MPID/mpid.py

from kiwisolver import Constraint
import numpy as np
import matplotlib.pyplot as plt
plt.rcParams.update({'font.size': 14})
import os
import pyfftw
import nlopt
from autograd import tensor_jacobian_product, grad as gd
import autograd.numpy as npa
from filters import conic_filter

def make_2Dplot_of(given_field:np.ndarray, grid_X:np.ndarray, grid_Y:np.ndarray, plot_zoom_x:float,plot_zoom_y:float,choose_quantity="amplitude",save_name="plot") -> None:
    '''Makes a plot of the given 2D field in a zoomed region. 
    Saves the plot with the chosen filename to a PDF file. 
    Args:
        given_field: the 2D field to be plotted (flattened)
        choose_quantity: either "amplitude" or "phase" to select quantity to plot
        save_name: name of the file to save the plot (without extension)
        plot_zoom_x: zoom level for the x-axis (in micrometers)
        plot_zoom_y: zoom level for the y-axis (in micrometers)
    Returns:
        None'''
    
    given_field_2d = given_field.reshape((grid_X.shape[0], grid_X.shape[1])) #assure the field is 2D before plotting
    fig, ax = plt.subplots(figsize=(6, 6))
    if choose_quantity == "amplitude":
        ax.pcolormesh(grid_X*1e6,grid_Y*1e6,np.abs(given_field_2d),rasterized=True)
        #add a colorbar for amplitude
        plt.colorbar(ax.pcolormesh(grid_X*1e6,grid_Y*1e6,np.abs(given_field_2d),rasterized=True), ax=ax)
    elif choose_quantity == "phase":
        ax.pcolormesh(grid_X*1e6,grid_Y*1e6,(np.angle(given_field_2d)+2*np.pi)%(2*np.pi), cmap='hsv', vmin=0, vmax=2*np.pi, rasterized=True)
    elif choose_quantity == "phase_mask":
        ax.pcolormesh(grid_X*1e6,grid_Y*1e6,(given_field_2d+2*np.pi)%(2*np.pi), cmap='hsv', vmin=0, vmax=2*np.pi, rasterized=True)
    else:
        raise ValueError("Unexpected value for choose_quantity")

    ax.set_xlim(-plot_zoom_x, plot_zoom_x)
    ax.set_ylim(-plot_zoom_y, plot_zoom_y)
    ax.set_xlabel("x [um]")
    ax.set_ylabel("y [um]")
    plt.tight_layout()
    plt.savefig(save_name + ".pdf")
    plt.close()

def make_1Dplot_of(x_axis,y_axis,plot_zoom_x,save_name="plot_1D",) -> None:
    '''Makes a 1D plot of the given data and saves it to a PDF file.
    Args:
        x_axis: list of x-axis data (list of 1D arrays)
        y_axis: list of y-axis data (list of 1D arrays)
        plot_zoom_x: zoom level for the x-axis (in micrometers)
        save_name: name of the file to save the plot (without extension)
    Returns:
        None
    '''
    if len(x_axis) != len(y_axis):
        raise ValueError("Lists x_axis and y_axis must have the same length.")
    plt.figure()
    for i in range(len(x_axis)):
        if x_axis[i] is None:
            plt.plot(y_axis[i])
        else:
            plt.plot(x_axis[i], y_axis[i])
    plt.xlabel("x [um]")
    plt.tight_layout()
    if plot_zoom_x is None:
        pass
    else:
        plt.xlim(-plot_zoom_x, plot_zoom_x)
    plt.savefig(save_name + ".pdf")
    plt.close()

class SpaceGrid:
    '''
    Class representing the spatial grid for the simulation.
    Spatial dimensions are intended to be measured in micrometers [um].
    '''
    def __init__(self, side_pixels: int, unit_cell_pitch: float, materials_refr_index: np.ndarray, prop_distances: np.ndarray = None, xy_symmetry=False):
        if prop_distances is None:
            self.propagation_distances_set = False
            self.d = None
        else:
            self.propagation_distances_set = True
            self.d = prop_distances * 1e-6
        
        self.materials_refr_index = materials_refr_index

        self.num_phase_masks = 0
        if self.propagation_distances_set:
            self.num_phase_masks = len(self.d) - 1

        #determine the number of phase masks required based on the number of propagation distances
        self.num_phase_masks = 0
        if self.propagation_distances_set:
            self.num_phase_masks = len(self.d) - 1
        
        self.Nx = side_pixels#for the moment we consider only square grids
        self.Ny = side_pixels
        self.unit_cell_pitch = unit_cell_pitch * 1e-6 # convert to [m]
        self.nx = (self.Nx - 1) // 2
        self.ny = (self.Ny - 1) // 2
        self.xy_symmetry = xy_symmetry
        self.S = self.Nx * self.Ny

        if self.xy_symmetry:
            self.dof = self.num_phase_masks * ((self.nx + 1)**2)
            self.S_symm = (self.nx + 1)**2
        else:
            self.dof = self.num_phase_masks * self.S

        self.size_x = self.unit_cell_pitch * self.Nx
        self.size_y = self.unit_cell_pitch * self.Ny
        self.xs = np.arange(-self.Nx//2+1, self.Nx//2+1) * (self.size_x / self.Nx)
        self.ys = np.arange(-self.Ny//2+1, self.Ny//2+1) * (self.size_y / self.Ny)
        self.X, self.Y = np.meshgrid(self.xs, self.ys)
        self.rho = np.sqrt(self.X**2 + self.Y**2)
        self.sampling_period = self.unit_cell_pitch

    def get_num_phase_masks(self):
        return self.num_phase_masks
        
    def get_grid_shape(self):
        return (self.Nx, self.Ny)

    def get_materials_refr_index(self):
        return self.materials_refr_index

    def get_distances(self):
        return self.d

    def get_num_distances(self):
        return len(self.d)
    
    def get_sampling_period(self):
        return self.sampling_period

    def get_resolution(self):
        '''
        Returns the resolution of the spatial grid in micrometers [um].
        '''
        return self.unit_cell_pitch * 1e6 # returns [um]

    def get_unit_cell_pitch(self) -> float:
        '''
        Returns the unit cell pitch of the spatial grid in micrometers [um].
        '''
        return self.unit_cell_pitch * 1e6 # returns [um]

    def get_size_x(self):
        return self.size_x

    def get_size_y(self):
        return self.size_y

    def get_Nx(self):
        return self.Nx

    def get_Ny(self):
        return self.Ny

    def get_nx(self):
        return self.nx

    def get_ny(self):
        return self.ny

    def get_dof(self):
        return self.dof

    def get_S(self):
        return self.S

    def get_S_symm(self):
        if not self.xy_symmetry:
            raise ValueError("S_symm is only defined when xy_symmetry is set True")
        return self.S_symm

    def get_X(self):
        return self.X

    def get_Y(self):
        return self.Y

    def get_XY(self):
        return self.X, self.Y

    def get_rho(self):
        return self.rho
    
class Field:
    def __init__(self, input_field: np.ndarray, wavelength: float, center: np.ndarray = np.array([0,0])):
        self.center = center * 1e-6
        self.input_field = input_field
        self.wavelength = wavelength * 1e-6

    def get_field(self, space_grid: SpaceGrid = None, flatten=False):
        if space_grid is None:
            raise ValueError("A SpaceGrid must be provided when invoking get_field()")
        self.space_grid = space_grid
        if flatten:
            return self._shift_field(self.input_field).flatten()
        return self._shift_field(self.input_field)

    def get_field_arr(self):
        return self.input_field

    def get_wavelength(self):
        return self.wavelength

    def get_center(self):
        return self.center

    def _shift_field(self,input_field):
        #take the input field and shift it according to the center
        shift_field_x = np.roll(input_field, shift=int(self.center[0]/self.space_grid.get_sampling_period()), axis=1)
        shift_field_y = np.roll(shift_field_x, shift=int(self.center[1]/self.space_grid.get_sampling_period()), axis=0)
        return shift_field_y

    def plot2D(self, plot_zoom_x:float, plot_zoom_y:float, choose_quantity="amplitude", save_name="results/plot_out"):
        return 0 #broken atm
        #make_2Dplot_of(self.input_field, 
        #               self.space_grid.X, 
        #               self.space_grid.Y,
        #               plot_zoom_x, 
        #               plot_zoom_y, 
        #               choose_quantity, 
        #               save_name)

