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This commit is contained in:
Benoît Sierro
2021-09-22 11:32:18 +02:00
parent 8d87c70bca
commit 98445271b8
13 changed files with 488 additions and 86 deletions
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4
setup.cfg
View File

@@ -30,9 +30,7 @@ install_requires =
[options.package_data]
scgenerator =
data/hr_t.npz
data/default_params.json
data/gas.json
data/silica.json
data/materials.toml
[options.packages.find]
where = src

2
src/scgenerator/cli/cli.py
View File

@@ -186,7 +186,7 @@ def prep_ray():
def plot_all(args):
opts = {}
if args.options is not None:
opts |= dict([o.split("=")[:2] for o in re.split("[, ]", args.options)])
opts |= dict([o.split("=")[:2] for o in re.split("[, ]+", args.options)])
root = Path(args.sim_dir).resolve()
scripts.plot_all(root, args.spectrum_limits, show=args.show, **opts)

252
src/scgenerator/data/materials.toml Normal file
View File

@@ -0,0 +1,252 @@
[silica.sellmeier]
B = [0.6961663, 0.4079426, 0.8974794]
C = [4.67914826e-15, 1.35120631e-14, 9.79340025e-11]
kind = 1
reference = [
"I. H. Malitson. Interspecimen comparison of the refractive index of fused silica, J. Opt. Soc. Am. 55, 1205-1208 (1965)",
"C. Z. Tan. Determination of refractive index of silica glass for infrared wavelengths by IR spectroscopy, J. Non-Cryst. Solids 223, 158-163 (1998)",
]
[nbk7.sellmeier]
B = [1.03961212, 0.231792344, 1.01046945]
C = [6.00069867e-15, 2.00179144e-14, 1.03560653e-10]
kind = 1
reference = [
"SCHOTT Zemax catalog 2017-01-20b (obtained from http://www.schott.com)",
]
[e7.sellmeier]
B = [0.0, 7.2e-15, 3e-28]
C = []
kind = 3
reference = [
"J. Li, C. H. Wen, S. Gauza, R. Lu and S. T. Wu. Refractive indices of liquid crystals for display applications, J. Disp. Technol. 1, 51-61, 2005",
]
[d-zlaf52la.sellmeier]
B = [
-8.48750283e9,
3.1753525,
3.71301651e-14,
-1.09609062e-27,
2.4418582e-40,
-8.94583294e-54,
]
C = []
kind = 3
reference = ["CDGM Zemax catalog 2017-09 (obtained from http://www.cdgmgd.com)"]
# -----
# GASES
# -----
[air]
a = 0.1358
b = 3.64e-5
[air.sellmeier]
B = [57921050000.0, 1679170000.0]
C = [238018500000000.0, 57362000000000.0]
P0 = 101325
T0 = 288.15
kind = 2
[air.kerr]
P0 = 101325
T0 = 293.15
n2 = 4.0e-23
source = "Pigeon, J. J., Tochitsky, S. Y., Welch, E. C., & Joshi, C. (2016). Measurements of the nonlinear refractive index of air, N 2, and O 2 at 10 μm using four-wave mixing. Optics letters, 41(17), 3924-3927."
[nitrogen]
a = 0.137
b = 1.709e-5
[nitrogen.sellmeier]
B = [32431570000.0]
C = [144000000000000.0]
P0 = 101325
T0 = 273.15
const = 6.8552e-5
kind = 2
[nitrogen.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 2.2e-23
source = "Wahlstrand, J. K., Cheng, Y. H., & Milchberg, H. M. (2012). High field optical nonlinearity and the Kramers-Kronig relations. Physical review letters, 109(11), 113904."
[helium]
a = 0.00346
b = 2.38e-5
[helium.sellmeier]
B = [2.16463842e-5, 2.10561127e-7, 4.7509272e-5]
C = [-6.80769781e-16, 5.13251289e-15, 3.18621354e-15]
P0 = 101325
T0 = 273.15
kind = 1
source = "A. Ermolov, K. F. Mak, M. H. Frosz, J. C. Travers, P. St. J. Russell, Supercontinuum generation in the vacuum ultraviolet through dispersive-wave and soliton-plasma interaction in a noble-gas-filled hollow-core photonic crystal fiber, Phys. Rev. A 92, 033821 (2015)"
[helium.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 3.1e-25
source = "Wahlstrand, J. K., Cheng, Y. H., & Milchberg, H. M. (2012). High field optical nonlinearity and the Kramers-Kronig relations. Physical review letters, 109(11), 113904."
[helium_alt]
a = 0.00346
b = 2.38e-5
[helium_alt.sellmeier]
B = [14755297000.0]
C = [426297400000000.0]
P0 = 101325
T0 = 273.15
kind = 2
source = " C. Cuthbertson and M. Cuthbertson. The refraction and dispersion of neon and helium. Proc. R. Soc. London A 135, 40-47 (1936)"
