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irp
Fresnel
Commits
bc06658c
Commit
bc06658c
authored
Feb 10, 2021
by
Leon Merten Lohse
Browse files
fix missing wavelength
parent
441a23a0
Changes
3
Hide whitespace changes
Inline
Side-by-side
examples/Test2d.ipynb
View file @
bc06658c
%% Cell type:code id: tags:
```
python
import
numpy
as
np
import
xraylib
as
xrl
import
matplotlib.pyplot
as
plt
import
fresnel.propagate
as
propagate
```
%% Cell type:code id: tags:
```
python
from
platform
import
python_version
print
(
python_version
())
```
%%%% Output: stream
3.8.7
%% Cell type:code id: tags:
```
python
%
matplotlib
inline
```
%% Cell type:code id: tags:
```
python
#xrl.GetCompoundDataNISTByName("Kapton Polyimide Film")
```
%% Cell type:code id: tags:
```
python
# simulation box
energy
=
12.
# keV
wavelength
=
1.2398
/
(
energy
*
1e3
)
*
1e-3
# mm
nx
=
1200
nz
=
10000
wg_radius
=
25e-6
xtot
=
10
*
wg_radius
# mm
ztot
=
0.4
# mm
# units
dx
=
xtot
/
nx
/
wavelength
dz
=
ztot
/
nz
/
wavelength
print
(
f
"dx:
{
dx
}
, dz:
{
dz
}
wavelengths"
)
```
%%%% Output: stream
dx: 2.0164542668172287, dz: 387.1592192289079 wavelengths
%% Cell type:code id: tags:
```
python
# slice thickness according to "Multislice does it all"
eps1
=
0.1
eps2
=
0.1
wl0
=
1
dz_max
=
eps2
/
eps1
**
2
*
dx
**
2
/
wl0
print
(
dz_max
)
```
%%%% Output: stream
40.66087810165406
%% Cell type:code id: tags:
```
python
# materials and geometry
density_Ge
=
xrl
.
ElementDensity
(
xrl
.
SymbolToAtomicNumber
(
'Ge'
))
density_Polyimide
=
1.42
density_Si
=
xrl
.
ElementDensity
(
xrl
.
SymbolToAtomicNumber
(
'Si'
))
n_Ge
=
xrl
.
Refractive_Index
(
'Ge'
,
energy
,
density_Ge
)
n_Si
=
xrl
.
Refractive_Index
(
'Si'
,
energy
,
density_Si
)
n_PI
=
xrl
.
Refractive_Index
(
'Kapton Polyimide Film'
,
energy
,
density_Polyimide
)
xx
=
np
.
linspace
(
-
xtot
/
2
,
xtot
/
2
,
nx
)
core
=
(
np
.
abs
(
xx
)
<
wg_radius
)
cladding
=
~
core
refractive_index
=
n_Ge
*
cladding
+
1
*
core
```
%% Cell type:code id: tags:
```
python
boundary
=
(
0
,
0
,)
u0
=
np
.
exp
(
-
xx
**
2
/
(
2
*
(
2
*
wg_radius
)
**
2
)).
astype
(
np
.
complex128
)
```
%% Cell type:code id: tags:
```
python
propagator
=
propagate
.
FDPropagator2d
(
refractive_index
,
u0
,
dz
,
dx
)
```
%% Cell type:code id: tags:
```
python
field
=
np
.
zeros
((
nz
,
nx
),
dtype
=
np
.
complex128
)
field
[
0
,...]
=
u0
for
iz
in
range
(
1
,
nz
):
boundary
=
(
0
,
0
)
field
[
iz
,
...]
=
propagator
.
step
(
refractive_index
,
boundary
)
```
%% Cell type:code id: tags:
```
python
result
=
field
.
transpose
()
fig
,
ax
=
plt
.
subplots
()
im
=
ax
.
imshow
(
np
.
abs
(
result
[:,:])
**
2
,
aspect
=
'auto'
,
clim
=
(
0
,
3
),
cmap
=
'cubehelix'
,
extent
=
[
0
,
ztot
,
-
xtot
/
2
*
1e6
,
xtot
/
2
*
1e6
])
ax
.
set_ylim
(
-
2e6
*
wg_radius
,
2e6
*
wg_radius
)
fig
.
colorbar
(
im
)
ax
.
set_xlabel
(
r
'$z$ (mm)'
)
ax
.
set_ylabel
(
r
'$x$ (nm)'
)
```
%%%% Output: execute_result
Text(0, 0.5, '$x$ (nm)')
%%%% Output: display_data
%% Cell type:code id: tags:
```
python
fresnel
propagator
=
propagate
.
MultislicePropagator
(
u0
,
(
dz
,
dx
,))
multislice
propagator
=
propagate
.
