nabu 2024.1.1__py3-none-any.whl → 2024.1.3__py3-none-any.whl

build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/algotom_convert_sino.py

@@ -1,276 +0,0 @@
-"""
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-   Copyright [2021] [Nghia T. Vo, Diamond Light Source Ltd]
-
-   Licensed under the Apache License, Version 2.0 (the "License");
-   you may not use this file except in compliance with the License.
-   You may obtain a copy of the License at
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-"""
-
-import numpy as np
-from scipy.ndimage import shift
-
-"""
-This function was taken from "algotom" (3b9a75a5f7b4d407ce142964ca683c067be8c246),
-with the following minor differences:
-  - That the center of rotation is kept where it is, so that the sinogram is
-    not shifted to have the CoR in the middle.
-  - When CoR is on the left, use 2*cor instead of 2*cor+2 for overlapping region
-"""
-
-
-def extend_sinogram(sino_360, cor, apply_log=True, shift_sinogram=True):
-    """
-    Extend a 360-degree sinogram (with offset center-of-rotation) for
-    later reconstruction (Ref. [1]).
-
-    Parameters
-    ----------
-    sino_360 : array_like
-        2D array. 360-degree sinogram.
-    cor : float or tuple of float
-        Center-of-rotation or (Overlap_area, overlap_side).
-    apply_log : bool, optional
-        Apply the logarithm function if True.
-
-    Returns
-    -------
-    sino_pad : array_like
-        Extended sinogram.
-    cor : float
-        Updated center-of-rotation referred to the converted sinogram.
-
-    References
-    ----------
-    .. [1] https://doi.org/10.1364/OE.418448
-    """
-    if apply_log is True:
-        sino_360 = -np.log(sino_360)
-    else:
-        sino_360 = np.copy(sino_360)
-    (nrow, ncol) = sino_360.shape
-    xcenter = (ncol - 1.0) * 0.5
-    if isinstance(cor, tuple):
-        (overlap, side) = cor
-    else:
-        if cor <= xcenter:
-            overlap = 2 * (cor + 0)  # was + 1
-            side = 0
-        else:
-            overlap = 2 * (ncol - cor - 1)
-            side = 1
-    overlap_int = int(np.floor(overlap))
-    sub_pixel = overlap - overlap_int
-    if side == 1:
-        if sub_pixel > 0.0 and shift_sinogram:
-            sino_360 = shift(sino_360, (0, sub_pixel), mode='nearest')
-        wei_list = np.linspace(1.0, 0.0, overlap_int)
-        wei_mat = np.tile(wei_list, (nrow, 1))
-        sino_360[:, -overlap_int:] = sino_360[:, -overlap_int:] * wei_mat
-        pad_wid = ncol - overlap_int
-        sino_pad = np.pad(sino_360, ((0, 0), (0, pad_wid)), mode="edge")
-    else:
-        if sub_pixel > 0.0 and shift_sinogram:
-            sino_360 = shift(sino_360, (0, -sub_pixel), mode='nearest')
-        wei_list = np.linspace(0.0, 1.0, overlap_int)
-        wei_mat = np.tile(wei_list, (nrow, 1))
-        sino_360[:, :overlap_int] = sino_360[:, :overlap_int] * wei_mat
-        pad_wid = ncol - overlap_int
-        sino_pad = np.pad(sino_360, ((0, 0), (pad_wid, 0)), mode="edge")
-    cor = (sino_pad.shape[1] - 1.0) / 2.0
-    return sino_pad, cor

build/lib/build/lib/build/lib/build/lib/build/lib/nabu/thirdparty/pore3d_deringer_munch.py

