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Merge pull request #2492 from ma-laforge/hdf5

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Fix broken hdf5 "backend".
This commit is contained in:
Michael Krabbe Borregaard 2020-03-20 10:40:28 +01:00 committed by GitHub
commit fba6802066
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1 changed files with 66 additions and 36 deletions
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102
src/backends/hdf5.jl
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@ -83,6 +83,7 @@ if length(HDF5PLOT_MAP_TELEM2STR) < 1
"ARRAY" => Array, #Dict won't allow Array to be key in HDF5PLOT_MAP_TELEM2STR "ARRAY" => Array, #Dict won't allow Array to be key in HDF5PLOT_MAP_TELEM2STR
#Sub-structure types: #Sub-structure types:
"ATTR" => Attr,
"FONT" => Font, "FONT" => Font,
"BOUNDINGBOX" => BoundingBox, "BOUNDINGBOX" => BoundingBox,
"GRIDLAYOUT" => GridLayout, "GRIDLAYOUT" => GridLayout,
@ -109,7 +110,7 @@ _hdf5_datapath(subpath::String) = "$_hdf5_dataroot/$subpath"
_hdf5_map_str2telem(k::String) = HDF5PLOT_MAP_STR2TELEM[k] _hdf5_map_str2telem(k::String) = HDF5PLOT_MAP_STR2TELEM[k]
_hdf5_map_str2telem(v::Vector) = HDF5PLOT_MAP_STR2TELEM[v[1]] _hdf5_map_str2telem(v::Vector) = HDF5PLOT_MAP_STR2TELEM[v[1]]
function _hdf5_merge!(dest, src) function _hdf5_merge!(dest::AKW, src::AKW)
for (k, v) in src for (k, v) in src
if isa(v, Axis) if isa(v, Axis)
_hdf5_merge!(dest[k].plotattributes, v.plotattributes) _hdf5_merge!(dest[k].plotattributes, v.plotattributes)
@ -263,6 +264,15 @@ function _hdf5plot_gwrite(grp, k::String, v::Array{T}) where T<:Number #Default
grp[k] = v grp[k] = v
_hdf5plot_writetype(grp, k, HDF5PlotNative) _hdf5plot_writetype(grp, k, HDF5PlotNative)
end end
function _hdf5plot_gwrite(grp, k::String, v::Dict)
#=
tstr = string(Dict)
path = HDF5.name(grp) * "/" * k
@info("Type not supported: $tstr\npath: $path")
=#
#No support for structures with Dicts different than KW (plotattributes)
end
#= #=
function _hdf5plot_gwrite(grp, k::String, v::Array{Any}) function _hdf5plot_gwrite(grp, k::String, v::Array{Any})
# @show grp, k # @show grp, k
@ -295,7 +305,8 @@ function _hdf5plot_gwrite(grp, k::String, v::Tuple)
end end
#NOTE: _hdf5plot_overwritetype overwrites "Array" type with "Tuple". #NOTE: _hdf5plot_overwritetype overwrites "Array" type with "Tuple".
end end
function _hdf5plot_gwrite(grp, k::String, plotattributes::AKW) function _hdf5plot_gwrite(grp, k::String, plotattributes::KW)
#NOTE: Can only write directly to group, not a subi-item
# @warn("Cannot write dict: $k=$plotattributes") # @warn("Cannot write dict: $k=$plotattributes")
end end
function _hdf5plot_gwrite(grp, k::String, v::AbstractRange) function _hdf5plot_gwrite(grp, k::String, v::AbstractRange)
@ -376,13 +387,22 @@ function _hdf5plot_gwrite(grp, k::String, v::Subplot)
_hdf5plot_writetype(grp, Subplot) _hdf5plot_writetype(grp, Subplot)
return return
end end
function _hdf5plot_write(grp, plotattributes::AKW)
function _hdf5plot_write(grp, plotattributes::KW)
for (k, v) in plotattributes for (k, v) in plotattributes
kstr = string(k) kstr = string(k)
_hdf5plot_gwrite(grp, kstr, v) _hdf5plot_gwrite(grp, kstr, v)
end end
return return
end end
function _hdf5plot_write(grp, plotattributes::Attr)
for (k, v) in plotattributes
kstr = string(k)
_hdf5plot_gwrite(grp, kstr, v)
end
_hdf5plot_writetype(grp, Attr)
end
# Write main plot structures: # Write main plot structures:
# ---------------------------------------------------------------- # ----------------------------------------------------------------
@ -445,20 +465,14 @@ _hdf5plot_convert(T::Type{Extrema}, v) = Extrema(v[1], v[2])
# Read data structures: # Read data structures:
# ---------------------------------------------------------------- # ----------------------------------------------------------------
function _hdf5plot_read(grp, k::String, T::Type, dtid) function _hdf5plot_read(grp, k::String, T::Type)
v = HDF5.d_read(grp, k) v = HDF5.d_read(grp, k)
return _hdf5plot_convert(T, v) return _hdf5plot_convert(T, v)