MultislicePropagator
(
u0
,
(
dz
,
dx
,))
```
%% Cell type:code id: tags:
```
python
field
=
np
.
zeros
((
nz
,
nx
),
dtype
=
np
.
complex128
)
field
[
0
,...]
=
u0
for
iz
in
range
(
1
,
nz
):
field
[
iz
,
...]
=
fresnelpropagator
.
step
(
refractive_index
)
```
%% Cell type:code id: tags:
```
python
result
=
field
.
transpose
()
fig
,
ax
=
plt
.
subplots
()
im
=
ax
.
imshow
(
np
.
abs
(
result
[:,:])
**
2
,
aspect
=
'auto'
,
clim
=
(
0
,
3
),
cmap
=
'cubehelix'
,
extent
=
[
0
,
ztot
,
-
xtot
/
2
*
1e6
,
xtot
/
2
*
1e6
])
ax
.
set_ylim
(
-
2e6
*
wg_radius
,
2e6
*
wg_radius
)
fig
.
colorbar
(
im
)
ax
.
set_xlabel
(
r
'$z$ (mm)'
)
ax
.
set_ylabel
(
r
'$x$ (nm)'
)
```
%%%% Output: execute_result
Text(0, 0.5, '$x$ (nm)')
%%%% Output: display_data
%% Cell type:code id: tags:
```
python
```
...
...
examples/Test3d.ipynb
View file @
bc06658c
%% Cell type:code id: tags:
```
python
import
numpy
as
np
import
xraylib
as
xrl
import
matplotlib.pyplot
as
plt
import
fresnel.propagate
as
propagate
```
%% Cell type:code id: tags:
```
python
%
matplotlib
inline
```
%% Cell type:code id: tags:
```
python
energy
=
12.
# keV
# geometry
wavelength
=
1.2398
/
(
energy
*
1e3
)
*
1e-3
# mm
nx
=
1024
ny
=
512
nz
=
800
ztot
=
0.4
# mm
wg_radius
=
25e-6
xtot
=
10
*
wg_radius
# mm
ytot
=
10
*
wg_radius
# units
dx
=
xtot
/
nx
/
wavelength
dy
=
ytot
/
ny
/
wavelength
dz
=
ztot
/
nz
/
wavelength
print
(
f
"dx:
{
dx
}
, dy:
{
dy
}
, dz:
{
dz
}
wavelengths"
)
```
%%%% Output: stream
dx: 2.36303234392644, dy: 4.72606468785288, dz: 4839.490240361349 wavelengths
%% Cell type:code id: tags:
```
python
density_Ge
=
xrl
.
ElementDensity
(
xrl
.
SymbolToAtomicNumber
(
'Ge'
))
density_Polyimide
=
1.42
density_Si
=
xrl
.
ElementDensity
(
xrl
.
SymbolToAtomicNumber
(
'Si'
))
n_Ge
=
xrl
.
Refractive_Index
(
'Ge'
,
energy
,
density_Ge
)
n_Si
=
xrl
.
Refractive_Index
(
'Si'
,
energy
,
density_Si
)
n_PI
=
xrl
.
Refractive_Index
(
'Kapton Polyimide Film'
,
energy
,
density_Polyimide
)
print
(
'Ge'
,
n_Ge
-
1
)
print
(
'Si'
,
n_Si
-
1
)
print
(
'PI'
,
n_PI
-
1
)
xx
=
np
.
linspace
(
-
xtot
/
2
,
xtot
/
2
,
nx
).
reshape
([
1
,
-
1
])
yy
=
np
.
linspace
(
-
ytot
/
2
,
ytot
/
2
,
ny
).
reshape
([
-
1
,
1
])
core
=
(
np
.
abs
(
xx
)
<
wg_radius
)
*
(
np
.
abs
(
yy
)
<
wg_radius
)
cladding
=
~
core
refractive_index
=
n_Ge
*
cladding
+
1
*
core
```
%%%% Output: stream
Ge (-6.426292114225518e-06+7.120128111534574e-07j)
Si (-3.3845180545943876e-06+3.810012288290064e-08j)
PI (-2.1023289580313076e-06+2.2059592416020462e-09j)
%% Cell type:code id: tags:
```
python
u0
=
np
.
exp
(
-
(
xx
**
2
+
yy
**
2
)
/
(
2
*
(
2
*
wg_radius
)
**
2
)).
astype
(
np
.
complex128
)
boundary
=
(
0
,
0
,
0
,
0
)
propagator
=
propagate
.
