diff --git a/REQUIRE b/REQUIRE index 22f785ac..2f70e7f9 100644 --- a/REQUIRE +++ b/REQUIRE @@ -9,3 +9,4 @@ Measures Showoff StatsBase 0.14.0 JSON +NaNMath diff --git a/src/Plots.jl b/src/Plots.jl index 7e630ad7..4842a039 100644 --- a/src/Plots.jl +++ b/src/Plots.jl @@ -10,6 +10,7 @@ using Base.Meta @reexport using PlotThemes import Showoff import StatsBase +import NaNMath # define functions that ignores NaNs. To overcome the destructive effects of https://github.com/JuliaLang/julia/pull/12563 export grid, diff --git a/src/axes.jl b/src/axes.jl index a5882d9a..0d855190 100644 --- a/src/axes.jl +++ b/src/axes.jl @@ -118,7 +118,7 @@ Base.show(io::IO, axis::Axis) = dumpdict(axis.d, "Axis", true) # Base.getindex(axis::Axis, k::Symbol) = getindex(axis.d, k) Base.setindex!(axis::Axis, v, ks::Symbol...) = setindex!(axis.d, v, ks...) Base.haskey(axis::Axis, k::Symbol) = haskey(axis.d, k) -Base.extrema(axis::Axis) = (ex = axis[:extrema]; (ex.emin, ex.emax)) +NaNMath.extrema(axis::Axis) = (ex = axis[:extrema]; (ex.emin, ex.emax)) const _scale_funcs = Dict{Symbol,Function}( @@ -260,8 +260,8 @@ end function expand_extrema!(ex::Extrema, v::Number) - ex.emin = min(v, ex.emin) - ex.emax = max(v, ex.emax) + ex.emin = NaNMath.min(v, ex.emin) + ex.emax = NaNMath.max(v, ex.emax) ex end @@ -276,8 +276,8 @@ expand_extrema!(axis::Axis, ::Bool) = axis[:extrema] function expand_extrema!{MIN<:Number,MAX<:Number}(axis::Axis, v::Tuple{MIN,MAX}) ex = axis[:extrema] - ex.emin = min(v[1], ex.emin) - ex.emax = max(v[2], ex.emax) + ex.emin = NaNMath.min(v[1], ex.emin) + ex.emax = NaNMath.max(v[2], ex.emax) ex end function expand_extrema!{N<:Number}(axis::Axis, v::AVec{N}) @@ -349,11 +349,11 @@ function expand_extrema!(sp::Subplot, d::KW) bw = d[:bar_width] if bw == nothing - bw = d[:bar_width] = mean(diff(data)) + bw = d[:bar_width] = NaNMath.mean(diff(data)) end axis = sp.attr[Symbol(dsym, :axis)] - expand_extrema!(axis, maximum(data) + 0.5maximum(bw)) - expand_extrema!(axis, minimum(data) - 0.5minimum(bw)) + expand_extrema!(axis, NaNMath.maximum(data) + 0.5maximum(bw)) + expand_extrema!(axis, NaNMath.minimum(data) - 0.5minimum(bw)) end end @@ -368,8 +368,8 @@ end # push the limits out slightly function widen(lmin, lmax) span = lmax - lmin - # eps = max(1e-16, min(1e-2span, 1e-10)) - eps = max(1e-16, 0.03span) + # eps = NaNMath.max(1e-16, min(1e-2span, 1e-10)) + eps = NaNMath.max(1e-16, 0.03span) lmin-eps, lmax+eps end @@ -425,7 +425,7 @@ function discrete_value!(axis::Axis, dv) # @show axis[:discrete_map], axis[:discrete_values], dv if cv_idx == -1 ex = axis[:extrema] - cv = max(0.5, ex.emax + 1.0) + cv = NaNMath.max(0.5, ex.emax + 1.0) expand_extrema!(axis, cv) push!(axis[:discrete_values], dv) push!