nabu 2024.1.1__py3-none-any.whl → 2024.1.2__py3-none-any.whl

build/lib/nabu/preproc/ctf.py

@@ -1,361 +0,0 @@
-import math
-import numpy as np
-from scipy.fft import rfft2, irfft2, fft2, ifft2
-from ..resources.logger import LoggerOrPrint
-from ..misc import fourier_filters
-from ..misc.padding import pad_interpolate, recut
-from ..utils import get_num_threads, deprecation_warning
-
-
-class GeoPars:
-    """
-    A class to describe the geometry of a phase contrast radiography with
-    a source obtained by a focussing system, possibly astigmatic, which is
-    at distance z1_vh from the sample. The detector is at z2 from the sample
-    """
-
-    def __init__(
-        self,
-        z1_vh=None,
-        z2=None,
-        pix_size_det=None,
-        wavelength=None,
-        magnification=True,
-        length_scale=10.0e-6,
-        logger=None,
-    ):
-        """
-        Parameters
-        ----------
-        z1_vh : None, a float, or a sequence of two floats
-           the source sample distance (meters), if None the parallel beam is assumed.
-           If two floats are given then they are taken as the distance of the vertically focused source (horizontal line)
-           and the horizontaly focused source (vertical line) for KB mirrors.
-        z2 : float
-           the sample detector distance (meters).
-        pix_size_det: float
-           pixel size (meters)
-        wavelength: float
-           beam wave length (meters).
-        magnification: boolean defaults to True
-           if false no magnification is considered
-        length_scale: float
-            rescaling length scale, meant to avoid having too big or too small numbers.
-            defaults to 10.0e-6
-        logger: Logger, optional
-            A logging object
-        """
-        self.logger = LoggerOrPrint(logger)
-        if z1_vh is None:
-            self.z1_vh = None
-        else:
-            if hasattr(type(z1_vh), "__iter__"):
-                self.z1_vh = np.array(z1_vh)
-            else:
-                self.z1_vh = np.array([z1_vh, z1_vh])
-        self.z2 = z2
-        self.magnification = magnification
-        self.pix_size_det = pix_size_det
-
-        if self.magnification and self.z1_vh is not None:
-            self.M_vh = (self.z1_vh + self.z2) / self.z1_vh
-        else:
-            self.M_vh = np.array([1, 1])
-
-        self.logger.debug("Magnification : h ({}) ;  v ({}) ".format(self.M_vh[1], self.M_vh[0]))
-
-        self.length_scale = length_scale
-        self.wavelength = wavelength
-
-        self.maxM = self.M_vh.max()
-
-        self.pix_size_rec = self.pix_size_det / self.maxM  # we bring everything to highest magnification
-
-        which_unit = int(np.sum(np.array([self.pix_size_rec > small for small in [1.0e-6, 1.0e-7]]).astype(np.int32)))
-        self.pixelsize_string = [
-            "{:.1f} nm".format(self.pix_size_rec * 1e9),
-            "{:.3f} um".format(self.pix_size_rec * 1e6),
-            "{:.1f} um".format(self.pix_size_rec * 1e6),
-        ][which_unit]
-
-        if self.magnification:
-            self.logger.debug(
-                "All images are resampled to smallest pixelsize: {}".format(self.pixelsize_string),
-            )
-        else:
-            self.logger.debug("Pixelsize images:  {}".format(self.pixelsize_string))
-
-
-class CTFPhaseRetrieval:
-    """
-    This class implements the CTF formula of [1] in its regularised form which avoids the zeros
-    of unregularised_filter_denominator (unreg_filter_denom is the so here named denominator/delta_beta
-    of equation 8).
-
-    References
-    -----------
-    [1] B. Yu, L. Weber, A. Pacureanu, M. Langer, C. Olivier, P. Cloetens, and F. Peyrin,
-    "Evaluation of phase retrieval approaches in magnified X-ray phase nano computerized tomography applied to bone tissue",
-    Optics Express, Vol 26, No 9, 11110-11124 (2018)
-    """
-
-    def __init__(
-        self,
-        shape,
-        geo_pars,
-        delta_beta,
-        padded_shape="auto",
-        padding_mode="reflect",
-        translation_vh=None,
-        normalize_by_mean=False,
-        lim1=1.0e-5,
-        lim2=0.2,
-        use_rfft=False,
-        fftw_num_threads=None,
-        fft_num_threads=None,
-        logger=None,
-    ):
-        """
-        Initialize a Contrast Transfer Function phase retrieval.