[helium_alt.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 3.1e-25
[hydrogen]
a = 0.02453
b = 2.651e-5
[hydrogen.sellmeier]
B = [0.0148956, 0.0049037]
C = [1.807e-10, 9.2e-11]
P0 = 101325
T0 = 273.15
kind = 2
source = "E. R. Peck and S. Hung. Refractivity and dispersion of hydrogen in the visible and near infrared, J. Opt. Soc. Am. 67, 1550-1554 (1977)"
[hydrogen.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 6.36e-24
source = "Shelton, D. P., & Rice, J. E. (1994). Measurements and calculations of the hyperpolarizabilities of atoms and small molecules in the gas phase. Chemical Reviews, 94(1), 3-29"
[neon]
a = 0.02135
b = 1.709e-5
[neon.sellmeier]
B = [1281450000.0, 22048600000.0]
C = [184661000000000.0, 376840000000000.0]
P0 = 101325
T0 = 273.15
kind = 2
[neon.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 8.7e-25
source = "Wahlstrand, J. K., Cheng, Y. H., & Milchberg, H. M. (2012). High field optical nonlinearity and the Kramers-Kronig relations. Physical review letters, 109(11), 113904."
[argon]
a = 0.1355
b = 3.201e-5
[argon.sellmeier]
B = [2501410000.0, 500283000.0, 52234300000.0]
C = [91012000000000.0, 87892000000000.0, 214020000000000.0]
P0 = 101325
T0 = 273.15
kind = 2
source = "A. Bideau-Mehu, Y. Guern, R. Abjean, A. Johannin-Gilles. Measurement of refractive indices of neon, argon, krypton and xenon in the 253.7-140.4 nm wavelength range. Dispersion relations and estimated oscillator strengths of the resonance lines. J. Quant. Spectrosc. Rad. Transfer 25, 395-402 (1981)"
[argon.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 9.7e-24
source = "Wahlstrand, J. K., Cheng, Y. H., & Milchberg, H. M. (2012). High field optical nonlinearity and the Kramers-Kronig relations. Physical review letters, 109(11), 113904."
[argon_alt]
a = 0.1355
b = 3.201e-5
[argon_alt.sellmeier]
B = [0.0002033229, 0.0003445831]
C = [2.0612e-16, 8.066e-15]
P0 = 101325
T0 = 273.15
kind = 1
source = "A. Börzsönyi, Z. Heiner, M. P. Kalashnikov, A. P. Kovács, and K. Osvay, Dispersion measurement of inert gases and gas mixtures at 800 nm, Appl. Opt. 47, 4856-4863 (2008)"
[argon_alt.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 9.7e-24
source = "Wahlstrand, J. K., Cheng, Y. H., & Milchberg, H. M. (2012). High field optical nonlinearity and the Kramers-Kronig relations. Physical review letters, 109(11), 113904."
[argon_alt2]
a = 0.1355
b = 3.201e-5
[argon_alt2.sellmeier]
B = [0.030182943]
C = [144000000000000.0]
P0 = 101325
T0 = 273.15
const = 6.7867e-5
kind = 2
source = "E. R. Peck and D. J. Fisher. Dispersion of argon, J. Opt. Soc. Am. 54, 1362-1364 (1964)"
[argon_alt2.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 9.7e-24
source = "Wahlstrand, J. K., Cheng, Y. H., & Milchberg, H. M. (2012). High field optical nonlinearity and the Kramers-Kronig relations. Physical review letters, 109(11), 113904."
[krypton]
a = 0.2349
b = 3.978e-5
[krypton.sellmeier]
B = [2536370000.0, 2736490000.0, 62080200000.0]
C = [65474200000000.0, 73698000000000.0, 181080000000000.0]
P0 = 101325
T0 = 273.15
kind = 2
[krypton.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 2.2e-23
source = "Wahlstrand, J. K., Cheng, Y. H., & Milchberg, H. M. (2012). High field optical nonlinearity and the Kramers-Kronig relations. Physical review letters, 109(11), 113904."
[xenon]
a = 0.425
b = 5.105e-5
[xenon.sellmeier]
B = [3228690000.0, 3553930000.0, 60676400000.0]
C = [46301000000000.0, 59578000000000.0, 112740000000000.0]
P0 = 101325
T0 = 273.15
kind = 2
[xenon.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 5.8e-23
source = "Wahlstrand, J. K., Cheng, Y. H., & Milchberg, H. M. (2012). High field optical nonlinearity and the Kramers-Kronig relations. Physical review letters, 109(11), 113904."
[vacuum]
a = 0
b = 0
[vacuum.sellmeier]
B = []
C = []
P0 = 101325
T0 = 273.15
kind = 1
[vacuum.kerr]
P0 = 30400.0
T0 = 273.15
n2 = 0
source = "none"