class Source(Field):
    def __init__(self, input_field: np.ndarray | str, wavelength: float, field_norm = False, center: np.ndarray = np.array([0,0])):
        if isinstance(input_field, str):
            input_field_to_constr = np.load(input_field)
            input_field_shape = input_field_to_constr.shape
            input_field_to_constr = (input_field_to_constr / np.sqrt(np.sum(np.abs(input_field_to_constr)**2))).reshape(input_field_shape)
        else:
            input_field_to_constr = input_field

        if field_norm:
            input_field_to_constr = input_field_to_constr / np.sqrt(np.sum(np.abs(input_field_to_constr)**2))

        super().__init__(input_field_to_constr, wavelength, center=center)
        self.type = "source"

    def get_type(self):
        return self.type

class GaussianBeam():
    def __init__(self, beam_waist: float, space_grid: SpaceGrid, center=np.array([0,0]), field_norm = False):
        self.beam_waist = beam_waist
        self.center = center
        self.space_grid = space_grid
        generated_field = self._generate_gaussian_beam()
        if field_norm:
            self.field = generated_field / np.sqrt(np.sum(np.abs(generated_field)**2))
        else:
            self.field = generated_field
        
    def _generate_gaussian_beam(self):
        X = self.space_grid.X - self.center[0]
        Y = self.space_grid.Y - self.center[1]
        r_squared = X**2 + Y**2
        return np.exp(-r_squared / self.beam_waist**2)

    def get_field(self):
        return self.field

    def get_space_grid(self):
        return self.space_grid

class Target(Field):
    def __init__(self, input_field: np.ndarray | str | Field ,
                 associated_source: Source, 
                 wavelength: float, 
                 field_norm = False, 
                 center = np.array([0,0])):
        if isinstance(input_field, str):
            input_field_to_constr = np.load(input_field)
            input_field_shape = input_field_to_constr.shape
            input_field_to_constr = (input_field_to_constr / np.sqrt(np.sum(np.abs(input_field_to_constr)**2))).reshape(input_field_shape)
        else:
            input_field_to_constr = input_field

        if field_norm:
            input_field_to_constr = input_field_to_constr / np.sqrt(np.sum(np.abs(input_field_to_constr)**2))

        super().__init__(input_field_to_constr, wavelength, center=center)
        self.type = "target"

        if associated_source.get_wavelength() != self.get_wavelength():
            raise ValueError("Associated source must have the same wavelength as the target.")
        else:
            self.associated_source = associated_source
        
    def get_type(self):
        return self.type

    def get_associated_source(self):
        return self.associated_source

class PlotArray():
    def __init__(self, input_field: np.ndarray, space_grid: SpaceGrid):
        self.input_field = input_field
        self.array_shape = input_field.shape
        self.space_grid = space_grid
        self.type = "plot_array"

    def get_type(self):
        return self.type

    def plot2D(self, plot_zoom_x, plot_zoom_y, choose_quantity="amplitude", save_name="results/plot2D_out"):
        if len(self.array_shape) == 2:
            make_2Dplot_of(self.input_field, 
                        self.space_grid.X, 
                        self.space_grid.Y,
                        plot_zoom_x, 
                        plot_zoom_y, 
                        choose_quantity, 
                        save_name)
        else:
            raise ValueError("Input field must be 2D for plot2D.")

    def plot1D(self, plot_zoom_x, save_name="results/plot1D_out"):
        if len(self.array_shape) == 1:
            make_1Dplot_of([self.space_grid.X.flatten()], 
                           [self.input_field.flatten()], 
                           plot_zoom_x, 
                           save_name)
        else:
            raise ValueError("Input field must be 1D for plot1D.")

class Simulation:
    def  __init__(self, sources:list[Source], 
                  targets:list[Target], 
                  central_wavelength: float, 
                  space_grid: SpaceGrid = None, 
                  n_cpu: int = 1):

        self.sources = sources
        self.targets = targets
        self.eps_0 = 8.854e-12
        self.mu_0 = 4*np.pi*1e-7
        self.central_wavelength = central_wavelength * 1e-6 #central_wavelength parameter has little sense to exist. Revise
        self.operating_wavelength = self.central_wavelength #initially, the operating_wavelength is the central wavelength
        self.n_cpu = n_cpu

        if space_grid is not None:
            self.set_space_grid(space_grid)

        self._configure_fftw(self.n_cpu)
        
        self.is_optimization_set = False
        self.is_optimized_flag = False
        self.results_while_solving = True
        self.opt_history = []
        self.results_folder = "results"
        if not os.path.exists(self.results_folder):
            os.makedirs(self.results_folder)

    def _configure_fftw(self, n_cpu = 1, planner_effort='FFTW_ESTIMATE'):
        pyfftw.config.NUM_THREADS = n_cpu
        pyfftw.interfaces.cache.disable()
        pyfftw.config.PLANNER_EFFORT = planner_effort

    def set_optimization(self, 
                         opt_param_min, 
                         opt_param_max, 
                         ms_max_avail_diameter, 
                         phase_mask_init_size, 
                         opt_max_eval, 
                         conic_filter_radius = None, 
                         results_while_solving=True, 
                         custom_mask = None, 
                         strategy = 'mean',
                         save_results = True):
        '''
        Sets the optimization parameters for the simulation.
        Arguments related to physical dimensions are expected to be in micrometers [um].
        Args:
            optimization_params (dict): A dictionary containing optimization parameters.
        '''
        self.is_optimization_set = True
        self.iter_num = [0]
        self.norm_phase_min = opt_param_min
        self.norm_phase_max = opt_param_max
        self.ms_max_avail_diameter = ms_max_avail_diameter * 1e-6
        self.phase_mask_init_size = phase_mask_init_size * 1e-6
        self.opt_max_eval = opt_max_eval
        self.results_while_solving = results_while_solving
        self.custom_mask = custom_mask #future: one might be able to directly pass a custom mask
        self.strategy = strategy
        self.save_results = save_results

        if conic_filter_radius is None:
            self.use_filtering = False
        else:
            self.use_filtering = True
            self.filter_radius = None

        if conic_filter_radius is not None:
            self.filter_radius = conic_filter_radius 
        else:
            self.filter_radius = None

    def get_sources(self):
        return self.sources

    def get_targets(self):
        return self.targets

    def get_num_targets(self):
        return len(self.targets)

    def get_space_grid(self):
        return self.space_grid

    def get_ms_max_avail_diameter(self):
        return self.ms_max_avail_diameter

    def get_central_wavelength(self):
        return self.central_wavelength

    def get_operating_wavelength(self):
        return self.operating_wavelength

    def get_k_vectors(self):
        return self.k_vectors

    def get_wvl_all_targets(self, unit_measure = 1):
        return [target.get_wavelength() * unit_measure for target in self.targets]

    def _update_wavelength(self, new_wavelength):
        '''
        Updates the operating wavelength and related vectors (lda_vector and k_vectors) based on the new wavelength.
        The new_wavelength should be provided in meters.
        Args:
            new_wavelength (float): The new operating wavelength in meters.
        '''
        assert new_wavelength > 0, "Wavelength must be positive."
        self.operating_wavelength = new_wavelength

        self.lda_vector = [self.operating_wavelength / n for n in self.space_grid.get_materials_refr_index()]
        self.eps_r = (self.space_grid.get_materials_refr_index())**2
        self.k_vectors = [2 * np.pi / lda for lda in self.lda_vector]
        
        self.phase_factors = [self.k_vectors[i] * self.space_grid.get_distances()[i] * np.sqrt(1 - (self.lda_vector[i] * self.nu_parallel) ** 2 + 0*1j) for i in range(len(self.k_vectors))]
        
        self.P = [np.exp(1j * self.phase_factors[i]) for i in range(len(self.phase_factors))]
        self.P_nat = [np.fft.ifftshift(self.P[i]) for i in range(len(self.P))]
        self.P_dagger_nat = [self.P_nat[i].T.conj() for i in range(len(self.P_nat))]

    def _phase_given_w(self):
        return 2 * np.pi * self.w_norm

    def _phase_given_w(self, input_normalized_phase):
        return 2 * np.pi * input_normalized_phase

    def _w_given_phase(self, input_phase):
        return input_phase / (2 * np.pi)

