Welcome to 3D Welcome to 3D Visualization and the Visualization and the GeowallGeowall

Christian Educators Annual Fall ConferenceOctober 2005

The King’s University College, Edmonton

Dr. Brian MartinDr. Peter MahaffyThe King’s Centre for Visualization in Science

The Myth of Visualization as “Seeing is Believing” A Simple Task…

Watch the white team and count the exact number of times the white team passes the ball back and forth

Workshop Goals… Acquaint you with current best practices in

developing science visualizations Provide you with sufficient technical understanding

to set up your own Geowall Provide you with insights into presently available

software options to use with Geowall Assist you in applying Geowall technology to your

visualization interests Work collectively on understanding the educational

application of Geowall The best kept secret

The King’s Center for Visualization in Science (KCVS)

Explore ways in which visualization (not just computer based) can be used to enhance understanding: Among students Among researchers

Explore ways to implement visualizations into teaching at both secondary and post secondary levels

To work within international communities of scholars researching topics related to visualization

KCVS: Past, Present, Future

Modular Approach to Physics Project (MAP) 1997 – 2004

Gordon Research Conferences Centres for Research in Youth, Science

Teaching and Learning - CRYSTALS

Gordon Research Conference on Visualization in

Science & Education,Oxford, July 2005

Mahaffy (Chair)Martin (Workshop Leader)

Flowing water in SE Jordan

NASA Satellite Image

New emphases

Visualization in nanotechnology Best practices in production and dissemination of

educational visualizations Visualization in genomics and systems biology Computer graphics / cognitive science interface Visualization for public understanding of science Physical models and touch in forming mental models Geo-Wall 3D visualization applied to other disciplines

http://www.grc.org/

King’s, KCVS and CRYSTALS

5 year, 200K/a, Mahaffy (co-PI), Martin (management team &co-PI)

Project involves U of A, King’s, 3 other post-secondaries, Edmonton Schools, Telus World of Science and others

Current projects KCVS will play a role in: Visualizing Global Climate Change (with NSF)

Ethical Use of Chemicals (with IUPAC)

Major role for undergraduate student researcher/programmers

Car on a banked roadway

Applets that Help the Student Visualize Complex Phenomena

Thin Film Interference

Applets that Help the Student Visualize Complex Phenomena

First … a fast breaking news story

Refresher course on polarized light… Plane polarized light – what is it? Simple (and fun!) demos with polarized light

Scotch Plastics De-polarizers

Tape!

I. Geowall – Technical Considerations Uses 2-matched DLP

projectors (“left” & “right”) each outputting a plane polarized image rotated 900 wrt the other.

Screen is “daylite” type – polarization preserving

Eyeglasses “decode” left and right eye information – your brain does the rest!

Geowall – Technical Considerations

Left-channel image Right-channel image

Left channel image is projected through the

left channel DLP projector and is plane-polarized as shown

Right channel image is projected through the

right channel DLP projector and is plane-

polarized as shown

Geowall – Technical Considerations Projectors are stacked

vertically with 3 rotational and translational degrees-of-freedom

Computer should be equipped with a video board capable of running 2 monitors

Passive stereo – image “stacking”

Crude alignment can be achieved using separate monitor windows from each projector

Geowall – Technical Considerations Left and Right channel

polaroids are placed in front of the lens – avoid touching the lenses as conducted heat will quickly (< 1 hour) degrade filters

Final alignment achieved by using stereoviewer and the Geowall alignment image

Not quite!BetterGood (not perfect)!

Congratulations – you are readyCongratulations – you are ready for stereo projection!for stereo projection!

II. Software – Creating Stereo Images Two parts:

Creating or capturing L and R channel images

Combining L and R channel images.

More on Creating Stereo Images Digital

Camera Two images

contain all of the stereo information needed for your brain to produce a stereo pair

Translate camera L to R

More on Creating Stereo Images 3D Image rendering

software Blender – freeware

(outstanding package but steep learning curve)

Bryce (more accessible but not free)

Either offset “camera” or scene and render both L and R channel images.

