camera.py

import os
import yaml
import numpy as np
import scipy.ndimage as nd
from astropy.io import fits

from .config import cpism_refdata, solar_spectrum, MAG_SYSTEM
from .utils import region_replace, random_seed_select
from .io import log
from .optics import filter_throughput


def sky_frame_maker(band, skybg, platescale, shape):
    """
    generate a sky background frame.

    Parameters
    ----------
    band : str
        The band of the sky background.
    skybg : str
        The sky background file name.
    platescale : float
        The platescale of the camera in arcsec/pixel.
    shape : tuple
        The shape of the output frame. (y, x)

    Returns
    -------
    sky_bkg_frame : numpy.ndarray
        The sky background frame.
    """
    filter = filter_throughput(band)
    sk_spec = solar_spectrum.renorm(skybg, MAG_SYSTEM, filter)
    sky_bkg_frame = np.zeros(shape)
    sky_bkg_frame += (sk_spec * filter).integrate() * platescale**2
    return sky_bkg_frame


class CRobj(object):
    """
    Cosmic ray object.

    Attributes
    ----------
    flux : float
        The flux of the cosmic ray.
    angle : float
        The angle of the cosmic ray.
    sigma : float
        The width of the cosmic ray.
    length : int
        The length of the cosmic ray.
    """

    def __init__(self, flux, angle, sigma, length) -> None:
        self.flux = flux
        self.angle = angle
        self.sigma = sigma
        self.length = length


class CosmicRayFrameMaker(object):
    """
    Cosmic ray frame maker.

    Parameters
    ----------
    depth : float
        The depth of the camera pixel in um.
    pitch : float
        The pitch of the camera pixel in um.
    cr_rate : float
        The cosmic ray rate per second per cm2.

    """

    def __init__(self) -> None:
        self.tmp_size = [7, 101]
        self.freq_power = -0.9
        self.trail_std = 0.1
        self.depth = 10  # um
        self.pitch = 13  # um
        self.cr_rate = 1  # particle per s per cm2 from Miles et al. 2021

    def make_CR(self, length, sigma, seed=-1):
        """
        make a image of cosmic ray with given length and sigma.

        Parameters
        ----------
        length : int
            The length of the cosmic ray in pixel.
        sigma : float
            The width of the cosmic ray in pixel.

        Returns
        -------
        output : numpy.ndarray
            The image of cosmic ray.
        """
        h = self.tmp_size[0]
        w = self.tmp_size[1]

        freq = ((w-1)/2-np.abs(np.arange(w)-(w-1)/2)+1)**(self.freq_power)

        x = np.arange(w) - (w-1)/2
        hl = (length-1)/2
        x_wing = np.exp(-(np.abs(x)-hl)**2/sigma/sigma/2)
        x_wing[np.abs(x) < hl] = 1

        cr = np.zeros([h, w])
        center = (h-1)/2

        for i in range(h):
            phase = np.random.rand(w)*2*np.pi
            trail0 = abs(np.fft.fft(freq*np.sin(phase) + 1j*x*np.cos(phase)))
            # TODO maybe somthing wrong
            trail_norm = (trail0 - trail0.mean())/trail0.std()
            cr[i, :] = np.exp(-(i - center)**2/sigma/sigma/2) \
                * (trail_norm * self.trail_std + 1) * x_wing

        output = np.zeros([w, w])
        d = (w-h)//2
        output[d:d+h, :] = cr
        return output

    def _length_rand(self, N, seed=-1):
        """
        randomly generate N cosmic ray length.
        """
        len_out = []
        seed = random_seed_select(seed=seed)
        log.debug(f"cr length seed: {seed}")
        for i in range(N):
            x2y2 = 2
            while x2y2 > 1:
                lx = 1 - 2 * np.random.rand()
                ly = 1 - 2 * np.random.rand()
                x2y2 = lx * lx + ly * ly