-
-        Parameters
-        ----------
-        geo_pars: GeoPars
-            the geometry description
-        delta_beta : float
-            the delta/beta ratio
-        padded_shape: str or tuple, optional
-            Padded image shape, in the form (num_rows, num_columns) i.e (vertical, horizontal).
-            By default, it is twice the image shape.
-        padding_mode: str
-            Padding mode. It must be valid for the numpy.pad function
-        translation_vh: array, optional
-            Shift in the form (y, x). It is used to perform a translation of the image before applying the CTF filter.
-        normalize_by_mean: bool
-            Whether to divide the (padded) image with its mean before applying the CTF filter.
-        lim1: float >0
-            the regulariser strenght at low  frequencies
-        lim2: float >0
-            the regulariser strenght at high frequencies
-        use_rfft: bool, optional
-            Whether to use real-to-complex (R2C) FFT instead of usual complex-to-complex (C2C).
-        fftw_num_threads: bool or None or int, optional
-            DEPRECATED - please use fft_num_threads instead.
-        fft_num_threads: bool or None or int, optional
-            Number of threads to use for FFT.
-            If a number is provided: number of threads to use for FFT.
-            You can pass a negative number to use N - fft_num_threads cores.
-        logger: optional
-            a logger object
-        """
-        self.logger = LoggerOrPrint(logger)
-        if not isinstance(geo_pars, GeoPars):
-            raise ValueError("Expected GeoPars instance for 'geo_pars' parameter")
-        self.geo_pars = geo_pars
-        self._calc_shape(shape, padded_shape, padding_mode)
-        self.delta_beta = delta_beta
-
-        # COMPAT.
-        if fftw_num_threads is not None:
-            deprecation_warning("'fftw_num_threads' is replaced with 'fft_num_threads'", func_name="ctf_fftw")
-            fft_num_threads = fftw_num_threads
-        # ---
-
-        self.lim = None
-        self.lim1 = lim1
-        self.lim2 = lim2
-        self.normalize_by_mean = normalize_by_mean
-        self.translation_vh = translation_vh
-        self._setup_fft(use_rfft, fft_num_threads)
-        self._get_ctf_filter()
-
-    def _calc_shape(self, shape, padded_shape, padding_mode):
-        if np.isscalar(shape):
-            shape = (shape, shape)
-        else:
-            assert len(shape) == 2
-        self.shape = shape
-        if padded_shape is None or padded_shape is False:
-            padded_shape = self.shape  # no padding
-        elif isinstance(padded_shape, (tuple, list, np.ndarray)):
-            pass
-        elif padded_shape == "auto":
-            padded_shape = (2 * self.shape[0], 2 * self.shape[1])
-        self.shape_padded = tuple(padded_shape)
-        self.padding_mode = padding_mode
-
-    def _setup_fft(self, use_rfft, fft_num_threads):
-        self.use_rfft = use_rfft
-        self._fft_func = rfft2 if use_rfft else fft2
-        self._ifft_func = irfft2 if use_rfft else ifft2
-        self.fft_num_threads = get_num_threads(fft_num_threads)
-
-    def _get_ctf_filter(self):
-        """
-        The parameter "length_scale" was mentioned, in the octave code,
-        as a rescaling length scale, which is meant to avoid
-        having too big or too small numbers.
-        From the mathematical point of view, it is infact completely trasparent:
-        its action is on fsamplex, fsampley and  betash, betasv.
-        But these latters ( beta's)  are multiplied by  the formers (fsample's) so that
-        "length_scale" mathematically disappears, however in case of simple precision float
-        the exponent of a float number ranges from -38 to 38, and one could approach it
-        as an example by taking the square of a very small number ( 1.0e-19), and losing significant bits
-        in he mantissa or getting zero, or the square of a big number, thus generting inf
-        Althought the values involved in our x-ray regimes seems safe, with respect to these problems,
-        this length_scale parameters does not hurt.