(axis[:continuous_values], cv) diff --git a/src/backends/glvisualize.jl b/src/backends/glvisualize.jl index f5168e16..c09fcab0 100644 --- a/src/backends/glvisualize.jl +++ b/src/backends/glvisualize.jl @@ -304,7 +304,7 @@ function extract_any_color(d, kw_args) kw_args[:color_norm] = Vec2f0(clims) end elseif clims == :auto - kw_args[:color_norm] = Vec2f0(extrema(d[:y])) + kw_args[:color_norm] = Vec2f0(NaNMath.extrema(d[:y])) end end else @@ -315,7 +315,7 @@ function extract_any_color(d, kw_args) kw_args[:color_norm] = Vec2f0(clims) end elseif clims == :auto - kw_args[:color_norm] = Vec2f0(extrema(d[:y])) + kw_args[:color_norm] = Vec2f0(NaNMath.extrema(d[:y])) else error("Unsupported limits: $clims") end @@ -367,14 +367,14 @@ end dist(a, b) = abs(a-b) -mindist(x, a, b) = min(dist(a, x), dist(b, x)) +mindist(x, a, b) = NaNMath.min(dist(a, x), dist(b, x)) function gappy(x, ps) n = length(ps) x <= first(ps) && return first(ps) - x for j=1:(n-1) p0 = ps[j] - p1 = ps[min(j+1, n)] + p1 = ps[NaNMath.min(j+1, n)] if p0 <= x && p1 >= x return mindist(x, p0, p1) * (isodd(j) ? 1 : -1) end @@ -482,7 +482,7 @@ function hover(to_hover, to_display, window) end function extract_extrema(d, kw_args) - xmin, xmax = extrema(d[:x]); ymin, ymax = extrema(d[:y]) + xmin, xmax = NaNMath.extrema(d[:x]); ymin, ymax = NaNMath.extrema(d[:y]) kw_args[:primitive] = GeometryTypes.SimpleRectangle{Float32}(xmin, ymin, xmax-xmin, ymax-ymin) nothing end @@ -509,7 +509,7 @@ function extract_colornorm(d, kw_args) else d[:y] end - kw_args[:color_norm] = Vec2f0(extrema(z)) + kw_args[:color_norm] = Vec2f0(NaNMath.extrema(z)) kw_args[:intensity] = map(Float32, collect(z)) end end @@ -781,7 +781,7 @@ function gl_bar(d, kw_args) # compute half-width of bars bw = nothing hw = if bw == nothing - mean(diff(x)) + NaNMath.mean(diff(x)) else Float64[cycle(bw,i)*0.5 for i=1:length(x)] end @@ -864,7 +864,7 @@ function gl_boxplot(d, kw_args) end # change q1 and q5 to show outliers # using maximum and minimum values inside the limits - q1, q5 = extrema(inside) + q1, q5 = NaNMath.extrema(inside) end # Box if notch @@ -1318,7 +1318,7 @@ function gl_contour(x, y, z, kw_args) T = eltype(z) levels = Contour.contours(map(T, x), map(T, y), z, h) result = Point2f0[] - zmin, zmax = get(kw_args, :limits, Vec2f0(extrema(z))) + zmin, zmax = get(kw_args, :limits, Vec2f0(NaNMath.extrema(z))) cmap = get(kw_args, :color_map, get(kw_args, :color, RGBA{Float32}(0,0,0,1))) colors = RGBA{Float32}[] for c in levels.contours @@ -1339,7 +1339,7 @@ end function gl_heatmap(x,y,z, kw_args) - get!(kw_args, :color_norm, Vec2f0(extrema(z))) + get!(kw_args, :color_norm, Vec2f0(NaNMath.extrema(z))) get!(kw_args, :color_map, Plots.make_gradient(cgrad())) delete!(kw_args, :intensity) I = GLVisualize.Intensity{1, Float32} diff --git a/src/backends/gr.jl b/src/backends/gr.jl index 9958e0a5..0c34b5d4 100644 --- a/src/backends/gr.jl +++ b/src/backends/gr.jl @@ -264,7 +264,7 @@ end normalize_zvals(zv::Void) = zv function normalize_zvals(zv::AVec) - vmin, vmax = extrema(zv) + vmin, vmax = NaNMath.extrema(zv) if vmin == vmax zeros(length(zv)) else @@ -428,7 +428,7 @@ function gr_set_viewport_polar() ymax -= 0.05 * (xmax - xmin) xcenter = 0.5 * (xmin + xmax) ycenter = 0.5 * (ymin + ymax) - r = 0.5 * min(xmax - xmin, ymax - ymin) + r = 0.5 * NaNMath.min(xmax - xmin, ymax - ymin) GR.setviewport(xcenter -r, xcenter + r, ycenter - r, ycenter + r) GR.setwindow(-1, 1, -1, 1) r @@ -639,7 +639,7 @@ function gr_display(sp::Subplot{GRBackend}, w, h, viewport_canvas) elseif ispolar(sp) r = gr_set_viewport_polar() - rmin, rmax = GR.adjustrange(minimum(r), maximum(r)) + rmin, rmax = GR.adjustrange(NaNMath.minimum(r), NaNMath.maximum(r)) # rmin, rmax = axis_limits(sp[:yaxis]) gr_polaraxes(rmin, rmax) @@ -824,7 +824,7 @@ function gr_display(sp::Subplot{GRBackend}, w, h, viewport_canvas) # create the colorbar of contour levels if sp[:colorbar] != :none gr_set_viewport_cmap(sp) - l = round(Int32, 1000 + (h - minimum(h)) / (maximum(h) - minimum(h)) * 255) + l = round(Int32, 1000 + (h - NaNMath.minimum(h)) / (NaNMath.maximum(h) - NaNMath.minimum(h)) * 255) GR.setwindow(xmin, xmax, zmin, zmax) GR.cellarray(xmin, xmax, zmax, zmin, 1, length(l), l) ztick = 0.5 * GR.tick(zmin, zmax) diff --git a/src/backends/inspectdr.jl b/src/backends/inspectdr.jl index c58ef884..18b5b541 100644 --- a/src/backends/inspectdr.jl +++ b/src/backends/inspectdr.jl @@ -349,7 +349,7 @@ function _inspectdr_setupsubplot(sp::Subplot{InspectDRBackend}) ymin, ymax = axis_limits(yaxis) if ispolar(sp) #Plots.jl appears to give (xmin,xmax) ≜ (Θmin,Θmax) & (ymin,ymax) ≜ (rmin,rmax) - rmax = max(abs(ymin), abs(ymax)) + rmax = NaNMath.max(abs(ymin), abs(ymax)) xmin, xmax = -rmax, rmax ymin, ymax = -rmax, rmax end diff --git a/src/backends/plotly.jl b/src/backends/plotly.jl index 814e4775..9232fb85 100644 --- a/src/backends/plotly.jl +++ b/src/backends/plotly.jl @@ -546,7 +546,7 @@ function plotly_series(plt::Plot, series::Series) else # grad = ColorGradient(series[:markercolor], alpha=series[:markeralpha]) grad = as_gradient(series[:markercolor], series[:markeralpha]) - zmin, zmax = extrema(series[:marker_z]) + zmin, zmax = NaNMath.extrema(series[:marker_z]) zrange = zmax == zmin ? 1 : zmax - zmin # if all marker_z values are the same, plot all markers same color (avoids division by zero in next line) [rgba_string(grad[(zi - zmin) / zrange]) for zi in series[:marker_z]] end diff --git a/src/backends/pyplot.jl b/src/backends/pyplot.jl index 69fbe426..49760a75 100644 --- a/src/backends/pyplot.jl +++ b/src/backends/pyplot.jl @@ -705,11 +705,11 @@ function py_add_series(plt::Plot{PyPlotBackend}, series::Series) # contours on the axis planes if series[:contours] for (zdir,mat) in (("x",x), ("y",y), ("z",z)) - offset = (zdir == "y" ? maximum : minimum)(mat) + offset = (zdir == "y" ? NaNMath.maximum : NaNMath.minimum)(mat) handle = ax[:contourf](x, y, z, levelargs...; zdir = zdir, cmap = py_fillcolormap(series), - offset = (zdir == "y" ? maximum : minimum)(mat) # where to draw the contour plane + offset = (zdir == "y" ? NaNMath.maximum : NaNMath.minimum)(mat) # where to draw the contour plane ) push!