Combining Left and Right Channels “Do-it-yourself”:

GIMP (freeware – excellent!) Fireworks, Photoshop etc

Stereo Image Software Pokescope (low cost < $30USD)

III. Free Software that Supports Stereo Projection Chemistry/Biology:

JMOL Pymol VMD Protein Explorer

Physics/Astronomy VPython Astrowall suite Wallview

IV. Using 3D Projection to Enhance Student Understanding Astronomy:

Understanding phases, eclipses Physics

Magnetic fields around wires Organic Chemistry

Stereo chemistry Biochemistry

DNA, protein structure, etc

Visualizing the World Too Small To See:

Small Matters Christina deMatteis, University of Nottingham

The Importance of Multiple Representations at the Molecular LevelRoy Tasker, Univ. Western SydneyModels in Chemistry

“The most powerful thing you can do when you’re learning chemistry is to zoom down, in your mind’s eye, to the molecular level and try to imagine what is going on and in a sense, try to understand the personalities of the reactants and products…

Having each type of model show a different aspect is ideal. Because then students don’t look at a particular model and say: that’s reality.”

"Since garlic hath powers to save from death, bear with it though it makes unsavory breath"

Robert of Normandy, 1100 AD Literature Reports

Allium sativum

• Broad spectrum antibacterial activity, including Helicobacter pylori• Antifungal activity• Antiviral activity• Normalization of plasma lipid levels• Stimulates lymphocytes and elicits

anti-tumor effects• Anti-hypertensive effects• Bacillus anthracis inhibition?

2D TLC of dichloromethane

garlic extract

Several compounds

inhibit Bacillus subtilis growth

1st D

imen

sion

– L

ess

Pola

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olv

en

t

2nd Dimension–More Polar Solvent

Initial Spot

AllicinAllicin

Bioactive Compound: Allicin

E. Block.Agnew. Chem. Int. Ed. Engl. 1992, 31, 1135-1178

Mode of Action of Allicin

Interferes with microbial cellular function

DNA & RNA synthesisSignal transduction & apoptosis

Blocks the active site on sulfhydryl enzymes

Investigative laboratoriesFor majors and non-majors

SH

sulfhydryl enzyme

SH

sulfhydryl enzyme

SSR

from visual import *

#simple program to illustrate lunar nodes and eclipse conditions#In this example an eclipse is possible - the line of nodes points at the sunscene.stereo='passive'scene.stereodepth = 1scene.ambient = 0.005scene.lights = [vector(1,0,0)]scene.ambient=0.1

orb1=ring(pos=(1,1,1), axis=(0,1,0), radius=50, thickness=0.2, color = color.red)orb2=ring(pos=(1,1,1), axis=(0,1,0.2), radius=50 , thickness=0.2)earth = sphere(pos=(1,1,1), radius=5, color=color.blue)#sun = sphere(pos=(500,0,1), radius=15, color = color.yellow)lineofnodes = cylinder(pos=(-50,1,1), axis=(100,0,0), color=color.yellow, radius =0.4)moon = sphere(pos=(50,1,1), radius = 2)

angle = 0delta = 2e-2while 1: rate(10) angle = delta moon.rotate(angle=angle, axis=(0,1,0), origin=(1,1,1)) #lineofnodes.rotate(angle=angle/100, axis=(0,1,0), origin=(1,1,1))

Example using VPython

…easy as this!

Resources…

Geowall Site: http://geowall.geo.lsa.umich.edu/ Vpython: http://vpython.org/ VMD: http://www.ks.uiuc.edu/Research/vmd/ Protein Explorer:

http://www.umass.edu/microbio/chime/pe/protexpl/frntdoor.htm Gimp: http://www.gimp.org/ Blender: http://blender.org/

Contacts: Paul Morin @ Geowall (lpaul@umn.edu) Brian Martin (brian.martin@kingsu.ca)