            z = 1 - 2 * x2y2
            r = 2 * np.sqrt(x2y2 * (1 - x2y2))
            length = abs(r / z * self.depth)
            pitch = self.pitch

            len_out.append(int(length/pitch))
        return np.array(len_out)

    def _number_rand(self, expt, pixsize, random=False, seed=-1):
        """
        randomly generate the number of cosmic rays.
        """
        area = (self.pitch / 1e4)**2 * pixsize[0] * pixsize[1]
        ncr = area * expt * self.cr_rate
        if random:
            seed = random_seed_select(seed=seed)
            log.debug(f"cr count: {seed}")
            ncr = np.random.poisson(ncr)
        else:
            ncr = int(ncr)
        self.ncr = ncr
        return ncr

    def _sigma_rand(self, N, seed=-1):
        """
        randomly generate N cosmic ray sigma.
        """
        sig_sig = 0.5  # asuming the sigma of size of cosmic ray is 0.5
        seed = random_seed_select(seed=seed)
        log.debug(f"cr width seed: {seed}")
        sig = abs(np.random.randn(N))*sig_sig + 1/np.sqrt(12) * 1.2
        # assume sigma is 1.2 times of pictch sig
        return sig

    def _flux_rand(self, N, seed=-1):
        """
        randomly generate N cosmic ray flux.
        """
        seed = random_seed_select(seed=seed)
        log.debug(f"cr flux seed: {seed}")
        u = np.random.rand(N)
        S0 = 800
        lam = 0.57
        S = (-np.log(1-u)/lam + S0**0.25)**4
        return S

    def random_CR_parameter(self, expt, pixsize):
        """
        randomly generate cosmic ray parameters, including number, length, flux, sigma and angle.

        Parameters
        ----------
        expt : float
            The exposure time in second.
        pixsize : list
            The size of the image in pixel.

        Returns
        -------
        CRs : list
            A list of cosmic ray objects.

        """
        N = self._number_rand(expt, pixsize)
        log.debug(f"cr count: {N}")
        length = self._length_rand(N)
        if N > 0:
            log.debug(f"cr length, max: {length.max()}, min: {length.min()}")
            flux = self._flux_rand(N)
            log.debug(f"cr flux, max: {flux.max()}, min: {flux.min()}")
            sig = self._sigma_rand(N)
            log.debug(f"cr width, max: {sig.max()}, min: {sig.min()}")
            seed = random_seed_select(seed=-1)
            log.debug(f"cr angle seed: {seed}")
            angle = np.random.rand(N) * 180

        CRs = []
        for i in range(N):
            CRs.append(CRobj(flux[i], angle[i], sig[i], length[i]))
        return CRs

    def make_cr_frame(self, shape, expt, seed=-1):
        """
        make a cosmic ray frame.

        Parameters
        ----------
        shape : list
            The size of the image in pixel.
        expt : float
            The exposure time in second.
        seed : int, optional
            The random seed. The default is -1. If seed is -1, the seed will be randomly selected.

        Returns
        -------
        image : numpy.ndarray
            The cosmic ray frame.
        """
        image = np.zeros(shape)
        sz = shape
        cr_array = self.random_CR_parameter(expt, shape)
        cr_center = (self.tmp_size[1] - 1)/2
        seed = random_seed_select(seed=seed)
        log.debug(f"cr position seed: {seed}")

        for i in range(len(cr_array)):
            cr = cr_array[i]
            x = np.random.rand() * sz[1]
            y = np.random.rand() * sz[0]
            cr_img = self.make_CR(cr.length, cr.sigma)
            cr_img *= cr.flux
            cr_img = abs(nd.rotate(cr_img, cr.angle, reshape=False))

            if i == 0:
                pdin = False
            else:
                pdin = True

            if i == len(cr_array) - 1:
                pdout = False
            else:
                pdout = True

            image = region_replace(
                image, cr_img,
                [y-cr_center, x-cr_center],
                padded_in=pdin,
                padded_out=pdout, subpix=True
            )
            image = np.maximum(image, 0)
        log.debug(f"cr image max: {image.max()}, min: {image.min()}")
        return image


class EMCCD(object):
    """
    EMCCD camera class

    Parameters
    ----------
    config_file : str
        config file name

    Attributes
    ----------
    switch : dict
        switch for each camera effects, including:
            - 'flat': bool,
            - 'dark': bool,
            - 'stripe': bool,
            - 'cic': bool,
            - 'cte': bool,
            - 'badcolumn': bool,
            - 'nonlinear': bool,
            - 'cosmicray': bool,
            - 'blooming': bool,