FDPropagator3d
(
refractive_index
,
u0
,
dz
,
dy
,
dx
)
```
%% Cell type:code id: tags:
```
python
field
=
np
.
zeros
((
nz
,
ny
,
nx
),
dtype
=
np
.
complex128
)
field
[
0
,...]
=
u0
for
iz
in
range
(
1
,
nz
):
boundary
=
(
0
,
0
,
0
,
0
)
field
[
iz
,
...]
=
propagator
.
step
(
refractive_index
,
boundary
)
if
iz
%
100
==
0
:
print
(
iz
)
```
%%%% Output: stream
100
200
300
400
500
600
700
%% Cell type:code id: tags:
```
python
result
=
field
[:,
ny
//
2
,
:].
transpose
()
fig
,
ax
=
plt
.
subplots
()
im
=
ax
.
imshow
(
np
.
abs
(
result
)
**
2
,
aspect
=
'auto'
,
clim
=
(
0
,
4
),
cmap
=
'cubehelix'
,
extent
=
[
0
,
ztot
,
-
xtot
/
2
*
1e6
,
xtot
/
2
*
1e6
])
ax
.
set_ylim
(
-
2e6
*
wg_radius
,
2e6
*
wg_radius
)
fig
.
colorbar
(
im
)
ax
.
set_xlabel
(
r
'$z$ (mm)'
)
ax
.
set_ylabel
(
r
'$x$ (nm)'
)
result
=
field
[:,:,
nx
//
2
].
transpose
()
fig
,
ax
=
plt
.
subplots
()
im
=
ax
.
imshow
(
np
.
abs
(
result
)
**
2
,
aspect
=
'auto'
,
clim
=
(
0
,
4
),
cmap
=
'cubehelix'
,
extent
=
[
0
,
ztot
,
-
xtot
/
2
*
1e6
,
xtot
/
2
*
1e6
])
ax
.
set_ylim
(
-
2e6
*
wg_radius
,
2e6
*
wg_radius
)
fig
.
colorbar
(
im
)
ax
.
set_xlabel
(
r
'$z$ (um)'
)
ax
.
set_ylabel
(
r
'$y$ (nm)'
)
```
%%%% Output: execute_result
Text(0, 0.5, '$y$ (nm)')
%%%% Output: display_data
%%%% Output: display_data
%% Cell type:code id: tags:
```
python
fresnel
propagator
=
propagate
.
FresnelPropagator
(
u0
,
(
dz
,
dy
,
dx
))
multislice
propagator
=
propagate
.
FresnelPropagator
(
u0
,
(
dz
,
dy
,
dx
))
```
%% Cell type:code id: tags:
```
python
field
=
np
.
zeros
((
nz
,
ny
,
nx
),
dtype
=
np
.
complex128
)
field
[
0
,...]
=
u0
for
iz
in
range
(
1
,
nz
):
field
[
iz
,
...]
=
fresnel
propagator
.
step
(
refractive_index
)
field
[
iz
,
...]
=
multislice
propagator
.
step
(
refractive_index
)
if
iz
%
100
==
0
:
print
(
iz
)
```
%%%% Output: stream
100
200
300
400
500
600
700
%% Cell type:code id: tags:
```
python
result
=
field
[:,
ny
//
2
,
:].
transpose
()
fig
,
ax
=
plt
.
subplots
()
im
=
ax
.
imshow
(
np
.
abs
(
result
)
**
2
,
aspect
=
'auto'
,
clim
=
(
0
,
4
),
cmap
=
'cubehelix'
,
extent
=
[
0
,
ztot
,
-
xtot
/
2
*
1e6
,
xtot
/
2
*
1e6
])
ax
.
set_ylim
(
-
2e6
*
wg_radius
,
2e6
*
wg_radius
)
fig
.
colorbar
(
im
)
ax
.
set_xlabel
(
r
'$z$ (mm)'
)
ax
.
set_ylabel
(
r
'$x$ (nm)'
)
result
=
field
[:,:,
nx
//
2
].
transpose
()
fig
,
ax
=
plt
.
subplots
()
im
=
ax
.
imshow
(
np
.
abs
(
result
)
**
2
,
aspect
=
'auto'
,
clim
=
(
0
,
4
),
cmap
=
'cubehelix'
,
extent
=
[
0
,
ztot
,
-
xtot
/
2
*
1e6
,
xtot
/
2
*
1e6
])
ax
.
set_ylim
(
-
2e6
*
wg_radius
,
2e6
*
wg_radius
)
fig
.
colorbar
(
im
)
ax
.
set_xlabel
(
r
'$z$ (um)'
)
ax
.
set_ylabel
(
r
'$y$ (nm)'
)
```
%%%% Output: execute_result
Text(0, 0.5, '$y$ (nm)')
%%%% Output: display_data
%%%% Output: display_data