    def _symmetrize(self, w):
        '''
        Takes an input array, which must be full in size, turns it into a 2D array, and symmetrizes it along the x and y axes.
        Returns the first quadrant of shape (nx,ny), including the zero axis, flattened
        '''
        try:
            w_2d = w.reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))
        except:
            raise ValueError(f"Wrong shape for input array. Current shape: {w.shape}")

        w_symm = np.zeros((self.space_grid.get_nx()+1, self.space_grid.get_ny()+1))
        w_symm[:,:] = w_2d[:self.space_grid.get_nx()+1, :self.space_grid.get_ny()+1]

        return w_symm.flatten()

    def _build_circular_mask(self, center, radius):
        '''
        Builds a circular mask centered at the given position with the specified radius.
        '''
        x_center, y_center = center
        X, Y = self.space_grid.get_XY()
        rho = np.sqrt((X - x_center)**2 + (Y - y_center)**2)
        return np.where(rho.flatten() < radius, 1, 0)

    def _initialize_phase_masks(self):
        '''
        Initializes the phase masks for the simulation.
        This method should be called once, before iterating over the targets.
        If multiple source/targets are present in this simulation instance, the mask
        is locally initialized around each source and target.
        '''
    
        source_Efields = [source.get_field(space_grid=self.space_grid, flatten=True) for source in self.sources]
        source_centers = [source.get_center() for source in self.sources]

        target_Efields = [target.get_field(space_grid=self.space_grid, flatten=True) for target in self.targets]
        target_centers = [target.get_center() for target in self.targets]

        self.w_norm = np.zeros((self.num_phase_masks*self.space_grid.get_S()))

        circular_mask_source = [self._build_circular_mask(source_center, self.phase_mask_init_size) for source_center in source_centers]
        circular_mask_target = [self._build_circular_mask(target_center, self.phase_mask_init_size) for target_center in target_centers]

        source_pattern_phase = [(np.angle(source_Efields[i]) + 2 * np.pi) % (2 * np.pi) * circular_mask_source[i] for i in range(len(source_Efields))] #make sure the phase is between 0 and 2pi
        target_pattern_phase = [(np.angle(target_Efields[i]) + 2 * np.pi) % (2 * np.pi) * circular_mask_target[i] for i in range(len(target_Efields))] #make sure the phase is between 0 and 2pi

        #initialize mask on source side
        cumulated_source_phase = np.zeros_like(self.w_norm[:self.space_grid.get_S()])
        for _, source_phase in enumerate(source_pattern_phase):
            cumulated_source_phase += source_phase / (2 * np.pi) #normalize the source phase to be between 0 and 1

        self.w_norm[:self.space_grid.get_S()] = ((cumulated_source_phase + 2*np.pi) % (2*np.pi)) / (2*np.pi)

        #initialize mask on target side
        cumulated_target_phase = np.zeros(self.space_grid.get_S())
        for _, target_phase in enumerate(target_pattern_phase):
            cumulated_target_phase += target_phase / (2 * np.pi) #normalize the target phase to be between 0 and 1

        if self.num_phase_masks ==2:
            self.w_norm[self.space_grid.get_S():] = ((cumulated_target_phase + 2*np.pi) % (2*np.pi)) / (2*np.pi)
        elif self.num_phase_masks == 3:
            self.w_norm[2*self.space_grid.get_S():] = ((cumulated_target_phase + 2*np.pi) % (2*np.pi)) / (2*np.pi)

        
        if self.space_grid.xy_symmetry:
            if self.num_phase_masks == 2:
                w_norm_symm_1 = self._symmetrize(self.w_norm[:self.space_grid.get_S()])
                w_norm_symm_2 = self._symmetrize(self.w_norm[self.space_grid.get_S():])
            elif self.num_phase_masks == 3:
                w_norm_symm_1 = self._symmetrize(self.w_norm[:self.space_grid.get_S()])
                w_norm_symm_2 = self._symmetrize(self.w_norm[self.space_grid.get_S():2*self.space_grid.get_S()])
                w_norm_symm_3 = self._symmetrize(self.w_norm[2*self.space_grid.get_S():])

            if self.num_phase_masks == 2:
                self.w_norm_symm[:] = np.concatenate((w_norm_symm_1, w_norm_symm_2), axis=0)
            elif self.num_phase_masks == 3:
                self.w_norm_symm[:] = np.concatenate((w_norm_symm_1, w_norm_symm_2, w_norm_symm_3), axis=0)

        self.phase_mask[:] = self._phase_given_w(self.w_norm)
                
    def _phase_filter(self, phase_mask: np.ndarray) -> np.ndarray:
        '''Applies a conic filter on the phase mask. The filtering action is equivalent to a local weighted averaging of the phase.
        Note that due to the circular behavior of phase, a direct averaging of phase values can lead to incorrect results. 
        The following code averages the sine and cosine components separately and then reconstructs the phase mask through the arctangent.
        A practical example might help: if the phase mask contains values close to 0 and 2π, a direct averaging would incorrectly yield a value around π. 
        By averaging the sine and cosine components separately, the correct average near 0 (or 2π) is obtained.

        Args:
            phase_mask (ndarray): The input phase mask to be filtered.

        Returns:
            ndarray: The filtered phase mask.
        '''
        if self.filter_radius is None:
            raise ValueError("Filter radius is not set.")

        phase_mask_cos = npa.cos(phase_mask)
        phase_mask_sin = npa.sin(phase_mask)

        phase_mask_filtered_cos = conic_filter(
            phase_mask_cos,
            self.filter_radius,
            self.space_grid,
        )

        phase_mask_filtered_sin = conic_filter(
            phase_mask_sin,
            self.filter_radius,
            self.space_grid,
        )
        return npa.arctan2(phase_mask_filtered_sin, phase_mask_filtered_cos)

    def _forward_propagate(self, source_object: Source, returns_field: bool = False):
        #source field
        source_to_propagate = source_object.get_field(space_grid=self.space_grid)

        #we retrieve the phase masks by managing the filtered phase mask array
        #depending on the number of phase masks, we will split the filtered phase mask array accordingly
        if self.num_phase_masks == 2:
            filtered_phase_mask_1 = self.filtered_phase_mask[:self.space_grid.get_S()]
            filtered_phase_mask_2 = self.filtered_phase_mask[self.space_grid.get_S():]
        elif self.num_phase_masks == 3:
            filtered_phase_mask_1 = self.filtered_phase_mask[:self.space_grid.get_S()]
            filtered_phase_mask_2 = self.filtered_phase_mask[self.space_grid.get_S():2*self.space_grid.get_S()]
            filtered_phase_mask_3 = self.filtered_phase_mask[2*self.space_grid.get_S():]

        self.fft_input_array[:,:] = np.fft.ifftshift(source_to_propagate.reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny())))
        self.fft_operator()

        self.ifft_input_array[:,:] = self.fft_operator.output_array * self.P_nat[0]
        
        self.ifft_operator()

        #field before MS1
        self.intermediate_electric_fields[0] = np.fft.fftshift(self.ifft_operator.output_array)

        input_field = self.intermediate_electric_fields[0].flatten()

        self.fft_input_array[:,:] = np.fft.ifftshift((input_field * np.exp(1j * filtered_phase_mask_1)).reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny())))
        self.fft_operator()
        self.ifft_input_array[:,:] = self.fft_operator.output_array * self.P_nat[1] #element wise product
        self.ifft_operator()

        #field before MS2
        self.intermediate_electric_fields[1] = np.fft.fftshift(self.ifft_operator.output_array.copy())

        #print("Field intensity after first phase mask and propagation: %.4e" % np.sum(np.abs(self.intermediate_electric_fields[0])**2))

        self.fft_input_array[:,:] = np.fft.ifftshift(np.fft.fftshift(self.ifft_operator.output_array) * np.exp(1j * filtered_phase_mask_2.reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))))
        self.fft_operator()
        self.ifft_input_array[:,:] = self.fft_operator.output_array * self.P_nat[2] #element wise product
        self.ifft_operator()

        #output field if the number of phase masks is 2, otherwise this is the input field on MS3
        self.intermediate_electric_fields[2] = np.fft.fftshift(self.ifft_operator.output_array.copy())

