Merge remote-tracking branch 'JuliaPlots/master'

src/Plots.jl

@@ -1,4 +1,4 @@
-__precompile__(false)
+__precompile__(true)
 
 module Plots
 

src/arg_desc.jl

@@ -29,6 +29,7 @@ const _arg_desc = KW(
 :z                 	=> "Various. Input data. Third Dimension. May be wrapped by a `Surface` for surface and heatmap types.",
 :marker_z          	=> "AbstractVector, Function `f(x,y,z) -> z_value`, or nothing. z-values for each series data point, which correspond to the color to be used from a markercolor gradient.",
 :line_z          	=> "AbstractVector, Function `f(x,y,z) -> z_value`, or nothing. z-values for each series line segment, which correspond to the color to be used from a linecolor gradient.  Note that for N points, only the first N-1 values are used (one per line-segment).",
+:fill_z           => "Matrix{Float64} of the same size as z matrix, which specifies the color of the 3D surface; the default value is `nothing`.",
 :levels            	=> "Integer, NTuple{2,Integer}. Number of levels (or x-levels/y-levels) for a contour type.",
 :orientation       	=> "Symbol.  Horizontal or vertical orientation for bar types.  Values `:h`, `:hor`, `:horizontal` correspond to horizontal (sideways, anchored to y-axis), and `:v`, `:vert`, and `:vertical` correspond to vertical (the default).",
 :bar_position      	=> "Symbol.  Choose from `:overlay` (default), `:stack`.  (warning: May not be implemented fully)",

src/args.jl

@@ -188,6 +188,7 @@ const _series_defaults = KW(
     :z                 => nothing,   # depth for contour, surface, etc
     :marker_z          => nothing,   # value for color scale
     :line_z            => nothing,
+    :fill_z            => nothing,
     :levels            => 15,
     :orientation       => :vertical,
     :bar_position      => :overlay,  # for bar plots and histograms: could also be stack (stack up) or dodge (side by side)
@@ -431,6 +432,7 @@ add_aliases(:zguide, :zlabel, :zlab, :zl)
 add_aliases(:zlims, :zlim, :zlimit, :zlimits)
 add_aliases(:zticks, :ztick)
 add_aliases(:zrotation, :zrot, :zr)
+add_aliases(:fill_z, :fillz, :fz, :surfacecolor, :surfacecolour, :sc, :surfcolor, :surfcolour)
 add_aliases(:legend, :leg, :key)
 add_aliases(:colorbar, :cb, :cbar, :colorkey)
 add_aliases(:clims, :clim, :cbarlims, :cbar_lims, :climits, :color_limits)

src/backends.jl

@@ -276,6 +276,7 @@ end
 @init_backend GR
 @init_backend GLVisualize
 @init_backend PGFPlots
+@init_backend InspectDR
 
