G4DAE : Export Geant4 Geometry to COLLADA/DAE XML files

http://simoncblyth.bitbucket.io/env/presentation/g4dae_geometry_exporter.html http://simoncblyth.bitbucket.io/env/presentation/gpu_optical_photon_simulation.html

Exporter details
What is COLLADA/DAE ?
Validating exports
General viewing of exports
Custom use: bridging to GPU
OpenGL Viewer implementation
Optical Photon Data handling
Introducing Chroma
Chroma raycasting
Chroma photon propagation
G4DAE Exporter status
Conclusion

Simon C Blyth, Daya Bay Collaboration, National Taiwan University

19th Geant4 Collaboration Meeting, Okinawa, Sept 2014, Parallel Session B2, Visualization Group (Invited Speaker)

https://bitbucket.org/simoncblyth/g4dae

Exports Geant4 Geometry into COLLADA/DAE standard 3D files, based on GDML writer code, same XercesC dependency for XML handling. Export includes:

volume tree: solid/physical volume/logical volume heirarchy
geometry: vertices, triangles+quads (triangulation from G4Polyhedron)
materials and surfaces with properties as function of wavelength (using DAE extra XML elements)

/env/geant4/geometry/collada/g4dae/g4dae_bitbucket.png

COLLADA : Standard for 3D Digital Asset Exchange (DAE)

https://www.khronos.org/collada/

/env/graphics/collada/collada_khronos.png

Compare DAE Exports to GDML and VRML2(WRL)

Export validation:

Comparison of all vertices/faces reveals boolean solids are discrepant.

Perfect [1] DAE WRL agreement achieved by cheating : perform triangulation once and reuse.

Boolean solid triangulation sensitivity must be kept in mind as a potential systematic for computational uses

DAE not much bigger than GDML, despite including all triangles/vertices [2]

Qty	DayaBay	Lingao	Far	Juno x0.5
Volumes	12,229	12,229	18,903	25,000
Triangles	2,448,064	2,448,064	4,189,680	21,886,158
Vertices	1,245,996	1,245,996	2,128,208	10,993,079
DAE/GDML/WRL (MB)	6.9/4.0/98	6.9/4.0/96	8.6/6.0/167	6.1/-/-

VGDX_20140414 counts using g4daeview.py -g 0: --with-chroma, Juno geometry truncated

[1]	Maximum DAE WRL offset < 0.13 mm, after patching VRML2 export precision bug (fixed in current G4). Details: http://simoncblyth.bitbucket.io/env/notes/geant4/geometry/collada/dae_cf_wrl/

[2]	Geometry is not repeated, instead the COLLADA format uses geometry instancing and a tree of transforms, just like GDML

Tested G4DAE reading applications and frameworks

Commercial:

Finder/Quicklook/Preview/Xcode (standard OSX 10.8+)
- Xcode : useful effect tweaking interface
- Preview : set black background for visibility
Sketchup 8 free (OSX) [also Windows]
ESKO Studio Viewer free (iOS on iPad)

Open source:

Meshlab (OSX/Linux), slow DAE loading, OK interface [also Windows]
Blender (OSX), painful GUI [also Windows/Linux]

Frameworks:

pycollada, Python COLLADA parsing/construction, lxml + numpy powered fast parsing
threejs, Javascript COLLADA loading, renders HTML canvas with WebGL
SceneKit, Objective C Framework used by OSX apps

Many more applications and frameworks listed http://en.wikipedia.org/wiki/COLLADA

http://meshlab.sourceforge.net https://bitbucket.org/simoncblyth/meshlab (fork improves COLLADA loading speed)

G4DAE export in OSX Finder, Interactive Quicklook (1)

Coverflow through geometries:

/env/geant4/geometry/collada/osx_finder/g4dae_osx_finder.png

G4DAE export in OSX 10.8+ Finder, Rotate/Pan/Zoom

Rotate/Pan/Zoom in the Finder:

/env/geant4/geometry/collada/osx_finder/g4dae_osx_finder_2.png

G4DAE export view/edit with OSX Xcode.app (1)

Deep tree makes choice of default appearance problematic. Useful editing.

/env/geant4/geometry/collada/xcode/g4dae_xcode.png

G4DAE export view/edit with OSX Xcode.app (2)

Bialkali PMT cathode highlighted by Xcode effect edit.

/env/geant4/geometry/collada/xcode/g4dae_xcode_2.png

G4DAE export in OSX 10.8+ Preview : Daya Bay Antineutrino Detector

Set black background for visibility Preview > Preferences... > General [Window Background]
Control with iOS-like gestures, pinch/rotate etc..

/env/geant4/geometry/collada/osx_preview/g4dae_osx_preview.png

G4DAE export in OSX Sketchup

Available for Windows too.

