"""
The imaging module provides simulations of different imaging systems
and acquisition techniques for microscopy.

**Conventions:**

arrays follow the ZXY convention, with

    - Z : depth axis (axial, focus axis)
    - X : horizontal axis (lateral)
    - Y : vertical axis (lateral, rotation axis when relevant)

sinograms follow the TPY convention, with

    - T : angles (theta)
    - P : captor axis
    - Y : rotation axis
"""

# Copyright (c) 2020 Idiap Research Institute, http://www.idiap.ch/
# Written by <NAME> <<EMAIL>>
#
# This file is part of CBI Toolbox.
#
# CBI Toolbox is free software: you can redistribute it and/or modify
# it under the terms of the 3-Clause BSD License.
#
# CBI Toolbox is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# 3-Clause BSD License for more details.
#
# You should have received a copy of the 3-Clause BSD License along
# with CBI Toolbox. If not, see https://opensource.org/licenses/BSD-3-Clause.
#
# SPDX-License-Identifier: BSD-3-Clause

import scipy.signal as sig
import numpy as np
import numpy.random as random
from scipy import ndimage
from cbi_toolbox import splineradon as spl


def widefield(obj, psf, pad=False):
    """
    Simulate the widefield imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged
    psf : array [ZXY]
        the PSF of the imaging system
    pad : bool, optional
        extend the field of view to see all contributions, by default False
        if False, the image will have the same size as the object

    Returns
    -------
    numpy.ndarray
        the widefield image
    """

    mode = 'full' if pad else 'same'

    image = sig.fftconvolve(obj, psf, mode=mode)
    image.clip(0, None, out=image)
    return image


def opt(obj, psf, theta=None, pad=False):
    """
    Simulate the OPT imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged, ZX must be square
    psf : array [ZXY]
        the PSF of the imaging system, Z dimension must match object ZX
    theta : array, optional
        array of rotation angles (in degrees), by default None
        If None, uses numpy.arange(180).
    pad : bool, optional
        extend the field of view to see all contributions
        (needed if the object is not contained in the inner cylinder to the array), by default False

    Returns
    -------
    array [TPY]
        the imaged sinogram

    Raises
    ------
    ValueError
        if the PSF dimension does not match the object
    """

    if not obj.shape[0] == obj.shape[1]:
        raise NotImplementedError(
            'Please provide a square object in ZX dimensions')

    if psf.shape[0] % 2 != obj.shape[0] % 2:
        raise ValueError('In order to correctly center the PSF,'
                         ' please profide a PSF with the same Z axis parity as the object Z axis')

    if theta is None:
        theta = np.arange(180)

    full_size = obj.shape[0]

    if pad:
        full_size = int(full_size * np.sqrt(2)) + 1
        pad_size = (full_size - obj.shape[0]) // 2
        full_size = obj.shape[0] + 2 * pad_size

    if psf.shape[0] < full_size:
        raise ValueError('PSF Z size must be greater than padded object Z size: {} >= {}'.format(
            psf.shape[0], full_size))

    if pad and pad_size:
        obj = np.pad(obj, ((pad_size,), (pad_size,), (0,)))

    if pad:
        mode = 'full'
        sinogram = np.empty(
            (theta.size, obj.shape[0] + psf.shape[1] - 1,
             obj.shape[-1] + psf.shape[-1] - 1))
    else:
        mode = 'same'
        sinogram = np.empty(
            (theta.size, obj.shape[0], obj.shape[-1]))

    splimage = ndimage.spline_filter1d(obj, axis=0)
    splimage = ndimage.spline_filter1d(obj, axis=1, output=splimage)

    crop_size = (psf.shape[0] - obj.shape[0]) // 2
    if crop_size:
        psf = psf[crop_size:-crop_size, ...]

    psf = np.flip(psf, 0)

    for idx, angle in enumerate(theta):
        rotated = ndimage.rotate(
            splimage, angle, prefilter=False, reshape=False)

        rotated = sig.fftconvolve(rotated, psf, axes=(1, 2), mode=mode)

        sinogram[idx, ...] = rotated.sum(0)

    return sinogram


def fps_opt(obj, psf, pad=False, **kwargs):
    """
    Simulate the FPS-OPT (focal plane scanning) imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged
    psf : array [ZXY] or array [XY]
        the PSF of the system, or projected PSF along the Z axis
    pad : bool, optional
        pad the vield of view to see all contributions
        (required if the sample is not contained in the inner cylinder of the object),
        by default False