-        """
-        padded_img_shape = self.shape_padded
-        fsample_vh = np.array(
-            [
-                self.geo_pars.length_scale / self.geo_pars.pix_size_rec,
-                self.geo_pars.length_scale / self.geo_pars.pix_size_rec,
-            ]
-        )
-
-        if not self.use_rfft:
-            ff_index_vh = list(map(np.fft.fftfreq, padded_img_shape))
-        else:
-            ff_index_vh = [np.fft.fftfreq(padded_img_shape[0]), np.fft.rfftfreq(padded_img_shape[1])]
-
-        # if padded_img_shape[1]%2 == 0 : # change to holotomo_slave indexing (by a transparent 2pi shift)
-        #     ff_index_x[ ff_index_x  == -0.5    ] =  +0.5
-        # if padded_img_shape[0]%2 == 0 : # change to holotomo_slave indexing (by a transparent 2pi shift)
-        #     ff_index_y[ ff_index_y  == -0.5    ] =  +0.5
-
-        frequencies_vh = np.array(
-            np.meshgrid(ff_index_vh[0] * fsample_vh[0], ff_index_vh[1] * fsample_vh[1], indexing="ij")
-        )
-
-        frequencies_squared_vh = frequencies_vh * frequencies_vh
-
-        """
-        ---------------  fresnelnumbers and forward propagators -------------------
-        In the limit of parallel beam, z1_h and z1_v would be infinite
-        so that the here below distances becomes z2
-        which is sample-detector distance.
-        """
-
-        if self.geo_pars.z1_vh is not None:
-            distances_vh = (self.geo_pars.z1_vh * self.geo_pars.z2) / (self.geo_pars.z1_vh + self.geo_pars.z2)
-        else:
-            distances_vh = np.array([self.geo_pars.z2, self.geo_pars.z2])
-
-        """
-        Citing David Paganin (2002) :
-        The intensity I_{R_1}(r⊥,z) at a distance z  of a weakly refracting object illuminated by a
-        point source at distance R1  behind the said object, is related to the intensity
-        I∞(r⊥,z), which would result from normally
-        incident collimated illumination of the same object, by (Pogany et al., 1997):
-          I_{R_1}(r⊥,z) = 1/{M^2} I∞(r⊥/M , z/M)
-        where M is the magnification.
-        This explains the effective distance formula expressed by
-        distancesh, distancesv  above.
-        ------------------------------------------------------------------------------
-        """
-
-        lambda_dist_vh = self.geo_pars.wavelength * distances_vh / (self.geo_pars.length_scale**2)
-
-        """
-        ---------------------------------------------------------------------------------------
-        -> cut_v at first maximum of ctf largest distance
-
-        In the paraxial expansion of the Fresnel propagator, the phase is equal to
-                          1/2 K_{parallel}^2 wavelength * Distance /2 / pi
-
-        When this is equal to a multiple of 2 pi, the effect of propagation disappears
-        and we have a singularity in equation 8.
-
-        The sampling in the reciprocal space is done with  a step length of 2*pi*fsamplex,y
-          (note: fsamples are the plain inverse of pixel size)
-        The first singularity occurs  at a frequence number
-                        K_{parallel}/2/pi/ fsamplex
-
-         for K_{parallel}^2 = 2 * (2pi)^2 /( wavelength * distance  )
-
-         which would correspond to
-                   K_{parallel}/2/pi/ fsamplex  =  sqrt( 2/wavelength*distance) / fsample
-
-        Question:( why the factor 2 appear at the denominator in the square root below?)
-        Answer : the below defined cut corresponds to the first maximum of the denominator,
-        before arriving to the first zero. In this way the regularisation
-        is already at ( almost) full strenght on the first pole.ation
-        ## is already at ( almost) full strenght on the first pole.