 # ---------------------------------------------------------
 

src/backends/inspectdr.jl

@@ -0,0 +1,531 @@
+
+# https://github.com/ma-laforge/InspectDR.jl
+
+#=TODO:
+    Tweak scale factor for width & other sizes
+
+Not supported by InspectDR:
+    :foreground_color_grid
+    :foreground_color_border
+    :polar,
+
+Add in functionality to Plots.jl:
+    :aspect_ratio,
+=#
+
+# ---------------------------------------------------------------------------
+#TODO: remove features
+const _inspectdr_attr = merge_with_base_supported([
+    :annotations,
+    :background_color_legend, :background_color_inside, :background_color_outside,
+    :foreground_color_grid, :foreground_color_legend, :foreground_color_title,
+    :foreground_color_axis, :foreground_color_border, :foreground_color_guide, :foreground_color_text,
+    :label,
+    :linecolor, :linestyle, :linewidth, :linealpha,
+    :markershape, :markercolor, :markersize, :markeralpha,
+    :markerstrokewidth, :markerstrokecolor, :markerstrokealpha,
+    :markerstrokestyle, #Causes warning not to have it... what is this?
+    :fillcolor, :fillalpha, #:fillrange,
+#    :bins, :bar_width, :bar_edges, :bar_position,
+    :title, :title_location, :titlefont,
+    :window_title,
+    :guide, :lims, :scale, #:ticks, :flip, :rotation,
+    :tickfont, :guidefont, :legendfont,
+    :grid, :legend, #:colorbar,
+#    :marker_z,
+#    :line_z,
+#    :levels,
+ #   :ribbon, :quiver, :arrow,
+#    :orientation,
+    :overwrite_figure,
+    :polar,
+#    :normalize, :weights,
+#    :contours, :aspect_ratio,
+    :match_dimensions,
+#    :clims,
+#    :inset_subplots,
+    :dpi,
+#    :colorbar_title,
+  ])
+const _inspectdr_style = [:auto, :solid, :dash, :dot, :dashdot]
+const _inspectdr_seriestype = [
+        :path, :scatter, :shape #, :steppre, :steppost
+    ]
+#see: _allMarkers, _shape_keys
+const _inspectdr_marker = Symbol[
+    :none, :auto,
+    :circle, :rect, :diamond,
+    :cross, :xcross,
+    :utriangle, :dtriangle, :rtriangle, :ltriangle,
+    :pentagon, :hexagon, :heptagon, :octagon,
+    :star4, :star5, :star6, :star7, :star8,
+    :vline, :hline, :+, :x,
+]
+
+const _inspectdr_scale = [:identity, :ln, :log2, :log10]
+
+is_marker_supported(::InspectDRBackend, shape::Shape) = true
+
+_inspectdr_to_pixels(bb::BoundingBox) =
+    InspectDR.BoundingBox(to_pixels(left(bb)), to_pixels(right(bb)), to_pixels(top(bb)), to_pixels(bottom(bb)))
+
+#Do we avoid Map to avoid possible pre-comile issues?
+function _inspectdr_mapglyph(s::Symbol)
+    s == :rect && return :square
+    return s
+end
+
+function _inspectdr_mapglyph(s::Shape)
+    x, y = coords(s)
+    return InspectDR.GlyphPolyline(x, y)
+end
+
+# py_marker(markers::AVec) = map(py_marker, markers)
+function _inspectdr_mapglyph(markers::AVec)
+    warn("Vectors of markers are currently unsupported in InspectDR.")
+    _inspectdr_mapglyph(markers[1])
+end
+
+_inspectdr_mapglyphsize(v::Real) = v
+function _inspectdr_mapglyphsize(v::Vector)
+    warn("Vectors of marker sizes are currently unsupported in InspectDR.")
+    _inspectdr_mapglyphsize(v[1])
+end
+
+_inspectdr_mapcolor(v::Colorant) = v
+function _inspectdr_mapcolor(g::PlotUtils.ColorGradient)
+    warn("Color gradients are currently unsupported in InspectDR.")
+    #Pick middle color:
+    _inspectdr_mapcolor(g.colors[div(1+end,2)])
+end
+function _inspectdr_mapcolor(v::AVec)
+    warn("Vectors of colors are currently unsupported in InspectDR.")
+    #Pick middle color:
+    _inspectdr_mapcolor(v[div(1+end,2)])
+end
+
+#Hack: suggested point size does not seem adequate relative to plot size, for some reason.
+_inspectdr_mapptsize(v) = 1.5*v
+
+function _inspectdr_add_annotations(plot, x, y, val)
+    #What kind of annotation is this?
+end
+
+#plot::InspectDR.Plot2D
+function _inspectdr_add_annotations(plot, x, y, val::PlotText)
+    vmap = Dict{Symbol, Symbol}(:top=>:t, :bottom=>:b) #:vcenter
+    hmap = Dict{Symbol, Symbol}(:left=>:l, :right=>:r) #:hcenter
+    align = Symbol(get(vmap, val.font.valign, :c), get(hmap, val.font.halign, :c))
+    fnt = InspectDR.Font(val.font.family, val.font.pointsize,
+        color =_inspectdr_mapcolor(val.font.color)
+    )
+    ann = InspectDR.atext(val.str, x=x, y=y,
+        font=fnt, angle=val.font.rotation, align=align
+    )
+    InspectDR.add(plot, ann)
+    return
+end
+
+# ---------------------------------------------------------------------------
+
+function _inspectdr_getscale(s::Symbol, yaxis::Bool)
+#TODO: Support :asinh, :sqrt
+    kwargs = yaxis? (:tgtmajor=>8, :tgtminor=>2): () #More grid lines on y-axis
+    if :log2 == s
+        return InspectDR.AxisScale(:log2; kwargs...)
+    elseif :log10 == s
+        return InspectDR.AxisScale(:log10; kwargs...)
+    elseif :ln == s
+        return InspectDR.AxisScale(:ln; kwargs...)
+    else #identity
