GR: Plotting with Python or Julia - Scientific IT

Member of the Helmholtz Association
GR: Plotting with Python or Julia
July 11th – 17th, 2016
Scientific Computing with Python • Austin, Texas | Josef Heinen | @josef_heinen
http://goo.gl/XQsXhi
The main ideas behind GR
✓ procedural graphics backend (completely written in C) ➟ presentation of continuous data streams
✓ builtin support for 2D plotting and OpenGL (GR3) ➟ coexistent 2D and 3D world
✓ support for different programming languages including Python, Julia and
JavaScript
✓ backend support for Matplotlib (Python) and Plots (Julia)
✓ interoperability with GUIs (Qt, wx, Gtk) and web applications (Jupyter)
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
2
Use GR as a backend for Matplotlib
✓ combine the power of Matplotlib and GR ➟ select GR as a backend by setting the MPLBACKEND environment variable
export MPLBACKEND="module://gr.matplotlib.backend_gr"
✓ significantly improve the performance of existing Matplotlib applications
✓ create plots containing both 2D and 3D graphics elements (from different
packages)
✓ produce video contents on the fly by adding a single line of code ➟ no need to import an animation module or write extra code
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
3
Matplotlib using the GR backend
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July 11th – 17th, 2016
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Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
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… with Matplotlib’s new colormaps
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47
magma
plasma
inferno
viridis
terrain
seismic
rainbow
ocean
gnuplot2
gnuplot
cubehelix
CMRmap
coolwarm
bwr
brg
afmhot
gist_stern
gist_rainbow
gist_ncar
gist_heat
gist_earth
winter
summer
spring
spectral
pink
jet
hsv
hot
gray
copper
cool
bone
autumn
pilatus
brownscale
flame
redscale
magentascale
bluescale
cyanscale
greenscale
geologic
rainbowlike
glowing
grayscale
temperature
uniform
5
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
July 11th – 17th, 2016
Use GR as a MATLAB–like plot interface
Advanced LIGO WHITENED strain data near GW150914
using GR
figure(figsize=(6,4))
4
2
whitented strain
tevent = 1126259462.422
d = readdlm("strain.dat")
time, H1_strain, L1_strain = d[:,1], d[:,2], d[:,3]
d = readdlm("nr_waveform.dat")
NRtime, NR_H1_whitenbp = d[:,1],d[:,2]
H1 strain
L1 strain
matched NR waveform
xlim([-0.1, +0.05])
ylim([-4,+4])
legend("H1 strain", "L1 strain”, "matched NR waveform")
xlabel(@sprintf("time (s) since %.3f", tevent))
ylabel("whitented strain")
title("Advanced LIGO WHITENED strain data near GW150914")
plot(time-tevent, H1_strain, "r",
time-tevent, L1_strain, "g",
NRtime+0.002, NR_H1_whitenbp, "k")
0
−2
−4
−0.10
−0.05
0
0.05
time (s) since 1126259462.422
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
6
… for 2D
using LsqFit
x = -16:0.5:35
y = 19.4./((x - 7).^2 + 15.8) + randn(size(x))./10;
1.0
model(x, p) = p[1]./((x-p[2]).^2+p[3])
fit = curve_fit(model, x, y, [25.,10.,10.])