        #if the number of phase masks is 2, stop here
        if self.num_phase_masks == 2:
            self.output_field = self.intermediate_electric_fields[-1].flatten()
            if returns_field:
                return self.output_field
            else:
                return None

        self.fft_input_array[:,:] = np.fft.ifftshift(np.fft.fftshift(self.ifft_operator.output_array) * np.exp(1j * filtered_phase_mask_3.reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))))
        self.fft_operator()
        self.ifft_input_array[:,:] = self.fft_operator.output_array * self.P_nat[3] #element wise product
        self.ifft_operator()

        self.intermediate_electric_fields[3] = np.fft.fftshift(self.ifft_operator.output_array.copy())

        self.output_field = self.intermediate_electric_fields[-1].flatten()        

        if returns_field:
            return self.output_field
        else:
            return None
        #make a plot of intermediate fields
        #for i, field in enumerate(self.intermediate_electric_fields):
        #    make_2Dplot_of(field, self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=60, plot_zoom_y=60, choose_quantity="amplitude", save_name=f"results/intermediate_field_{i+1}_plot")


    def _reduce_symmetrized_gradient(self, g_full):
        '''
        Utility function that takes a spatial full size gradient and reduces it 
        to a smaller, symmetrized representation. In other words, it combines
        the contributions from the other quadrants into the selected quadrant.
        '''
        g_2d = g_full.reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))

        third = g_2d[self.space_grid.get_nx()+1:,:self.space_grid.get_ny()+1]
        second = g_2d[:self.space_grid.get_nx()+1, self.space_grid.get_ny()+1:]
        fourth = g_2d[self.space_grid.get_nx()+1:, self.space_grid.get_ny()+1:]

        g_2d[:self.space_grid.get_nx(), self.space_grid.get_ny()+1:] += np.flip(fourth, axis = 0)
        g_2d[:self.space_grid.get_nx(), :self.space_grid.get_ny()+1] += np.flip(third, axis = 0)
        g_2d[:self.space_grid.get_nx()+1, :self.space_grid.get_ny()] += np.flip(second, axis = 1)
        
        return g_2d[:self.space_grid.get_nx()+1, :self.space_grid.get_ny()+1].flatten()

    def _adjoint_propagate(self, target):
        #we need to manage the case of two or three phase masks by defining the associated filtered phase masks
        if self.num_phase_masks == 2:
            filtered_phase_mask_1 = self.filtered_phase_mask[:self.space_grid.get_S()]
            filtered_phase_mask_2 = self.filtered_phase_mask[self.space_grid.get_S():]
        elif self.num_phase_masks == 3:
            filtered_phase_mask_1 = self.filtered_phase_mask[:self.space_grid.get_S()]
            filtered_phase_mask_2 = self.filtered_phase_mask[self.space_grid.get_S():2*self.space_grid.get_S()]
            filtered_phase_mask_3 = self.filtered_phase_mask[2*self.space_grid.get_S():]

        Phi_dagger = []
        Phi_1_dagger = np.exp(-1j * filtered_phase_mask_1).reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))
        Phi_2_dagger = np.exp(-1j * filtered_phase_mask_2).reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))
        Phi_dagger.append(Phi_1_dagger)
        Phi_dagger.append(Phi_2_dagger)
        if self.num_phase_masks == 3:
            Phi_3_dagger = np.exp(-1j * filtered_phase_mask_3).reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))
            Phi_dagger.append(Phi_3_dagger)


        grad_C_phi = [None] * self.num_phase_masks
        #compute the adjoint source
        S = np.sum(self.intermediate_electric_fields[-1] * np.conj(target.get_field(space_grid=self.space_grid)))
        a = S * target.get_field(space_grid=self.space_grid)
        
        self.fft_input_array[:,:] = np.fft.ifftshift(a)
        self.fft_operator()
        self.ifft_input_array[:,:] = self.fft_operator.output_array * self.P_dagger_nat[-1]
        self.ifft_operator()
        self.fft_input_array[:,:] = np.fft.ifftshift(np.fft.fftshift(self.ifft_operator.output_array) * Phi_dagger[-1])

        grad_C_phi[-1] = 2 * np.real(-1j * self.intermediate_electric_fields[-2].conj() * np.fft.fftshift(self.fft_input_array)).flatten() 
        #grad_C_phi_2 = 2 * np.real(-1j * self.intermediate_electric_fields[1].conj() * np.fft.fftshift(self.fft_input_array)).flatten() 

        self.fft_operator()
        self.ifft_input_array[:,:] = self.fft_operator.output_array * self.P_dagger_nat[-2] #element wise
        self.ifft_operator()
        self.fft_input_array[:,:] = np.fft.ifftshift(np.fft.fftshift(self.ifft_operator.output_array) * Phi_dagger[-2])

        grad_C_phi[-2] = 2 * np.real(-1j * self.intermediate_electric_fields[-3].conj() * np.fft.fftshift(self.fft_input_array)).flatten()

        if self.num_phase_masks == 2:
            return grad_C_phi

        self.fft_operator()
        self.ifft_input_array[:,:] = self.fft_operator.output_array * self.P_dagger_nat[-3] #element wise
        self.ifft_operator()
        self.fft_input_array[:,:] = np.fft.ifftshift(np.fft.fftshift(self.ifft_operator.output_array) * Phi_dagger[-3])

        grad_C_phi[-3] = 2 * np.real(-1j * self.intermediate_electric_fields[-4].conj() * np.fft.fftshift(self.fft_input_array)).flatten()

        return grad_C_phi
        #return grad_C_phi_1, grad_C_phi_2

    def _value_and_grad(self, target):
        '''

        '''
        source = target.get_associated_source()
        wavelength = source.get_wavelength()

        self._update_wavelength(wavelength)

        self._forward_propagate(source)

        C_s = np.real(np.abs(np.sum(self.output_field * np.conj(target.get_field(space_grid=self.space_grid, flatten=True)))) ** 2)
        grads = self._adjoint_propagate(target)

        return C_s, grads

    def _expand_symmetrize(self, w_symm):
        '''
        Takes a array of shape (nx+1, ny+1), representing the first quadrant, including zero axes, and 
        expands it to a full 2D array of shape (Nx, Ny) by mirroring, flattened.
        '''
        w_symm_2d = w_symm.reshape((self.space_grid.get_nx()+1, self.space_grid.get_ny()+1))

        w_full = np.zeros((self.space_grid.get_Nx(), self.space_grid.get_Ny()))

        w_full[:self.space_grid.get_nx()+1, :self.space_grid.get_ny()+1] = w_symm_2d
        w_full[:self.space_grid.get_nx()+1, self.space_grid.get_ny()+1:] = np.flip(w_full[:self.space_grid.get_nx()+1, :self.space_grid.get_ny()], axis=1)
        w_full[self.space_grid.get_nx()+1:, :self.space_grid.get_ny()+1] = np.flip(w_full[:self.space_grid.get_nx(), :self.space_grid.get_ny()+1], axis=0)
        w_full[self.space_grid.get_nx()+1:, self.space_grid.get_ny()+1:] = np.flip(np.flip(w_full[:self.space_grid.get_nx(), :self.space_grid.get_ny()], axis=1), axis=0)
        w_full[self.space_grid.get_nx(), self.space_grid.get_ny()] = w_symm_2d[-1, -1]

        return w_full.flatten()

    def _epigraph_constraint(self, result, epigraph_and_weights, gradient)->None:
        '''
        Constraint function for the epigraph formulation. 
        Check nlopt documentation about Vector-valued constraints for additional details.
        
        Args:
            result: 1D array, modified in place, with the results of this constraint
                evaluation. Dimensionality should match the number of constraints.
        
            epigraph_and_weights: 1D array of epigraph (first element) and 
                design weights (remaining elements)
            
            gradient: a 2D array of gradients, modified in place, of the constraint function with respect to the design weights.
            Shape should be mxn, where m is the number of constraints and n is the number of design weights.

