Post on 19-Dec-2015
description
Scientific Visualization
May 22, 2014 !PGI-1 / IAS-1 | Scientific Visualization Workshop | Josef Heinen
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
✓ Motivation
✓ Scientific visualization software
✓ Visualization with Python
✓ Python performance optimizations
✓ Development tools
✓ Conclusion
✓ Future plans
✓ Discussion
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Outline
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
We need easy-to-use methods for:
✓ visualizing and analyzing two- and three-dimensional data sets, perhaps with a dynamic component
✓ creating publication-quality graphics
✓ making glossy figures for high impact journals or press releases
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Motivation
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
✓ line / bar graphs, curve plots
✓ scatter plots
✓ surface plots, mesh rendering with iso-surface generation
✓ contour plots
✓ vector / streamline plots
✓ volume graphics
✓ molecule plots
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Scientific plotting methods
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Scientific visualization tools
✓ Gnuplot
✓ Xmgrace
✓ OpenDX
✓ ParaView
✓ Mayavi2
✓ MATLAB
✓ Mathematica
✓ Octave, Scilab, Freemat
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
… drawbacks
✓ Gnuplot — limited functionality
✓ Xmgrace — too old, requires OSF/Motif (X11)
✓ OpenDX — no longer maintained (2007)
✓ ParaView — not very intuitive
✓ Mayavi2 — not very responsive
✓ MATLAB — 5 floating, 3 user licenses (16K €/year)
✓ Mathematica — expensive (~2.500 €/user)
✓ Octave, Scilab, Freemat — no syntax compatibility
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Scientific visualization APIs
✓ Matplotlib
✓ mlab, VTK
✓ OpenGL
✓ pgplot
✓ PyQtGraph
✓ PyQwt / PyQwt3D
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Scientific visualization APIs
✓ Matplotlib — de-facto standard (“workhorse”)
✓ mlab, VTK — versatile, but difficult to learn; slow
✓ OpenGL — large and complex
✓ pgplot — too old
✓ PyQtGraph — no yet mature
✓ PyQwt / PyQwt3D — currently unmaintained
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Remaining solutions
GUI + API:
✓ ParaView
✓ Mayavi2
API:
✓ matplotlib
✓ n.n. ← Let’s talk about this later …
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both based on VTK}
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems 10
ParaView
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems 11
Mayavi2
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems 12
matplotlib
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Problems so far
✓ separated 2D and (hardware accelerated) 3D world
✓ some graphics backends "only" produce pictures ➟ no presentation of continuous data streams
✓ bare minimum level of interoperability ➟ limited user interaction
✓ poor performance on large data sets
✓ APIs are partly device- and platform-dependent
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Isn’t there an all-in-one solution?
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All these components provide powerful APIsfor Python !
!
There must be a reason for that …
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
… so let’s push for Python
✓ free and open
✓ dynamic typed language, easy to understand
✓ powerful modules for science, technology, engineering and mathematics (STEM): NumPy, SciPy, Pandas, SymPy
✓ great visualization libraries: Matplotlib, MayaVi, VTK, PyOpenGL
✓ techniques to boost execution speed: PyPy, Cython, PyOpenCL, PyCUDA, Numba
✓ wrapper for GUI toolkits: PyQt4, PyGTK, wxWidgets
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
… get it up and running
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IPython + NumPy + SciPy + Matplotlib
What else do we need?
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
… achieve more Python performance
Numba: compiles annotated Python and NumPy code to LLVM (through decorators)
✓ just-in-time compilation
✓ vectorization
✓ parallelization
NumbaPro: adds support for multicore and GPU architectures
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(* Numba (Pro) is part of Anaconda (Accelerate), a (commercial) Python distribution from Continuum Analytics
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
… achieve more graphics performance and interop
GR framework: a universal framework for cross-platform visualization (*
✓ procedural graphics backend➟ presentation of continuous data streams
✓ coexistent 2D and 3D world
✓ interoperability with GUI toolkits➟ good user interaction
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(* The GR framework is an in-house project initiated by the group Scientific IT Systems
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
“Our” Scientific Python distribution
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IPython + NumPy + SciPy + Numba + GR framework +
PyOpenGL + PyOpenCL + PyCUDA + PyQt4/PyGTK/wxWidgets
➟ more performance and interoperability
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
How can we use it?