/env/geant4/geometry/collada/sketchup/g4dae_sketchup.png

My Modules/Applications using G4DAE exports (OSX/Linux)

g4daenode.py pycollada based G4DAE parser

reconstructs Geant4 volume tree from raw tree
parses extra material/surface properties
provides partial geometry tree creation

g4daeserver.py threejs/WebGL (client) and pycollada/webpy (server) based webapp:

3D geometry viewer in the browser, NO client installation
useful for debugging single volumes
did not pursue as python development more flexible than Javascript in browser

g4daeview.py pyopengl/pycollada/numpy based 3D viewer app

many interactive features detailed later
integrates with GPU/CUDA based Chroma project
live link to Geant4 (via StackAction sending optical photons over ZeroMQ message queue)

https://bitbucket.org/simoncblyth/env/src/tip/geant4/geometry/collada/g4daenode.py https://bitbucket.org/simoncblyth/env/src/tip/geant4/geometry/g4daeserver/ https://bitbucket.org/simoncblyth/env/src/tip/geant4/geometry/collada/g4daeview/g4daeview.py

g4daeview.py : Fast OpenGL 3D viewer for G4DAE files

G4DAE visualization [3] implemented with PyCollada, PyOpenGL and Glumpy

very fast/responsive 3D OpenGL visualization [4]
flexible tree/list based partial geometry loading
intuitive virtual trackball translate/rotate
parallel or perspective projections
interactive fov and near/far plane clipping
persistent viewpoint bookmarks
animation by interpolation between bookmarks or orbiting
numerical control via UDP remote messaging
live Geant4 connection, photon visualization, single stepping
easily extensible python implementation [5]
photon picking interface, with property inspection

Also used for testing GPU photon propagation with Chroma project

interactive raycasting, including animated
propagation visualization, with time slider

[3]	http://simoncblyth.bitbucket.io/env/notes/geant4/geometry/collada/g4daeview/g4daeview_usage/

[4]	Implemented with single OpenGL Vertex Buffer Object (VBO) for entire geometry

[5]	https://bitbucket.org/simoncblyth/env/src/tip/geant4/geometry/collada/g4daeview/

g4daeview.py : Initial Photon Positions

Initial photon positions of a Geant4 simulated muon that crosses between the Dayabay Near hall ADs. Colors represent photon wavelengths. Optical photons: collected in G4 StackAction, serialized, sent over ZeroMQ, deserialized, presented using OpenGL GLSL shaders.

/env/geant4/geometry/collada/g4daeview/20140518-174941.png

g4daeview.py : Implementation

Based on glumpy [6] and pyopengl [7]

started from .obj viewer [8]
added vertices, triangles from G4DAE export
- entire geometry in single VBO
- only one OpenGL command needed to draw
immediately (few hrs): shockingly fast graphics
- smoothly slinging around ~2.5M triangles, no stuttering

[6]	https://code.google.com/p/glumpy/ many useful examples of pyopengl usage

[7]	http://pyopengl.sourceforge.net cross platform Python binding to OpenGL and related APIs

[8]	http://bitbucket.org/simoncblyth/env/src/tip/graphics/glumpy/glumpy_examples/obj-viewer-structured.py

g4daeview.py : Optical Photon (OP) Data Handling

Photon data flow:

OP collected in StackAction::ClassifyNewTrack and killed [9]
NewStage send OP lists [10] to CUDA/Chroma process, propagated on GPU
reply back to NewStage to form hits

When visualizing/debugging:

populate OpenGL VBO data structure
on load, propagate, saving steps into VBO slots
presentation, every frame:
- photon styles, GLSL shaders: spagetti, confetti, noodles, ...
- simple CUDA presenter kernel to interpolate between steps based on an input time

[9]	Would be more efficient to collect OP inside Cerenkov and Scintillation processes, avoiding creating and stacking only to immediately kill.

[10]	ROOT TObject (de)serialization, network message queue ZeroMQ

g4daeview.py : Status

Not mature, but intend to facilitate usage anyhow.

Plan:

break out into separate bitbucket repository
- https://bitbucket.org/simoncblyth/env/src/tip/geant4/geometry/collada/g4daeview/

degrade to OpenGL only features, when CUDA not available
- glumpy/pyopengl/numpy/pycollada : visualization/navigation/bookmarks
- Chroma/PyCUDA/Chroma : photon propagation, raycasting

document installation and usage

Chroma : Ultra-fast Photon MC, Developed by Stan Seibert, University of Pennsylvania

http://chroma.bitbucket.org

Chroma tracks photons through a triangle-mesh detector geometry, simulating processes like diffuse and specular reflections, refraction, Rayleigh scattering and absorption. Using triangle meshes eliminate geometry code as just one code path.

200x performance claim:

With a CUDA GPU Chroma has propagated 2.5M photons per second in a detector with 29k photomultiplier tubes. This is 200x faster than GEANT4.