        '''
        print("evaluating epigraph constraint")
        epigraph = epigraph_and_weights[0]
        x = epigraph_and_weights[1:]
        #we need to manage the number of phase masks, depending on the current object instance
        if self.space_grid.xy_symmetry:
            if self.num_phase_masks == 2:
                ms1_first_quadrant = x[:self.space_grid.get_S_symm()].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms2_first_quadrant = x[self.space_grid.get_S_symm():].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms1 = self._expand_symmetrize(ms1_first_quadrant)
                ms2 = self._expand_symmetrize(ms2_first_quadrant)
            elif self.num_phase_masks == 3:
                ms1_first_quadrant = x[:self.space_grid.get_S_symm()].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms2_first_quadrant = x[self.space_grid.get_S_symm(): 2*self.space_grid.get_S_symm()].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms3_first_quadrant = x[2*self.space_grid.get_S_symm():].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms1 = self._expand_symmetrize(ms1_first_quadrant)
                ms2 = self._expand_symmetrize(ms2_first_quadrant)
                ms3 = self._expand_symmetrize(ms3_first_quadrant)
        else:
            if self.num_phase_masks == 2:
                ms1 = x[:self.space_grid.get_S()]
                ms2 = x[self.space_grid.get_S():]
            elif self.num_phase_masks == 3:
                ms1 = x[:self.space_grid.get_S()]
                ms2 = x[self.space_grid.get_S(): 2*self.space_grid.get_S()]
                ms3 = x[2*self.space_grid.get_S():]

        if self.num_phase_masks == 2:
            all_ms = np.concatenate((ms1, ms2))
        elif self.num_phase_masks == 3:
            all_ms = np.concatenate((ms1, ms2, ms3))

        self.w_norm[:] = all_ms
        self.phase_mask[:] = self._phase_given_w(self.w_norm)

        if self.use_filtering:
            if self.num_phase_masks == 2:
                phase_mask_1 = self.phase_mask[:self.space_grid.get_S()]
                phase_mask_2 = self.phase_mask[self.space_grid.get_S():]
                filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
                self.filtered_phase_mask[:] = np.concatenate((filtered_phase_mask_1, filtered_phase_mask_2))
            elif self.num_phase_masks == 3:
                phase_mask_1 = self.phase_mask[:self.space_grid.get_S()]
                phase_mask_2 = self.phase_mask[self.space_grid.get_S(): 2*self.space_grid.get_S()]
                phase_mask_3 = self.phase_mask[2*self.space_grid.get_S():]
                filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
                filtered_phase_mask_3 = self._phase_filter(phase_mask_3)
                self.filtered_phase_mask[:] = np.concatenate((filtered_phase_mask_1, filtered_phase_mask_2, filtered_phase_mask_3))
        else:
            self.filtered_phase_mask[:] = self.phase_mask

        #after the phase masks are set, we need to compute value and gradients for each target
        grads_matrix = np.zeros((len(self.targets), self.space_grid.get_dof()))
        results_array = np.zeros(len(self.targets))

        for idx, target in enumerate(self.targets):

            C, full_grads = self._value_and_grad(target) 
            #minus sign required because the constraint is in the form of f - t < 0 and we minimize the epigraph t
            results_array[idx] = - C 

            if self.use_filtering:
                if self.num_phase_masks == 2:
                    jac_grad_1 = tensor_jacobian_product(self._phase_filter)(phase_mask_1, full_grads[0])
                    print("jac 1 done")
                    jac_grad_2 = tensor_jacobian_product(self._phase_filter)(phase_mask_2, full_grads[1])
                    print("jac 2 done")
                elif self.num_phase_masks == 3:
                    jac_grad_1 = tensor_jacobian_product(self._phase_filter)(phase_mask_1, full_grads[0])
                    print("jac 1 done")
                    jac_grad_2 = tensor_jacobian_product(self._phase_filter)(phase_mask_2, full_grads[1])
                    print("jac 2 done")
                    jac_grad_3 = tensor_jacobian_product(self._phase_filter)(phase_mask_3, full_grads[2])
                    print("jac 3 done")
            else:
                if self.num_phase_masks == 2:
                    jac_grad_1 = full_grads[0]
                    jac_grad_2 = full_grads[1]
                elif self.num_phase_masks == 3:
                    jac_grad_1 = full_grads[0]
                    jac_grad_2 = full_grads[1]
                    jac_grad_3 = full_grads[2]

            if self.space_grid.xy_symmetry:
                jac_grad_1_symm = self._reduce_symmetrized_gradient(jac_grad_1)
                jac_grad_2_symm = self._reduce_symmetrized_gradient(jac_grad_2)
                if self.num_phase_masks == 3:
                    jac_grad_3_symm = self._reduce_symmetrized_gradient(jac_grad_3)
                    jac_grad = np.concatenate((jac_grad_1_symm, jac_grad_2_symm, jac_grad_3_symm), axis=0)
                else:
                    jac_grad = np.concatenate((jac_grad_1_symm, jac_grad_2_symm), axis=0)
            else:
                if self.num_phase_masks == 2:
                    jac_grad = np.concatenate((jac_grad_1, jac_grad_2), axis=0)
                elif self.num_phase_masks == 3:
                    jac_grad = np.concatenate((jac_grad_1, jac_grad_2, jac_grad_3), axis=0)

            grads_matrix[idx, :] = jac_grad

        result[:] = results_array - epigraph

        if gradient.size > 0:
            gradient[:,0] = -1
            gradient[:,1:] = - grads_matrix * 2 * np.pi


    def _obj_fun(self, epigraph_and_weights, grad):
        ''' Objective function for the epigraph formulation
            
            Args:
                epigraph_and_weights: 1D array of epigraph (first element) and 
                    design weights (remaining elements)
                grad: gradient of the objective function with respect to the design weights, modified in place
            Returns:
                The scalar epigraph variable (the objective function)
        '''

        epigraph = epigraph_and_weights[0]

        if grad.size > 0:
            grad[0] = 1
            grad[1:] = 0

        self.iter_num[0] = self.iter_num[0] + 1
        self.opt_history.append(epigraph)

        self._plot_history()
        self.iter_num[:] += [self.iter_num[0]+1]
        
        return epigraph

    def _cost_fun(self, x, grad):
        self.iter_num[0] = self.iter_num[0] + 1
        if self.space_grid.xy_symmetry:
            if self.num_phase_masks == 2:
                ms1_first_quadrant = x[:self.space_grid.get_S_symm()].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms2_first_quadrant = x[self.space_grid.get_S_symm():].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms1 = self._expand_symmetrize(ms1_first_quadrant)
                ms2 = self._expand_symmetrize(ms2_first_quadrant)
            elif self.num_phase_masks == 3:
                ms1_first_quadrant = x[:self.space_grid.get_S_symm()].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms2_first_quadrant = x[self.space_grid.get_S_symm():2*self.space_grid.get_S_symm()].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms3_first_quadrant = x[2*self.space_grid.get_S_symm():].reshape(self.space_grid.get_Nx()//2+1, self.space_grid.get_Ny()//2+1)
                ms1 = self._expand_symmetrize(ms1_first_quadrant)
                ms2 = self._expand_symmetrize(ms2_first_quadrant)
                ms3 = self._expand_symmetrize(ms3_first_quadrant)
        else:
            if self.num_phase_masks == 2:
                ms1 = x[:self.space_grid.get_dof()//2]
                ms2 = x[self.space_grid.get_dof()//2:]
            elif self.num_phase_masks == 3:
                ms1 = x[:self.space_grid.get_dof()//3]
                ms2 = x[self.space_grid.get_dof()//3:2*self.space_grid.get_dof()//3]
                ms3 = x[2*self.space_grid.get_dof()//3:]

        if self.num_phase_masks == 2:
            all_ms = np.concatenate((ms1, ms2))
        elif self.num_phase_masks == 3:
            all_ms = np.concatenate((ms1, ms2, ms3))

        self.w_norm[:] = all_ms
        self.phase_mask[:] = self._phase_given_w(self.w_norm)
        
        if self.use_filtering:
            if self.num_phase_masks == 2:
                phase_mask_1 = self.phase_mask[:self.space_grid.get_S()]
                phase_mask_2 = self.phase_mask[self.space_grid.get_S():]
                filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
            elif self.num_phase_masks == 3:
                phase_mask_1 = self.phase_mask[:self.space_grid.get_S()]
                phase_mask_2 = self.phase_mask[self.space_grid.get_S():2*self.space_grid.get_S()]
                phase_mask_3 = self.phase_mask[2*self.space_grid.get_S():]
                filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
                filtered_phase_mask_3 = self._phase_filter(phase_mask_3)

            if self.num_phase_masks == 2:
                self.filtered_phase_mask[:] = np.concatenate((filtered_phase_mask_1, filtered_phase_mask_2))
            elif self.num_phase_masks == 3:
                self.filtered_phase_mask[:] = np.concatenate((filtered_phase_mask_1, filtered_phase_mask_2, filtered_phase_mask_3))
        else:
            self.filtered_phase_mask[:] = self.phase_mask