    """

    def __init__(self, config_file="emccd_config.yaml"):
        self.plszx = 1024
        self.plszy = 1024
        self.pscan1 = 8
        self.pscan2 = 0
        self.oscan1 = 16
        self.oscan2 = 18
        self.udark = 6
        self.bdark = 2
        self.ldark = 16
        self.rdark = 16

        self.fullwell = 80_000
        self.em_fullwell = 780_000

        # if config file exists, load it, otherwise use default values
        config_file = cpism_refdata + '/camera/' + config_file
        log.debug(f"emccd config file: {config_file}")
        if os.path.exists(config_file):
            self.load_config(config_file)

        else:  # pragma: no cover
            # set default values for EMCCD
            # note: these values are default values, you can change them by load_config()
            # ↓↓↓↓↓↓↓start default values setting↓↓↓↓↓↓

            self.readout_noise = 40
            self.ph_per_adu = 8
            self.bias_level = 30
            self.max_adu = 16_383

            self.switch = {
                'flat': True,
                'dark': True,
                'stripe': True,
                'cic': False,
                'cte': False,
                'badcolumn': True,
                'nonlinear': False,
                'cosmicray': True,
                'blooming': False,
            }

            self.dark_file = cpism_refdata + '/camera/emccd_dark_current.fits'
            self.flat_file = cpism_refdata + '/camera/emccd_flat_field.fits'
            self.cic_file = cpism_refdata + '/camera/emcid_cic.fits'
            self.bad_col_file = cpism_refdata + '/camera/emccd_bad_columns.fits'
            # ↑↑↑↑↑↑↑end default values setting↑↑↑↑↑↑
            # note: these values are default values, you can change them by load_config()

        self.flat_shape = [self.plszy, self.plszx]

        darksz_x = self.plszx + self.rdark + self.ldark
        darksz_y = self.plszy + self.udark + self.bdark
        self.dark_shape = [darksz_y, darksz_x]

        biassz_x = darksz_x + self.pscan1 + self.oscan1
        biassz_y = darksz_y + self.pscan2 + self.oscan2
        self.image_shape = [biassz_y, biassz_x]

        self.flat = fits.getdata(self.flat_file)
        self.cic = fits.getdata(self.cic_file)
        self.dark = fits.getdata(self.dark_file)
        self.bad_col = fits.getdata(self.bad_col_file)

    def load_config(self, config_file):
        """
        load config file. Only for internal use.
        """

        with open(config_file, 'r') as f:
            config = yaml.load(f, Loader=yaml.FullLoader)

        self.switch = config['switch']

        self.readout_noise = config['readout_noise']
        self.ph_per_adu = config['ph_per_adu']
        self.bias_level = config['bias_level']
        self.max_adu = config['max_adu']

        self.dark_file = cpism_refdata + "/camera/" + config['dark_file']
        self.flat_file = cpism_refdata + "/camera/" + config['flat_file']
        self.cic_file = cpism_refdata + "/camera/" + config['cic_file']
        self.bad_col_file = cpism_refdata + \
            "/camera/" + config['bad_col_file']