-        """
-        self.cut_v = math.sqrt(1.0 / 2 / lambda_dist_vh[0]) / fsample_vh[0]
-        self.cut_v = min(self.cut_v, 0.5)
-
-        self.logger.debug("Normalized cut-off = {:5.3f}".format(self.cut_v))
-
-        self.r = fourier_filters.get_lowpass_filter(
-            padded_img_shape,
-            cutoff_par=(
-                0.5 / (self.cut_v + 1.0 / padded_img_shape[0]),
-                0.01 * padded_img_shape[0] / (1 + self.cut_v * padded_img_shape[0]),
-            ),
-            use_rfft=self.use_rfft,
-        )
-        self.r /= self.r[0, 0]
-
-        self.lim = self.lim1 * self.r + self.lim2 * (1 - self.r)
-
-        # more methods exist in the original code, and they are initialized starting from here
-        # (ht_app1, ht_app2... ht_app7)
-
-        fresnel_phase = (
-            np.pi * lambda_dist_vh[1] * frequencies_squared_vh[1]
-            + np.pi * lambda_dist_vh[0] * frequencies_squared_vh[0]
-        )
-
-        if self.delta_beta:
-            unreg_filter_denom = np.sin(fresnel_phase) + (1.0 / self.delta_beta) * np.cos(fresnel_phase)
-        else:
-            unreg_filter_denom = np.sin(fresnel_phase)
-        self.unreg_filter_denom = unreg_filter_denom.astype(np.float32)
-        self._ctf_filter_denom = (2 * self.unreg_filter_denom * self.unreg_filter_denom + self.lim).astype(np.complex64)
-
-    def _apply_filter(self, img):
-        img_f = self._fft_func(img, workers=self.fft_num_threads)
-        img_f *= self.unreg_filter_denom
-
-        unreg_filter_denom_0_mean = self.unreg_filter_denom[0, 0]
-        nf, mf = img.shape
-
-        # here it is assumed that the average of img is 1 and the DC component is removed
-        img_f[0, 0] -= nf * mf * unreg_filter_denom_0_mean
-
-        ## formula 8, with regularisation to stay at a safe distance from the poles
-        img_f /= self._ctf_filter_denom
-        ph = self._ifft_func(img_f, workers=self.fft_num_threads).real
-        return ph
-
-    def retrieve_phase(self, img, output=None):
-        """
-        Apply the CTF filter to retrieve the phase.
-
-        Parameters
-        ----------
-        img: np.ndarray
-            Projection image. It must have been already flat-fielded.
-
-        Returns
-        --------
-        ph: numpy.ndarray
-            Phase image
-        """
-        padded_img = pad_interpolate(
-            img, self.shape_padded, translation_vh=self.translation_vh, padding_mode=self.padding_mode
-        )
-        if self.normalize_by_mean:
-            padded_img /= padded_img.mean()
-        phase_img = self._apply_filter(padded_img)
-        res = recut(phase_img, img.shape)
-        if output is not None:
-            output[:, :] = res[:, :]
-            return output
-        return res
-
-    __call__ = retrieve_phase
-
-
-CtfFilter = CTFPhaseRetrieval

build/lib/nabu/preproc/ctf_cuda.py

@@ -1,142 +0,0 @@
-import numpy as np
-from ..utils import calc_padding_lengths, updiv, get_cuda_srcfile, docstring
-from ..cuda.processing import CudaProcessing
-from ..cuda.utils import __has_pycuda__
-from ..processing.padding_cuda import CudaPadding
-from ..processing.fft_cuda import get_fft_class
-from .phase_cuda import CudaPaganinPhaseRetrieval
-from .ctf import CTFPhaseRetrieval
-
-if __has_pycuda__:
-    from pycuda import gpuarray as garray
-
-
-# TODO:
-#  - better padding scheme (for now 2*shape)
-#  - rework inheritance scheme ? (base class SingleDistancePhaseRetrieval and its cuda counterpart)
-class CudaCTFPhaseRetrieval(CTFPhaseRetrieval):
-
-    """
-    Cuda back-end of CTFPhaseRetrieval
-    """
-
-    @docstring(CTFPhaseRetrieval)
-    def __init__(
-        self,
-        shape,
-        geo_pars,
-        delta_beta,
-        padded_shape="auto",
-        padding_mode="reflect",
-        translation_vh=None,
-        normalize_by_mean=False,
-        lim1=1.0e-5,
-        lim2=0.2,
-        use_rfft=True,
-        fftw_num_threads=None,  # COMPAT.
