ii escuela de optica biomedica, puebla, 2011 monte carlo, euler and quaternions jessica c....
TRANSCRIPT
![Page 1: II Escuela de Optica Biomedica, Puebla, 2011 Monte Carlo, Euler and Quaternions Jessica C. Ramella-Roman](https://reader038.vdocuments.net/reader038/viewer/2022110209/56649e175503460f94b032a4/html5/thumbnails/1.jpg)
II Escuela de Optica Biomedica, Puebla, 2011
Monte Carlo, Euler and Quaternions
Jessica C. Ramella-Roman
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II Escuela de Optica Biomedica, Puebla, 2011
Stokes vector reference
• Yesterday, Meridian plane– Three steps– “Rotate” to scattering plane• Rotational matrix
– Scatter• Scattering matrix
– “Rotate” to a new plane• Rotational matrix
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II Escuela de Optica Biomedica, Puebla, 2011
Today Monte Carlo
• Reference frame is a triplet of unit vectors
• Rotation are about an axis and follow a specific order
http://www.grc.nasa.gov/WWW/K-12/airplane
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II Escuela de Optica Biomedica, Puebla, 2011
Today Monte Carlo
• Reference frame is a triplet of unit vectors
• Rotation of the frame is done in two steps.
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II Escuela de Optica Biomedica, Puebla, 2011
Euler and Quaternion
• The only difference between today programs is the way we handle these rotations
• Euler angles rotation Quaternions algebra
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II Escuela de Optica Biomedica, Puebla, 2011
Euler Monte Carlo
• The photon polarization reference frame is tracked at any time via a triplet of unit vectors that are rotated by an azimuth and scattering angle according to a predefined order
• Introduced by Bartel et al. (*)
* S. Bartel, A. Hielsher, “Monte Carlo simulations of the diffuse backscattering Mueller matrix for highly scattering media,” Applied Optics, Vol. 39, No. 10; (2000).
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II Escuela de Optica Biomedica, Puebla, 2011
Euler matrices
• Euler's rotation theorem: any rotation may be described using three angles.
• And three rotation matrices– About z axis
– About x’ axis
– About z’ axis
Drawings, Wolfram, Mathworld
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II Escuela de Optica Biomedica, Puebla, 2011
Euler cnt.
• We only need TWO vectors and TWO rotations
• Two unit vectors v and u
• The third unit vector is defined by the cross product of v and u and is calculated only when a photon reaches a boundary.
€
v=[ vx , vy , vz ] = [0,1,0]
u=[ ux , uy , uz ] =[ 0,0,1]
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II Escuela de Optica Biomedica, Puebla, 2011
Euler cnt.
• Advantage – Stokes vector is rotated only once for each
scattering event instead of twice as in the meridian plane method.
– Simple to implement and visualize
• Drawback – – Gimbal lock - makes the rotation fail for angles
exactly equal to 90˚ (rare event).
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II Escuela de Optica Biomedica, Puebla, 2011
Monte Carlo flow chart
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II Escuela de Optica Biomedica, Puebla, 2011
Launch
• The two unit vector v and u
• v and u define the starting Stokes vector reference plane.
• The unit vector u represents the direction of photon propagation.
€
v=[ vx , vy , vz ] = [0,1,0]
u=[ ux , uy , uz ] =[ 0,0,1]
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II Escuela de Optica Biomedica, Puebla, 2011
Move
• The photon is moved a distance Ds, the new coordinates of the photon are
€
′ x =x+uxΔs
′ y =y+uyΔs
′ z =z+uzΔs
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II Escuela de Optica Biomedica, Puebla, 2011
Drop
• Reduction of photon weight (W)
• According to material albedo
• albedo = ms/(ms+ ma)
• absorbed = W*(1-albedo)
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II Escuela de Optica Biomedica, Puebla, 2011
Scatter
• The rejection method establishes the scattering angle q and azimuth angle f.
• The Stokes vector must be rotated by an angle f into the scattering plane before scattering can occur.