    **kwargs :
        to be passed to the radon call

    Returns
    -------
    array [TPY]
        the imaged sinogram

    Raises
    ------
    ValueError
        if the PSF is not 2D or 3D
    """

    if psf.ndim == 3:
        psf = psf.sum(0, keepdims=True)
    elif psf.ndim == 2:
        psf = psf[None, ...]
    else:
        raise ValueError("Invalid dimensions for PSF: {}".format(psf.ndim))

    sinogram = spl.radon(obj, circle=(not pad), **kwargs)

    mode = 'full' if pad else 'same'

    image = sig.fftconvolve(sinogram, psf, axes=(1, 2), mode=mode)
    return image


def fss_opt(obj, psf, illu, pad=False, **kwargs):
    """
    Simulate the FSS-OPT (focal sheet scanning) imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged
    psf : array [ZXY] or array [XY]
        the PSF of the system
    illu : array [ZXY]
        the illumination function of the SPIM
    pad : bool, optional
        pad the vield of view to see all contributions
        if used, illu will be required to be bigger
        (required if the sample is not contained in the inner cylinder of the object),
        by default False

    **kwargs :
        to be passed to the radon call

    Returns
    -------
    array [TPY]
        the imaged sinogram

    Raises
    ------
    ValueError
        if the PSF dimensions do not fit the illumination
        if the illumination function has an incorrect shape
    """

    if pad:
        # TODO use bigger SPIM illumination function to fit padded sinogram
        raise NotImplementedError()

    if psf.shape[0] % 2 != illu.shape[0] % 2:
        raise ValueError('In order to correctly center the illumination on the PSF,'
                         ' please profide a PSF with the same Z axis parity'
                         'as the illumination Z axis')

    if not (psf.shape[1] % 2 and psf.shape[2] % 2):
        raise ValueError('In order to correctly center the PSF on the pixels,'
                         ' please provide a PSF with odd parity on X and Y axis')

    crop = (psf.shape[0] - illu.shape[0]) // 2
    if crop:
        psf = psf[crop:-crop, ...]
    psf = np.flip(psf)

    sinogram = spl.radon(obj, circle=(not pad), **kwargs)

    psf_xw = psf.shape[1]
    psf_yw = psf.shape[2]
    pad_x = psf_xw // 2
    pad_y = psf_yw // 2

    illu = np.pad(illu, ((0,), (pad_x,), (pad_y,)))

    image = np.zeros((sinogram.shape[0], sinogram.shape[1] + psf_xw - 1, sinogram.shape[2] + psf_yw - 1), dtype=sinogram.dtype)

    for x in range(sinogram.shape[1]):
        for y in range(sinogram.shape[2]):
            local = np.sum(illu[:, x:x+psf_xw, y:y+psf_yw] * psf, 0)
            pixel = sinogram[:, x, y]
            spread = pixel[:, None, None] * local[None, ...]

            image[:, x:x+psf_xw, y:y+psf_xw] += spread

    if not pad:
        image = image[:, pad_x:-pad_x, pad_y:-pad_y]

    return image


def spim(obj, psf, illu, pad=False):
    """
    Simulate the SPIM imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged
    psf : array [ZXY]
        the PSF of the imaging objective
    illu : array [ZXY]
        the illumination function of the SPIM
    pad : bool, optional
        pad the vield of view to see all contributions, by default False
    """

    if psf.shape[0] % 2 != illu.shape[0] % 2:
        raise ValueError('In order to correctly center the illumination on the PSF,'
                         ' please profide a PSF with the same Z axis parity'
                         'as the illumination Z axis')

    if psf.shape[0] < illu.shape[0]:
        raise ValueError(
            'PSF depth must be bigger than SPIM illumination depth (Z axis) - {} < {}'.format(psf.shape[0], illu.shape[0]))