(handles, handle) needs_colorbar = true @@ -778,7 +778,7 @@ function py_add_series(plt::Plot{PyPlotBackend}, series::Series) end clims = sp[:clims] - zmin, zmax = extrema(z) + zmin, zmax = NaNMath.extrema(z) extrakw[:vmin] = (is_2tuple(clims) && isfinite(clims[1])) ? clims[1] : zmin extrakw[:vmax] = (is_2tuple(clims) && isfinite(clims[2])) ? clims[2] : zmax @@ -926,14 +926,14 @@ function py_compute_axis_minval(axis::Axis) for series in series_list(sp) v = series.d[axis[:letter]] if !isempty(v) - minval = min(minval, minimum(abs(v))) + minval = NaNMath.min(minval, NaNMath.minimum(abs(v))) end end end # now if the axis limits go to a smaller abs value, use that instead vmin, vmax = axis_limits(axis) - minval = min(minval, abs(vmin), abs(vmax)) + minval = NaNMath.min(minval, abs(vmin), abs(vmax)) minval end @@ -954,7 +954,7 @@ function py_set_scale(ax, axis::Axis) elseif scale == :log10 10 end - kw[Symbol(:linthresh,letter)] = max(1e-16, py_compute_axis_minval(axis)) + kw[Symbol(:linthresh,letter)] = NaNMath.max(1e-16, py_compute_axis_minval(axis)) "symlog" end func(arg; kw...) diff --git a/src/components.jl b/src/components.jl index b20eb3d0..4a11bd7e 100644 --- a/src/components.jl +++ b/src/components.jl @@ -501,7 +501,7 @@ immutable ZValues zrange::Tuple{Float64,Float64} end -function zvalues{T<:Real}(values::AVec{T}, zrange::Tuple{T,T} = (minimum(values), maximum(values))) +function zvalues{T<:Real}(values::AVec{T}, zrange::Tuple{T,T} = (NaNMath.minimum(values), NaNMath.maximum(values))) ZValues(collect(float(values)), map(Float64, zrange)) end @@ -645,8 +645,8 @@ function (bc::BezierCurve)(t::Real) p end -Base.mean(x::Real, y::Real) = 0.5*(x+y) -Base.mean{N,T<:Real}(ps::FixedSizeArrays.Vec{N,T}...) = sum(ps) / length(ps) +# mean(x::Real, y::Real) = 0.5*(x+y) #commented out as I cannot see this used anywhere and it overwrites a Base method with different functionality +# mean{N,T<:Real}(ps::FixedSizeArrays.Vec{N,T}...) = sum(ps) / length(ps) # I also could not see this used anywhere, and it's type piracy - implementing a NaNMath version for this would just involve converting to a standard array @deprecate curve_points coords @@ -659,7 +659,7 @@ function directed_curve(args...; kw...) end function extrema_plus_buffer(v, buffmult = 0.2) - vmin,vmax = extrema(v) + vmin,vmax = NaNMath.extrema(v) vdiff = vmax-vmin buffer = vdiff * buffmult vmin - buffer, vmax + buffer diff --git a/src/layouts.jl b/src/layouts.jl index a5814ba1..003c63c1 100644 --- a/src/layouts.jl +++ b/src/layouts.jl @@ -704,7 +704,7 @@ function link_axes!(axes::Axis...) a1 = axes[1] for i=2:length(axes) a2 = axes[i] - expand_extrema!(a1, extrema(a2)) + expand_extrema!(a1, NaNMath.extrema(a2)) for k in (:extrema, :discrete_values, :continuous_values, :discrete_map) a2[k] = a1[k] end diff --git a/src/pipeline.jl b/src/pipeline.jl index 70644055..3a68e4a4 100644 --- a/src/pipeline.jl +++ b/src/pipeline.jl @@ -153,7 +153,7 @@ function _add_smooth_kw(kw_list::Vector{KW}, kw::KW) if get(kw, :smooth, false) x, y = kw[:x], kw[:y] β, α = convert(Matrix{Float64}, [x ones(length(x))]) \ convert(Vector{Float64}, y) - sx = [minimum(x), maximum(x)] + sx = [NaNMath.minimum(x), NaNMath.maximum(x)] sy = β * sx + α push!