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