    if illu.shape[1] != obj.shape[1] or illu.shape[2] != obj.shape[2]:
        raise ValueError(
            'SPIM illumination XY must match object XY dimensions - [{},{}] != [{},{}]'.format(
                illu.shape[1], illu.shape[2], obj.shape[1], obj.shape[2]))

    thickness = illu.shape[0]
    crop = (psf.shape[0] - thickness) // 2
    if crop:
        psf = psf[crop:-crop, ...]
    psf = np.flip(psf, 0)

    if pad:
        image = np.empty(
            (obj.shape[0] + thickness - 1, obj.shape[1] + psf.shape[1] - 1, obj.shape[2] + psf.shape[2] - 1))
        mode = 'full'
        obj = np.pad(obj, ((thickness - 1,), (0,), (0,)))

    else:
        image = np.empty(
            (obj.shape[0], obj.shape[1], obj.shape[2]))
        mode = 'same'
        obj = np.pad(obj, ((thickness // 2,), (0,), (0,)))

    for index in range(image.shape[0]):
        sliced = obj[index:index+thickness, ...] * illu
        sliced = sig.fftconvolve(sliced, psf, axes=(1, 2), mode=mode)
        image[index, ...] = sliced.sum(0)

    return image


def noise(image, photons=200, background=3, seed=None, in_place=False):
    """
    Simulate the acquisition noise of the camera:
        noise = shot noise

    Parameters
    ----------
    image : array [ZXY]
        the clean image
    photons : int, optional
        the max level of photons per pixel, by default 150
    background : int, optional
        the background level of photons per pixel, by default 3
    seed : int, optional
        the seed for rng, by default None
    in_place: bool, optional
        perform computations in-place and store the results in the input array, by default False

    Returns
    -------
    array [ZXY]
        the noisy image
    """

    if not in_place:
        image = image.copy()

    amp = image.max()

    image *= (photons - background) / amp
    image += background
    rng = random.default_rng(seed)
    poisson = rng.poisson(image)

    return amp * poisson / poisson.max()


if __name__ == "__main__":
    from cbi_toolbox.simu import primitives, optics
    import napari
    import time

    TEST_SIZE = 64

    sample = primitives.boccia(
        TEST_SIZE, radius=(0.8 * TEST_SIZE) // 2, n_stripes=4)
    s_psf = optics.gaussian_psf(
        numerical_aperture=0.3,
        npix_axial=TEST_SIZE+1, npix_lateral=TEST_SIZE+1)
    opt_psf = optics.gaussian_psf(
        numerical_aperture=0.1, npix_axial=TEST_SIZE, npix_lateral=TEST_SIZE+1)
    spim_illu = optics.openspim_illumination(
        slit_opening=2e-3,
        npix_fov=TEST_SIZE, simu_size=4*TEST_SIZE, rel_thresh=1e-3)
    s_theta = np.arange(90)

    start = time.time()
    s_widefield = widefield(sample, s_psf)
    print('Time for widefield: \t{}s'.format(time.time() - start))
    start = time.time()
    noisy = noise(s_widefield)
    print('Time for noise: \t{}s'.format(time.time() - start))

    start = time.time()
    s_spim = spim(sample, s_psf, spim_illu)
    print('Time for SPIM: \t{}s'.format(time.time() - start))

    start = time.time()
    s_opt = opt(sample, opt_psf, theta=s_theta)
    print('Time for OPT: \t{}s'.format(time.time() - start))

    start = time.time()
    s_fpsopt = fps_opt(sample, s_psf, theta=s_theta)
    print('Time for FPS-OPT: \t{}s'.format(time.time() - start))

    start = time.time()
    s_fssopt = fss_opt(sample, s_psf, spim_illu, theta=s_theta)
    print('Time for FSS-OPT: \t{}s'.format(time.time() - start))

    start = time.time()
    s_radon = spl.radon(sample, theta=s_theta, circle=True)
    print('Time for radon: \t{}s'.format(time.time() - start))

    viewer = napari.view_image(sample)
    viewer.add_image(s_widefield)
    viewer.add_image(noisy)
    viewer.add_image(s_spim)

    viewer = napari.view_image(s_radon)
    viewer.add_image(s_opt)
    viewer.add_image(s_fpsopt)
    viewer.add_image(s_fssopt)

    napari.run()

"""
The imaging module provides simulations of different imaging systems
and acquisition techniques for microscopy.