+        return InspectDR.AxisScale(:lin; kwargs...)
+    end
+end
+
+# ---------------------------------------------------------------------------
+
+function add_backend_string(::InspectDRBackend)
+    """
+    if !Plots.is_installed("InspectDR")
+        Pkg.add("InspectDR")
+    end
+    """
+end
+
+function _initialize_backend(::InspectDRBackend; kw...)
+    @eval begin
+        import InspectDR
+        export InspectDR
+
+        #Glyph used when plotting "Shape"s:
+        const INSPECTDR_GLYPH_SHAPE = InspectDR.GlyphPolyline(
+            2*InspectDR.GLYPH_SQUARE.x, InspectDR.GLYPH_SQUARE.y
+        )
+
+        type InspecDRPlotRef
+            mplot::Union{Void, InspectDR.Multiplot}
+            gui::Union{Void, InspectDR.GtkPlot}
+        end
+
+        _inspectdr_getmplot(::Any) = nothing
+        _inspectdr_getmplot(r::InspecDRPlotRef) = r.mplot
+
+        _inspectdr_getgui(::Any) = nothing
+        _inspectdr_getgui(gplot::InspectDR.GtkPlot) = (gplot.destroyed? nothing: gplot)
+        _inspectdr_getgui(r::InspecDRPlotRef) = _inspectdr_getgui(r.gui)
+    end
+end
+
+# ---------------------------------------------------------------------------
+
+# Create the window/figure for this backend.
+function _create_backend_figure(plt::Plot{InspectDRBackend})
+    mplot = _inspectdr_getmplot(plt.o)
+    gplot = _inspectdr_getgui(plt.o)
+
+    #:overwrite_figure: want to reuse current figure
+    if plt[:overwrite_figure] && mplot != nothing
+        mplot.subplots = [] #Reset
+        if gplot != nothing #Ensure still references current plot
+            gplot.src = mplot
+        end
+    else #want new one:
+        mplot = InspectDR.Multiplot()
+        gplot = nothing #Will be created later
+    end
+
+    #break link with old subplots
+    for sp in plt.subplots
+        sp.o = nothing
+    end
+
+    return InspecDRPlotRef(mplot, gplot)
+end
+
+# ---------------------------------------------------------------------------
+
+# # this is called early in the pipeline, use it to make the plot current or something
+# function _prepare_plot_object(plt::Plot{InspectDRBackend})
+# end
+
+# ---------------------------------------------------------------------------
+
+# Set up the subplot within the backend object.
+function _initialize_subplot(plt::Plot{InspectDRBackend}, sp::Subplot{InspectDRBackend})
+    plot = sp.o
+
+    #Don't do anything without a "subplot" object:  Will process later.
+    if nothing == plot; return; end
+    plot.data = []
+    plot.markers = [] #Clear old markers
+    plot.atext = [] #Clear old annotation
+    plot.apline = [] #Clear old poly lines
+
+    return plot
+end
+
+# ---------------------------------------------------------------------------
+
+# Add one series to the underlying backend object.
+# Called once per series
+# NOTE: Seems to be called when user calls plot()... even if backend
+#       plot, sp.o has not yet been constructed...
+function _series_added(plt::Plot{InspectDRBackend}, series::Series)
+    st = series[:seriestype]
+    sp = series[:subplot]
+    plot = sp.o
+
+    #Don't do anything without a "subplot" object:  Will process later.
+    if nothing == plot; return; end
+
+    _vectorize(v) = isa(v, Vector)? v: collect(v) #InspectDR only supports vectors
+    x = _vectorize(series[:x]); y = _vectorize(series[:y])
+
+    #No support for polar grid... but can still perform polar transformation:
+    if ispolar(sp)
+        Θ = x; r = y
+        x = r.*cos(Θ); y = r.*sin(Θ)
+    end
+
+    # doesn't handle mismatched x/y - wrap data (pyplot behaviour):
+    nx = length(x); ny = length(y)
+    if nx < ny
+        series[:x] = Float64[x[mod1(i,nx)] for i=1:ny]
+    elseif ny > nx
+        series[:y] = Float64[y[mod1(i,ny)] for i=1:nx]
+    end
+
+#= TODO: Eventually support
+    series[:fillcolor] #I think this is fill under line
+    zorder = series[:series_plotindex]
+
+For st in :shape:
+    zorder = series[:series_plotindex],
+=#
+
+    if st in (:shape,)
+        nmax = 0
+        for (i,rng) in enumerate(iter_segments(x, y))
+            nmax = i
+            if length(rng) > 1
+                linewidth = series[:linewidth]
+                linecolor = _inspectdr_mapcolor(cycle(series[:linecolor], i))
+                fillcolor = _inspectdr_mapcolor(cycle(series[:fillcolor], i))
+                line = InspectDR.line(
+                    style=:solid, width=linewidth, color=linecolor
+                )
+                apline = InspectDR.PolylineAnnotation(
+                    x[rng], y[rng], line=line, fillcolor=fillcolor
+                )
+                push!(plot.apline, apline)
+            end
+        end
+
+        i = (nmax >= 2? div(nmax, 2): nmax) #Must pick one set of colors for legend
+        if i > 1 #Add dummy waveform for legend entry:
+            linewidth = series[:linewidth]