✓ GR framework (and other mentioned packages) available on all Linux and OS X machines(Python and IPython) at PGI / JCNS:% gr % igr"
✓ GR framework can also be used with Anaconda:% anaconda
✓ Windows version(s) on request
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Batteries included
✓ NumPy — package for numerical computation
✓ SciPy — collection of numerical algorithms and specific toolboxes
✓ Matplotlib — popular plotting package
✓ Pandas — provides high-performance, easy to use data structures
✓ SymPy — symbolic mathematics and computer algebra
✓ IPython — rich interactive interface (including IPython notebook)
✓ Mayavi2 — 3D visualization framework, based on VTK
✓ scikit-image — algorithms for image processing
✓ h5py, PyTables — managing hierarchical datasets (HDF5)
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Visualization with Python
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GKS logical device drivers
C / C++
GKS
GR
OpenGL (WGL / CGL / GLX)
POV-Raygeneration
off-screen rendering
direct rendering
Browser
JavaScriptgeneration
WebGL
IPython / PyPy/ Anaconda
Win32X11
GKSTermgksqt
Java
gksweb
Qt Quartz PDF
C / ObjC
OpenGL ES
glgr / iGR Appsocket
communication
Qt / wxevent loop
0MQ OpenGL
More logical device drivers / plugins: – CGM, GKSM, GIF, RF, UIL – WMF, Xfig – GS (BMP, JPEG, PNG, TIFF)
...
HTML5
wx
POV-Ray
GLUT wxGLCanvas QGLWidget
...
SVGPSMOV
GR3
Highlights: – simultaneous output to multiple output devices – direct generation of MPEG4 image sequences – flicker-free display ("double buffering")
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Presentation of continuous data streams in 2D ...
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from numpy import sin, cos, sqrt, pi, array import gr !def rk4(x, h, y, f): k1 = h * f(x, y) k2 = h * f(x + 0.5 * h, y + 0.5 * k1) k3 = h * f(x + 0.5 * h, y + 0.5 * k2) k4 = h * f(x + h, y + k3) return x + h, y + (k1 + 2 * (k2 + k3) + k4) / 6.0 !def damped_pendulum_deriv(t, state): theta, omega = state return array([omega, -gamma * omega - 9.81 / L * sin(theta)]) !def pendulum(t, theta, omega) gr.clearws() ... # draw pendulum (pivot point, rod, bob, ...) gr.updatews() !theta = 70.0 # initial angle gamma = 0.1 # damping coefficient L = 1 # pendulum length t = 0 dt = 0.04 state = array([theta * pi / 180, 0]) !while t < 30: t, state = rk4(t, dt, state, damped_pendulum_deriv) theta, omega = state pendulum(t, theta, omega)
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
... with full 3D functionality
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from numpy import sin, cos, array import gr, gr3 !def rk4(x, h, y, f): k1 = h * f(x, y) k2 = h * f(x + 0.5 * h, y + 0.5 * k1) k3 = h * f(x + 0.5 * h, y + 0.5 * k2) k4 = h * f(x + h, y + k3) return x + h, y + (k1 + 2 * (k2 + k3) + k4) / 6.0 !def pendulum_derivs(t, state): t1, w1, t2, w2 = state a = (m1 + m2) * l1 b = m2 * l2 * cos(t1 - t2) c = m2 * l1 * cos(t1 - t2) d = m2 * l2 e = -m2 * l2 * w2**2 * sin(t1 - t2) - 9.81 * (m1 + m2) * sin(t1) f = m2 * l1 * w1**2 * sin(t1 - t2) - m2 * 9.81 * sin(t2) return array([w1, (e*d-b*f) / (a*d-c*b), w2, (a*f-c*e) / (a*d-c*b)]) !def double_pendulum(theta, length, mass): gr.clearws() gr3.clear() ! ... # draw pivot point, rods, bobs (using 3D meshes) ! gr3.drawimage(0, 1, 0, 1, 500, 500, gr3.GR3_Drawable.GR3_DRAWABLE_GKS) gr.updatews()
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
... in real-time