**Conventions:**

arrays follow the ZXY convention, with

    - Z : depth axis (axial, focus axis)
    - X : horizontal axis (lateral)
    - Y : vertical axis (lateral, rotation axis when relevant)

sinograms follow the TPY convention, with

    - T : angles (theta)
    - P : captor axis
    - Y : rotation axis
"""

# Copyright (c) 2020 Idiap Research Institute, http://www.idiap.ch/
# Written by <NAME> <<EMAIL>>
#
# This file is part of CBI Toolbox.
#
# CBI Toolbox is free software: you can redistribute it and/or modify
# it under the terms of the 3-Clause BSD License.
#
# CBI Toolbox is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# 3-Clause BSD License for more details.
#
# You should have received a copy of the 3-Clause BSD License along
# with CBI Toolbox. If not, see https://opensource.org/licenses/BSD-3-Clause.
#
# SPDX-License-Identifier: BSD-3-Clause

import scipy.signal as sig
import numpy as np
import numpy.random as random
from scipy import ndimage
from cbi_toolbox import splineradon as spl


def widefield(obj, psf, pad=False):
    """
    Simulate the widefield imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged
    psf : array [ZXY]
        the PSF of the imaging system
    pad : bool, optional
        extend the field of view to see all contributions, by default False
        if False, the image will have the same size as the object

    Returns
    -------
    numpy.ndarray
        the widefield image
    """

    mode = 'full' if pad else 'same'

    image = sig.fftconvolve(obj, psf, mode=mode)
    image.clip(0, None, out=image)
    return image


def opt(obj, psf, theta=None, pad=False):
    """
    Simulate the OPT imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged, ZX must be square
    psf : array [ZXY]
        the PSF of the imaging system, Z dimension must match object ZX
    theta : array, optional
        array of rotation angles (in degrees), by default None
        If None, uses numpy.arange(180).
    pad : bool, optional
        extend the field of view to see all contributions
        (needed if the object is not contained in the inner cylinder to the array), by default False

    Returns
    -------
    array [TPY]
        the imaged sinogram

    Raises
    ------
    ValueError
        if the PSF dimension does not match the object
    """

    if not obj.shape[0] == obj.shape[1]:
        raise NotImplementedError(
            'Please provide a square object in ZX dimensions')

    if psf.shape[0] % 2 != obj.shape[0] % 2:
        raise ValueError('In order to correctly center the PSF,'
                         ' please profide a PSF with the same Z axis parity as the object Z axis')

    if theta is None:
        theta = np.arange(180)

    full_size = obj.shape[0]

    if pad:
        full_size = int(full_size * np.sqrt(2)) + 1
        pad_size = (full_size - obj.shape[0]) // 2
        full_size = obj.shape[0] + 2 * pad_size

    if psf.shape[0] < full_size:
        raise ValueError('PSF Z size must be greater than padded object Z size: {} >= {}'.format(
            psf.shape[0], full_size))

    if pad and pad_size:
        obj = np.pad(obj, ((pad_size,), (pad_size,), (0,)))

    if pad:
        mode = 'full'
        sinogram = np.empty(
            (theta.size, obj.shape[0] + psf.shape[1] - 1,
             obj.shape[-1] + psf.shape[-1] - 1))
    else:
        mode = 'same'
        sinogram = np.empty(
            (theta.size, obj.shape[0], obj.shape[-1]))

    splimage = ndimage.spline_filter1d(obj, axis=0)
    splimage = ndimage.spline_filter1d(obj, axis=1, output=splimage)

    crop_size = (psf.shape[0] - obj.shape[0]) // 2
    if crop_size:
        psf = psf[crop_size:-crop_size, ...]