31
src/scgenerator/data/silica.toml
View File

@@ -1,4 +1,29 @@
[sellmeier]
B = [ 0.6961663, 0.4079426, 0.8974794,]
C = [ 4.67914826e-15, 1.35120631e-14, 9.79340025e-11,]
[silica.sellmeier]
B = [0.6961663, 0.4079426, 0.8974794]
C = [4.67914826e-15, 1.35120631e-14, 9.79340025e-11]
kind = 1
reference = [
"I. H. Malitson. Interspecimen comparison of the refractive index of fused silica, J. Opt. Soc. Am. 55, 1205-1208 (1965)",
"C. Z. Tan. Determination of refractive index of silica glass for infrared wavelengths by IR spectroscopy, J. Non-Cryst. Solids 223, 158-163 (1998)",
]
[nbk7.sellmeier]
B = [1.03961212, 0.231792344, 1.01046945]
C = [6.00069867e-15, 2.00179144e-14, 1.03560653e-10]
kind = 1
reference = [
"SCHOTT Zemax catalog 2017-01-20b (obtained from http://www.schott.com)",
]
[d-zlaf52la.sellmeier]
B = [
-8.48750283e9,
3.1753525,
3.71301651e-14,
-1.09609062e-27,
2.4418582e-40,
-8.94583294e-54,
]
C = []
kind = 3
reference = ["CDGM Zemax catalog 2017-09 (obtained from http://www.cdgmgd.com)"]

63
src/scgenerator/physics/__init__.py
View File

@@ -11,6 +11,7 @@ from scipy.optimize import minimize_scalar
from .. import math
from . import fiber, materials, units, pulse
from .. import utils
from ..utils import cache
T = TypeVar("T")
@@ -21,8 +22,9 @@ def group_delay_to_gdd(wavelength: np.ndarray, group_delay: np.ndarray) -> np.nd
return gdd
@cache.np_cache
def material_dispersion(
wavelengths,
wavelengths: np.ndarray,
material: str,
pressure=None,
temperature=None,
@@ -52,17 +54,6 @@ def material_dispersion(
w = units.m(wavelengths)
order = np.argsort(w)
material_dico = utils.load_material_dico(material)
if ideal:
n_gas_2 = materials.sellmeier(wavelengths, material_dico, pressure, temperature) + 1
else:
N_1 = materials.number_density_van_der_waals(
pressure=pressure, temperature=temperature, material_dico=material_dico
)
N_0 = materials.number_density_van_der_waals(material_dico=material_dico)
n_gas_2 = materials.sellmeier(wavelengths, material_dico) * N_1 / N_0 + 1
if safe:
disp = np.zeros(len(w))
ind = w > 0
@@ -71,7 +62,18 @@ def material_dispersion(
)
return disp
else:
return fiber.beta2(w[order], np.sqrt(n_gas_2[order]))[order]
material_dico = utils.load_material_dico(material)
if ideal:
n_gas_2 = materials.sellmeier(wavelengths, material_dico, pressure, temperature) + 1
else:
N_1 = materials.number_density_van_der_waals(
pressure=pressure, temperature=temperature, material_dico=material_dico
)
N_0 = materials.number_density_van_der_waals(material_dico=material_dico)
n_gas_2 = materials.sellmeier(wavelengths, material_dico) * N_1 / N_0 + 1
order = np.argsort(w)
unorder = np.argsort(order)
return fiber.beta2(w[order], np.sqrt(n_gas_2[order]))[unorder]
def find_optimal_depth(
@@ -108,15 +110,30 @@ def find_optimal_depth(
def score(z):
return -np.nansum(integrate(z) ** 6)
# import matplotlib.pyplot as plt
# to_test = np.linspace(0, max_z, 200)
# scores = [score(z) for z in to_test]
# fig, ax = plt.subplots()
# ax.plot(to_test, scores / np.min(scores))
# plt.show()
# plt.close(fig)
# ama = np.argmin(scores)
opti = minimize_scalar(score, method="bounded", bounds=(0, max_z))
return propagate(opti.x), opti
def propagate_field(t: np.ndarray, field: np.ndarray, z: float, material: str) -> np.ndarray:
"""propagates a field through bulk material
Parameters
----------
t : np.ndarray, shape (n,)
time grid
field : np.ndarray, shape (n,)
corresponding complex field
z : float
distance to propagate in m
material : str
material name
Returns
-------
np.ndarray, shape (n,)
propagated field
"""
w_c = math.wspace(t)
l = units.m(w_c + units.nm(1540))
disp = material_dispersion(l, material)
return np.fft.ifft(np.fft.fft(field) * np.exp(0.5j * disp * w_c ** 2 * z))