+            linecolor = _inspectdr_mapcolor(cycle(series[:linecolor], i))
+            fillcolor = _inspectdr_mapcolor(cycle(series[:fillcolor], i))
+            wfrm = InspectDR.add(plot, Float64[], Float64[], id=series[:label])
+            wfrm.line = InspectDR.line(
+                style=:none, width=linewidth, #linewidth affects glyph
+            )
+            wfrm.glyph = InspectDR.glyph(
+                shape = INSPECTDR_GLYPH_SHAPE, size = 8,
+                color = linecolor, fillcolor = fillcolor
+            )
+        end
+   elseif st in (:path, :scatter) #, :steppre, :steppost)
+        #NOTE: In Plots.jl, :scatter plots have 0-linewidths (I think).
+        linewidth = series[:linewidth]
+        #More efficient & allows some support for markerstrokewidth:
+        _style = (0==linewidth? :none: series[:linestyle])
+        wfrm = InspectDR.add(plot, x, y, id=series[:label])
+        wfrm.line = InspectDR.line(
+            style = _style,
+            width = series[:linewidth],
+            color = series[:linecolor],
+        )
+        #InspectDR does not control markerstrokewidth independently.
+        if :none == _style
+            #Use this property only if no line is displayed:
+            wfrm.line.width = series[:markerstrokewidth]
+        end
+        wfrm.glyph = InspectDR.glyph(
+            shape = _inspectdr_mapglyph(series[:markershape]),
+            size = _inspectdr_mapglyphsize(series[:markersize]),
+            color = _inspectdr_mapcolor(series[:markerstrokecolor]),
+            fillcolor = _inspectdr_mapcolor(series[:markercolor]),
+        )
+    end
+
+    # this is all we need to add the series_annotations text
+    anns = series[:series_annotations]
+    for (xi,yi,str,fnt) in EachAnn(anns, x, y)
+        _inspectdr_add_annotations(plot, xi, yi, PlotText(str, fnt))
+    end
+    return
+end
+
+# ---------------------------------------------------------------------------
+
+# When series data is added/changed, this callback can do dynamic updates to the backend object.
+# note: if the backend rebuilds the plot from scratch on display, then you might not do anything here.
+function _series_updated(plt::Plot{InspectDRBackend}, series::Series)
+    #Nothing to do
+end
+
+# ---------------------------------------------------------------------------
+
+function _inspectdr_setupsubplot(sp::Subplot{InspectDRBackend})
+    const gridon = InspectDR.GridRect(vmajor=true, hmajor=true)
+    const gridoff = InspectDR.GridRect()
+    const plot = sp.o
+    const strip = plot.strips[1] #Only 1 strip supported with Plots.jl
+
+	#No independent control of grid???
+	strip.grid = sp[:grid]? gridon: gridoff
+
+    xaxis = sp[:xaxis]; yaxis = sp[:yaxis]
+        plot.xscale = _inspectdr_getscale(xaxis[:scale], false)
+        strip.yscale = _inspectdr_getscale(yaxis[:scale], true)
+        xmin, xmax  = axis_limits(xaxis)
+        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))
+            xmin, xmax = -rmax, rmax
+            ymin, ymax = -rmax, rmax
+        end
+        plot.xext = InspectDR.PExtents1D() #reset
+        strip.yext = InspectDR.PExtents1D() #reset
+        plot.xext_full = InspectDR.PExtents1D(xmin, xmax)
+        strip.yext_full = InspectDR.PExtents1D(ymin, ymax)
+    a = plot.annotation
+        a.title = sp[:title]
+        a.xlabel = xaxis[:guide]; a.ylabels = [yaxis[:guide]]
+
+    l = plot.layout
+        l.frame.fillcolor = _inspectdr_mapcolor(sp[:background_color_subplot])
+        l.framedata.fillcolor = _inspectdr_mapcolor(sp[:background_color_inside])
+        l.framedata.line.color = _inspectdr_mapcolor(xaxis[:foreground_color_axis])
+        l.fnttitle = InspectDR.Font(sp[:titlefont].family,
+            _inspectdr_mapptsize(sp[:titlefont].pointsize),
+            color = _inspectdr_mapcolor(sp[:foreground_color_title])
+        )
+        #Cannot independently control fonts of axes with InspectDR:
+        l.fntaxlabel = InspectDR.Font(xaxis[:guidefont].family,
+            _inspectdr_mapptsize(xaxis[:guidefont].pointsize),
+            color = _inspectdr_mapcolor(xaxis[:foreground_color_guide])
+        )
+        l.fntticklabel = InspectDR.Font(xaxis[:tickfont].family,
+            _inspectdr_mapptsize(xaxis[:tickfont].pointsize),
+            color = _inspectdr_mapcolor(xaxis[:foreground_color_text])
+        )
+    leg = l.legend
+        leg.enabled = (sp[:legend] != :none)
+        #leg.width = 150 #TODO: compute???
+        leg.font = InspectDR.Font(sp[:legendfont].family,
+            _inspectdr_mapptsize(sp[:legendfont].pointsize),
+            color = _inspectdr_mapcolor(sp[:foreground_color_legend])
+        )
+        leg.frame.fillcolor = _inspectdr_mapcolor(sp[:background_color_legend])
+end
+
+# called just before updating layout bounding boxes... in case you need to prep
+# for the calcs