    psf = np.flip(psf, 0)

    for idx, angle in enumerate(theta):
        rotated = ndimage.rotate(
            splimage, angle, prefilter=False, reshape=False)

        rotated = sig.fftconvolve(rotated, psf, axes=(1, 2), mode=mode)

        sinogram[idx, ...] = rotated.sum(0)

    return sinogram


def fps_opt(obj, psf, pad=False, **kwargs):
    """
    Simulate the FPS-OPT (focal plane scanning) imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged
    psf : array [ZXY] or array [XY]
        the PSF of the system, or projected PSF along the Z axis
    pad : bool, optional
        pad the vield of view to see all contributions
        (required if the sample is not contained in the inner cylinder of the object),
        by default False

    **kwargs :
        to be passed to the radon call

    Returns
    -------
    array [TPY]
        the imaged sinogram

    Raises
    ------
    ValueError
        if the PSF is not 2D or 3D
    """

    if psf.ndim == 3:
        psf = psf.sum(0, keepdims=True)
    elif psf.ndim == 2:
        psf = psf[None, ...]
    else:
        raise ValueError("Invalid dimensions for PSF: {}".format(psf.ndim))

    sinogram = spl.radon(obj, circle=(not pad), **kwargs)

    mode = 'full' if pad else 'same'

    image = sig.fftconvolve(sinogram, psf, axes=(1, 2), mode=mode)
    return image


def fss_opt(obj, psf, illu, pad=False, **kwargs):
    """
    Simulate the FSS-OPT (focal sheet scanning) imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged
    psf : array [ZXY] or array [XY]
        the PSF of the system
    illu : array [ZXY]
        the illumination function of the SPIM
    pad : bool, optional
        pad the vield of view to see all contributions
        if used, illu will be required to be bigger
        (required if the sample is not contained in the inner cylinder of the object),
        by default False

    **kwargs :
        to be passed to the radon call

    Returns
    -------
    array [TPY]
        the imaged sinogram

    Raises
    ------
    ValueError
        if the PSF dimensions do not fit the illumination
        if the illumination function has an incorrect shape
    """

    if pad:
        # TODO use bigger SPIM illumination function to fit padded sinogram
        raise NotImplementedError()

    if psf.shape[0] % 2 != illu.shape[0] % 2:
        raise ValueError('In order to correctly center the illumination on the PSF,'
                         ' please profide a PSF with the same Z axis parity'
                         'as the illumination Z axis')

    if not (psf.shape[1] % 2 and psf.shape[2] % 2):
        raise ValueError('In order to correctly center the PSF on the pixels,'
                         ' please provide a PSF with odd parity on X and Y axis')

    crop = (psf.shape[0] - illu.shape[0]) // 2
    if crop:
        psf = psf[crop:-crop, ...]
    psf = np.flip(psf)

    sinogram = spl.radon(obj, circle=(not pad), **kwargs)

    psf_xw = psf.shape[1]
    psf_yw = psf.shape[2]
    pad_x = psf_xw // 2
    pad_y = psf_yw // 2

    illu = np.pad(illu, ((0,), (pad_x,), (pad_y,)))

    image = np.zeros((sinogram.shape[0], sinogram.shape[1] + psf_xw - 1, sinogram.shape[2] + psf_yw - 1), dtype=sinogram.dtype)

    for x in range(sinogram.shape[1]):
        for y in range(sinogram.shape[2]):
            local = np.sum(illu[:, x:x+psf_xw, y:y+psf_yw] * psf, 0)
            pixel = sinogram[:, x, y]
            spread = pixel[:, None, None] * local[None, ...]

            image[:, x:x+psf_xw, y:y+psf_xw] += spread

    if not pad:
        image = image[:, pad_x:-pad_x, pad_y:-pad_y]

    return image


def spim(obj, psf, illu, pad=False):
    """
    Simulate the SPIM imaging of an object