        #after the phase mask is set, we test the same mask across all targets
        C_all_wavelengths = []
        tested_wavelengths = []
        grad_partial = np.zeros_like(grad)

        for target in self.targets:

            C, full_grads = self._value_and_grad(target) 

            C_all_wavelengths.append(C)
            tested_wavelengths.append(target.get_wavelength())
            if self.use_filtering:
                if self.num_phase_masks == 2:
                    full_grad_1, full_grad_2 = full_grads
                    jac_grad_1 = tensor_jacobian_product(self._phase_filter)(phase_mask_1, full_grad_1)
                    jac_grad_2 = tensor_jacobian_product(self._phase_filter)(phase_mask_2, full_grad_2)
                elif self.num_phase_masks == 3:
                    full_grad_1, full_grad_2, full_grad_3 = full_grads
                    jac_grad_1 = tensor_jacobian_product(self._phase_filter)(phase_mask_1, full_grad_1)
                    jac_grad_2 = tensor_jacobian_product(self._phase_filter)(phase_mask_2, full_grad_2)
                    jac_grad_3 = tensor_jacobian_product(self._phase_filter)(phase_mask_3, full_grad_3)
            else:
                if self.num_phase_masks == 2:
                    full_grad_1, full_grad_2 = full_grads
                    jac_grad_1 = full_grad_1
                    jac_grad_2 = full_grad_2
                elif self.num_phase_masks == 3:
                    full_grad_1, full_grad_2, full_grad_3 = full_grads
                    jac_grad_1 = full_grad_1
                    jac_grad_2 = full_grad_2
                    jac_grad_3 = full_grad_3

            if self.space_grid.xy_symmetry:
                jac_grad_1_symm = self._reduce_symmetrized_gradient(jac_grad_1)
                jac_grad_2_symm = self._reduce_symmetrized_gradient(jac_grad_2)
                if self.num_phase_masks == 2:
                    jac_grad = np.concatenate((jac_grad_1_symm, jac_grad_2_symm), axis=0)
                elif self.num_phase_masks == 3:
                    jac_grad_3_symm = self._reduce_symmetrized_gradient(jac_grad_3)
                    jac_grad = np.concatenate((jac_grad_1_symm, jac_grad_2_symm, jac_grad_3_symm), axis=0)
            else:
                if self.num_phase_masks == 2:
                    jac_grad = np.concatenate((jac_grad_1, jac_grad_2),axis=0)
                elif self.num_phase_masks == 3:
                    jac_grad = np.concatenate((jac_grad_1, jac_grad_2, jac_grad_3),axis=0)

            grad_partial[:] += jac_grad

        if grad.size > 0:
            grad[:] = grad_partial * 2 * np.pi / len(self.targets) 

        #the new cost function considers the average overlap across all wavelengths.
        self.opt_history.append(np.mean(C_all_wavelengths))

        self._plot_history()

        if self.iter_num[0] % 5 == 0 and self.results_while_solving:
            fig, ax = plt.subplots()
            ax.plot(np.array(tested_wavelengths)*1e6, C_all_wavelengths, 'o-')
            ax.set_xlabel('Wavelength [um]')
            ax.set_ylabel('Overlap')
            ax.set_title('Overlap Across Wavelengths')
            fig.tight_layout()
            fig.savefig(f"{self.results_folder}/overlap_across_wavelengths.pdf")
            plt.close(fig)

        return np.mean(C_all_wavelengths) 

    def _plot_history(self):
        '''
        Utility function to plot the optimization history and the cost function
        '''
        print("Iteration:", self.iter_num[0])
        if self.iter_num[0] % 5 == 0 and self.results_while_solving:
            fig, ax = plt.subplots()
            ax.plot(self.opt_history)
            ax.set_xlabel('Iteration')
            ax.set_ylabel('Epigraph value')
            ax.set_title('Optimization History')
            fig.tight_layout()
            fig.savefig(f"{self.results_folder}/optimization_history.pdf")
            plt.close(fig)

    def _solver_init(self):
        '''
        This method sets up the optimizer based on the chosen strategy.

        '''
        if self.use_filtering:
            if self.num_phase_masks == 2:
                filtered_phase_mask_1 = self._phase_filter(self.phase_mask[:self.space_grid.get_S()])
                filtered_phase_mask_2 = self._phase_filter(self.phase_mask[self.space_grid.get_S():])
                self.filtered_phase_mask = np.concatenate((filtered_phase_mask_1, filtered_phase_mask_2))
            elif self.num_phase_masks == 3:
                filtered_phase_mask_1 = self._phase_filter(self.phase_mask[:self.space_grid.get_S()])
                filtered_phase_mask_2 = self._phase_filter(self.phase_mask[self.space_grid.get_S():2*self.space_grid.get_S()])
                filtered_phase_mask_3 = self._phase_filter(self.phase_mask[2*self.space_grid.get_S():])
                self.filtered_phase_mask = np.concatenate((filtered_phase_mask_1, filtered_phase_mask_2, filtered_phase_mask_3))
        else:
            self.filtered_phase_mask = self.phase_mask

        mask_upper_bounds = self.norm_phase_max * np.where(self.space_grid.get_X().flatten()**2 + self.space_grid.get_Y().flatten()**2 < (self.ms_max_avail_diameter/2)**2, 1, 0)
        mask_upper_bounds_full = np.tile(mask_upper_bounds,self.num_phase_masks)
        mask_lower_bounds_full = np.zeros_like(mask_upper_bounds_full)
        
        if self.space_grid.xy_symmetry:
            mask_upper_bounds_symm = mask_upper_bounds.reshape((self.space_grid.get_Nx(),self.space_grid.get_Ny()))[:self.space_grid.get_nx()+1, :self.space_grid.get_ny()+1].flatten()
            mask_upper_bounds_symm_full = np.tile(mask_upper_bounds_symm,self.num_phase_masks)
            mask_lower_bounds_symm_full = np.zeros_like(mask_upper_bounds_symm_full)
            self.chosen_mask_upper_bounds = mask_upper_bounds_symm_full
            self.chosen_mask_lower_bounds = mask_lower_bounds_symm_full
        else:
            self.chosen_mask_upper_bounds = mask_upper_bounds_full
            self.chosen_mask_lower_bounds = mask_lower_bounds_full

        if self.strategy == 'mean':

            self.solver = nlopt.opt(nlopt.LD_CCSAQ, self.space_grid.get_dof())

            self.solver.set_lower_bounds(self.chosen_mask_lower_bounds.flatten())
            self.solver.set_upper_bounds(self.chosen_mask_upper_bounds.flatten())

            self.solver.set_max_objective(self._cost_fun)
            self.solver.set_maxeval(self.opt_max_eval)

        elif self.strategy == 'epigraph':

            self.solver = nlopt.opt(nlopt.LD_CCSAQ, self.space_grid.get_dof() + 1)

            epigraph_and_weights_lower_bounds = np.insert(self.chosen_mask_lower_bounds.flatten(), 0, -np.inf)
            epigraph_and_weights_upper_bounds = np.insert(self.chosen_mask_upper_bounds.flatten(), 0, np.inf)

            self.solver.set_lower_bounds(epigraph_and_weights_lower_bounds)
            self.solver.set_upper_bounds(epigraph_and_weights_upper_bounds)

            self.solver.set_min_objective(self._obj_fun)
            epigraph_tolerance = np.array([1e-4] * self.get_num_targets())
            self.solver.add_inequality_mconstraint(
                lambda result_, epigraph_and_weights_, grad_: self._epigraph_constraint(
                    result_, 
                    epigraph_and_weights_, 
                    grad_
                ),
                epigraph_tolerance
            )
            self.solver.set_maxeval(self.opt_max_eval)
        else:
            raise ValueError(f"Unknown optimization strategy: {self.strategy}")
        
        self.solver.set_param("dual_ftol_rel", 1e-5)
        self.solver.set_param("inner_maxeval", 30)
        self.solver.set_param("verbosity", 0)

    def _export_results(self):
        '''
        Placeholder method for exporting the results of the optimization.
        This method should be implemented to save the relevant data.
        '''
        #intermediate fields
        #intermediate_field[0] is on MS1
        #intermediate_field[1] is on MS2
        #intermediate_field[2] is the output
        for i,field in enumerate(self.intermediate_electric_fields):
            np.save(f"{self.results_folder}/intermediate_electric_fields_{i}.npy", field)
            make_2Dplot_of(field, self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="amplitude", save_name=f"{self.results_folder}/intermediate_electric_fields_{i}_plot")
            make_2Dplot_of(field, self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="phase", save_name=f"{self.results_folder}/intermediate_electric_fields_{i}_phase_plot")