p = fit.param
f = p[1]./((x-p[2]).^2+p[3])
0.5
using GR
plot(x, y, "d", x, f, "-", linewidth=2)
0
- 20
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
0
20
40
7
… for 2D (line, scatter)
1.0
1.0
J0
J1
J2
J3
0.8
0.5
0.6
0.4
0
0.2
- 0.5
July 11th – 17th, 2016
0
5
10
15
20
0
0
0.2
0.4
0.6
0.8
1.0
using GR
using GR
x = linspace(0,20,200)
for order in 0:3
plot(x, besselj(order, x))
hold(true)
end
legend("J_0", "J_1", "J_2", “J_3")
n = 500
x = rand(n)
y = rand(n)
area = pi .* (15 .* rand(n)).^2
scatter(x, y, area, 1:n, alpha=0.5)
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
8
… or 2D (filled contours)
using GR
6000
figure(size=(1000,500))
5000
600
4000
z = readdlm("TerrainHeight.txt")
3000
400
contourf(max(z’,-1500),
xlim=(0,1440), ylim=(0,720),
colormap=GR.COLORMAP_TERRAIN)
2000
1000
200
0
- 1000
0
0
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
500
1000
9
… or 3D (surface)
using GR
inline("mov")
figure(size=(800,800))
z = Z = readdlm("sans.dat")
G = [ exp(-x^2 -y^2) for
x in linspace(-1.5, 1.5, 128),
y in linspace(-1.5, 1.5, 128) ]
for t = 0:500
surface(z, title="Time: $t s")
z += 0.05 * Z .* G .* rand((128, 128))
end
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
10
… or 3D (iso surface)
using GR
inline("mov")
Ψv = calculate_electronic_density(3, 2, 0)
for alpha in 30:210
isosurface(Ψv, isovalue=0.25, rotation=alpha)
end
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
11
Mix 2D and 3D scenes and create video content on the fly
jlgr
GR3
GR
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
12
Use GR with Interact
using Interact
using GR
inline()
z = peaks()
maps = Dict(“gnuplot"=>39,
“viridis"=>44,
"inferno"=>45)
@manipulate for θ=20:1:70, Φ=20:1:70,
cmap=radiobuttons([“gnuplot",
“viridis",
"inferno"])
surface(z, rotation=θ, tilt=Φ,
colormap=maps[cmap])
end
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
13
… or with JavaScript
JavaScript
GR can be transpiled to JS ➟ gr.js (Emscripten: LLVM–to–JavaScript compiler)
➟ call GR functions from JS <canvas id="canvas" width="500" height="500"></canvas>
<script type="text/javascript" src="gr.js"></script>
<script type="text/javascript">
GR.ready(function() {
var gr = new GR();
var t = 0;
var x = new Array(629);
var y = new Array(629);
var draw = function() {
gr_clearws();
var i;
for (i = 0; i < 629; i++) {
x[i] = i / 630.0 * 2 * Math.PI;
y[i] = Math.sin(x[i] + t / 10.0);
}
Use cases:
gr_setviewport(0.1, 0.95, 0.1, 0.95);
gr_setwindow(0, 8, -1, 1);
gr_setcharheight(0.020);
gr_grid(0.5, 0.1, 0, -1, 4, 5);
gr_axes(0.5, 0.1, 0, -1, 4, 5, 0.01);
gr_polyline(629, x, y);
gr_updatews();
t = t + 1;
if (t < 200) {
setTimeout(draw, 1);
}
✓ embed JS code in Jypyter
✓ interpret GR display list in the browser
};
draw();
});
</script>
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
14
Use GR with Gtk …
function paint(w)
ctx = Gtk.getgc(w)
Gtk.show_text(ctx, "Contour Plot using Gtk ...")