    Parameters
    ----------
    obj : array [ZXY]
        the object to be imaged
    psf : array [ZXY]
        the PSF of the imaging objective
    illu : array [ZXY]
        the illumination function of the SPIM
    pad : bool, optional
        pad the vield of view to see all contributions, by default False
    """

    if psf.shape[0] % 2 != illu.shape[0] % 2:
        raise ValueError('In order to correctly center the illumination on the PSF,'
                         ' please profide a PSF with the same Z axis parity'
                         'as the illumination Z axis')

    if psf.shape[0] < illu.shape[0]:
        raise ValueError(
            'PSF depth must be bigger than SPIM illumination depth (Z axis) - {} < {}'.format(psf.shape[0], illu.shape[0]))

    if illu.shape[1] != obj.shape[1] or illu.shape[2] != obj.shape[2]:
        raise ValueError(
            'SPIM illumination XY must match object XY dimensions - [{},{}] != [{},{}]'.format(
                illu.shape[1], illu.shape[2], obj.shape[1], obj.shape[2]))

    thickness = illu.shape[0]
    crop = (psf.shape[0] - thickness) // 2
    if crop:
        psf = psf[crop:-crop, ...]
    psf = np.flip(psf, 0)

    if pad:
        image = np.empty(
            (obj.shape[0] + thickness - 1, obj.shape[1] + psf.shape[1] - 1, obj.shape[2] + psf.shape[2] - 1))
        mode = 'full'
        obj = np.pad(obj, ((thickness - 1,), (0,), (0,)))

    else:
        image = np.empty(
            (obj.shape[0], obj.shape[1], obj.shape[2]))
        mode = 'same'
        obj = np.pad(obj, ((thickness // 2,), (0,), (0,)))

    for index in range(image.shape[0]):
        sliced = obj[index:index+thickness, ...] * illu
        sliced = sig.fftconvolve(sliced, psf, axes=(1, 2), mode=mode)
        image[index, ...] = sliced.sum(0)

    return image


def noise(image, photons=200, background=3, seed=None, in_place=False):
    """
    Simulate the acquisition noise of the camera:
        noise = shot noise

    Parameters
    ----------
    image : array [ZXY]
        the clean image
    photons : int, optional
        the max level of photons per pixel, by default 150
    background : int, optional
        the background level of photons per pixel, by default 3
    seed : int, optional
        the seed for rng, by default None
    in_place: bool, optional
        perform computations in-place and store the results in the input array, by default False

    Returns
    -------
    array [ZXY]
        the noisy image
    """

    if not in_place:
        image = image.copy()

    amp = image.max()

    image *= (photons - background) / amp
    image += background
    rng = random.default_rng(seed)
    poisson = rng.poisson(image)

    return amp * poisson / poisson.max()


if __name__ == "__main__":
    from cbi_toolbox.simu import primitives, optics
    import napari
    import time

    TEST_SIZE = 64

    sample = primitives.boccia(
        TEST_SIZE, radius=(0.8 * TEST_SIZE) // 2, n_stripes=4)
    s_psf = optics.gaussian_psf(
        numerical_aperture=0.3,
        npix_axial=TEST_SIZE+1, npix_lateral=TEST_SIZE+1)
    opt_psf = optics.gaussian_psf(
        numerical_aperture=0.1, npix_axial=TEST_SIZE, npix_lateral=TEST_SIZE+1)
    spim_illu = optics.openspim_illumination(
        slit_opening=2e-3,
        npix_fov=TEST_SIZE, simu_size=4*TEST_SIZE, rel_thresh=1e-3)
    s_theta = np.arange(90)

    start = time.time()
    s_widefield = widefield(sample, s_psf)
    print('Time for widefield: \t{}s'.format(time.time() - start))
    start = time.time()
    noisy = noise(s_widefield)
    print('Time for noise: \t{}s'.format(time.time() - start))

    start = time.time()
    s_spim = spim(sample, s_psf, spim_illu)
    print('Time for SPIM: \t{}s'.format(time.time() - start))

    start = time.time()
    s_opt = opt(sample, opt_psf, theta=s_theta)
    print('Time for OPT: \t{}s'.format(time.time() - start))

    start = time.time()
    s_fpsopt = fps_opt(sample, s_psf, theta=s_theta)
    print('Time for FPS-OPT: \t{}s'.format(time.time() - start))

    start = time.time()
    s_fssopt = fss_opt(sample, s_psf, spim_illu, theta=s_theta)
    print('Time for FSS-OPT: \t{}s'.format(time.time() - start))

    start = time.time()
    s_radon = spl.radon(sample, theta=s_theta, circle=True)
    print('Time for radon: \t{}s'.format(time.time() - start))

    viewer = napari.view_image(sample)
    viewer.add_image(s_widefield)
    viewer.add_image(noisy)
    viewer.add_image(s_spim)

    viewer = napari.view_image(s_radon)
    viewer.add_image(s_opt)
    viewer.add_image(s_fpsopt)
    viewer.add_image(s_fssopt)

    napari.run()