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import wave, pyaudio import numpy import gr !SAMPLES=1024 FS=44100 # Sampling frequency !f = [FS/float(SAMPLES)*t for t in range(1, SAMPLES/2+1)] !wf = wave.open('Monty_Python.wav', 'rb') pa = pyaudio.PyAudio() stream = pa.open(format=pa.get_format_from_width(wf.getsampwidth()), channels=wf.getnchannels(), rate=wf.getframerate(), output=True) !... !data = wf.readframes(SAMPLES) while data != '' and len(data) == SAMPLES * wf.getsampwidth(): stream.write(data) amplitudes = numpy.fromstring(data, dtype=numpy.short) power = abs(numpy.fft.fft(amplitudes / 65536.0))[:SAMPLES/2] ! gr.clearws() ... gr.polyline(SAMPLES/2, f, power) gr.updatews() data = wf.readframes(SAMPLES)
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
... with user interaction
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import gr3 from OpenGL.GLUT import * # ... Read MRI data
width = height = 1000 isolevel = 100 angle = 0 !def display(): vertices, normals = gr3.triangulate(data, (1.0/160, 1.0/160, 1.0/200), (-0.5, -0.5, -0.5), isolevel) mesh = gr3.createmesh(len(vertices)*3, vertices, normals, np.ones(vertices.shape)) gr3.drawmesh(mesh, 1, (0,0,0), (0,0,1), (0,1,0), (1,1,1), (1,1,1)) gr3.cameralookat(-2*math.cos(angle), -2*math.sin(angle), -0.25, 0, 0, -0.25, 0, 0, -1) gr3.drawimage(0, width, 0, height, width, height, gr3.GR3_Drawable.GR3_DRAWABLE_OPENGL) glutSwapBuffers() gr3.clear() gr3.deletemesh(ctypes.c_int(mesh.value)) def motion(x, y): isolevel = 256*y/height angle = -math.pi + 2*math.pi*x/width glutPostRedisplay() glutInit() glutInitWindowSize(width, height) glutCreateWindow("Marching Cubes Demo") !glutDisplayFunc(display) glutMotionFunc(motion) glutMainLoop()
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
... with Qt
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
... and wxWidgets
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Scalable graphics in Web browsers
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Import PDF
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import gr (w, h, data) = gr.readimage("fs.pdf") if w < h: r = float(w)/h gr.setviewport(0.5*(1-r), 0.5*(1+r), 0, 1); else: r = float(h)/w gr.setviewport(0, 1, 0.5*(1-r), 0.5*(1+r)); gr.drawimage(0, 1, 0, 1, w, h, data) gr.updatews()
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Success stories (I)
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World’s most powerful laboratory small-angle X-ray scattering facility at
Forschungszentrum Jülich
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Success stories (II)
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BornAgain A software to simulate and fit neutron
and x-ray scattering at grazing incidence (GISANS and GISAXS), using distorted-
wave Born approximation (DWBA)
Nframes = 100 radius = 1 height = 4 distance = 5 !def RunSimulation(): # defining materials mAir = HomogeneousMaterial("Air", 0.0, 0.0) mSubstrate = HomogeneousMaterial("Substrate", 6e-6, 2e-8) mParticle = HomogeneousMaterial("Particle", 6e-4, 2e-8) # collection of particles cylinder_ff = FormFactorCylinder(radius, height) cylinder = Particle(mParticle, cylinder_ff) particle_layout = ParticleLayout() particle_layout.addParticle(cylinder) # interference function interference = InterferenceFunction1DParaCrystal(distance, 3 * nanometer) particle_layout.addInterferenceFunction(interference) # air layer with particles and substrate form multi layer air_layer = Layer(mAir) air_layer.setLayout(particle_layout) substrate_layer = Layer(mSubstrate) multi_layer = MultiLayer() multi_layer.addLayer(air_layer) multi_layer.addLayer(substrate_layer) # build and run experiment simulation = Simulation() simulation.setDetectorParameters(250, -4*degree, 4*degree, 250, 0*degree, 8*degree) simulation.setBeamParameters(1.0 * angstrom, 0.2 * degree, 0.0 * degree) simulation.setSample(multi_layer) simulation.runSimulation() return simulation.getIntensityData().getArray() def SetParameters(i): radius = (1. + (3.0/Nframes)*i) * nanometer height = (1. + (4.0/Nframes)*i) * nanometer distance = (10. - (1.0/Nframes)*i) * nanometer !for i in range(100): SetParameters(i) result = RunSimulation() gr.pygr.imshow(numpy.log10(numpy.rot90(result, 1)), cmap=gr.COLORMAP_PILATUS)
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Success stories (III)
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NICOS a network-based control
system written for neutron scattering
instruments at the FRM II
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Coming soon:Python moldyn package …
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
… with video output
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
… and POV-Ray output
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
… in highest resolution
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Performance optimizations
✓ NumPymodule for handling multi-dimensional arrays (ndarray)
✓ Numba (Anaconda)
✓ just-in-time compilation driven by @autojit- or @jit-decorators (LLVM)
✓ vectorization of ndarray based functions (ufuncs)
✓ Numba Pro (Anaconda Accelerate)
✓ parallel loops and ufuncs
✓ execution of ufunfs on GPUs
✓ “Python” GPU kernels
✓ GPU optimized libraries (cuBLAS, cuFFT, cuRAND)
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Realization
✓ NumPyvector operations on ndarrays instead of loops➟ works in any NumPy Python environment
✓ Numba (Anaconda)add @jit and @autojit decorators➟ useful for “many” function calls with “big” arrays
✓ Numba Pro (Anaconda Accelerate)add @vectorize decoratorsimplementation of multi-core / GPU kernels in "Python" switch to GPU-optimized features➟ useful only for "large" arrays
performance
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Particle simulation
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import numpy as np !!N = 300 # number of particles M = 0.05 * np.ones(N) # masses size = 0.04 # particle size !!def step(dt, size, a): a[0] += dt * a[1] # update positions ! n = a.shape[1] D = np.empty((n, n), dtype=np.float) for i in range(n): for j in range(n): dx = a[0, i, 0] - a[0, j, 0] dy = a[0, i, 1] - a[0, j, 1] D[i, j] = np.sqrt(dx*dx + dy*dy) ! ... # find pairs of particles undergoing a collision ... # check for crossing boundary return a ... !a[0, :] = -0.5 + np.random.random((N, 2)) # positions a[1, :] = -0.5 + np.random.random((N, 2)) # velocities a[0, :] *= (4 - 2*size) dt = 1. / 30 !while True: a = step(dt, size, a) ....
!from numba.decorators import autojit !!!!!@autojit !!!!!!!!!!!!!!!!!!!!!!!
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Diffusion
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import numpy !!dx = 0.005 dy = 0.005 a = 0.5 dt = dx*dx*dy*dy/(2*a*(dx*dx+dy*dy)) timesteps = 300 !nx = int(1/dx) ny = int(1/dy) ui = numpy.zeros([nx,ny]) u = numpy.zeros([nx,ny]) !!def diff_step(u, ui): for i in range(1,nx-1): for j in range(1,ny-1): uxx = ( ui[i+1,j] - 2*ui[i,j] + ui[i-1, j] )/(dx*dx) uyy = ( ui[i,j+1] - 2*ui[i,j] + ui[i, j-1] )/(dy*dy) u[i,j] = ui[i,j]+dt*a*(uxx+uyy) !!!for m in range(timesteps): diff_step (u, ui) ui = numpy.copy(u) ...
!from numba.decorators import jit !!!!!!!!!!!!!!!!!!!!diff_step_numba = jit('void(f8[:,:], f8[:,:])')(diff_step) !! diff_step_numba(u, ui) !