15
src/scgenerator/physics/materials.py
View File

@@ -113,8 +113,8 @@ def sellmeier(lambda_, material_dico, pressure=None, temperature=None):
logger = get_logger(__name__)
WL_THRESHOLD = 8.285e-6
temp_l = lambda_[lambda_ < WL_THRESHOLD]
kind = 1
ind = lambda_ < WL_THRESHOLD
temp_l = lambda_[ind]
B = material_dico["sellmeier"]["B"]
C = material_dico["sellmeier"]["C"]
@@ -125,13 +125,20 @@ def sellmeier(lambda_, material_dico, pressure=None, temperature=None):
chi = np.zeros_like(lambda_) # = n^2 - 1
if kind == 1:
logger.debug("materials : using Sellmeier 1st kind equation")
for b, c in zip(B, C):
chi[lambda_ < WL_THRESHOLD] += temp_l ** 2 * b / (temp_l ** 2 - c)
chi[ind] += temp_l ** 2 * b / (temp_l ** 2 - c)
elif kind == 2: # gives n-1
logger.debug("materials : using Sellmeier 2nd kind equation")
for b, c in zip(B, C):
chi[lambda_ < WL_THRESHOLD] += b / (c - 1 / temp_l ** 2)
chi[ind] += b / (c - 1 / temp_l ** 2)
chi += const
chi = (chi + 1) ** 2 - 1
elif kind == 3: # Schott formula
logger.debug("materials : using Schott equation")
for i, b in reversed(list(enumerate(B))):
chi[ind] += b * temp_l ** (-2 * (i - 1))
chi[ind] = chi[ind] - 1
else:
raise ValueError(f"kind {kind} is not recognized.")

11
src/scgenerator/physics/simulate.py
View File

@@ -44,6 +44,12 @@ class RK4IP:
"""
self.set(params, save_data, job_identifier, task_id)
def __iter__(self) -> Generator[tuple[int, int, np.ndarray], None, None]:
yield from self.irun()
def __len__(self) -> int:
return self.len
def set(
self,
params: Parameters,
@@ -73,6 +79,7 @@ class RK4IP:
self.alpha = params.alpha_arr
self.spec_0 = np.sqrt(params.input_transmission) * params.spec_0
self.z_targets = params.z_targets
self.len = len(params.z_targets)
self.z_final = params.length
self.beta2_coefficients = (
params.beta_func if params.beta_func is not None else params.beta2_coefficients
@@ -189,7 +196,7 @@ class RK4IP:
"""
utils.save_data(data, self.data_dir, name)
def run(self):
def run(self) -> list[np.ndarray]:
time_start = datetime.today()
for step, num, _ in self.irun():
@@ -480,7 +487,7 @@ class Simulations:
def _run_available(self):
for variable, params in self.configuration:
v_list_str = format_variable_list(variable)
v_list_str = format_variable_list(variable, add_iden=True)
utils.save_parameters(params.prepare_for_dump(), Path(params.output_path))
self.new_sim(v_list_str, params)