The imaging module provides simulations of different imaging systems and acquisition techniques for microscopy.  **Conventions:**  arrays follow the ZXY convention, with      - Z : depth axis (axial, focus axis)     - X : horizontal axis (lateral)     - Y : vertical axis (lateral, rotation axis when relevant)  sinograms follow the TPY convention, with      - T : angles (theta)     - P : captor axis     - Y : rotation axis # Copyright (c) 2020 Idiap Research Institute, http://www.idiap.ch/ # Written by <NAME> <<EMAIL>> # # This file is part of CBI Toolbox. # # CBI Toolbox is free software: you can redistribute it and/or modify # it under the terms of the 3-Clause BSD License. # # CBI Toolbox is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # 3-Clause BSD License for more details. # # You should have received a copy of the 3-Clause BSD License along # with CBI Toolbox. If not, see https://opensource.org/licenses/BSD-3-Clause. # # SPDX-License-Identifier: BSD-3-Clause Simulate the widefield imaging of an object      Parameters     ----------     obj : array [ZXY]         the object to be imaged     psf : array [ZXY]         the PSF of the imaging system     pad : bool, optional         extend the field of view to see all contributions, by default False         if False, the image will have the same size as the object      Returns     -------     numpy.ndarray         the widefield image Simulate the OPT imaging of an object      Parameters     ----------     obj : array [ZXY]         the object to be imaged, ZX must be square     psf : array [ZXY]         the PSF of the imaging system, Z dimension must match object ZX     theta : array, optional         array of rotation angles (in degrees), by default None         If None, uses numpy.arange(180).     pad : bool, optional         extend the field of view to see all contributions         (needed if the object is not contained in the inner cylinder to the array), by default False      Returns     -------     array [TPY]         the imaged sinogram      Raises     ------     ValueError         if the PSF dimension does not match the object Simulate the FPS-OPT (focal plane scanning) imaging of an object      Parameters     ----------     obj : array [ZXY]         the object to be imaged     psf : array [ZXY] or array [XY]         the PSF of the system, or projected PSF along the Z axis     pad : bool, optional         pad the vield of view to see all contributions         (required if the sample is not contained in the inner cylinder of the object),         by default False      **kwargs :         to be passed to the radon call      Returns     -------     array [TPY]         the imaged sinogram      Raises     ------     ValueError         if the PSF is not 2D or 3D Simulate the FSS-OPT (focal sheet scanning) imaging of an object      Parameters     ----------     obj : array [ZXY]         the object to be imaged     psf : array [ZXY] or array [XY]         the PSF of the system     illu : array [ZXY]         the illumination function of the SPIM     pad : bool, optional         pad the vield of view to see all contributions         if used, illu will be required to be bigger         (required if the sample is not contained in the inner cylinder of the object),         by default False      **kwargs :         to be passed to the radon call      Returns     -------     array [TPY]         the imaged sinogram      Raises     ------     ValueError         if the PSF dimensions do not fit the illumination         if the illumination function has an incorrect shape # TODO use bigger SPIM illumination function to fit padded sinogram Simulate the SPIM imaging of an object      Parameters     ----------     obj : array [ZXY]         the object to be imaged     psf : array [ZXY]         the PSF of the imaging objective     illu : array [ZXY]         the illumination function of the SPIM     pad : bool, optional         pad the vield of view to see all contributions, by default False Simulate the acquisition noise of the camera:         noise = shot noise      Parameters     ----------     image : array [ZXY]         the clean image     photons : int, optional         the max level of photons per pixel, by default 150     background : int, optional         the background level of photons per pixel, by default 3     seed : int, optional         the seed for rng, by default None     in_place: bool, optional         perform computations in-place and store the results in the input array, by default False      Returns     -------     array [ZXY]         the noisy image