end end
function _hdf5plot_read(grp, k::String, T::Type{Length}, dtid::Vector)
v = HDF5.d_read(grp, k)
TU = Symbol(dtid[2])
T = typeof(v)
return Length{TU,T}(v)
end
# Read more complex data structures: # Read more complex data structures:
# ---------------------------------------------------------------- # ----------------------------------------------------------------
function _hdf5plot_read(grp, k::String, T::Type{Font}, dtid) function _hdf5plot_read(grp, k::String, T::Type{Font})
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
family = _hdf5plot_read(grp, "family") family = _hdf5plot_read(grp, "family")
@ -469,7 +483,7 @@ function _hdf5plot_read(grp, k::String, T::Type{Font}, dtid)
color = _hdf5plot_read(grp, "color") color = _hdf5plot_read(grp, "color")
return Font(family, pointsize, halign, valign, rotation, color) return Font(family, pointsize, halign, valign, rotation, color)
end end
function _hdf5plot_read(grp, k::String, T::Type{Array}, dtid) #ANY function _hdf5plot_read(grp, k::String, T::Type{Array}) #ANY
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
sz = _hdf5plot_read(grp, "dim") sz = _hdf5plot_read(grp, "dim")
if [0] == sz; return []; end if [0] == sz; return []; end
@ -488,18 +502,18 @@ function _hdf5plot_read(grp, k::String, T::Type{Array}, dtid) #ANY
result = [result[iter] for iter in eachindex(result)] #Potentially make more specific result = [result[iter] for iter in eachindex(result)] #Potentially make more specific
return reshape(result, sz) return reshape(result, sz)
end end
function _hdf5plot_read(grp, k::String, T::Type{HDF5CTuple}, dtid) function _hdf5plot_read(grp, k::String, T::Type{HDF5CTuple})
v = _hdf5plot_read(grp, k, Array, dtid) v = _hdf5plot_read(grp, k, Array)
return tuple(v...) return tuple(v...)
end end
function _hdf5plot_read(grp, k::String, T::Type{PlotText}, dtid) function _hdf5plot_read(grp, k::String, T::Type{PlotText})
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
str = _hdf5plot_read(grp, "str") str = _hdf5plot_read(grp, "str")
font = _hdf5plot_read(grp, "font") font = _hdf5plot_read(grp, "font")
return PlotText(str, font) return PlotText(str, font)
end end
function _hdf5plot_read(grp, k::String, T::Type{SeriesAnnotations}, dtid) function _hdf5plot_read(grp, k::String, T::Type{SeriesAnnotations})
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
strs = _hdf5plot_read(grp, "strs") strs = _hdf5plot_read(grp, "strs")
@ -508,29 +522,29 @@ function _hdf5plot_read(grp, k::String, T::Type{SeriesAnnotations}, dtid)
scalefactor = _hdf5plot_read(grp, "scalefactor") scalefactor = _hdf5plot_read(grp, "scalefactor")
return SeriesAnnotations(strs, font, baseshape, scalefactor) return SeriesAnnotations(strs, font, baseshape, scalefactor)
end end
function _hdf5plot_read(grp, k::String, T::Type{Shape}, dtid) function _hdf5plot_read(grp, k::String, T::Type{Shape})
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
x = _hdf5plot_read(grp, "x") x = _hdf5plot_read(grp, "x")
y = _hdf5plot_read(grp, "y") y = _hdf5plot_read(grp, "y")
return Shape(x, y) return Shape(x, y)
end end
function _hdf5plot_read(grp, k::String, T::Type{ColorGradient}, dtid) function _hdf5plot_read(grp, k::String, T::Type{ColorGradient})
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
colors = _hdf5plot_read(grp, "colors") colors = _hdf5plot_read(grp, "colors")
values = _hdf5plot_read(grp, "values") values = _hdf5plot_read(grp, "values")
return ColorGradient(colors, values) return ColorGradient(colors, values)
end end
function _hdf5plot_read(grp, k::String, T::Type{BoundingBox}, dtid) function _hdf5plot_read(grp, k::String, T::Type{BoundingBox})
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
x0 = _hdf5plot_read(grp, "x0") x0 = _hdf5plot_read(grp, "x0")
a = _hdf5plot_read(grp, "a") a = _hdf5plot_read(grp, "a")
return BoundingBox(x0, a) return BoundingBox(x0, a)
end end
_hdf5plot_read(grp, k::String, T::Type{RootLayout}, dtid) = RootLayout() _hdf5plot_read(grp, k::String, T::Type{RootLayout}) = RootLayout()