1
src/scgenerator/physics/units.py
View File

@@ -48,6 +48,7 @@ def unit(tpe: str, label: str, inv: Callable = None):
setattr(To, name, inv.__call__)
func.type = tpe
func.label = label
func.name = name
func.inv = inv
if name in units_map:
raise NameError(f"Two unit functions with the same name {name!r} were defined")

68
src/scgenerator/plotting.py
View File

@@ -543,7 +543,7 @@ def transform_mean_values(
values = abs2(values)
new_axis, ind, ext = sort_axis(x_axis, plt_range)
values = values[:, ind]
if plt_range.unit.type == "WL":
if plt_range.unit.type == "WL" and plt_range.conserved_quantity:
values = np.apply_along_axis(units.to_WL, -1, values, new_axis)
if isinstance(spacing, (float, np.floating)):
@@ -735,14 +735,13 @@ def transform_1D_values(
x axis and values
"""
if len(values.shape) != 1:
print(f"Shape was {values.shape}. Can only plot 1D arrays")
return
raise ValueError("Can only plot 1D values")
is_complex, x_axis, plt_range = prep_plot_axis(values, plt_range, params)
if is_complex:
values = abs2(values)
new_axis, ind, ext = sort_axis(x_axis, plt_range)
values = values[ind]
if plt_range.unit.type == "WL":
if plt_range.unit.type == "WL" and plt_range.conserved_quantity:
values = units.to_WL(values, new_axis)
if isinstance(spacing, (float, np.floating)):
@@ -1000,3 +999,64 @@ def arrowstyle(direction=1, color="white"):
color=color,
backgroundcolor=(0.5, 0.5, 0.5, 0.5),
)
def measure_and_annotate_fwhm(
ax: plt.Axes,
t: np.ndarray,
field: np.ndarray,
side: Literal["left", "right"] = "right",
unit="fs",
arrow_length_pts: float = 20.0,
arrow_props: dict[str, Any] = None,
) -> float:
"""measured the FWHM of a pulse and plots it
Parameters
----------
ax : plt.Axes
ax on which to plot
t : np.ndarray, shape (n,)
time in s
field : np.ndarray, shape (n,)
complex field
side : Literal["left", "right"]
whether to write the text on the right or left side
unit : str, optional
units of the plot, by default "fs"
arrow_length_pts : float, optional
length of the arrows in pts, by default 20.0
arrow_props : dict[str, Any], optional
style of the arrow to be passed to plt.annotate, by default None
Returns
-------
float
FWHM in units
"""
unit = units.get_unit(unit)
if np.iscomplexobj(field):
field = abs2(field)
_, (left, right), *_ = pulse.find_lobe_limits(unit.inv(t), field)
arrow_label = f"{right - left:.1f} {unit.name}"
arrow_dict = dict(arrowstyle="->")
if arrow_props is not None:
arrow_dict |= arrow_props
ax.annotate(
"" if side == "right" else arrow_label,
(left, field.max() / 2),
xytext=(-arrow_length_pts, 0),
ha="right",
va="center",
textcoords="offset points",
arrowprops=arrow_dict,
)
ax.annotate(
"" if side == "left" else arrow_label,
(right, field.max() / 2),
xytext=(arrow_length_pts, 0),
textcoords="offset points",
arrowprops=arrow_dict,
va="center",
)
return right - left

2
src/scgenerator/scripts/__init__.py
View File

@@ -31,6 +31,8 @@ def plot_all(sim_dir: Path, limits: list[str], show=False, **opts):
for k, v in opts.items():
if k in ["skip"]:
opts[k] = int(v)
if k in {"log", "renormalize"}:
opts[k] = True if v == "True" else False
dir_list = list(p for p in sim_dir.glob("*") if p.is_dir())
if len(dir_list) == 0:
dir_list = [sim_dir]

