepsizes starting | ||
| from `origin[i] + (stepsizes[i]/N)/2` | ||
| """ | ||
| function fill_hyperrectangle_3D(origin, stepsizes, N = 10) | ||
| xs, ys, zs = ([LinRange(origin[i] + stepsizes[i]/N/2, origin[i] + stepsizes[i] - stepsizes[i]/N/2, N) for i = 1:length(origin)]...,) | ||
| pts = zeros(Float64, 3, length(xs)^3) | ||
| i = 0 | ||
| for x in xs | ||
| for y in ys | ||
| for z in zs | ||
| i += 1 | ||
| pts[:, i] = [x, y, z] | ||
| end | ||
| end | ||
| end | ||
| pts | ||
| end |
Oops, something went wrong.