function _hdf5plot_read(grp, k::String, T::Type{GridLayout}, dtid) function _hdf5plot_read(grp, k::String, T::Type{GridLayout})
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
# parent = _hdf5plot_read(grp, "parent") # parent = _hdf5plot_read(grp, "parent")
@ -544,22 +558,36 @@ parent = RootLayout()
return GridLayout(parent, minpad, bbox, grid, widths, heights, attr) return GridLayout(parent, minpad, bbox, grid, widths, heights, attr)
end end
function _hdf5plot_read(grp, k::String, T::Type{Axis}, dtid) function _hdf5plot_read(grp, T::Type{Attr})
grp = HDF5.g_open(grp, k) attr = Attr(KW(), _plot_defaults)
kwlist = KW() v = _hdf5plot_read(grp, attr)
_hdf5plot_read(grp, kwlist) return attr
return Axis([], kwlist)
end end
function _hdf5plot_read(grp, k::String, T::Type{Surface}, dtid) function _hdf5plot_read(grp, k::String, T::Type{Axis})
grp = HDF5.g_open(grp, k)
plotattributes = Attr(KW(), _plot_defaults)
_hdf5plot_read(grp, plotattributes)
return Axis([], plotattributes)
end
function _hdf5plot_read(grp, k::String, T::Type{Surface})
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
data2d = _hdf5plot_read(grp, "data2d") data2d = _hdf5plot_read(grp, "data2d")
return Surface(data2d) return Surface(data2d)
end end
function _hdf5plot_read(grp, k::String, T::Type{Subplot}, dtid) function _hdf5plot_read(grp, k::String, T::Type{Subplot})
grp = HDF5.g_open(grp, k) grp = HDF5.g_open(grp, k)
idx = _hdf5plot_read(grp, "index") idx = _hdf5plot_read(grp, "index")
return HDF5PLOT_PLOTREF.ref.subplots[idx] return HDF5PLOT_PLOTREF.ref.subplots[idx]
end end
#Most types don't need dtid for read!!:
_hdf5plot_read(grp, k::String, T::Type, dtid) = _hdf5plot_read(grp, k, T)
function _hdf5plot_read(grp, k::String, T::Type{Length}, dtid::Vector)
v = HDF5.d_read(grp, k)
TU = Symbol(dtid[2])
T = typeof(v)
return Length{TU,T}(v)
end
function _hdf5plot_read(grp, k::String) function _hdf5plot_read(grp, k::String)
dtid = HDF5.a_read(grp[k], _hdf5plot_datatypeid) dtid = HDF5.a_read(grp[k], _hdf5plot_datatypeid)
T = _hdf5_map_str2telem(dtid) #expect exception T = _hdf5_map_str2telem(dtid) #expect exception
@ -567,7 +595,7 @@ function _hdf5plot_read(grp, k::String)
end end
#Read in values in group to populate plotattributes: #Read in values in group to populate plotattributes:
function _hdf5plot_read(grp, plotattributes::AKW) function _hdf5plot_readattr(grp, plotattributes::AbstractDict)
gnames = names(grp) gnames = names(grp)
for k in gnames for k in gnames
try try
@ -581,6 +609,8 @@ function _hdf5plot_read(grp, plotattributes::AKW)
end end
return return
end end
_hdf5plot_read(grp, plotattributes::KW) = _hdf5plot_readattr(grp, plotattributes)
_hdf5plot_read(grp, plotattributes::Attr) = _hdf5plot_readattr(grp, plotattributes)
# Read main plot structures: # Read main plot structures:
# ---------------------------------------------------------------- # ----------------------------------------------------------------
@ -593,17 +623,17 @@ function _hdf5plot_read(sp::Subplot, subpath::String, f)
for i in 1:nseries for i in 1:nseries
grp = HDF5.g_open(f, _hdf5_plotelempath("$subpath/series_list/series$i")) grp = HDF5.g_open(f, _hdf5_plotelempath("$subpath/series_list/series$i"))
kwlist = KW() seriesinfo = Attr(KW(), _plot_defaults)
_hdf5plot_read(grp, kwlist) _hdf5plot_read(grp, seriesinfo)
plot!(sp, kwlist[:x], kwlist[:y]) #Add data & create data structures plot!(sp, seriesinfo[:x], seriesinfo[:y]) #Add data & create data structures
_hdf5_merge!(sp.series_list[end].plotattributes, kwlist) _hdf5_merge!(sp.series_list[end].plotattributes, seriesinfo)
end end
#Perform after adding series... otherwise values get overwritten: #Perform after adding series... otherwise values get overwritten:
grp = HDF5.g_open(f, _hdf5_plotelempath("$subpath/attr")) grp = HDF5.g_open(f, _hdf5_plotelempath("$subpath/attr"))
kwlist = KW() attr = Attr(KW(), _plot_defaults)
_hdf5plot_read(grp, kwlist) _hdf5plot_read(grp, attr)
_hdf5_merge!(sp.attr, kwlist) _hdf5_merge!(sp.attr, attr)
return return
end end