241 lines
12 KiB
Python
241 lines
12 KiB
Python
from .IPSF import IPSF
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from ...lib.helpers import rasterizeCircle
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from ..sensor.PixelMask import PixelMask
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from ...lib.logger import logger
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import numpy as np
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import astropy.units as u
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import re
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from typing import Union
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from scipy.optimize import bisect
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from scipy.signal import fftconvolve
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from scipy.interpolate import interp2d
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class Zemax(IPSF):
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"""
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A class for modelling the PSF from a Zemax output file
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"""
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@u.quantity_input(wl="length", d_aperture="length", pixel_size="length")
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def __init__(self, file: str, f_number: float, wl: u.Quantity, d_aperture: u.Quantity, osf: float,
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pixel_size: u.Quantity):
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"""
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Initialize a new PSF from a Zemax file.
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Parameters
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----------
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file : str
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Path to the Zemax-file. The origin of the coordinate system is in the lower left corner of the matrix
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f_number : float
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The working focal number of the optical system
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wl : Quantity
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The central wavelength which is used for calculating the PSF
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d_aperture : Quantity
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The diameter of the telescope's aperture.
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osf : float
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The oversampling factor to be used for oversampling the PSF with regards to the pixel size.
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pixel_size : Quantity
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The size of a pixel as length-quantity.
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"""
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# Store parameters
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self.__f_number = f_number
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self.__wl = wl
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self.__d_aperture = d_aperture
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self.__osf = osf
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self.__pixel_size = pixel_size
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# Read PSF from file
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with open(file, encoding="utf16") as fp:
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self.__psf = np.genfromtxt((x.replace(",", ".") for x in fp), delimiter='\t', skip_header=21)
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# Read header parameters from the file
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with open(file, encoding="utf16") as fp:
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head = [next(fp) for _ in range(21)]
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# Parse shape of the grid and check the read PSF-array
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shape = [int(x) for x in re.findall("[0-9]+", list(filter(re.compile("Image grid size: ").match, head))[0])]
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if shape != list(self.__psf.shape):
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logger.warning("Not all PSF entries read.")
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# Parse and calculate the grid width
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grid_delta = [float(x.replace(",", ".")) for x in
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re.findall("[0-9]+,*[0-9]*", list(filter(re.compile("Data area is ").match, head))[0])]
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unit = re.findall(".+(?=\\.$)", re.sub("Data area is [0-9]+,*[0-9]* by [0-9]+,*[0-9]* ", "",
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list(filter(re.compile("Data area is ").match, head))[0]))[0]
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# noinspection PyArgumentList
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self.__grid_delta = np.array(grid_delta) / np.array(shape) << u.Unit(unit)
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# Parse the center point of the PSF in the grid
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self.__center_point = [int(x) for x in
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re.findall("[0-9]+", list(filter(re.compile("Center point is: ").match, head))[0])]
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self.__center_point[0] = self.__psf.shape[0] - self.__center_point[0]
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self.__center_point[1] -= 1
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self.__center_point_os = None
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self.__psf_os = None
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self.__psf_osf = None
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# @u.quantity_input(jitter_sigma=u.arcsec)
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def calcReducedObservationAngle(self, contained_energy: Union[str, int, float, u.Quantity],
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jitter_sigma: u.Quantity = None, obstruction: float = 0.0) -> u.Quantity:
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"""
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Calculate the reduced observation angle in lambda / d_ap for the given contained energy.
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Parameters
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----------
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contained_energy : Union[str, int, float, u.Quantity]
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The percentage of energy to be contained within a circle with the diameter reduced observation angle.
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jitter_sigma : Quantity
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Sigma of the telescope's jitter in arcsec
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obstruction : float
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The central obstruction as ratio A_ob / A_ap
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Returns
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-------
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reduced_observation_angle: Quantity
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The reduced observation angle in lambda / d_ap
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"""
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# Parse the contained energy
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if type(contained_energy) == str:
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try:
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contained_energy = float(contained_energy) / 100.0 * u.dimensionless_unscaled
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except ValueError:
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logger.error("Could not convert encircled energy to float.")