44
src/scgenerator/spectra.py
View File

@@ -1,7 +1,7 @@
import os
from collections.abc import Sequence
from pathlib import Path
from typing import Callable, Dict, Iterable, Union
from typing import Callable, Dict, Iterable, Optional, Union
import matplotlib.pyplot as plt
import numpy as np
@@ -17,6 +17,7 @@ from .plotting import (
transform_2D_propagation,
)
from .utils.parameter import Parameters, PlotRange
from .utils import load_spectrum
class Spectrum(np.ndarray):
@@ -152,7 +153,7 @@ class Pulse(Sequence):
self.params = Parameters.load(self.path / "params.toml")
self.params.compute(["name", "t", "l", "w_c", "w0", "z_targets"])
if self.params.fiber_map is None:
self.params.fiber_map = {0.0: self.params.name}
self.params.fiber_map = [(0.0, self.params.name)]
try:
self.z = np.load(os.path.join(path, "z.npy"))
@@ -161,7 +162,6 @@ class Pulse(Sequence):
self.z = self.params.z_targets
else:
raise
self.cache: Dict[int, Spectrum] = {}
self.nmax = len(list(self.path.glob("spectra_*.npy")))
if self.nmax <= 0:
raise FileNotFoundError(f"No appropriate file in specified folder {self.path}")
@@ -306,12 +306,9 @@ class Pulse(Sequence):
def _load1(self, i: int):
if i < 0:
i = self.nmax + i
if i in self.cache:
return self.cache[i]
spec = np.load(self.path / SPECN_FN.format(i))
spec = load_spectrum(self.path / SPECN_FN.format(i))
spec = np.atleast_2d(spec)
spec = Spectrum(spec, self.params)
self.cache[i] = spec
return spec
def plot_2D(
@@ -324,8 +321,9 @@ class Pulse(Sequence):
sim_ind: int = 0,
**kwargs,
):
plt_range, vals = self.retrieve_plot_values(left, right, unit, z_pos, sim_ind)
return propagation_plot(vals, plt_range, self.params, ax, **kwargs)
plot_range = PlotRange(left, right, unit)
vals = self.retrieve_plot_values(plot_range, z_pos, sim_ind)
return propagation_plot(vals, plot_range, self.params, ax, **kwargs)
def plot_1D(
self,
@@ -337,8 +335,9 @@ class Pulse(Sequence):
sim_ind: int = 0,
**kwargs,
):
plt_range, vals = self.retrieve_plot_values(left, right, unit, z_pos, sim_ind)
return single_position_plot(vals, plt_range, self.params, ax, **kwargs)
plot_range = PlotRange(left, right, unit)
vals = self.retrieve_plot_values(plot_range, z_pos, sim_ind)
return single_position_plot(vals, plot_range, self.params, ax, **kwargs)
def plot_mean(
self,
@@ -349,20 +348,25 @@ class Pulse(Sequence):
z_pos: int,
**kwargs,
):
plt_range, vals = self.retrieve_plot_values(left, right, unit, z_pos, slice(None))
return mean_values_plot(vals, plt_range, self.params, ax, **kwargs)
plot_range = PlotRange(left, right, unit)
vals = self.retrieve_plot_values(plot_range, z_pos, slice(None))
return mean_values_plot(vals, plot_range, self.params, ax, **kwargs)
def retrieve_plot_values(self, left, right, unit, z_pos, sim_ind):
plt_range = PlotRange(left, right, unit)
if plt_range.unit.type == "TIME":
def retrieve_plot_values(
self, plot_range: PlotRange, z_pos: Optional[Union[int, float]], sim_ind: Optional[int]
):
if plot_range.unit.type == "TIME":
vals = self.all_fields(ind=z_pos)
else:
vals = self.all_spectra(ind=z_pos)
if vals.ndim == 3:
vals = vals[:, sim_ind]
if sim_ind is None:
return vals
elif z_pos is None:
return vals[:, sim_ind]
else:
vals = vals[sim_ind]
return plt_range, vals
return vals[sim_ind]
def rin_propagation(
self, left: float, right: float, unit: str