-        fft_num_threads=None,
-        logger=None,
-        cuda_options=None,
-        fft_backend="skcuda",
-    ):
-        """
-        Initialize a CudaCTFPhaseRetrieval.
-
-        Parameters
-        ----------
-        shape: tuple
-            Shape of the images to process
-        padding_mode: str
-            Padding mode. Default is "reflect".
-
-        Other parameters
-        -----------------
-        Please refer to CTFPhaseRetrieval documentation.
-        """
-        if not use_rfft:
-            raise ValueError("Only use_rfft=True is supported")
-        self.cuda_processing = CudaProcessing(**(cuda_options or {}))
-        super().__init__(
-            shape,
-            geo_pars,
-            delta_beta,
-            padded_shape=padded_shape,
-            padding_mode=padding_mode,
-            translation_vh=translation_vh,
-            normalize_by_mean=normalize_by_mean,
-            lim1=lim1,
-            lim2=lim2,
-            logger=logger,
-            use_rfft=True,
-            fft_num_threads=False,
-        )
-        self._init_ctf_filter()
-        self._init_cuda_padding()
-        self._init_fft(fft_backend)
-        self._init_mult_kernel()
-
-    def _init_ctf_filter(self):
-        self._mean_scale_factor = self.unreg_filter_denom[0, 0] * np.prod(self.shape_padded)
-        self._d_filter_num = self.cuda_processing.to_device("_d_filter_num", self.unreg_filter_denom).astype("f")
-        self._d_filter_denom = self.cuda_processing.to_device(
-            "_d_filter_denom", (1.0 / (2 * self.unreg_filter_denom * self.unreg_filter_denom + self.lim)).astype("f")
-        )
-
-    def _init_cuda_padding(self):
-        pad_width = calc_padding_lengths(self.shape, self.shape_padded)
-        # Custom coordinate transform to get directly FFT layout
-        R, C = np.indices(self.shape, dtype=np.int32, sparse=True)
-        coords_R = np.roll(np.pad(R.ravel(), pad_width[0], mode=self.padding_mode), -pad_width[0][0])
-        coords_C = np.roll(np.pad(C.ravel(), pad_width[1], mode=self.padding_mode), -pad_width[1][0])
-        self.cuda_padding = CudaPadding(
-            self.shape,
-            (coords_R, coords_C),
-            mode=self.padding_mode,
-            # propagate cuda options ?
-        )
-
-    def _init_fft(self, fft_backend):
-        fft_cls = get_fft_class(backend=fft_backend)
-        self.cufft = fft_cls(shape=self.shape_padded, dtype=np.float32, r2c=True)
-        self.d_radio_padded = self.cuda_processing.allocate_array("d_radio_padded", self.shape_padded, "f")
-        self.d_radio_f = self.cuda_processing.allocate_array("d_radio_f", self.cufft.shape_out, np.complex64)
-
-    def _init_mult_kernel(self):
-        self.cpxmult_kernel = self.cuda_processing.kernel(
-            "CTF_kernel",
-            filename=get_cuda_srcfile("ElementOp.cu"),
-            signature="PPPfii",
-        )
-        Nx = np.int32(self.shape_padded[1] // 2 + 1)
-        Ny = np.int32(self.shape_padded[0])
-        self._cpxmult_kernel_args = [
-            self.d_radio_f,
-            self._d_filter_num,
-            self._d_filter_denom,
-            np.float32(self._mean_scale_factor),
-            Nx,
-            Ny,
-        ]
-        blk = (32, 32, 1)
-        grd = (updiv(Nx, blk[0]), updiv(Ny, blk[1]))
-        self._cpxmult_kernel_kwargs = {"grid": grd, "block": blk}
-
-    set_input = CudaPaganinPhaseRetrieval.set_input
-
-    def retrieve_phase(self, image, output=None):
-        """
-        Perform padding on an image. Please see the documentation of CTFPhaseRetrieval.retrieve_phase().