+function _before_layout_calcs(plt::Plot{InspectDRBackend})
+    const mplot = _inspectdr_getmplot(plt.o)
+    if nothing == mplot; return; end
+
+    mplot.title = plt[:plot_title]
+    if "" == mplot.title
+        #Don't use window_title... probably not what you want.
+        #mplot.title = plt[:window_title]
+    end
+    mplot.frame.fillcolor = _inspectdr_mapcolor(plt[:background_color_outside])
+
+    resize!(mplot.subplots, length(plt.subplots))
+    nsubplots = length(plt.subplots)
+    for (i, sp) in enumerate(plt.subplots)
+        if !isassigned(mplot.subplots, i)
+            mplot.subplots[i] = InspectDR.Plot2D()
+        end
+        sp.o = mplot.subplots[i]
+        plot = sp.o
+        _initialize_subplot(plt, sp)
+        _inspectdr_setupsubplot(sp)
+        graphbb = _inspectdr_to_pixels(plotarea(sp))
+        plot.plotbb = InspectDR.plotbounds(plot.layout, graphbb)
+
+        # add the annotations
+        for ann in sp[:annotations]
+            _inspectdr_add_annotations(plot, ann...)
+        end
+    end
+
+    #Do not yet support absolute plot positionning.
+    #Just try to make things look more-or less ok:
+    if nsubplots <= 1
+        mplot.ncolumns = 1
+    elseif nsubplots <= 4
+        mplot.ncolumns = 2
+    elseif nsubplots <= 6
+        mplot.ncolumns = 3
+    elseif nsubplots <= 12
+        mplot.ncolumns = 4
+    else
+        mplot.ncolumns = 5
+    end
+
+    for series in plt.series_list
+        _series_added(plt, series)
+    end
+    return
+end
+
+# ----------------------------------------------------------------
+
+# Set the (left, top, right, bottom) minimum padding around the plot area
+# to fit ticks, tick labels, guides, colorbars, etc.
+function _update_min_padding!(sp::Subplot{InspectDRBackend})
+    plot = sp.o
+    if !isa(plot, InspectDR.Plot2D); return sp.minpad; end
+    #Computing plotbounds with 0-BoundingBox returns required padding:
+    bb = InspectDR.plotbounds(plot.layout, InspectDR.BoundingBox(0,0,0,0))
+    #NOTE: plotbounds always pads for titles, legends, etc. even if not in use.
+    #TODO: possibly zero-out items not in use??
+
+    # add in the user-specified margin to InspectDR padding:
+    leftpad   = abs(bb.xmin)*px + sp[:left_margin]
+    toppad    = abs(bb.ymin)*px + sp[:top_margin]
+    rightpad  = abs(bb.xmax)*px + sp[:right_margin]
+    bottompad = abs(bb.ymax)*px + sp[:bottom_margin]
+    sp.minpad = (leftpad, toppad, rightpad, bottompad)
+end
+
+# ----------------------------------------------------------------
+
+# Override this to update plot items (title, xlabel, etc), and add annotations (d[:annotations])
+function _update_plot_object(plt::Plot{InspectDRBackend})
+    mplot = _inspectdr_getmplot(plt.o)
+    if nothing == mplot; return; end
+
+    #TODO: should plotbb be computed here??
+
+    gplot = _inspectdr_getgui(plt.o)
+    if nothing == gplot; return; end
+
+    gplot.src = mplot #Ensure still references current plot
+    InspectDR.refresh(gplot)
+    return
+end
+
+# ----------------------------------------------------------------
+
+const _inspectdr_mimeformats_dpi = Dict(
+    "image/png"               => "png"
+)
+const _inspectdr_mimeformats_nodpi = Dict(
+    "image/svg+xml"           => "svg",
+    "application/eps"         => "eps",
+    "image/eps"               => "eps",
+#    "application/postscript"  => "ps", #TODO: support once Cairo supports PSSurface
+    "application/pdf"         => "pdf"
+)
+_inspectdr_show(io::IO, mime::MIME, ::Void, w, h) =
+    throw(ErrorException("Cannot show(::IO, ...) plot - not yet generated"))
+function _inspectdr_show(io::IO, mime::MIME, mplot, w, h)
+    InspectDR._show(io, mime, mplot, Float64(w), Float64(h))
+end
+
+for (mime, fmt) in _inspectdr_mimeformats_dpi
+    @eval function _show(io::IO, mime::MIME{Symbol($mime)}, plt::Plot{InspectDRBackend})
+        dpi = plt[:dpi]#TODO: support
+        _inspectdr_show(io, mime, _inspectdr_getmplot(plt.o), plt[:size]...)
+    end
+end
+for (mime, fmt) in _inspectdr_mimeformats_nodpi
+    @eval function _show(io::IO, mime::MIME{Symbol($mime)}, plt::Plot{InspectDRBackend})
+        _inspectdr_show(io, mime, _inspectdr_getmplot(plt.o), plt[:size]...)
+    end
+end
+_show(io::IO, mime::MIME"text/plain", plt::Plot{InspectDRBackend}) = nothing #Don't show
+
+# ----------------------------------------------------------------
+
+# Display/show the plot (open a GUI window, or browser page, for example).
+function _display(plt::Plot{InspectDRBackend})
+    mplot = _inspectdr_getmplot(plt.o)
+    if nothing == mplot; return; end
+    gplot = _inspectdr_getgui(plt.o)
+
+    if nothing == gplot
+        gplot = display(InspectDR.GtkDisplay(), mplot)
+    else
+        #redundant... Plots.jl will call _update_plot_object:
+        #InspectDR.refresh(gplot)
+    end
+    plt.o = InspecDRPlotRef(mplot, gplot)
+    return gplot
+end