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II Escuela de Optica Biomedica, Puebla, 2011
Referencing to scattering plane
• Done as in meridian plane Monte Carlo
• Multiply the Stokes vector by matrix R
€
R φ( ) =
1 0 0 0
0 cos(2φ ) sin(2φ ) 0
0 − sin(2φ ) cos(2φ ) 0
0 0 0 1
⎡
⎣
⎢ ⎢ ⎢ ⎢
⎤
⎦
⎥ ⎥ ⎥ ⎥
Sout = R φ( )Sin
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II Escuela de Optica Biomedica, Puebla, 2011
Scatter cnt
• The interaction with a spherical particle is achieved by multiplying the Stokes vector with a scattering matrix M(q)
€
M θ( ) =
s11(θ ) s12(θ ) 0 0
s12(θ ) s11(θ ) 0 0
0 0 s33(θ ) s34(θ )
0 0 −s34(θ ) s33(θ )
⎡
⎣
⎢ ⎢ ⎢ ⎢
⎤
⎦
⎥ ⎥ ⎥ ⎥
Sout = M θ( )Sin
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II Escuela de Optica Biomedica, Puebla, 2011
M(q) elements
• s11 , s12 , s33 , s34 calculated with Mie theory
• Expressed as
• S1, S2* – Mie scattering
€
s11(θ )=12[ S2(θ )
2+ S1(θ )
2]
s12(θ )=12[ S2(θ )
2−S1(θ )
2]
s33(θ )=12[ S2
* (θ )S1(θ )+S2(θ )S1* (θ )]
s34(θ )= i2[ S2
* (θ )S1(θ )−S2(θ )S1* (θ )]
*http://omlc.ogi.edu/calc/mie_calc.html
C. Bohren and D. R. Huffman, Absorption and scattering of light by small particles, (Wiley Science Paperback Series,1998).
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II Escuela de Optica Biomedica, Puebla, 2011
Reference frame
• After scattering the Stokes vector the reference coordinate system v u must be updated.
• The two rotations, for the angles f and q can be obtained using Euler’s rotational matrices.
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II Escuela de Optica Biomedica, Puebla, 2011
Rotational matrix ROT
• Rodrigues’s rotational matrix ROT • Accomplishes the general case of rotating any
vector by an angle y about an axis K
• Where K is the rotational axis,• c=cos(y), s=sin(y) and v=1-cos(y).
€
ROT (K ,ψ ) =
kxkxv + c k ykxv − k zs k zkxv + k ys
kxk yv + k zs k yk yv + c k yk zv − kxs
kxk zv − k ys k yk zv + kxs k zk zv + c
⎡
⎣
⎢ ⎢ ⎢
⎤
⎦
⎥ ⎥ ⎥
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II Escuela de Optica Biomedica, Puebla, 2011
Vector rotation
• First the unit vector v is rotated about the vector u by an angle f
• Multiply v by the rotational matrix ROT(u,f); u remains unchanged
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II Escuela de Optica Biomedica, Puebla, 2011
Vector rotation
• Second u is rotated about the newly generated v by an angle q.
• This is done multiplying the unit vector u by the rotational matrix ROT(v,q).
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II Escuela de Optica Biomedica, Puebla, 2011
Update of direction cosines
• This is done as in standard Monte Carlo
• q and f
€
u^
x = (sin θ ) (cos φ)
u^
y = (sin θ ) (sin φ)
u^
z = (cosθ ) uzuz
If |uz| ≈ 1
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II Escuela de Optica Biomedica, Puebla, 2011
Update of direction cosines
€
u^
x =1
1−uz
2(sinθ )(uxuy (cosφ)−uy (sinφ))+ux (cosθ )
u^
y=1
1−uz
2(sinθ )(uxuz (cosφ)−ux (sinφ))+uy (cosθ )
u^
z = 1−uz
2 (sinθ ) (cosφ)(uyuz (cosφ)−ux (sinφ))+uz (cosθ )
If |uz| ≠ 1
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II Escuela de Optica Biomedica, Puebla, 2011
Photon life
• The life of a photon ends when the photon passes through a boundary or when its weight W value falls below a threshold.
• Roulette is used to terminate the photon packet when W £ Wth. – Gives the photon packet one chance of surviving– If the photon packet does not survive the roulette,
the photon weight is reduced to zero and the photon is terminated.
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II Escuela de Optica Biomedica, Puebla, 2011
Boundaries
• Two final rotations of the Stokes vector are necessary to put the photon status of polarization in the detector reference frame.
• This will be achieved with matrix multiplication of two rotational matrix by stokes vector
€
Sfinal=R(ψ )R( ε )S
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II Escuela de Optica Biomedica, Puebla, 2011
Boundaries – R(e)
• w is reconstructed as the cross product of v and u.
