tmove GSD plotting to io.jl, add grain-plotting function - Granular.jl - Julia package for granular dynamics simulation
(HTM) git clone git://src.adamsgaard.dk/Granular.jl
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---
(DIR) commit de89698ecd7d60173f5cfbf8e30b455452b8951c
(DIR) parent f8e0e4db6963a0e5775539a65d8f85add7af9565
(HTM) Author: Anders Damsgaard <andersd@riseup.net>
Date: Fri, 17 Nov 2017 22:48:10 -0500
move GSD plotting to io.jl, add grain-plotting function
Diffstat:
M src/grain.jl | 105 -------------------------------
M src/io.jl | 187 +++++++++++++++++++++++++++++++
2 files changed, 187 insertions(+), 105 deletions(-)
---
(DIR) diff --git a/src/grain.jl b/src/grain.jl
t@@ -2,15 +2,6 @@
using Compat.Test
-# load Homebrew/WinRPM for gnuplot and imagemagick
-if is_apple()
- using Homebrew
-end
-
-if is_windows()
- using WinRPM
-end
-
export addGrainCylindrical!
"""
function addGrainCylindrical!(simulation, lin_pos, contact_radius,
t@@ -725,102 +716,6 @@ function compareGrains(if1::GrainCylindrical, if2::GrainCylindrical)
nothing
end
-export plotGrainSizeDistribution
-"""
- plotGrainSizeDistribution(simulation, [filename_postfix], [nbins],
- [size_type], [figsize], [filetype])
-
-Plot the grain size distribution as a histogram and save it to the disk. The
-plot is saved accoring to the simulation id, the optional `filename_postfix`
-string, and the `filetype`, and is written to the current folder.
-
-# Arguments
-* `simulation::Simulation`: the simulation object containing the grains.
-* `filename_postfix::String`: optional string for the output filename.
-* `nbins::Int`: number of bins in the histogram (default = 12).
-* `size_type::String`: specify whether to use the `contact` or `areal` radius
- for the grain size. The default is `contact`.
-* `figsize::Tuple`: the output figure size in inches (default = (6,4).
-* `filetype::String`: the output file type (default = "png").
-* `verbose::String`: show output file as info message in stdout (default =
- true).
-* `skip_fixed::Bool`: ommit grains that are fixed in space from the size
- distribution (default = true).
-* `log_y::Bool`: plot y-axis in log scale.
-* `show_plot::Bool`: show plot in pop-up window in addition to writing to disk.
-"""
-function plotGrainSizeDistribution(simulation::Simulation;
- filename_postfix::String = "",
- nbins::Int=12,
- size_type::String = "contact",
- figsize::Tuple = (6,4),
- filetype::String = "png",
- gnuplot_terminal::String = "png",
- verbose::Bool = true,
- skip_fixed::Bool = true,
- log_y::Bool = false,
- show_plot::Bool = false)
-
- diameters = Float64[]
- for i=1:length(simulation.grains)
- if simulation.grains[i].fixed && skip_fixed
- continue
- end
- if size_type == "contact"
- push!(diameters, simulation.grains[i].contact_radius*2.)
- elseif size_type == "areal"
- push!(diameters, simulation.grains[i].areal_radius*2.)
- else
- error("size_type '$size_type' not understood")
- end
- end
-
- filename = string(simulation.id * filename_postfix *
- "-grain-size-distribution." * filetype)
-
- # write data to temporary file on disk
- datafile = Base.Filesystem.tempname()
- writedlm(datafile, diameters)
- gnuplotscript = Base.Filesystem.tempname()
-
- #if maximum(diameters) ≈ minimum(diameters)
- #info("Overriding `nbins = $nbins` -> `nbins = 1`.")