src/backends/pgfplots.jl

@@ -3,7 +3,7 @@
 # significant contributions by: @pkofod
 
 const _pgfplots_attr = merge_with_base_supported([
-    # :annotations,
+    :annotations,
     # :background_color_legend,
     :background_color_inside,
     # :background_color_outside,
@@ -27,12 +27,12 @@ const _pgfplots_attr = merge_with_base_supported([
     # :ribbon, :quiver, :arrow,
     # :orientation,
     # :overwrite_figure,
-    # :polar,
+    :polar,
     # :normalize, :weights, :contours,
     :aspect_ratio,
     # :match_dimensions,
   ])
-const _pgfplots_seriestype = [:path, :path3d, :scatter, :steppre, :stepmid, :steppost, :histogram2d, :ysticks, :xsticks, :contour]
+const _pgfplots_seriestype = [:path, :path3d, :scatter, :steppre, :stepmid, :steppost, :histogram2d, :ysticks, :xsticks, :contour, :shape]
 const _pgfplots_style = [:auto, :solid, :dash, :dot, :dashdot, :dashdotdot]
 const _pgfplots_marker = [:none, :auto, :circle, :rect, :diamond, :utriangle, :dtriangle, :cross, :xcross, :star5, :pentagon] #vcat(_allMarkers, Shape)
 const _pgfplots_scale = [:identity, :ln, :log2, :log10]
@@ -136,6 +136,20 @@ function pgf_marker(d::KW)
     }"""
 end
 
+function pgf_add_annotation!(o,x,y,val)
+    # Construct the style string.
+    # Currently supports color and orientation
+    halign = val.font.halign == :hcenter ? "" : string(val.font.halign)
+    cstr,a = pgf_color(val.font.color)
+    push!(o, PGFPlots.Plots.Node(val.str, # Annotation Text
+                                 x, y,
+                                 style="""
+                                 $halign,
+                                 color=$cstr, draw opacity=$(convert(Float16,a)),
+                                 rotate=$(val.font.rotation)
+                                 """))
+end
+
 # --------------------------------------------------------------------------------------
 
 function pgf_series(sp::Subplot, series::Series)
@@ -147,7 +161,7 @@ function pgf_series(sp::Subplot, series::Series)
     push!(style, pgf_linestyle(d))
     push!(style, pgf_marker(d))
 
-    if d[:fillrange] != nothing
+    if d[:fillrange] != nothing || st in (:shape,)
         push!(style, pgf_fillstyle(d))
     end
 
@@ -211,6 +225,9 @@ function pgf_axis(sp::Subplot, letter)
     # axis guide
     kw[Symbol(letter,:label)] = axis[:guide]
 
+    # Add ticklabel rotations
+    push!(style, "$(letter)ticklabel style={rotate = $(axis[:rotation])}")
+
     # flip/reverse?
     axis[:flip] && push!(style, "$letter dir=reverse")
 
@@ -249,8 +266,11 @@ end
 
 function _update_plot_object(plt::Plot{PGFPlotsBackend})
     plt.o = PGFPlots.Axis[]
+    # Obtain the total height of the plot by extracting the maximal bottom
+    # coordinate from the bounding box.
+    total_height = bottom(bbox(plt.layout))
     for sp in plt.subplots
-        # first build the PGFPlots.Axis object
+       # first build the PGFPlots.Axis object
         style = ["unbounded coords=jump"]
         kw = KW()
 
@@ -265,10 +285,12 @@ function _update_plot_object(plt::Plot{PGFPlotsBackend})
 
         # bounding box values are in mm
         # note: bb origin is top-left, pgf is bottom-left
+        # A round on 2 decimal places should be enough precision for 300 dpi
+        # plots.
         bb = bbox(sp)
         push!(style, """
             xshift = $(left(bb).value)mm,
-            yshift = $((height(bb) - (bottom(bb))).value)mm,
+            yshift = $(round((total_height - (bottom(bb))).value,2))mm,
             axis background/.style={fill=$(pgf_color(sp[:background_color_inside])[1])}
         """)
         kw[:width] = "$(width(bb).value)mm"
@@ -288,19 +310,34 @@ function _update_plot_object(plt::Plot{PGFPlotsBackend})
             kw[:legendPos] = _pgfplots_legend_pos[legpos]
         end
 
-        o = PGFPlots.Axis(; style = style, kw...)
+        axisf = PGFPlots.Axis
+        if sp[:projection] == :polar
+            axisf = PGFPlots.PolarAxis
+        end
+        o = axisf(; style = style, kw...)
 