24
src/scgenerator/utils/__init__.py
View File

@@ -17,11 +17,10 @@ from collections import abc
from io import StringIO
from pathlib import Path
from string import printable as str_printable
from functools import cache
from typing import Any, Callable, Generator, Iterable, MutableMapping, Sequence, TypeVar, Union
import numpy as np
from numpy.lib.arraysetops import isin
from numpy.lib.function_base import insert
import pkg_resources as pkg
import toml
from tqdm import tqdm
@@ -37,8 +36,7 @@ PathTree = list[tuple[Path, ...]]
class Paths:
_data_files = [
"silica.toml",
"gas.toml",
"materials.toml",
"hr_t.npz",
"submit_job_template.txt",
"start_worker.sh",
@@ -87,7 +85,12 @@ class Paths:
def load_previous_spectrum(prev_data_dir: str) -> np.ndarray:
prev_data_dir = Path(prev_data_dir)
num = find_last_spectrum_num(prev_data_dir)
return np.load(prev_data_dir / SPEC1_FN.format(num))
return load_spectrum(prev_data_dir / SPEC1_FN.format(num))
@cache
def load_spectrum(folder: os.PathLike) -> np.ndarray:
return np.load(folder)
def conform_toml_path(path: os.PathLike) -> str:
@@ -97,6 +100,12 @@ def conform_toml_path(path: os.PathLike) -> str:
return path
def open_single_config(path: os.PathLike) -> dict[str, Any]:
d = open_config(path)
f = d.pop("Fiber")[0]
return d | f
def open_config(path: os.PathLike):
"""returns a dictionary parsed from the specified toml file
This also handle having a 'INCLUDE' argument that will fill
@@ -215,10 +224,7 @@ def load_material_dico(name: str) -> dict[str, Any]:
----------
material_dico : dict
"""
if name == "silica":
return toml.loads(Paths.gets("silica"))
else:
return toml.loads(Paths.gets("gas"))[name]
return toml.loads(Paths.gets("materials"))[name]
def update_appended_params(source: Path, destination: Path, z: Sequence):