@@ -1,108 +0,0 @@
-"""
-The following de-striping method is adapted from the pore3d software.
-
-:Organization: Elettra - Sincrotrone Trieste S.C.p.A.
-
-:Version: 2013.05.01
-
-References
-----------
-[1] F. Brun, A. Accardo, G. Kourousias, D. Dreossi, R. Pugliese. Effective implementation
-of ring artifacts removal filters for synchrotron radiation microtomographic images. Proc.
-of the 8th International Symposium on Image and Signal Processing (ISPA), pp. 672-676, Sept. 4-6,
-Trieste (Italy), 2013.
-
-The license follows.
-"""
-# Copyright (c) 2013, Elettra - Sincrotrone Trieste S.C.p.A.
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-#
-# * Redistributions of source code must retain the above copyright
-#   notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-#   notice, this list of conditions and the following disclaimer in the
-#   documentation and/or other materials provided with the distribution.
-# * Neither the name of the copyright holders nor the names of any
-#   contributors may be used to endorse or promote products derived
-#   from this software without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-# ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
-# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
-# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
-# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
-# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-
-import numpy as np
-try:
-    import pywt
-    __has_pywt__ = True
-except ImportError:
-    __has_pywt__ = False
-
-
-def munchetal_filter(im, wlevel, sigma, wname='db15'):
-    """Process a sinogram image with the Munch et al. de-striping algorithm.
-
-    Parameters
-    ----------
-    im : array_like
-        Image data as numpy array.
-    wname : {'haar', 'db1'-'db20', 'sym2'-'sym20', 'coif1'-'coif5', 'dmey'}
-        The wavelet transform to use.
-    wlevel : int
-        Levels of the wavelet decomposition.
-    sigma : float
-        Cutoff frequency of the Butterworth low-pass filtering.
-
-    Example (using tiffile.py)
-    --------------------------
-    >>> im = imread('original.tif')
-    >>> im = munchetal_filter(im, 'db15', 4, 1.0)
-    >>> imsave('filtered.tif', im)
-
-    References
-    ----------
-    B. Munch, P. Trtik, F. Marone, M. Stampanoni, Stripe and ring artifact removal with
-    combined wavelet-Fourier filtering, Optics Express 17(10):8567-8591, 2009.
-    """
-    # Wavelet decomposition:
-    coeffs = pywt.wavedec2(im.astype(np.float32), wname, level=wlevel, mode="periodization")
-    coeffsFlt = [coeffs[0]]
-    # FFT transform of horizontal frequency bands:
-    for i in range(1, wlevel + 1):
-        # FFT:
-        fcV = np.fft.fftshift(np.fft.fft(coeffs[i][1], axis=0))
-        my, mx = fcV.shape
-        # Damping of vertical stripes:
-        damp = 1 - np.exp(-(np.arange(-np.floor(my / 2.), -np.floor(my / 2.) + my) ** 2) / (2 * (sigma ** 2)))
-        dampprime = np.kron(np.ones((1, mx)), damp.reshape((damp.shape[0], 1))) # np.tile(damp[:, np.newaxis], (1, mx))
-        fcV = fcV * dampprime
-        # Inverse FFT:
-        fcVflt = np.real(np.fft.ifft(np.fft.ifftshift(fcV), axis=0))
-        cVHDtup = (coeffs[i][0], fcVflt, coeffs[i][2])
-        coeffsFlt.append(cVHDtup)
-
-    # Get wavelet reconstruction:
-    im_f = np.real(pywt.waverec2(coeffsFlt, wname, mode="periodization"))
-    # Return image according to input type:
-    if (im.dtype == 'uint16'):
-        # Check extrema for uint16 images:
-        im_f[im_f < np.iinfo(np.uint16).min] = np.iinfo(np.uint16).min
-        im_f[im_f > np.iinfo(np.uint16).max] = np.iinfo(np.uint16).max
-        # Return filtered image (an additional row and/or column might be present):
-        return im_f[0:im.shape[0], 0:im.shape[1]].astype(np.uint16)
-    else:
-        return im_f[0:im.shape[0], 0:im.shape[1]]
-
-
-if not(__has_pywt__):
-    munchetal_filter = None