        #output fields
        output_field = []
        for i,source in enumerate(self.sources):
            self._forward_propagate(source)
            output_field.append(self.intermediate_electric_fields[-1])

            np.save(f"{self.results_folder}/output_fields_{i}.npy", output_field[-1])
            make_2Dplot_of(output_field[-1], self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="amplitude", save_name=f"{self.results_folder}/output_fields_{i}_plot")
            make_2Dplot_of(output_field[-1], self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="phase", save_name=f"{self.results_folder}/output_fields_{i}_phase_plot")

        #phase masks
        if self.num_phase_masks == 2:
            phase_mask_1 = self._phase_given_w(self.w_norm[:self.space_grid.get_S()]).reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))
            phase_mask_2 = self._phase_given_w(self.w_norm[self.space_grid.get_S():]).reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))
        elif self.num_phase_masks == 3:
            phase_mask_1 = self._phase_given_w(self.w_norm[:self.space_grid.get_S()]).reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))
            phase_mask_2 = self._phase_given_w(self.w_norm[self.space_grid.get_S():2*self.space_grid.get_S()]).reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))
            phase_mask_3 = self._phase_given_w(self.w_norm[2*self.space_grid.get_S():]).reshape((self.space_grid.get_Nx(), self.space_grid.get_Ny()))
        
        if self.use_filtering:
            if self.num_phase_masks == 2:
                filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
            elif self.num_phase_masks == 3:
                filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
                filtered_phase_mask_3 = self._phase_filter(phase_mask_3)
        else:
            if self.num_phase_masks == 2:
                filtered_phase_mask_1 = phase_mask_1
                filtered_phase_mask_2 = phase_mask_2
            elif self.num_phase_masks == 3:
                filtered_phase_mask_1 = phase_mask_1
                filtered_phase_mask_2 = phase_mask_2
                filtered_phase_mask_3 = phase_mask_3
        make_2Dplot_of(phase_mask_1, self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="phase_mask", save_name=f"{self.results_folder}/phase_mask_1_plot")
        make_2Dplot_of(phase_mask_2, self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="phase_mask", save_name=f"{self.results_folder}/phase_mask_2_plot")
        make_2Dplot_of(filtered_phase_mask_1, self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="phase_mask", save_name=f"{self.results_folder}/filtered_phase_mask_1_plot")
        make_2Dplot_of(filtered_phase_mask_2, self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="phase_mask", save_name=f"{self.results_folder}/filtered_phase_mask_2_plot")
        if self.num_phase_masks == 3:
            make_2Dplot_of(phase_mask_3, self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="phase_mask", save_name=f"{self.results_folder}/phase_mask_3_plot")
            make_2Dplot_of(filtered_phase_mask_3, self.space_grid.get_X(), self.space_grid.get_Y(), plot_zoom_x=1e6*self.get_ms_max_avail_diameter()/2, plot_zoom_y=1e6*self.get_ms_max_avail_diameter()/2, choose_quantity="phase_mask", save_name=f"{self.results_folder}/filtered_phase_mask_3_plot")

        np.save(f"{self.results_folder}/optimized_phase_mask_1.npy", phase_mask_1)
        np.save(f"{self.results_folder}/optimized_phase_mask_2.npy", phase_mask_2)
        np.save(f"{self.results_folder}/filtered_phase_mask_1.npy", filtered_phase_mask_1)
        np.save(f"{self.results_folder}/filtered_phase_mask_2.npy", filtered_phase_mask_2)
        if self.num_phase_masks == 3:
            np.save(f"{self.results_folder}/optimized_phase_mask_3.npy", phase_mask_3)
            np.save(f"{self.results_folder}/filtered_phase_mask_3.npy", filtered_phase_mask_3)

    def get_best_opt_val(self):
        if self.is_optimized_flag:
            return self.best_opt_val
        else:
            raise RuntimeError("Simulation object has not been optimized")

    def get_best_opt_and_distances(self):
        if self.is_optimized_flag:
            return self.best_opt_val, self.space_grid.d
        else:
            raise RuntimeError("Simulation object has not been optimized")

    def is_optimized(self):
        return self.is_optimized_flag

    def set_space_grid(self, new_space_grid: SpaceGrid):
        '''
        Update the space grid and associate parameters used for propagation.
        '''
        for source in self.sources:
            if source.get_field_arr().shape != new_space_grid.get_grid_shape():
                raise ValueError("The provided space grid is not compatible with the source fields.")
        for target in self.targets:
            if target.get_field_arr().shape != new_space_grid.get_grid_shape():
                raise ValueError("The provided space grid is not compatible with the target fields.")

        self.space_grid = new_space_grid
        self.num_phase_masks = self.space_grid.get_num_phase_masks()

        self.space_grid_is_set = False
        self.is_optimized_flag = False
        self.best_opt_val = 0

        if self.space_grid.get_distances() is not None:
            try:
                if self.space_grid.get_materials_refr_index().shape != self.space_grid.get_distances().shape:
                    raise ValueError("Materials array must have the same shape as d array.")
            except AttributeError:
                raise ValueError("Materials must be an Numpy array.")
            self.space_grid_is_set = True
            self.d = self.space_grid.get_distances()
            print("Using distances: ", self.d)
            self.ks = 2 * np.pi / self.space_grid.get_sampling_period()
            self.kappas = np.arange(-self.space_grid.get_Nx()//2+1, self.space_grid.get_Nx()//2+1) * self.ks / self.space_grid.get_Nx()
            self.KX, self.KY = np.meshgrid(self.kappas, self.kappas)
            self.K_parallel = np.sqrt(self.KX**2 + self.KY**2)
            self.nu_parallel = self.K_parallel / (2 * np.pi)
            
            #phase masks initialization
            self.w_norm = np.zeros((self.num_phase_masks*self.space_grid.get_S()))
            self.w_norm_symm = np.zeros(self.space_grid.get_dof())
            self.phase_mask = self._phase_given_w(self.w_norm)
            
            #initialize intermediate fields
            self.intermediate_electric_fields = [None] * (self.num_phase_masks + 1)
            self.intermediate_magnetic_fields = [None] * (self.num_phase_masks + 1)
            
            #pyfftw init
            self.fft_input_array = pyfftw.empty_aligned((self.space_grid.get_Nx(), self.space_grid.get_Ny()), dtype='complex128', n=16)
            self.fft_output_array = pyfftw.empty_aligned((self.space_grid.get_Nx(), self.space_grid.get_Ny()), dtype='complex128', n=16)
            self.ifft_input_array = pyfftw.empty_aligned((self.space_grid.get_Nx(), self.space_grid.get_Ny()), dtype='complex128', n=16)
            self.ifft_output_array = pyfftw.empty_aligned((self.space_grid.get_Nx(), self.space_grid.get_Ny()), dtype='complex128', n=16)
            self.fft_input_array.fill(0)
            self.fft_output_array.fill(0)
            self.ifft_input_array.fill(0)
            self.ifft_output_array.fill(0)
            self.fft_operator = pyfftw.FFTW(self.fft_input_array, self.fft_output_array, axes=(0,1), direction='FFTW_FORWARD', threads=self.n_cpu, flags=('FFTW_ESTIMATE',))
            self.ifft_operator = pyfftw.FFTW(self.ifft_input_array, self.ifft_output_array, axes=(0,1), direction='FFTW_BACKWARD', threads=self.n_cpu, flags=('FFTW_ESTIMATE',))
        else:
            self.space_grid_is_set = False

    def update_propagation_distances(self, new_distances: np.ndarray):
        '''
        Update the propagation distances of the simulation by creating a new space grid 
        with the specified distances while maintaining the other properties of the current space grid.
        '''
        self.opt_history = [] #updating distances resets the history
        new_space_grid = SpaceGrid(
                side_pixels=self.space_grid.get_Nx(), 
                unit_cell_pitch=self.space_grid.get_unit_cell_pitch(),
                prop_distances=new_distances, 
                materials_refr_index=self.space_grid.get_materials_refr_index(),
                xy_symmetry=True,
            )
        
        self.set_space_grid(new_space_grid)