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elif type(contained_energy) in [int, float]:
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contained_energy = contained_energy / 100 * u.dimensionless_unscaled
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center_point, psf, psf_osf = self.__calcPSF(jitter_sigma)
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# Calculate the maximum possible radius for the circle containing the photometric aperture
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r_max = max(np.sqrt(center_point[0] ** 2 + center_point[1] ** 2),
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np.sqrt((psf.shape[0] - center_point[0]) ** 2 + center_point[1] ** 2),
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np.sqrt(center_point[0] ** 2 + (psf.shape[1] - center_point[1]) ** 2),
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np.sqrt((psf.shape[0] - center_point[0]) ** 2 + (psf.shape[1] - center_point[1]) ** 2))
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# Calculate the total contained energy of the PSF
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total = np.sum(psf)
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# Iterate the optimal radius for the contained energy
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r = bisect(lambda r_c: contained_energy.value - np.sum(
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psf * rasterizeCircle(np.zeros((psf.shape[0], psf.shape[0])), r_c, center_point[0],
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center_point[1])) / total, 0, r_max, xtol=1e-1) * 2
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# Calculate the reduced observation angle in lambda / d_ap
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# noinspection PyTypeChecker
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reduced_observation_angle = r / psf_osf * self.__grid_delta[0] / (
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self.__f_number * self.__d_aperture) * self.__d_aperture / self.__wl
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return reduced_observation_angle * u.dimensionless_unscaled
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def __calcPSF(self, jitter_sigma: u.Quantity = None):
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"""
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Calculate the PSF from the Zemax-file. This includes oversampling the PSF and convolving with the
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jitter-gaussian.
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Parameters
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----------
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jitter_sigma : Quantity
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Sigma of the telescope's jitter in arcsec.
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Returns
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-------
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center_point : ndarray
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The indices of the PSF's center point on the grid.
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psf : ndarray
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The PSF.
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psf_osf : float
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The oversampling factor of the returned PSF.
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"""
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# Calculate the psf for the PSF based on the current resolution of the PSF
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psf_osf = np.ceil(max(self.__grid_delta) / (2 * self.__pixel_size / self.__osf)).value * 2
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if psf_osf == 1.0:
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# No oversampling is necessary
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psf = self.__psf
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center_point = self.__center_point
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else:
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# Oversampling is necessary, oversample the PSF and calculate the new center point.
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f = interp2d(x=np.arange(self.__psf.shape[1]) - self.__center_point[1],
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y=np.arange(self.__psf.shape[0]) - self.__center_point[0], z=self.__psf,
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kind='cubic', copy=False, bounds_error=False, fill_value=None)
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center_point = [(x + 0.5) * psf_osf - 0.5 for x in self.__center_point]
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psf = f((np.arange(self.__psf.shape[1] * psf_osf) - center_point[1]) / psf_osf,
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(np.arange(self.__psf.shape[0] * psf_osf) - center_point[0]) / psf_osf)
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if jitter_sigma is not None:
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# Convert angular jitter to jitter on focal plane
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jitter_sigma_um = (jitter_sigma.to(u.rad) * self.__f_number * self.__d_aperture / u.rad).to(u.um)
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# Jitter is enabled. Calculate the corresponding gaussian bell and convolve it with the PSF
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if min(self.__grid_delta) / psf_osf < 6 * jitter_sigma_um:
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# 3-sigma interval of the gaussian bell is larger than the grid width
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# Calculate the necessary grid length for the 3-sigma interval of the gaussian bell
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jitter_grid_length = np.ceil(6 * jitter_sigma_um / (min(self.__grid_delta) / psf_osf)).value
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# Make sure, the grid size is odd in order to have a defined kernel center
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jitter_grid_length = int(jitter_grid_length if jitter_grid_length % 2 == 1 else jitter_grid_length + 1)
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# Create a meshgrid containing the x and y coordinates of each point within the first quadrant of the
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# gaussian kernel
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xv, yv = np.meshgrid(range(-int((jitter_grid_length - 1) / 2), 1),
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range(-int((jitter_grid_length - 1) / 2), 1))
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# Calculate the gaussian kernel in the first quadrant
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kernel = 1 / (2 * np.pi * jitter_sigma_um.value ** 2) * np.exp(
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-((xv * min(self.__grid_delta.value) / psf_osf) ** 2 +
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(yv * min(self.__grid_delta.value) / psf_osf) ** 2) / (2 * jitter_sigma_um.value ** 2))
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# Mirror the kernel from the first quadrant to all other quadrants
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kernel = np.concatenate((kernel, np.flip(kernel, axis=1)[:, 1:]), axis=1)
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kernel = np.concatenate((kernel, np.flip(kernel, axis=0)[1:, :]), axis=0)
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# Normalize kernel
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kernel = kernel / np.sum(kernel)
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# Convolve PSF with gaussian kernel
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psf = fftconvolve(np.pad(psf, int((jitter_grid_length - 1) / 2), mode="constant", constant_values=0),
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kernel, mode="same")
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# Calculate new center point
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center_point = [x + int((jitter_grid_length - 1) / 2) for x in center_point]
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# Save the values as object attribute
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self.__center_point_os = center_point
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self.__psf_os = psf
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self.__psf_osf = psf_osf
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return center_point, psf, psf_osf
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def mapToPixelMask(self, mask: PixelMask, jitter_sigma: u.Quantity = None, obstruction: float = 0.0) -> PixelMask:
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"""
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Map the integrated PSF values to a sensor grid.