(kw_list, merge(copy(kw), KW( :seriestype => :path, diff --git a/src/recipes.jl b/src/recipes.jl index d3fe10fa..68ffd407 100644 --- a/src/recipes.jl +++ b/src/recipes.jl @@ -225,7 +225,7 @@ end fr = if yaxis[:scale] == :identity 0.0 else - min(axis_limits(yaxis)[1], minimum(y)) + NaNMath.min(axis_limits(yaxis)[1], NaNMath.minimum(y)) end end newx, newy = zeros(3n), zeros(3n) @@ -338,7 +338,7 @@ end # compute half-width of bars bw = d[:bar_width] hw = if bw == nothing - 0.5mean(diff(procx)) + 0.5NaNMath.mean(diff(procx)) else Float64[0.5cycle(bw,i) for i=1:length(procx)] end @@ -366,7 +366,7 @@ end end # widen limits out a bit - expand_extrema!(axis, widen(extrema(xseg.pts)...)) + expand_extrema!(axis, widen(NaNMath.extrema(xseg.pts)...)) # switch back if !isvertical(d) @@ -414,8 +414,8 @@ end function _preprocess_binbarlike_weights{T<:AbstractFloat}(::Type{T}, w, wscale::Symbol) w_adj = _scale_adjusted_values(T, w, wscale) - w_min = minimum(w_adj) - w_max = maximum(w_adj) + w_min = NaNMath.minimum(w_adj) + w_max = NaNMath.maximum(w_adj) baseline = _binbarlike_baseline(w_min, wscale) w_adj, baseline end @@ -548,9 +548,9 @@ Plots.@deps stepbins path function _auto_binning_nbins{N}(vs::NTuple{N,AbstractVector}, dim::Integer; mode::Symbol = :auto) - _cl(x) = max(ceil(Int, x), 1) + _cl(x) = ceil(Int, NaNMath.max(x, one(x))) _iqr(v) = quantile(v, 0.75) - quantile(v, 0.25) - _span(v) = maximum(v) - minimum(v) + _span(v) = NaNMath.maximum(v) - NaNMath.minimum(v) n_samples = length(linearindices(first(vs))) # Estimator for number of samples in one row/column of bins along each axis: @@ -919,7 +919,7 @@ end # get the joined vector function get_xy(v::AVec{OHLC}, x = 1:length(v)) - xdiff = 0.3mean(abs(diff(x))) + xdiff = 0.3NaNMath.mean(abs(diff(x))) x_out, y_out = zeros(0), zeros(0) for (i,ohlc) in enumerate(v) ox,oy = get_xy(ohlc, x[i], xdiff) @@ -984,8 +984,8 @@ end yflip := true aspect_ratio := 1 rs, cs, zs = findnz(z.surf) - xlim := extrema(cs) - ylim := extrema(rs) + xlim := NaNMath.extrema(cs) + ylim := NaNMath.extrema(rs) if d[:markershape] == :none markershape := :circle end @@ -1006,7 +1006,7 @@ end "Adds a+bx... straight line over the current plot" function abline!(plt::Plot, a, b; kw...) - plot!(plt, [extrema(plt)...], x -> b + a*x; kw...) + plot!(plt, [NaNMath.extrema(plt)...], x -> b + a*x; kw...) end abline!(args...; kw...) = abline!(current(), args...; kw...) diff --git a/src/utils.jl b/src/utils.jl index f5ae3733..dddfdf19 100644 --- a/src/utils.jl +++ b/src/utils.jl @@ -3,7 +3,7 @@ calcMidpoints(edges::AbstractVector) = Float64[0.5 * (edges[i] + edges[i+1]) for "Make histogram-like bins of data" function binData(data, nbins) - lo, hi = extrema(data) + lo, hi = NaNMath.extrema(data) edges = collect(linspace(lo, hi, nbins+1)) midpoints = calcMidpoints(edges) buckets = Int[max(2, min(searchsortedfirst(edges, x), length(edges)))-1 for x in data] @@ -109,7 +109,7 @@ function regressionXY(x, y) β, α = convert(Matrix{Float64}, [x ones(length(x))]) \ convert(Vector{Float64}, y) # make a line segment - regx = [minimum(x), maximum(x)] + regx = [NaNMath.minimum(x), NaNMath.maximum(x)] regy = β * regx + α regx, regy end @@ -283,9 +283,9 @@ unzip{T}(xyuv::FixedSizeArrays.Vec{4,T}) = T[xyuv[1]], T[xyuv[2]], T[xyuv[ # given 2-element lims and a vector of data x, widen lims to account for the extrema of x function _expand_limits(lims, x) try - e1, e2 = extrema(x) - lims[1] = min(lims[1], e1) - lims[2] = max(lims[2], e2) + e1, e2 = NaNMath.extrema(x) + lims[1] = NaNMath.min(lims[1], e1) + lims[2] = NaNMath.max(lims[2], e2) # catch err # warn(err) end @@ -334,17 +334,17 @@ sortedkeys(d::Dict) = sort(collect(keys(d))) "create an (n+1) list of the outsides of heatmap rectangles" function heatmap_edges(v::AVec) - vmin, vmax = extrema(v) + vmin, vmax = NaNMath.extrema(v) extra = 0.5 * (vmax-vmin) / (length(v)-1) vcat(vmin-extra, 0.5 * (v[1:end-1] + v[2:end]), vmax+extra) end function calc_r_extrema(x, y) - xmin, xmax = extrema(x) - ymin, ymax = extrema(y) - r = 0.5 * min(xmax - xmin, ymax - ymin) - extrema(r) + xmin, xmax = NaNMath.extrema(x) + ymin, ymax = NaNMath.extrema(y) + r = 0.5 * NaNMath.min(xmax - xmin, ymax - ymin) + NaNMath.extrema(r) end function convert_to_polar(x, y, r_extrema = calc_r_extrema(x, y)) @@ -645,7 +645,7 @@ end # used in updating an existing series extendSeriesByOne(v::UnitRange{Int}, n::Int = 1) = isempty(v) ? (1:n) : (minimum(v):maximum(v)+n) -extendSeriesByOne(v::AVec, n::Integer = 1) = isempty(v) ? (1:n) : vcat(v, (1:n) + maximum(v)) +extendSeriesByOne(v::AVec, n::Integer = 1) = isempty(v) ? (1:n) : vcat(v, (1:n) + NaNMath.maximum(v)) extendSeriesData{T}(v::Range{T}, z::Real) = extendSeriesData(float(collect(v)), z) extendSeriesData{T}(v::Range{T}, z::AVec) = extendSeriesData(float(collect(v)), z) extendSeriesData{T}(v::AVec{T}, z::Real) = (push!(v, convert(T, z)); v) @@ -871,9 +871,9 @@ mm2px(mm::Real) = float(px / MM_PER_PX) "Smallest x in plot" -xmin(plt::Plot) = minimum([minimum(series.d[:x]) for series in plt.series_list]) +xmin(plt::Plot) = NaNMath.minimum([NaNMath.minimum(series.d[:x]) for series in plt.series_list]) "Largest x in plot" -xmax(plt::Plot) = maximum([maximum(series.d[:x]) for series in plt.series_list]) +xmax(plt::Plot) = NaNMath.maximum([NaNMath.maximum(series.d[:x]) for series in plt.series_list]) "Extrema of x-values in plot" -Base.extrema(plt::Plot) = (xmin(plt), xmax(plt)) +NaNMath.extrema(plt::Plot) = (xmin(plt), xmax(plt)) diff --git a/test/runtests.jl b/test/runtests.jl index 94f95a1b..d7d4441c 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -78,12 +78,12 @@ facts("Axes") do @fact typeof(axis) --> Plots.Axis @fact Plots.discrete_value!(axis, "HI") --> (0.5, 1) @fact Plots.discrete_value!(axis, :yo) --> (1.5, 2) - @fact extrema(axis) --> (0.5,1.5) + @fact Plots.NaNMath.extrema(axis) --> (0.5,1.5) @fact axis[:discrete_map] --> Dict{Any,Any}(:yo => 2, "HI" => 1) Plots.discrete_value!(axis, ["x$i" for i=1:5]) Plots.discrete_value!(axis, ["x$i" for i=0:2]) - @fact extrema(axis) --> (0.5, 7.5) + @fact Plots.NaNMath.extrema(axis) --> (0.5, 7.5) end