    def vertical_blooming(self, image):
        """
        vertical blooming effect
        """
        fullwell = self.fullwell
        line = np.arange(image.shape[0])
        yp, xp = np.where(image > fullwell)
        n_saturated = len(xp)
        log.debug(f"{len(xp)} pixels are saturated!")
        if n_saturated > 5000:
            log.warning(f"More than 5000({len(xp)}) pixels are saturated!")
        img0 = image.copy()
        for x, y in zip(xp, yp):
            image[:, x] += np.exp(-(line-y)**2/20**2) * img0[y, x] * 0.2
        return np.minimum(image, fullwell)

    def nonlinear_effect(self, image):
        """
        nonlinear effect
        """
        fullwell = self.fullwell
        nonlinear_coefficient = 0.1
        log.debug(
            f"nonlinear effect added with coefficient {nonlinear_coefficient}")
        image += (image / fullwell)**2 * nonlinear_coefficient * fullwell

        return image

    def emregester_blooming(self, image, max_iteration=5):
        """
        emregester blooming effect
        """
        line = image.flatten().copy()

        curve_x = np.arange(1300)+2
        curve_y = np.exp(11*curve_x**(-0.19)-11)
        curve_y[0] = 0
        curve_y /= curve_y.sum()

        over_limit_coe = 0.999

        saturated = image > self.em_fullwell
        n_saturated = saturated.sum()
        if n_saturated > 0:
            log.debug(f"{n_saturated} pixels are saturated during EM process.")

        if n_saturated > 2000:
            log.warning(
                f"More than 2000 ({n_saturated}) pixels are saturated during EM process!")

        for index in range(max_iteration):
            over_limit = np.maximum(
                line - self.em_fullwell * over_limit_coe, 0)
            line = np.minimum(line, self.em_fullwell * over_limit_coe)
            blooming = np.convolve(over_limit, curve_y, mode='full')[
                :len(line)]
            line = line + blooming
            n_over = (line > self.em_fullwell).sum()
            if n_over <= 0:
                break

            log.debug(
                f'{index}/{max_iteration} loop: saturated pixel number: {n_over}')

        return line.reshape(image.shape)

    def cte(self, image):
        """
        cte effect
        """
        image = self.emregester_blooming(image, max_iteration=5)
        return image

    def readout(self, image_focal, emgain, expt, image_cosmic_ray=None):
        """
        emccd readout. Generate a image with emccd readout effect.

        Parameters
        ----------
        image_focal : numpy.ndarray
            image at focal plane. Unit: electron/second
        emgain : float
            emgain of emccd
        expt : float
            exposure time. Unit: second
        image_cosmic_ray : numpy.ndarray, optional
            cosmic ray image. Unit: electron/second, by default None

        Returns
        -------
        numpy.ndarray
            image with emccd readout effect. Unit: ADU

        Notes
        -----
        1. effects include: dark, flat, cte, blooming, nonlinear, etc. Can be turned on/off by switch.
        2. size of input image_focal must be 1024x1024
        3. size of output image is 1080x1056 (including overscan and dark reference region)
        4. Q.E is not included in this function. It should be included in image_focal. See optics.py for details.
        """
        log.debug(
            fr"EMCCD readout: {emgain=:}, {expt=:}, image_comic_ray:{'None' if image_cosmic_ray is None else 'Not None'}")

        log.debug(
            f"camera effects  switch={self.switch}"
        )
        image = image_focal * expt
        if self.switch['flat']:
            image = image * self.flat

        if self.switch['nonlinear']:
            image = self.nonlinear_effect(image)

        darksz_x = self.plszx + self.rdark + self.ldark
        darksz_y = self.plszy + self.udark + self.bdark
        img_dark = np.zeros((darksz_y, darksz_x))
        img_dark[
            self.bdark:self.plszy+self.bdark,
            self.ldark:self.ldark+self.plszx
        ] = image
        image = img_dark

        if self.switch['dark']:
            image += self.dark * expt

        if self.switch['cic']:
            image += self.cic

        if image_cosmic_ray is not None and self.switch['cosmicray']:
            image += image_cosmic_ray

        if self.switch['blooming']:
            image = self.vertical_blooming(image)

