use scikit-build

020c5a37 · Leon Merten Lohse · a295e825 · 020c5a37 · 020c5a37 · 020c5a37
Commit 020c5a37 authored Feb 09, 2021 by Leon Merten Lohse
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-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}")
--- a/examples/Test2d.ipynb
+++ b/examples/Test2d.ipynb
@@ -4,17 +4,30 @@
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "ImportError",
+     "evalue": "cannot import name '_solver' from 'fresnel' (/home/leon/.local/lib/python3.8/site-packages/fresnel/__init__.py)",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-1-566ac7b624d1>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      8\u001b[0m \u001b[0;31m# path to fresnel (adjust if necessary)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      9\u001b[0m \u001b[0;31m#sys.path.append(f'{Path.home()}/fresnel/')\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 10\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mfresnel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msolver\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0msolver\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     11\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mfresnel\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpropagation\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mpropagation\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/.local/lib/python3.8/site-packages/fresnel/solver.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mnumpy\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0;34m.\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0m_solver\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      4\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      5\u001b[0m \u001b[0m_k\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m2\u001b[0m \u001b[0;34m*\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpi\u001b[0m \u001b[0;31m# all lengths are in units of the wavelength\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mImportError\u001b[0m: cannot import name '_solver' from 'fresnel' (/home/leon/.local/lib/python3.8/site-packages/fresnel/__init__.py)"
+     ]
+    }
+   ],
   "source": [
    "import sys\n",
    "import numpy as np\n",
    "import xraylib as xrl\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
-    "from pathlib import Path\n",
+    "#from pathlib import Path\n",
    "\n",
    "# path to fresnel (adjust if necessary)\n",
-    "sys.path.append(f'{Path.home()}/fresnel/')\n",
+    "#sys.path.append(f'{Path.home()}/fresnel/')\n",
    "import fresnel.solver as solver\n",
    "import fresnel.propagation as propagation"
   ]

 %% 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
+
+    ---------------------------------------------------------------------------
+    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

    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

    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

    Text(0, 0.5, '$x$ (nm)')



 %% 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

    Text(0, 0.5, '$x$ (nm)')



 %% Cell type:code id: tags:

 ``` python
 ```

--- a/examples/Test3d.ipynb
+++ b/examples/Test3d.ipynb
@@ -11,10 +11,6 @@
    "import xraylib as xrl\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
-    "from pathlib import Path\n",
-    "\n",
-    "# path to fresnel (adjust if necessary)\n",
-    "sys.path.append(f'{Path.home()}/fresnel/')\n",
    "import fresnel.solver as solver"
   ]
  },

 %% 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

    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

    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

    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

    Text(0, 0.5, '$y$ (nm)')





 %% Cell type:code id: tags:

 ``` python
 ```

 %% Cell type:code id: tags:

 ``` python

 ```

--- a/examples/TestCS.ipynb
+++ b/examples/TestCS.ipynb
@@ -11,10 +11,6 @@
    "import xraylib as xrl\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
-    "from pathlib import Path\n",
-    "\n",
-    "# path to fresnel (adjust if necessary)\n",
-    "sys.path.append(f'{Path.home()}/fresnel/')\n",
    "import fresnel.solver as solver"
   ]
  },

 %% 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

    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
 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

    Text(0, 0.5, '$x$ (nm)')



 %% Cell type:code id: tags:

 ``` python
 ```

--- a/source/python.cpp
+++ b/source/python.cpp