         # add the series object to the PGFPlots.Axis
         for series in series_list(sp)
             push!(o, pgf_series(sp, series))
+
+            # add series annotations
+            anns = series[:series_annotations]
+            for (xi,yi,str,fnt) in EachAnn(anns, series[:x], series[:y])
+                pgf_add_annotation!(o, xi, yi, PlotText(str, fnt))
+            end
         end
 
+        # add the annotations
+        for ann in sp[:annotations]
+            pgf_add_annotation!(o,ann...)
+        end
+
+
         # add the PGFPlots.Axis to the list
         push!(plt.o, o)
     end
 end
 
-
 function _show(io::IO, mime::MIME"image/svg+xml", plt::Plot{PGFPlotsBackend})
     show(io, mime, plt.o)
 end

src/backends/plotly.jl

@@ -20,7 +20,7 @@ const _plotly_attr = merge_with_base_supported([
     :guide, :lims, :ticks, :scale, :flip, :rotation,
     :tickfont, :guidefont, :legendfont,
     :grid, :legend, :colorbar,
-    :marker_z, :levels,
+    :marker_z, :fill_z, :levels,
     :ribbon, :quiver,
     :orientation,
     # :overwrite_figure,
@@ -371,6 +371,7 @@ end
 plotly_colorscale(c, α) = plotly_colorscale(cgrad(alpha=α), α)
 # plotly_colorscale(c, alpha = nothing) = plotly_colorscale(cgrad(), alpha)
 
+
 const _plotly_markers = KW(
     :rect       => "square",
     :xcross     => "x",
@@ -488,6 +489,9 @@ function plotly_series(plt::Plot, series::Series)
             d_out[:contours] = KW(:x => wirelines, :y => wirelines, :z => wirelines)
         else
             d_out[:colorscale] = plotly_colorscale(series[:fillcolor], series[:fillalpha])
+            if series[:fill_z] != nothing
+                d_out[:surfacecolor] = plotly_surface_data(series, series[:fill_z])
+            end
         end
 
     elseif st == :pie

src/backends/plotlyjs.jl

@@ -102,8 +102,18 @@ _show(io::IO, ::MIME"image/png", plt::Plot{PlotlyJSBackend}) = plotlyjs_save_hac
 _show(io::IO, ::MIME"application/pdf", plt::Plot{PlotlyJSBackend}) = plotlyjs_save_hack(io, plt, "pdf")
 _show(io::IO, ::MIME"image/eps", plt::Plot{PlotlyJSBackend}) = plotlyjs_save_hack(io, plt, "eps")
 
+function write_temp_html(plt::Plot{PlotlyJSBackend})
+    filename = string(tempname(), ".html")
+    savefig(plt, filename)
+    filename
+end
+
 function _display(plt::Plot{PlotlyJSBackend})
-    display(plt.o)
+    if get(ENV, "PLOTS_USE_ATOM_PLOTPANE", true) in (true, 1, "1", "true", "yes")
+        display(plt.o)
+    else
+        standalone_html_window(plt)
+    end
 end
 
 

src/backends/pyplot.jl

@@ -18,8 +18,7 @@ const _pyplot_attr = merge_with_base_supported([
     :guide, :lims, :ticks, :scale, :flip, :rotation,
     :tickfont, :guidefont, :legendfont,
     :grid, :legend, :colorbar,
-    :marker_z,
+    :marker_z, :line_z, :fill_z,
-    :line_z,
     :levels,
     :ribbon, :quiver, :arrow,
     :orientation,
@@ -56,6 +55,10 @@ function add_backend_string(::PyPlotBackend)
     withenv("PYTHON" => "") do
         Pkg.build("PyPlot")
     end
+    import Conda
+    Conda.add("qt=4.8.5")
+
+    # now restart julia!
     """
 end
 
@@ -82,7 +85,17 @@ function _initialize_backend(::PyPlotBackend)
         const pycollections = PyPlot.pywrap(PyPlot.pyimport("matplotlib.collections"))
         const pyart3d = PyPlot.pywrap(PyPlot.pyimport("mpl_toolkits.mplot3d.art3d"))
     end
-
+    if is_linux()
+      @eval begin
+        # avoid Conda update that causes Segfault with qt >=4.8.6 on Ubuntu https://github.com/JuliaPy/PyPlot.jl/issues/234
+        import Conda
+        kw = Conda._installed_packages_dict()
+        if (!haskey(kw,"qt") || (qt_version=get(kw,"qt",0)[1]!=v"4.8.5"))
+          print("\n If the code has a Segmentation fault error switch to qt v4.8.5 by pasting the following code into julia: \n \n")
+          print(add_backend_string(PyPlotBackend()))
+        end
+      end
+    end
     # we don't want every command to update the figure
     PyPlot.ioff()
 end
@@ -124,8 +137,8 @@ end
 py_colormap(c) = py_colormap(cgrad())
 