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Mandelbrot set
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from numbapro import vectorize import numpy as np !@vectorize(['uint8(uint32, f8, f8, f8, f8, uint32, uint32, uint32)'], target='gpu') def mandel(tid, min_x, max_x, min_y, max_y, width, height, iters): pixel_size_x = (max_x - min_x) / width pixel_size_y = (max_y - min_y) / height ! x = tid % width y = tid / width ! real = min_x + x * pixel_size_x imag = min_y + y * pixel_size_y ! c = complex(real, imag) z = 0.0j ! for i in range(iters): z = z * z + c if (z.real * z.real + z.imag * z.imag) >= 4: return i ! return 255 !!def create_fractal(min_x, max_x, min_y, max_y, width, height, iters): tids = np.arange(width * height, dtype=np.uint32) return mandel(tids, np.float64(min_x), np.float64(max_x), np.float64(min_y), np.float64(max_y), np.uint32(height), np.uint32(width), np.uint32(iters))
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Performance comparison
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Calculation of Mandelbrot set
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Numba (Pro) review
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✓ functions with numerical code can be compiled with little effort and lead to impressive results
✓ numerical code should be separated from logic statements (and processing of lists, dictionaries)
✓ advanced Technologie due to LLVM intermediate language (LLVM IR)
✓ easy installation and maintenanceDownload link (Continuum Analytics): http://www.continuum.io/downloads
% bash Anaconda-1.x.x-[Linux|MacOSX]-x86[_64].sh % conda update conda % conda update anaconda
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Development tools
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You can use your favorite editor and start Python in a shell. Butthe impatient user should chose a development environment:
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
IPython console
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
IPython notebook
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Spyder
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
PyCharm
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Bokeh
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import numpy as np from scipy.integrate import odeint from bokeh.plotting import * !sigma = 10 rho = 28 beta = 8.0/3 theta = 3 * np.pi / 4 !def lorenz(xyz, t): x, y, z = xyz x_dot = sigma * (y - x) y_dot = x * rho - x * z - y z_dot = x * y - beta* z return [x_dot, y_dot, z_dot] !initial = (-10, -7, 35) t = np.arange(0, 100, 0.006) !solution = odeint(lorenz, initial, t) !x = solution[:, 0] y = solution[:, 1] z = solution[:, 2] xprime = np.cos(theta) * x - np.sin(theta) * y !colors = ["#C6DBEF", "#9ECAE1", "#6BAED6", “#4292C6", "#2171B5", "#08519C", "#08306B",] !output_file("lorenz.html", title="lorenz.py example") !multi_line(np.array_split(xprime, 7), np.array_split(z, 7), line_color=colors, line_alpha=0.8, line_width=1.5, tools=“pan,wheel_zoom,box_zoom,reset,previewsave", title="lorenz example", name="lorenz_example") !show() # open a browser
May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Resources
✓ Website: http://gr-framework.org
✓ PyPI: https://pypi.python.org/pypi/gr
✓ Git Repository: http://github.com/jheinen/gr
✓ Binstar: https://binstar.org/jheinen/gr
✓ Talk: Scientific Visualization Workshop (PDF, HTML)
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Website
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Git-Repo
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
PyPI
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Binstar
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Conclusion
✓ The use of Python with the GR framework and Numba (Pro) extensions allows the realization of high-performance visualization applications in scientific and technical environments
✓ The GR framework can seamlessly be integrated into "foreign" Python environments, e.g. Anaconda, by using the ctypes mechanism
✓ Anaconda (Accelerate) is an easy to manage (commercial) Python distribution that can be enhanced by the use of the GR framework with its functions for real-time or 3D visualization applications
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Future plans
✓ implement your(!) feature requests
✓ moldyn package for Python
✓ more
✓ tutorials
✓ convenience functions
✓ documentation
✓ examples (gallery)
✓ IPython notebook integration
✓ Bokeh integration
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May 22, 2014 Josef Heinen, Forschungszentrum Jülich, Peter Grünberg Institute, Scientific IT Systems
Thank you for your attentionReferences:
Numba, A Dynamic Python compiler for Science: http://lanyrd.com/2013/pycon/scdyzh Continuum Analytics: http://www.continuum.io
!Contact:
j.heinen@fz-juelich.de @josef_heinen"
!Thanks to: Florian Rhiem, Ingo Heimbach, Christian Felder, David Knodt, Jörg Winkler, Fabian Beule, Marcel Dück, Marvin Goblet, et al.
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