-        """
-        self.set_input(image)
-        self.cuda_padding.pad(image, output=self.d_radio_padded)
-        if self.normalize_by_mean:
-            m = garray.sum(self.d_radio_padded).get() / np.prod(self.shape_padded)
-            self.d_radio_padded /= m
-        self.cufft.fft(self.d_radio_padded, output=self.d_radio_f)
-        self.cpxmult_kernel(*self._cpxmult_kernel_args, **self._cpxmult_kernel_kwargs)
-        self.cufft.ifft(self.d_radio_f, output=self.d_radio_padded)
-
-        if output is None:
-            output = self.cuda_processing.allocate_array("d_output", self.shape)
-        output[:, :] = self.d_radio_padded[: self.shape[0], : self.shape[1]]
-        return output

build/lib/nabu/preproc/distortion.py

@@ -1,92 +0,0 @@
-import numpy as np
-from scipy.interpolate import RegularGridInterpolator
-from ..utils import check_supported
-from ..estimation.distortion import estimate_flat_distortion
-
-
-def correct_distortion_interpn(image, coords, bounds_error=False, fill_value=None):
-    """
-    Correct image distortion with scipy.interpolate.interpn.
-
-    Parameters
-    ----------
-    image: array
-        Distorted image
-    coords: array
-        Coordinates of the distortion correction to apply, with the shape (Ny, Nx, 2)
-    """
-    foo = RegularGridInterpolator(
-        (np.arange(image.shape[0]), np.arange(image.shape[1])),
-        image,
-        bounds_error=bounds_error,
-        method="linear",
-        fill_value=fill_value,
-    )
-    return foo(coords)
-
-
-class DistortionCorrection:
-    """
-    A class for estimating and correcting image distortion.
-    """
-
-    estimation_methods = {
-        "fft-correlation": estimate_flat_distortion,
-    }
-    correction_methods = {
-        "interpn": correct_distortion_interpn,
-    }
-
-    def __init__(
-        self,
-        estimation_method="fft-correlation",
-        estimation_kwargs=None,
-        correction_method="interpn",
-        correction_kwargs=None,
-    ):
-        """
-        Initialize a DistortionCorrection object.
-
-        Parameters
-        -----------
-        estimation_method: str
-            Name of the method to use for estimating the distortion
-        estimation_kwargs: dict, optional
-            Named arguments to pass to the estimation method, in the form of a dictionary.
-        correction_method: str
-            Name of the method to use for correcting the distortion
-        correction_kwargs: dict, optional
-            Named arguments to pass to the correction method, in the form of a dictionary.
-        """
-        self._set_estimator(estimation_method, estimation_kwargs)
-        self._set_corrector(correction_method, correction_kwargs)
-
-    def _set_estimator(self, estimation_method, estimation_kwargs):
-        check_supported(estimation_method, self.estimation_methods.keys(), "estimation method")
-        self.estimator = self.estimation_methods[estimation_method]
-        self._estimator_kwargs = estimation_kwargs or {}
-
-    def _set_corrector(self, correction_method, correction_kwargs):
-        check_supported(correction_method, self.correction_methods.keys(), "correction method")
-        self.corrector = self.correction_methods[correction_method]
-        self._corrector_kwargs = correction_kwargs or {}
-
-    def estimate_distortion(self, image, reference_image):
-        return self.estimator(image, reference_image, **self._estimator_kwargs)
-
-    estimate = estimate_distortion
-
-    def correct_distortion(self, image, coords):
-        image_corrected = self.corrector(image, coords, **self._corrector_kwargs)
-        fill_value = self._corrector_kwargs.get("fill_value", None)
-        if fill_value is not None and np.isnan(fill_value):
-            mask = np.isnan(image_corrected)
-            image_corrected[mask] = image[mask]
-        return image_corrected
-
-    correct = correct_distortion
-
-    def estimate_and_correct(self, image, reference_image):
-        coords = self.estimate_distortion(image, reference_image)
-        image_corrected = self.correct_distortion(image, coords)
-        return image_corrected