 
-function py_shading(c, z, α=nothing)
+function py_shading(c, z)
-    cmap = py_colormap(c, α)
+    cmap = py_colormap(c)
     ls = pycolors.pymember("LightSource")(270,45)
     ls[:shade](z, cmap, vert_exag=0.1, blend_mode="soft")
 end
@@ -668,21 +681,16 @@ function py_add_series(plt::Plot{PyPlotBackend}, series::Series)
                 x = repmat(x', length(y), 1)
                 y = repmat(y, 1, length(series[:x]))
             end
-            # z = z'
             z = transpose_z(series, z)
             if st == :surface
-                if series[:marker_z] != nothing
+                if series[:fill_z] != nothing
-                    extrakw[:facecolors] = py_shading(series[:fillcolor], series[:marker_z], series[:fillalpha])
+                    # the surface colors are different than z-value
+                    extrakw[:facecolors] = py_shading(series[:fillcolor], transpose_z(series, series[:fill_z].surf))
                     extrakw[:shade] = false
-                    clims = sp[:clims]
-                    if is_2tuple(clims)
-                        isfinite(clims[1]) && (extrakw[:vmin] = clims[1])
-                        isfinite(clims[2]) && (extrakw[:vmax] = clims[2])
-                    end
                 else
                     extrakw[:cmap] = py_fillcolormap(series)
-                    needs_colorbar = true
                 end
+                needs_colorbar = true
             end
             handle = ax[st == :surface ? :plot_surface : :plot_wireframe](x, y, z;
                 label = series[:label],

src/backends/web.jl

@@ -27,7 +27,7 @@ function open_browser_window(filename::AbstractString)
         return run(`xdg-open $(filename)`)
     end
     @static if is_windows()
-        return run(`$(ENV["COMSPEC"]) /c start $(filename)`)
+        return run(`$(ENV["COMSPEC"]) /c start "" "$(filename)"`)
     end
     warn("Unknown OS... cannot open browser window.")
 end

src/output.jl

@@ -302,6 +302,10 @@ function setup_atom()
                 Media.render(pane, Atom.div(".fill", Atom.HTML(stringmime(MIME("text/html"), plt))))
                 plt[:size] = sz
             end
+            # special handling for PlotlyJS
+            function Media.render(pane::Atom.PlotPane, plt::Plot{PlotlyJSBackend})
+                display(Plots.PlotsDisplay(), plt)
+            end
         else
             #
             function Media.render(pane::Atom.PlotPane, plt::Plot)
@@ -317,11 +321,5 @@ function setup_atom()
             s = "PlotPane turned off.  The plotly and plotlyjs backends cannot render in the PlotPane due to javascript issues."
             Media.render(pane, Atom.div(Atom.HTML(s)))
         end
-
-        # special handling for PlotlyJS to pass through to that render method
-        function Media.render(pane::Atom.PlotPane, plt::Plot{PlotlyJSBackend})
-            Plots.prepare_output(plt)
-            Media.render(pane, plt.o)
-        end
     end
 end

src/series.jl

@@ -257,12 +257,23 @@ end
 # # 1 argument
 # # --------------------------------------------------------------------
 
+# helper function to ensure relevant attributes are wrapped by Surface
+function wrap_surfaces(d::KW)
+    if haskey(d, :fill_z)
+        v = d[:fill_z]
+        if !isa(v, Surface)
+            d[:fill_z] = Surface(v)
+        end
+    end
+end
+
 @recipe f(n::Integer) = is3d(get(d,:seriestype,:path)) ? (SliceIt, n, n, n) : (SliceIt, n, n, nothing)
 
 # return a surface if this is a 3d plot, otherwise let it be sliced up
 @recipe function f{T<:Union{Integer,AbstractFloat}}(mat::AMat{T})
     if all3D(d)
         n,m = size(mat)
+        wrap_surfaces(d)
         SliceIt, 1:m, 1:n, Surface(mat)
     else
         SliceIt, nothing, mat, nothing
@@ -274,6 +285,7 @@ end
     if all3D(d)
         mat = fmt.data
         n,m = size(mat)
+        wrap_surfaces(d)
         SliceIt, 1:m, 1:n, Formatted(Surface(mat), fmt.formatter)
     else
         SliceIt, nothing, fmt, nothing
@@ -391,6 +403,7 @@ end
     #         seriestype := :path3d
     #     end
     # end
+    wrap_surfaces(d)
     SliceIt, x, y, z
 end
 
@@ -400,6 +413,7 @@ end
 @recipe function f(x::AVec, y::AVec, zf::Function)
     # x = X <: Number ? sort(x) : x
     # y = Y <: Number ? sort(y) : y
+    wrap_surfaces(d)
     SliceIt, x, y, Surface(zf, x, y)  # TODO: replace with SurfaceFunction when supported
 end
 
@@ -410,6 +424,7 @@ end
     if !like_surface(get(d, :seriestype, :none))
         d[:seriestype] = :contour
     end
+    wrap_surfaces(d)
     SliceIt, x, y, Surface(z)
 end