- #nbins = 1
- #end
-
- open(gnuplotscript, "w") do f
-
- write(f, """#!/usr/bin/env gnuplot
- set term $gnuplot_terminal
- set out "$(filename)"\n""")
- if log_y
- write(f, "set logscale y\n")
- end
- write(f, """set xlabel "Diameter [m]"
- set ylabel "Count [-]"
- binwidth = $((maximum(diameters) - minimum(diameters)+1e-7)/nbins)
- binstart = $(minimum(diameters))
- set boxwidth 1.0*binwidth
- set style fill solid 0.5
- set key off
- hist = 'u (binwidth*(floor((\$1-binstart)/binwidth)+0.5)+binstart):(1.0) smooth freq w boxes'
- plot "$(datafile)" i 0 @hist ls 1
- """)
- end
-
- try
- run(`gnuplot $gnuplotscript`)
- catch return_signal
- if isa(return_signal, Base.UVError)
- error("Could not launch external gnuplot process")
- end
- end
-
- if verbose
- info(filename)
- end
-end
-
export enableOceanDrag!
"""
enableOceanDrag!(grain)
(DIR) diff --git a/src/io.jl b/src/io.jl
t@@ -7,6 +7,15 @@ if typeof(Pkg.installed("JLD")) == VersionNumber
end
using Compat.DelimitedFiles
+# load Homebrew/WinRPM for gnuplot and imagemagick
+if is_apple()
+ using Homebrew
+end
+
+if is_windows()
+ using WinRPM
+end
+
## IO functions
export writeSimulation
t@@ -1057,3 +1066,181 @@ function removeSimulationFiles(simulation::Simulation; folder::String=".")
run(`bash -c "rm -rf $(folder)"`)
nothing
end
+
+export plotGrainSizeDistribution
+"""
+ plotGrainSizeDistribution(simulation, [filename_postfix, nbins,
+ size_type, filetype, gnuplot_terminal,
+ skip_fixed, log_y, verbose)
+
+Plot the grain size distribution as a histogram and save it to the disk. The
+plot is saved accoring to the simulation id, the optional `filename_postfix`
+string, and the `filetype`, and is written to the current folder.
+
+# Arguments
+* `simulation::Simulation`: the simulation object containing the grains.
+* `filename_postfix::String`: optional string for the output filename.
+* `nbins::Int`: number of bins in the histogram (default = 12).
+* `size_type::String`: specify whether to use the `contact` or `areal` radius
+ for the grain size. The default is `contact`.
+* `filetype::String`: the output file type (default = "png").
+* `gnuplot_terminal::String`: the gnuplot output terminal to use (default =
+ "png").
+* `skip_fixed::Bool`: ommit grains that are fixed in space from the size
+ distribution (default = true).
+* `log_y::Bool`: plot y-axis in log scale.
+* `verbose::String`: show output file as info message in stdout (default =
+ true).
+"""
+function plotGrainSizeDistribution(simulation::Simulation;
+ filename_postfix::String = "",
+ nbins::Int=12,
+ size_type::String = "contact",
+ filetype::String = "png",
+ gnuplot_terminal::String = "png",
+ skip_fixed::Bool = true,
+ log_y::Bool = false,
+ verbose::Bool = true)
+
+ diameters = Float64[]
+ for i=1:length(simulation.grains)
+ if simulation.grains[i].fixed && skip_fixed
+ continue
+ end
+ if size_type == "contact"
+ push!(diameters, simulation.grains[i].contact_radius*2.)
+ elseif size_type == "areal"
+ push!(diameters, simulation.grains[i].areal_radius*2.)
+ else
+ error("size_type '$size_type' not understood")
+ end
+ end
+
+ filename = string(simulation.id * filename_postfix *
+ "-grain-size-distribution." * filetype)
+
+ # write data to temporary file on disk
+ datafile = Base.Filesystem.tempname()
+ writedlm(datafile, diameters)
+ gnuplotscript = Base.Filesystem.tempname()
+
+ #if maximum(diameters) ≈ minimum(diameters)
+ #info("Overriding `nbins = $nbins` -> `nbins = 1`.")