        if self.switch['badcolumn']:
            for i in range(self.bad_col.shape[1]):
                deadpix_x = self.bad_col[0, i]
                deadpix_y = self.bad_col[1, i]
                image[deadpix_y:, deadpix_x] = 0

        biassz_x = darksz_x + self.pscan1 + self.oscan1
        biassz_y = darksz_y + self.pscan2 + self.oscan2
        img_bias = np.zeros((biassz_y, biassz_x), dtype=int)

        seed = random_seed_select()
        log.debug(f"photon noise seed: {seed}")
        img_bias[
            self.pscan2:self.pscan2+darksz_y,
            self.pscan1:self.pscan1+darksz_x
        ] = np.random.poisson(image)
        image = img_bias

        if self.switch['cte']:
            image = self.cte(image * emgain) / emgain

        seed = random_seed_select()
        log.debug(f"gamma noise seed: {seed}")
        if emgain != 1:
            image = np.random.gamma(image, emgain)

        image = np.minimum(image, self.em_fullwell)

        seed = random_seed_select()
        log.debug(f"readout noise seed: {seed}")
        image += np.random.randn(biassz_y, biassz_x) * self.readout_noise
        image = image / self.ph_per_adu + self.bias_level

        if self.switch['stripe']:
            image += self.add_stripe_effect(image)

        image = np.minimum(image, self.max_adu)
        image = np.maximum(image, 0)

        return image.astype(np.uint16)

    def add_stripe_effect(self, image):
        """
        add stripe effect
        """
        shape = image.shape

        v_width = 1
        v_amplitude = 30
        v_limit = 0.01
        v_base = 10

        h_width = 20
        h_amplitude = 10
        h_limit = 0.9
        h_base = 20

        index = np.linspace(0, np.pi, shape[0] * shape[1])

        def stripe(width, limit, amplitude, base, axis=0):
            seed = random_seed_select()
            log.debug(f"stripe noise seed: {seed}")
            dim_axis = shape[axis]
            dim_other = shape[0] * shape[1] // shape[axis]
            value = np.sin(index / width * dim_axis + np.pi *
                           dim_axis / width * np.random.randint(1024))

            value = np.maximum(value, -limit)
            value = np.minimum(value, limit)
            value = (value / limit + limit) / 2 * amplitude + base
            value = value.reshape(dim_axis, dim_other)

            if axis == 1:
                value = value.T

            return value

        output = stripe(v_width, v_limit, v_amplitude, v_base, axis=1)
        output += stripe(h_width, h_limit, h_amplitude, h_base, axis=0)
        return output

        # # plt.plot(horizontal_index, horizontal_value)
        # # # plt.xlim([0, 6.28])
        # # plt.show()

        # fits.writeto('horizontal_value.fits', output, overwrite=True)


# if __name__ == '__main__':
    # import matplotlib.pyplot as plt
    # emccd = EMCCD()
    # image_focal = np.zeros((emccd.plszy, emccd.plszx)) + 1000
    # image_focal[100:105, 100:105] = 10_000_000
    # after_cte = emccd.emregester_blooming(image_focal, max_iteration=100)
    # print(after_cte.sum(), image_focal.sum())

    # fits.writeto('after_cte.fits', after_cte, overwrite=True)

#     # darksz_x = emccd.plszx + emccd.rdark + emccd.ldark
#     # darksz_y = emccd.plszy + emccd.udark + emccd.bdark
#     # iamge_cosmic_ray = np.zeros((darksz_y, darksz_x))
#     # emgain = 10
#     # expt = 10
#     # image = emccd.readout(image_focal, emgain, expt, iamge_cosmic_ray)
#     # fits.writeto('test.fits', image, overwrite=True)

    # image = np.zeros((1000, 1000))
    # make_cosmic_ray_frame = CosmicRayFrameMaker()
    # crimage = make_cosmic_ray_frame(image.shape, 3000)
    # fits.writeto('crimage.fits', crimage, overwrite=True)

#     # emccd.add_stripe_effect(image)