BUT Chroma needs : triangles + inside/outside materials

http://on-demand.gputechconf.com/gtc/2013/presentations/S3304-Particle-Physics-With-PyCUDA.pdf

Chroma Raycasting : exercises geometry intersection

Raycasting exercises slowest part of optical photon propagation: geometry intersection.

/env/chroma/chroma_camera/chroma_raycast_illustration.png

Shoot rays thru every pixel out into geometry, 1 CUDA thread for each, typically >1M rays
Find triangle intersections using BVH [11] acceleration structure
Determine color based on ray to triangle normal angle
Alpha blend nearest 10 surfaces, providing transparency effect

[11]	Boundary Volume Heirarchy, a tree of bounding boxes with triangles inside leaf nodes

Chroma Raycast with entire geometry in view

Render Split into 3x3 CUDA kernel launches, 1 thread per pixel, ~1.8s for 1.23M pixels, 2.4M tris (with [12])

/env/chroma/chroma_camera/20140423-162109.png

[12]	MacBook Pro (2013), NVIDIA GeForce GT 750M 2048 MB ; Workstation GPUs such as NVIDIA Kepler K20 expected at least ~3x faster

g4daeview.py : Dayabay Chroma Photon Propagation (1)

Chroma GPU photon propagation at 12 nanoseconds. The photons are generated by Geant4 simulation of a 100 GeV muon travelling from right to left. Photon colors indicate reemission (green), absorption(red), specular reflection (magenta), scattering(blue), no history (white).

/env/geant4/geometry/collada/g4daeview/20140716-161445.png

g4daeview.py : Dayabay Chroma Photon Propagation (2)

Chroma GPU photon propagation at 14 nanoseconds. The interface provides interactive control of the propagation time allowing any stage of the propagation to be viewed by scrubbing time backwards/forwards. The speed of this visualization is achieved by interoperation of CUDA kernels and OpenGL shaders accessing the same GPU resident photon propagation data.

/env/geant4/geometry/collada/g4daeview/20140716-163403.png

G4DAE Exporter Status : almost feature complete

Development started with GDML from geant4.10.00.p01

made minor backports to work with geant4.9.2.p01
patched old version to give access to material property tables

Remaining tasks:

test with newer and latest versions of Geant4

implement parametrized/replica geometry handling, following GDML
confirm issue (inherited from GDML) of edge case skipped G4LogicalBorderSurface where a volume is shared between multiple volume pairs.

test on more geometries, currently mainly DayaBay and JUNO

export appearance adjustments
- current uniform translucent white, invisible when white background
- too many parameters, unclear what to use for defaults
- investigate propagating from G4VisAttributes

review code:
- remove: unused parsing inherited from GDML

G4DAE : Conclusion

https://bitbucket.org/simoncblyth/g4dae

I propose to contribute the COLLADA/DAE geometry exporter to the Geant4 collaboration, as I believe this can be useful for facilitating:

fast/flexible/ubiquitous visualization
external computation using geometry data such as
- GPU raycasting
- GPU optical photon simulation

Links for this presentation and another on GPU optical photon propagation:

Extra slides

g4daeserver.py : View exported geometry in web browser
g4daeserver.py : View exported geometry in web browser, details
g4daeview.py : Photon Selection Interface
g4daeview.py : Propagation Step Selection Interface

g4daeserver.py : View exported geometry in web browser

/env/geant4/geometry/collada/webgl_safari_daeserver/webgl_safari_daeserver.png

g4daeserver.py : View exported geometry in web browser, details

Select volume subtree by name or index and recursion depth

http://belle7.nuu.edu.tw/g4dae/tree/3150___1.html

Client in browser based on:

threejs, Javascript 3D library
- reads DAE geometry subtrees from server
- parses DAE and renders with WebGL (OpenGL GPU accelerated)

Server:

g4daenode.py, reconstructs Geant4 tree from G4DAE export using pycollada parser
webpy, serve .html and .dae subtrees at each request, running under apache mod_fcgi

Command line access to DAE subtrees:

curl -O http://belle7.nuu.edu.tw/g4dae/tree/3155___2.dae

http://threejs.org http://pycollada.github.io http://webpy.org https://bitbucket.org/simoncblyth/env/src/tip/geant4/geometry/g4daeserver/ https://bitbucket.org/simoncblyth/env/src/tip/geant4/geometry/collada/g4daenode.py

g4daeview.py : Photon Selection Interface

Propagation steps OR photons can be selected by materials, propagation history, or special selection by photon identifier. Photons can be selected by clicking their 3D representations allowing inspection of the propagation history of individual photons.

/env/geant4/geometry/collada/g4daeview/grab_glut_menu.png

g4daeview.py : Propagation Step Selection Interface

Photon propagation steps with material pair GdDopedLS,Acrylic. The larger squares represent selected photons, providing access to numerical details of propagation history.

/env/geant4/geometry/collada/g4daeview/20140716-183318.png