• An angle e is needed to rotate the Stokes vector into a scattering plane
€
w=v×u
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II Escuela de Optica Biomedica, Puebla, 2011
Boundaries – R(e)
• This is the ONLY reason we need the vector u, v, and w
€
ε =0 when vz =0 and uz =0
ε =tan−1( vz−wz
) in all other cases
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II Escuela de Optica Biomedica, Puebla, 2011
Boundaries – R(e)
• This rotation is about the direction of propagation of the photon, i.e. the axis u
• Resulting position of v
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II Escuela de Optica Biomedica, Puebla, 2011
Boundaries – R(y)
• A second rotation of an angle y about the Z axis
• Put the photon reference frame in the detector reference frame
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II Escuela de Optica Biomedica, Puebla, 2011
Boundaries – R(y)
• Transmission
• Reflection
€
ψ =tan−1(uy−ux
)
€
ψ =tan−1(uyux
)
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II Escuela de Optica Biomedica, Puebla, 2011
Boundaries End
• Stokes vector in the detector frame of reference
• We need vector u, v, and w to obtain these angles
€
Sfinal=R(ψ )R( ε )S
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II Escuela de Optica Biomedica, Puebla, 2011
Quaternion Monte Carlo
• Quaternion Monte Carlo simply uses Quaternion Algebra to handle vector rotation.
• Advantage – Stokes vector is rotated only once for each
scattering event instead of twice as in the meridian plane method.
– No issue with Gimbal lock – Optimized for computer simulations
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II Escuela de Optica Biomedica, Puebla, 2011
Quaternions
• A quaternion is a 4-tuple of real numbers; it is an element of R4.
• Quaternion can also be defined as the sum of a scalar part q0 and a vector part Q in R3 of the form
€
q = qo ,q1 ,q2 ,q3( )
€
q=q0 + Q = q0 + iq1 + jq2 + kq3
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II Escuela de Optica Biomedica, Puebla, 2011
Quaternions cnt.
• The vector part Q is the rotational axis and the scalar part is the angle of rotation.
• Multiplication of a vector t by the quaternion is equivalent to rotating the vector t around the vector Q of an angle q0.
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II Escuela de Optica Biomedica, Puebla, 2011
Vector rotation
• First the unit vector v is rotated about the vector u by an angle f
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II Escuela de Optica Biomedica, Puebla, 2011
Rotation - f
• The first rotation is about the vector u by an angle f.
• This is done generating the quaternion qf
• And then using the quaternion operator• q∗ vq on the vector v• q ∗ is the complex conjugate of q
€
qφ =φ + u = φ + iux + juy + kuz
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II Escuela de Optica Biomedica, Puebla, 2011
Vector rotation
• Second u is rotated about the newly generated v by an angle q.
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II Escuela de Optica Biomedica, Puebla, 2011
Rotation - q
• The second rotation is about the vector v by an angle q.
• This is done generating the quaternion qq
• And then using the quaternion operator• qq*uq q on the vector u
€
qφ =θ +v = φ + ivx + jvy + kvz
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II Escuela de Optica Biomedica, Puebla, 2011
Rotations
• These steps are repeated for every scattering event.
• At the boundaries the last aligning rotations are the same as in Euler Monte Carlo.
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II Escuela de Optica Biomedica, Puebla, 2011
Testing
• Comparison with Evans Code• In 1991 Evans designed an adding doubling code
that can calculate both the radiance and flux of a polarized light beam exiting the atmosphere
• plane parallel slab of thickness L = 4/µs,
• absorption coefficient µa=0, • unpolarized incident beam • wavelength l = 0.632 nm.
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II Escuela de Optica Biomedica, Puebla, 2011
Evans - Reflectance mode Diameter (nm) Evans
IThis code
IEvans
QThis code
Q10 0.6883 0.6886 -0.1041 -0.1042
100 0.6769 0.6769 -0.1015 -0.1009
1000 0.4479 0.4484 0.0499 0.0499
2000 0.2930 0.2931 0.0089 0.0088
Reflectance mode, comparison between Evans adding-doubling code and the meridian plane Monte Carlo program. The results do not include the final rotation for a single detector.