    def inject_phase_masks(self, input_phase_masks: list):
        """
        Inject the specified phase masks into the simulation.
        Args:
            input_phase_masks (list): A list of phase masks, flattened, to be injected into the simulation. 
        Returns:
            None
        """
        #check if the length of the list of input_phase_masks we are trying to inject
        #has the same number of phase masks in this simulation object.
        if len(input_phase_masks) != self.num_phase_masks:
            raise ValueError(f"Expected {self.num_phase_masks} phase masks, but got {len(input_phase_masks)}.")
        for i, phase_mask in enumerate(input_phase_masks):
            self.phase_mask[i*self.space_grid.get_S():(i+1)*self.space_grid.get_S()] = phase_mask
            self.w_norm[i*self.space_grid.get_S():(i+1)*self.space_grid.get_S()] = self._w_given_phase(phase_mask)
        if self.use_filtering:
            if self.num_phase_masks == 2:
                filtered_phase_mask_1 = self._phase_filter(self.phase_mask[:self.space_grid.get_S()])
                filtered_phase_mask_2 = self._phase_filter(self.phase_mask[self.space_grid.get_S():])
                self.filtered_phase_mask = np.concatenate((filtered_phase_mask_1, filtered_phase_mask_2))
            elif self.num_phase_masks == 3:
                filtered_phase_mask_1 = self._phase_filter(self.phase_mask[:self.space_grid.get_S()])
                filtered_phase_mask_2 = self._phase_filter(self.phase_mask[self.space_grid.get_S():2*self.space_grid.get_S()])
                filtered_phase_mask_3 = self._phase_filter(self.phase_mask[2*self.space_grid.get_S():])
                self.filtered_phase_mask = np.concatenate((filtered_phase_mask_1, filtered_phase_mask_2, filtered_phase_mask_3))
        else:
            self.filtered_phase_mask = self.phase_mask


    def source_sweep(self, distances: np.ndarray = None, input_phase_masks: list = None):
        """
        This method runs the propagation algorithm for the specified sources and targets in the simulation object.
        For every propagation step, it enforces the same phase masks. It can optionally update propagation distances and phase masks. 
        If not specified, it is assumed the simulation object has already been optimized and that the required quantities are already set.
        It is useful for studying the wavelength-dependent performance of the system.
        Args:
            distances (np.ndarray, optional): Array containing the propagation distances. If None, the current distances are used.
            input_phase_masks (list, optional): A list of phase masks to be injected into the simulation. If None, the current phase masks are used.
        Returns:
            dict: A dictionary mapping source wavelengths to the overlap between the output field and the associated target field.
        """
        results_dict = {}

        if distances is not None:
            self.update_propagation_distances(distances)

        if input_phase_masks is not None:
            self.inject_phase_masks(input_phase_masks)
        
        for target in self.targets:
            source = target.get_associated_source()
            self._update_wavelength(source.get_wavelength())
            output_field = self._forward_propagate(source, returns_field = True)
            #compute the overlap between the output field and associated target field
            target_field = target.get_field(self.get_space_grid(), flatten = True)

            overlap = np.abs(np.sum(np.conj(target_field) * output_field))**2
            results_dict[source.get_wavelength()] = overlap

        return results_dict
            
    def run(self):
        """
        Run the optimization process for the simulation.
        This method checks if the space grid and optimization settings are set,
        initializes the phase masks, and performs the optimization based on the chosen strategy.
        """
        if self.space_grid_is_set:
            if self.is_optimization_set:
                print(f"Using {self.num_phase_masks} phase masks")
                print("Initializing solver...")
                self._solver_init()
                print("Starting optimization...")
                self._initialize_phase_masks()
                #initialize nlopt solver

                if self.space_grid.xy_symmetry:
                    if self.strategy == 'epigraph':
                        epigraph_w_norm_symm = self.solver.optimize(np.insert(self.w_norm_symm, 0, 0))
                        self.w_norm_symm[:] = epigraph_w_norm_symm[1:]
                    elif self.strategy == 'mean':
                        self.w_norm_symm[:] = self.solver.optimize(self.w_norm_symm)
                    else:
                        raise ValueError(f"Unknown strategy: {self.strategy}")

                    self.is_optimized_flag = True
                    self.best_opt_val = self.solver.last_optimum_value()
                    if self.num_phase_masks == 2:
                        self.w_norm[:self.space_grid.get_S()] = self._expand_symmetrize(self.w_norm_symm[:self.space_grid.get_S_symm()])
                        self.w_norm[self.space_grid.get_S():] = self._expand_symmetrize(self.w_norm_symm[self.space_grid.get_S_symm():])
                        self.phase_mask[:] = self._phase_given_w(self.w_norm)
                    elif self.num_phase_masks == 3:
                        self.w_norm[:self.space_grid.get_S()] = self._expand_symmetrize(self.w_norm_symm[:self.space_grid.get_S_symm()])
                        self.w_norm[self.space_grid.get_S():2*self.space_grid.get_S()] = self._expand_symmetrize(self.w_norm_symm[self.space_grid.get_S_symm():2*self.space_grid.get_S_symm()])
                        self.w_norm[2*self.space_grid.get_S():] = self._expand_symmetrize(self.w_norm_symm[2*self.space_grid.get_S_symm():])
                        self.phase_mask[:] = self._phase_given_w(self.w_norm)

                    if self.use_filtering:
                        if self.num_phase_masks == 2:
                            phase_mask_1 = self.phase_mask[:self.space_grid.get_S()]
                            phase_mask_2 = self.phase_mask[self.space_grid.get_S():]
                            filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                            filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
                            self.filtered_phase_mask[:] = np.concatenate([filtered_phase_mask_1, filtered_phase_mask_2])
                        elif self.num_phase_masks == 3:
                            phase_mask_1 = self.phase_mask[:self.space_grid.get_S()]
                            phase_mask_2 = self.phase_mask[self.space_grid.get_S():2*self.space_grid.get_S()]
                            phase_mask_3 = self.phase_mask[2*self.space_grid.get_S():]
                            filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                            filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
                            filtered_phase_mask_3 = self._phase_filter(phase_mask_3)
                            self.filtered_phase_mask[:] = np.concatenate([filtered_phase_mask_1, filtered_phase_mask_2, filtered_phase_mask_3])
                    else:
                        self.filtered_phase_mask[:] = self.phase_mask
                    
                    self.is_optimization_set = True
                    self.best_opt_val = self.solver.last_optimum_value()
                else:
                    if self.strategy == 'epigraph':
                        self.epigraph_w_norm = np.insert(self.w_norm, 0, 0)
                        self.epigraph_w_norm[:] = self.solver.optimize(self.epigraph_w_norm)
                        self.w_norm[:] = self.epigraph_w_norm[1:]
                    elif self.strategy == 'mean':
                        self.w_norm[:] = self.solver.optimize(self.w_norm)
                    else:
                        raise ValueError(f"Unknown strategy: {self.strategy}")
                    self.phase_mask[:] = self._phase_given_w(self.w_norm)
                    
                    if self.use_filtering:
                        if self.num_phase_masks == 2:
                            phase_mask_1 = self.phase_mask[:self.space_grid.get_S()]
                            phase_mask_2 = self.phase_mask[self.space_grid.get_S():]
                            filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                            filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
                            self.filtered_phase_mask[:] = np.concatenate([filtered_phase_mask_1, filtered_phase_mask_2])
                        elif self.num_phase_masks == 3:
                            phase_mask_1 = self.phase_mask[:self.space_grid.get_S()]
                            phase_mask_2 = self.phase_mask[self.space_grid.get_S():2*self.space_grid.get_S()]
                            phase_mask_3 = self.phase_mask[2*self.space_grid.get_S():]
                            filtered_phase_mask_1 = self._phase_filter(phase_mask_1)
                            filtered_phase_mask_2 = self._phase_filter(phase_mask_2)
                            filtered_phase_mask_3 = self._phase_filter(phase_mask_3)
                            self.filtered_phase_mask[:] = np.concatenate([filtered_phase_mask_1, filtered_phase_mask_2, filtered_phase_mask_3])
                    else:
                        self.filtered_phase_mask[:] = self.phase_mask
                    
                    self.is_optimized_flag = True
                    self.best_opt_val = self.solver.last_optimum_value()

                if self.save_results:
                    self._export_results()

                self.iter_num[:] = [0]
                return self.best_opt_val
            else:
                raise RuntimeError("Optimization settings have not been specified.")
        else:
            raise RuntimeError("Space grid has not been specified.")