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irp
Fresnel
Commits
020c5a37
Commit
020c5a37
authored
Feb 09, 2021
by
Leon Merten Lohse
Browse files
use scikit-build
parent
a295e825
Changes
5
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CMakeLists.txt
View file @
020c5a37
cmake_minimum_required
(
VERSION 3.15
)
cmake_minimum_required
(
VERSION 3.15
..3.17
)
project
(
fresnel VERSION 0.1
)
set
(
CMAKE_CXX_STANDARD 14
)
set
(
CMAKE_CXX_STANDARD_REQUIRED ON
)
set
(
default_build_type
"Release"
)
include
(
GNUInstallDirs
)
#set(PYBIND11_PYTHON_VERSION 3.8)
find_package
(
Python COMPONENTS Interpreter Development
)
#
add_subdirectory (extern/pybind11)
find_package
(
pybind11 CONFIG
)
#
find_package (Python COMPONENTS Interpreter Development)
add_subdirectory
(
extern/pybind11
)
#
find_package (pybind11 CONFIG
REQUIRED
)
find_package
(
Eigen3 3.3 REQUIRED NO_MODULE
)
find_package
(
OpenMP
)
pybind11_add_module
(
_solver source/python.cpp
)
target_link_libraries
(
_solver PRIVATE Eigen3::Eigen
)
target_compile_options
(
_solver PRIVATE -Wpedantic -Wall -O3 -ffast-math
)
set
(
python_module_name _solver
)
pybind11_add_module
(
${
python_module_name
}
MODULE
source/solver_py.cpp
)
target_link_libraries
(
${
python_module_name
}
PRIVATE Eigen3::Eigen
)
target_compile_options
(
${
python_module_name
}
PRIVATE -Wpedantic -Wall -O3 -ffast-math
)
if
(
OpenMP_CXX_FOUND
)
target_link_libraries
(
_solver
PRIVATE OpenMP::OpenMP_CXX
)
target_link_libraries
(
${
python_module_name
}
PRIVATE OpenMP::OpenMP_CXX
)
endif
()
install
(
TARGETS _solver DESTINATION fresnel
)
install
(
DIRECTORY fresnel/ DESTINATION fresnel
FILES_MATCHING PATTERN
"*.py"
)
install
(
TARGETS
${
python_module_name
}
DESTINATION .
)
#install(DIRECTORY fresnel/ DESTINATION fresnel
# FILES_MATCHING PATTERN "*.py")
# Quiet a warning
set
(
ignoreMe
"
${
SKBUILD
}
"
)
examples/Test2d.ipynb
View file @
020c5a37
%% Cell type:code id: tags:
```
python
import
sys
import
numpy
as
np
import
xraylib
as
xrl
import
matplotlib.pyplot
as
plt
from
pathlib
import
Path
#
from pathlib import Path
# path to fresnel (adjust if necessary)
sys
.
path
.
append
(
f
'
{
Path
.
home
()
}
/fresnel/'
)
#
sys.path.append(f'{Path.home()}/fresnel/')
import
fresnel.solver
as
solver
import
fresnel.propagation
as
propagation
```
%%%% Output: error
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-566ac7b624d1> in <module>
8 # path to fresnel (adjust if necessary)
9 #sys.path.append(f'{Path.home()}/fresnel/')
---> 10 import fresnel.solver as solver
11 import fresnel.propagation as propagation
~/.local/lib/python3.8/site-packages/fresnel/solver.py in <module>
1 import numpy as np
2
----> 3 from . import _solver
4
5 _k = 2 * np.pi # all lengths are in units of the wavelength
ImportError: cannot import name '_solver' from 'fresnel' (/home/leon/.local/lib/python3.8/site-packages/fresnel/__init__.py)
%% 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
=
1010
nz
=
530
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: 2.395787247703638, dz: 7304.89092884732 wavelengths
%% 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
=
solver
.
Propagator2d
(
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
=
'jet'
,
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
fresnelpropagator
=
propagation
.
FresnelPropagator2d
(
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
,
...]
=
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
=
'jet'
,
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 @
020c5a37
%% Cell type:code id: tags:
```
python
import
sys
import
numpy
as
np
import
xraylib
as
xrl
import
matplotlib.pyplot
as
plt
from
pathlib
import
Path
# path to fresnel (adjust if necessary)
sys
.
path
.
append
(
f
'
{
Path
.
home
()
}
/fresnel/'
)
import
fresnel.solver
as
solver
```
%% 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
=
1000
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: 3871.592192289079 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
=
solver
.
Propagator3d
(
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
800
900
%% 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
``
`
%%
Cell
type
:
code
id
:
tags
:
```
python
```
...
...
examples/TestCS.ipynb
View file @
020c5a37
%% Cell type:code id: tags:
```
python
import
sys
import
numpy
as
np
import
xraylib
as
xrl
import
matplotlib.pyplot
as
plt
from
pathlib
import
Path
# path to fresnel (adjust if necessary)
sys
.
path
.
append
(
f
'
{
Path
.
home
()
}
/fresnel/'
)
import
fresnel.solver
as
solver
```
%% 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
=
1000
ztot
=
0.4
# mm
wg_radius
=
25e-6
xtot
=
10
*
wg_radius
# mm
# units
dx
=
xtot
/
nx
/
wavelength
dz
=
ztot
/
nz
/
wavelength
print
(
f
"dx:
{
dx
}
, dz:
{
dz
}
wavelengths"
)
```
%%%% Output: stream
dx: 2.36303234392644, dz: 3871.592192289079 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
)
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
=
solver
.
PropagatorCS
(
refractive_index
,
u0
,
dz
,
dx
)
```
%% Cell type:code id: tags:
```
python