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Parameters
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----------
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obstruction
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mask : PixelMask
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The pixel mask to map the values to. The values will only be mapped onto entries with the value 1.
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jitter_sigma : Quantity
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Sigma of the telescope's jitter in arcsec
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Returns
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-------
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mask : PixelMask
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The pixel mask with the integrated PSF values mapped onto each pixel.
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"""
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# Calculate the indices of all non-zero elements of the mask
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y_ind, x_ind = np.nonzero(mask)
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# Extract a rectangle containing all non-zero values of the mask
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mask_red = mask[y_ind.min():(y_ind.max() + 1), x_ind.min():(x_ind.max() + 1)]
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# Calculate the new PSF-center indices of the reduced mask
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psf_center_ind = [mask.psf_center_ind[0] - y_ind.min(), mask.psf_center_ind[1] - x_ind.min()]
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# Oversample the reduced mask
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mask_red_os = self._rebin(mask_red, self.__osf).view(PixelMask)
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# Calculate the new PSF-center indices of the reduced mask
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psf_center_ind = [x * self.__osf for x in psf_center_ind]
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# Get PSF values or calculate them if not available
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if self.__psf_os is not None and self.__center_point_os is not None and self.__psf_osf is not None:
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center_point = self.__center_point_os
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psf = self.__psf_os
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psf_osf = self.__psf_osf
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else:
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center_point, psf, psf_osf = self.__calcPSF(jitter_sigma)
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# Calculate the coordinates of each PSF value in microns
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x = (np.arange(psf.shape[1]) - center_point[1]) * self.__grid_delta[1].to(u.um).value / psf_osf
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y = (np.arange(psf.shape[0]) - center_point[0]) * self.__grid_delta[0].to(u.um).value / psf_osf
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# Initialize a two-dimensional cubic interpolation function for the PSF
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psf_interp = interp2d(x=x, y=y, z=psf, kind='cubic', copy=False, bounds_error=False, fill_value=None)
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# Calculate the values of the PSF for all elements of the reduced mask
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res = psf_interp((np.arange(mask_red_os.shape[1]) - psf_center_ind[1]) * mask_red_os.pixel_size.to(u.um).value,
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(np.arange(mask_red_os.shape[0]) - psf_center_ind[0]) * mask_red_os.pixel_size.to(u.um).value)
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# Bin the oversampled reduced mask to the original resolution and multiply with the reduced mask to select only
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# the relevant values
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res = mask_red * self._rebin(res, 1 / self.__osf)
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# Integrate the reduced mask and divide by the indefinite integral to get relative intensities
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res = res * mask_red_os.pixel_size.to(u.um).value ** 2 / (
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psf.sum() * (self.__grid_delta[0].to(u.um).value / psf_osf) ** 2)
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# reintegrate the reduced mask into the complete mask
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mask[y_ind.min():(y_ind.max() + 1), x_ind.min():(x_ind.max() + 1)] = res
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return mask
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