+ #nbins = 1
+ #end
+
+ open(gnuplotscript, "w") do f
+
+ write(f, """#!/usr/bin/env gnuplot
+ set term $gnuplot_terminal
+ set out "$(filename)"\n""")
+ if log_y
+ write(f, "set logscale y\n")
+ end
+ write(f, """set xlabel "Diameter [m]"
+ set ylabel "Count [-]"
+ binwidth = $((maximum(diameters) - minimum(diameters)+1e-7)/nbins)
+ binstart = $(minimum(diameters))
+ set boxwidth 1.0*binwidth
+ set style fill solid 0.5
+ set key off
+ hist = 'u (binwidth*(floor((\$1-binstart)/binwidth)+0.5)+binstart):(1.0) smooth freq w boxes'
+ plot "$(datafile)" i 0 @hist ls 1
+ """)
+ end
+
+ try
+ run(`gnuplot $gnuplotscript`)
+ catch return_signal
+ if isa(return_signal, Base.UVError)
+ error("Could not launch external gnuplot process")
+ end
+ end
+
+ if verbose
+ info(filename)
+ end
+end
+
+export plotGrains
+"""
+ plotGrains(simulation, [filetype, gnuplot_terminal, verbose])
+
+Plot the grains using Gnuplot and save the figure to disk.
+
+# Arguments
+* `simulation::Simulation`: the simulation object containing the grains.
+* `filetype::String`: the output file type (default = "png").
+* `gnuplot_terminal::String`: the gnuplot output terminal to use (default =
+ "png").
+* `verbose::String`: show output file as info message in stdout (default =
+ true).
+"""
+function plotGrains(sim::Simulation;
+ filetype::String = "png",
+ gnuplot_terminal::String = "png",
+ show_figure::Bool = true,
+ verbose::Bool = true)
+
+ mkpath(sim.id)
+ filename = string(sim.id, "/", sim.id, ".grains.", sim.file_number, ".",
+ filetype)
+
+ x = Float64[]
+ y = Float64[]
+ r = Float64[]
+ for grain in sim.grains
+ push!(x, grain.lin_pos[1])
+ push!(y, grain.lin_pos[2])
+ push!(r, grain.contact_radius)
+ end
+
+ # write data to temporary file on disk
+ datafile = Base.Filesystem.tempname()
+ writedlm(datafile, [x y r])
+ gnuplotscript = Base.Filesystem.tempname()
+
+ open(gnuplotscript, "w") do f
+
+ write(f, """#!/usr/bin/env gnuplot
+ set term $(gnuplot_terminal) crop size 1200,1200
+ set out "$(filename)"
+ set palette defined (0 "gray", 1 "white")
+ set xlabel "x [m]"
+ set ylabel "y [m]"\n""")
+ if typeof(sim.ocean.input_file) != Bool
+ write(f, "set xrange ")
+ write(f, "[$(sim.ocean.xq[1,1]):$(sim.ocean.xq[end,end])]\n")
+ write(f, "set yrange ")
+ write(f, "[$(sim.ocean.yq[1,1]):$(sim.ocean.yq[end,end])]\n")
+ else
+ write(f, "set xrange [$(minimum(x - r)):$(maximum(x + r))]\n")
+ write(f, "set yrange [$(minimum(y - r)):$(maximum(y + r))]\n")
+ end
+ write(f, """set cblabel "Diameter [m]"
+ set size ratio -1
+ set key off
+ plot "$(datafile)" with circles lt 1 lc rgb "black" t "Particle"
+ """)
+ end
+
+ try
+ run(`gnuplot $gnuplotscript`)
+ catch return_signal
+ if isa(return_signal, Base.UVError)
+ error("Could not launch external gnuplot process")
+ end
+ end
+
+ if verbose
+ info(filename)
+ end
+
+ if show_figure
+ if is_apple()
+ run(`open $(filename)`)
+ elseif is_linux()
+ run(`xdg-open $(filename)`)
+ end
+ end
+end