57
src/scgenerator/utils/parameter.py
View File

@@ -10,8 +10,9 @@ from copy import copy, deepcopy
from dataclasses import asdict, dataclass, fields
from functools import cache, lru_cache
from pathlib import Path
from typing import Any, Callable, Generator, Iterable, Literal, Optional, TypeVar, Union
from typing import Any, Callable, Generator, Iterable, Literal, Optional, Sequence, TypeVar, Union
import numpy as np
from numpy.lib import isin
from .. import math, utils
from ..const import PARAM_FN, PARAM_SEPARATOR, __version__
@@ -287,14 +288,14 @@ class Parameter:
def __set__(self, instance, value):
if isinstance(value, Parameter):
# defaut = None if self.default is None else copy(self.default)
# instance.__dict__[self.name] = defaut
instance.__dict__[self.name] = None
defaut = None if self.default is None else copy(self.default)
instance.__dict__[self.name] = defaut
# instance.__dict__[self.name] = None
else:
if value is not None:
self.validator(self.name, value)
if self.converter is not None:
value = self.converter(value)
self.validator(self.name, value)
instance.__dict__[self.name] = value
def display(self, num: float):
@@ -308,8 +309,11 @@ class Parameter:
return f"{num_str} {unit}"
def fiber_map_converter(d: dict[str, str]) -> dict[float, str]:
return {float(k): v for k, v in d.items()}
def fiber_map_converter(d: dict[str, str]) -> list[tuple[float, str]]:
if isinstance(d, dict):
return [(float(k), v) for k, v in d.items()]
else:
return [(float(k), v) for k, v in d]
@dataclass
@@ -340,7 +344,7 @@ class Parameters:
pitch_ratio: float = Parameter(in_range_excl(0, 1))
core_radius: float = Parameter(in_range_excl(0, 1e-3))
he_mode: tuple[int, int] = Parameter(int_pair, default=(1, 1))
fit_parameters: tuple[int, int] = Parameter(int_pair, default=(0.08, 200e-9))
fit_parameters: tuple[int, int] = Parameter(float_pair, default=(0.08, 200e-9))
beta2_coefficients: Iterable[float] = Parameter(num_list)
dispersion_file: str = Parameter(string)
model: str = Parameter(
@@ -425,13 +429,15 @@ class Parameters:
const_qty: np.ndarray = Parameter(type_checker(np.ndarray))
beta_func: Callable[[float], list[float]] = Parameter(func_validator)
gamma_func: Callable[[float], float] = Parameter(func_validator)
fiber_map: dict[float, str] = Parameter(type_checker(dict), converter=fiber_map_converter)
fiber_map: list[tuple[float, str]] = Parameter(
validator_list(type_checker(tuple)), converter=fiber_map_converter
)
datetime: datetime_module.datetime = Parameter(type_checker(datetime_module.datetime))
version: str = Parameter(string)
def prepare_for_dump(self) -> dict[str, Any]:
param = asdict(self)
param["fiber_map"] = {str(z): n for z, n in param.get("fiber_map", {}).items()}
param["fiber_map"] = [(str(z), n) for z, n in param.get("fiber_map", [])]
param = Parameters.strip_params_dict(param)
param["datetime"] = datetime_module.datetime.now()
param["version"] = __version__
@@ -896,7 +902,7 @@ class Configuration:
length = 0.0
fiber_map.append((length, this_conf["name"]))
params.output_path = str(sim_config.output_path)
params.fiber_map = dict(fiber_map)
params.fiber_map = fiber_map
yield sim_config.vary_list, params
def __iter_1_sim(
@@ -1020,7 +1026,7 @@ class DataPather:
def __init__(self, dl: list[dict[str, Any]]):
self.dict_list = dl
def dico_iterator(
def vary_list_iterator(
self, index: int
) -> Generator[tuple[tuple[tuple[int, ...]], list[list[tuple[str, Any]]]], None, None]:
"""iterates through every possible combination of a list of dict of lists
@@ -1050,6 +1056,8 @@ class DataPather:
[[(a, 57), (b, "!")], [(c, 1)]],
]
"""
if index < 0:
index = len(self.dict_list) - index
d_tem_list = [el for d in self.dict_list[: index + 1] for el in d.items()]
dict_pos = np.cumsum([0] + [len(d) for d in self.dict_list[: index + 1]])
ranges = [range(len(l)) for _, l in d_tem_list]
@@ -1062,7 +1070,7 @@ class DataPather:
yield pos, out
def all_vary_list(self, index):
for sim_index, l in self.dico_iterator(index):
for sim_index, l in self.vary_list_iterator(index):
unique_vary: list[tuple[str, Any]] = []
for ll in l[: index + 1]:
for pname, pval in ll:
@@ -1072,14 +1080,14 @@ class DataPather:
break
unique_vary.append((pname, pval))
yield sim_index, format_variable_list(
reduce_all_variable(l[:index])
), format_variable_list(reduce_all_variable(l)), unique_vary
reduce_all_variable(l[:index]), add_iden=True
), format_variable_list(reduce_all_variable(l), add_iden=True), unique_vary
def __repr__(self):
return f"DataPather([{', '.join(repr(d) for d in self.dict_list)}])"
@dataclass
@dataclass(frozen=True)
class PlotRange:
left: float = Parameter(type_checker(int, float))
right: float = Parameter(type_checker(int, float))
@@ -1194,7 +1202,7 @@ def _mock_function(num_args: int, num_returns: int) -> Callable:
return out_func
def format_variable_list(l: list[tuple[str, Any]]) -> str:
def format_variable_list(l: list[tuple[str, Any]], add_iden=False) -> str:
"""formats a variable list into a str such that each simulation has a unique
directory name. A u_XXX unique identifier and b_XXX (ignoring repeat simulations)
branch identifier are added at the beginning.
@@ -1203,6 +1211,8 @@ def format_variable_list(l: list[tuple[str, Any]]) -> str:
----------
l : list[tuple[str, Any]]
list of variable parameters
add_iden : bool
add unique simulation and parameter-set identifiers
Returns
-------
@@ -1215,6 +1225,8 @@ def format_variable_list(l: list[tuple[str, Any]]) -> str:
vs = format_value(p_name, p_value).replace("/", "").replace(PARAM_SEPARATOR, "")
str_list.append(ps + PARAM_SEPARATOR + vs)
tmp_name = PARAM_SEPARATOR.join(str_list)
if not add_iden:
return tmp_name
unique_id = "u_" + utils.to_62(hash(str(l)))
branch_id = "b_" + utils.to_62(hash(str([el for el in l if el[0] != "num"])))
return unique_id + PARAM_SEPARATOR + branch_id + PARAM_SEPARATOR + tmp_name
@@ -1324,6 +1336,17 @@ def reduce_all_variable(all_variable: list[list[tuple[str, Any]]]) -> list[tuple
return out
def strip_vary_list(all_variable: T) -> T:
if len(all_variable) == 0:
return all_variable
elif isinstance(all_variable[0], Sequence) and (
len(all_variable[0]) == 0 or not isinstance(all_variable[0][0], str)
):
return [strip_vary_list(el) for el in all_variable]
else:
return [el for el in all_variable if el[0] != "num"]
default_rules: list[Rule] = [
# Grid
*Rule.deduce(