nabu 2024.1.0rc4__py3-none-any.whl → 2024.1.1__py3-none-any.whl

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

@@ -0,0 +1,276 @@
+"""
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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
+
+       http://www.apache.org/licenses/LICENSE-2.0
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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/nabu/thirdparty/pore3d_deringer_munch.py

@@ -0,0 +1,108 @@
+"""
+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