Incident I=[1 0 0 0]
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II Escuela de Optica Biomedica, Puebla, 2011
Evans – Transmission mode Diameter (nm) Evans
I
This code
I
Evans
Q
This code
Q
10 0.33126 0.31133 -0.01228 -0.01233
100 0.32301 0.32305 -0.12844 -0.12770
1000 0.55201 0.55152 0.02340 0.02348
2000 0.70698 0.70689 0.01197 0.01205
Transmission mode, comparison between Evans adding doubling code and the meridian plane Monte Carlo program. The results are not corrected for a single detector
Incident I=[1 0 0 0]
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II Escuela de Optica Biomedica, Puebla, 2011
How to run the code
• Download the code
• http://faculty.cua.edu/ramella/MonteCarlo/index.html
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II Escuela de Optica Biomedica, Puebla, 2011
How to run the code
• Download the code
• http://faculty.cua.edu/ramella/MonteCarlo/index.html
![Page 45: II Escuela de Optica Biomedica, Puebla, 2011 Monte Carlo, Euler and Quaternions Jessica C. Ramella-Roman](https://reader038.vdocuments.net/reader038/viewer/2022110209/56649e175503460f94b032a4/html5/thumbnails/45.jpg)
II Escuela de Optica Biomedica, Puebla, 2011
Download the code
Programs
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II Escuela de Optica Biomedica, Puebla, 2011
Make
Command line
Compilation/linking step
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II Escuela de Optica Biomedica, Puebla, 2011
Run
This program will run a full Mueller matrix Monte Carlo launching four vectors[1 1 0 0] H 0 degree polarized[1 -1 0 0] V 90 degrees polarized[1 0 1 0] P 45 degrees polarized[1 0 0 1] R –Right circular
Command line
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II Escuela de Optica Biomedica, Puebla, 2011
Memory usage
• Intel (64-bit) – Macbook pro 2.3Ghz I7 8GB RAM
• Real mem 860 KB • Virtual mem 17 MB
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II Escuela de Optica Biomedica, Puebla, 2011
out
Output is a set of Stokes vector images for each launched Stokes vector
outHI -> Horizontal incident polarization and I portion of the Stokes vector
outHQ -> Horizontal incident polarization and Q portion of the Stokes vector
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II Escuela de Optica Biomedica, Puebla, 2011
Inside the code
GNU Licence
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II Escuela de Optica Biomedica, Puebla, 2011
Modifiable parameters
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II Escuela de Optica Biomedica, Puebla, 2011
Image related parameters
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II Escuela de Optica Biomedica, Puebla, 2011
Stokes vector launch
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II Escuela de Optica Biomedica, Puebla, 2011
Launch terms
Initial position
Initial orientation
Initial Stokes vector
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II Escuela de Optica Biomedica, Puebla, 2011
We can use the three Monte Carlo programs to understand how polarized light travels into
scattering media
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II Escuela de Optica Biomedica, Puebla, 2011
Light transfer –mono disperse particles
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II Escuela de Optica Biomedica, Puebla, 2011
Light transfer –mono disperse particles
• Experimental results– black circles
• Monte Carlo – black square
• Diameter 482 nm, • Wavelength was 543
nm.• nsphere =1.59
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II Escuela de Optica Biomedica, Puebla, 2011
Light transfer –mono disperse particles
• Experimental results– black circles
• Monte Carlo – black square
• Diameter 308 nm, • Wavelength was 543
nm.• nsphere =1.59
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II Escuela de Optica Biomedica, Puebla, 2011
Poly-disperse solutions
• Gamma distribution of particles
€
N(r )=arα (exp−brγ )
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II Escuela de Optica Biomedica, Puebla, 2011
Poly-disperse solutionsComparison with Evans
Results from a slab in reflectance
Incident I=[1 0 0 0]
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Poly-disperse solutions -DLP
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Map of polarized light distribution
d
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Map of polarized light distribution
d
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II Escuela de Optica Biomedica, Puebla, 2011
Map of polarized light distribution
d
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II Escuela de Optica Biomedica, Puebla, 2011
d
d
d
x y
d
x
y
D = 0.01 µmµs = 0.89 cm-1
l = 0.543µm
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II Escuela de Optica Biomedica, Puebla, 2011
D = 0.01µmµs = 0.89 cm-1
l = 0.543µm
y y
dd
x
y
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II Escuela de Optica Biomedica, Puebla, 2011
x y
d
d
d
D = 0.48 µmµs = 0.89 cm-1
l = 0.543µm
d
x
y
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II Escuela de Optica Biomedica, Puebla, 2011
D = 0.48 µmµs = 0.89 cm-1
l = 0.543µm
d
y y
d
x
y
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Isosurface Pol= 0.5
D = 0.01 µmµs = 0.89 cm-1
l = 0.543µm
xy
d
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Isosurface Pol = 0.9
D = 0.48 µmµs = 0.89 cm-1
l = 0.543µm
xy
d
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II Escuela de Optica Biomedica, Puebla, 2011
Poincaré sphere analysis, Ellipticity
Im()
Re()+1-1
+i
-i
tan() i tan(ε)
1 i tan(ε)tan()
I Ex
2 Ey2
Q Ex
2 Ey2 I cos(2ε)cos(2)
U 2Ex Ey cos() I cos(2ε)sin(2)
V 2Ex Ey sin() I sin(2ε)
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II Escuela de Optica Biomedica, Puebla, 2011
Ellipticity
0.01µm 10 µm
l = 543nm
2 scattering events19 scattering events
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II Escuela de Optica Biomedica, Puebla, 2011
Particle effect on polarization
• Depolarize faster• Less forward
directed• Turn incident
polarized light into another linear state
• Depolarize slower– Large g effect
• More forward directed
• Turn incident polarized light into elliptical states
Small spheres Large spheres