ENV["GKS_WSTYPE"] = "142"
ENV["GKSconid"] = @sprintf("%lu", UInt64(ctx.ptr))
…
x, y, z = gridit(xd, yd, zd, 200, 200)
h = linspace(-0.5, 0.5, 20)
surface(x, y, z, 5)
contour(x, y, h, z, 0)
polymarker(xd, yd)
axes(0.25, 0.25, -2, -2, 2, 2, 0.01)
end
win = @Window("Gtk")
canvas = @Canvas(600, 450)
Gtk.push!(win, canvas)
Gtk.draw(paint, canvas)
Gtk.showall(win)
…
Gtk.gtk_main()
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
15
… or with PyQt / PySide
class GrWidget(QtGui.QWidget):
def __init__(self):
QtGui.QWidget.__init__(self)
self.setup_ui(self)
self.rubberband = QtGui.QRubberBand(QtGui.QRubberBand.Rectangle, self)
self.setMouseTracking(True)
environ["GKS_WSTYPE"] = "381"
…
def paintEvent(self, ev):
self.painter.begin(self)
if have_pyside:
environ['GKSconid'] = "%x!%x" % (
long(shiboken.getCppPointer(self)[0]),
long(shiboken.getCppPointer(self.painter)[0]))
else:
environ["GKSconid"] = "%x!%x" % (unwrapinstance(self),
unwrapinstance(self.painter))
draw()
self.painter.end()
app = QtGui.QApplication(argv)
win = GrWidget()
win.show()
exit(app.exec_())
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
16
Use GR in Atom …
✓ powerful IDE
✓ syntax highlighting
✓ command completion
✓ inline graphics
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
17
… or in iTerm2
✓ terminal emulator for macOS
✓ syntax highlighting
✓ command completion
✓ inline graphics
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
18
Render molecules …
gr.setviewport(0, 1, 0, 1)
gr3.setbackgroundcolor(1, 1, 1, 1)
for angle in range(360):
gr.clearws()
gr3.clear()
gr3.drawmolecule('data/dna.xyz', bond_delta=2,
tilt=45, rotation=angle)
gr3.drawimage(0, 1, 0, 1, 1000, 1000,
gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.text(0.15, 0.95, "DNA rendered using gr3.drawmolecule")
gr.textext(0.15, 0.875, "\\alpha=%2d" % angle)
gr.updatews()
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
19
… and export a POV–Ray scene
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
20
Render spins
gr.setviewport(0, 1, 0, 1)
gr3.setbackgroundcolor(1, 1, 1, 1)
gr3.cameralookat(0, -60, 35, 0, -2, 0, 0, 2, 0)
for positions, directions, colors in …
gr.clearws()
gr3.clear()
gr3.drawspins(positions, directions, colors)
gr3.drawimage(0, 1, 0, 1, 1000, 1000,
gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.updatews()
gr3.export('spins.html', 1000, 1000)
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
21
Demos
✓ GR interoperability example
✓ interactive widget demo for a simple surface plot
✓ visualizing atomic orbitals in a Jupyter notebook
✓ use GR to visualize MRI data in an interactive notebook
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
22
Programs using GR: pyMolDyn
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
23
… GR as a backend for Plots.jl
julia> using Plots
julia> gr()
Plots.GRBackend()
10
10
250
8
75
250
y1
y2
8
200
200
6
150
100
4
6
150
100
4
50
2
Height
70
65
50
2
60
0
5
10
July 11th – 17th, 2016
15
20
5
10
15
20
2
4
6
8
VoicePart
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
24
Current Activities
✓ near completion of a “fully–featured” GR distribution for Windows based on
the MinGW–w64 toolchain
✓ improve the build and deployment process (self–contained GR packages)
✓ provide more (MATLAB–like) convenience functions
✓ proof–of–concept for an in–browser JavaScript–based GR interactive
renderer (based on gr.js)
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
25
What’s next?
IPython
QtTerm
C / C++ ...
GR3
GR
W
IP
off-screen
rendering
socket communication
direct
rendering
JavaScript generation
POV-Ray generation
QtTerm
✓ plattform–independent
Browser
Qt
WebGL
✓ interactive (zoom, pan, pick data, …)
OpenGL (WGL / CGL / GLX)
GKS
POV-Ray
EGS
✓ based on ModernGL
W
IP
✓ stand–alone viewer (C++, Qt 5.7)
Swift
PyPy
GKS logical device drivers
gksqt
wx
X11
Quartz
GKSTerm
Win32
Cairo
PNG
N
ew
Qt
X11
TikZ
LATEX
PDF
MOV
PS
0MQ
SVG
OpenGL
EGS ...
✓ extensibility using plugins
✓ combines 2D and 3D
HTML5
✓ high–performance rendering
✓ GKS driver
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
26
Why EGS? … because performance matters!
E.g. for the visualization of Micro Swimmers …
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
27
… or for the visualization of Skyrmion formations
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
28
Thank you for your attention
Questions?
Contact:
[email protected] @josef_heinen
Thanks to:
Florian Rhiem, Ingo Heimbach, Christian Felder, David Knodt, Jörg
Winkler, Fabian Beule, Philip Klinkhammer, Marvin Goblet, Daniel
Kaiser, et al.
July 11th – 17th, 2016
Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
29

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