httomolibgpu 3.1.1__py3-none-any.whl → 4.0__py3-none-any.whl

httomolibgpu/__init__.py

@@ -4,7 +4,7 @@ from httomolibgpu.misc.morph import sino_360_to_180, data_resampler
 from httomolibgpu.misc.rescale import rescale_to_int
 from httomolibgpu.prep.alignment import distortion_correction_proj_discorpy
 from httomolibgpu.prep.normalize import normalize
-from httomolibgpu.prep.phase import paganin_filter_tomopy
+from httomolibgpu.prep.phase import paganin_filter
 from httomolibgpu.prep.stripe import (
     remove_stripe_based_sorting,
     remove_stripe_ti,

httomolibgpu/prep/phase.py

@@ -18,7 +18,7 @@
 # Created By  : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
 # Created Date: 01 November 2022
 # ---------------------------------------------------------------------------
-"""Modules for phase retrieval and phase-contrast enhancement"""
+"""Modules for phase retrieval and phase-contrast enhancement. For more detailed information, see :ref:`phase_contrast_module`."""
 
 import numpy as np
 from httomolibgpu import cupywrapper
@@ -42,35 +42,36 @@ import math
 from httomolibgpu.misc.supp_func import data_checker
 
 __all__ = [
-    "paganin_filter_tomopy",
+    "paganin_filter",
 ]
 
 
-##-------------------------------------------------------------##
-# Adaptation of retrieve_phase (Paganin filter) from TomoPy
-def paganin_filter_tomopy(
+# This implementation originated from the TomoPy version. It has been modified to conform
+# different unit standards and also control of the filter driven by 'delta/beta' ratio
+# as opposed to 'alpha' in the TomoPy's implementation.
+def paganin_filter(
     tomo: cp.ndarray,
-    pixel_size: float = 1e-4,
-    dist: float = 50.0,
+    pixel_size: float = 1.28,
+    distance: float = 1.0,
     energy: float = 53.0,
-    alpha: float = 1e-3,
+    ratio_delta_beta: float = 250,
 ) -> cp.ndarray:
     """
-    Perform single-material phase retrieval from flats/darks corrected tomographic measurements. See
-    :cite:`Paganin02` for a reference.
+    Perform single-material phase retrieval from flats/darks corrected tomographic measurements. For more detailed information, see :ref:`phase_contrast_module`.
+    Also see :cite:`Paganin02` and :cite:`paganin2020boosting` for references.
 
     Parameters
     ----------
     tomo : cp.ndarray
         3D array of f/d corrected tomographic projections.
-    pixel_size : float, optional
-        Detector pixel size in cm.
-    dist : float, optional
-        Propagation distance of the wavefront in cm.
-    energy : float, optional
-        Energy of incident wave in keV.
-    alpha : float, optional
-        Regularization parameter, the ratio of delta/beta. Smaller values lead to less noise and more blur.
+    pixel_size : float
+        Detector pixel size (resolution) in micron units.
+    distance : float
+        Propagation distance of the wavefront from sample to detector in metre units.
+    energy : float
+        Beam energy in keV.
+    ratio_delta_beta : float
+        The ratio of delta/beta, where delta is the phase shift and real part of the complex material refractive index and beta is the absorption.
 
     Returns
     -------
@@ -84,7 +85,7 @@ def paganin_filter_tomopy(
             " please provide a stack of 2D projections."
         )
 
-    tomo = data_checker(tomo, verbosity=True, method_name="paganin_filter_tomopy")
+    tomo = data_checker(tomo, verbosity=True, method_name="paganin_filter")
 
     dz_orig, dy_orig, dx_orig = tomo.shape
 
@@ -98,11 +99,18 @@ def paganin_filter_tomopy(
     padded_tomo = cp.asarray(padded_tomo, dtype=cp.complex64)
     fft_tomo = fft2(padded_tomo, axes=(-2, -1), overwrite_x=True)
 
-    # Compute the reciprocal grid.
-    w2 = _reciprocal_grid(pixel_size, (dy, dx))
+    # calculate alpha constant
+    alpha = _calculate_alpha(energy, distance / 1e-6, ratio_delta_beta)
+
+    # Compute the reciprocal grid
+    indx = _reciprocal_coord(pixel_size, dy)
+    indy = _reciprocal_coord(pixel_size, dx)
+
+    # Build Lorentzian-type filter
+    phase_filter = fftshift(
+        1.0 / (1.0 + alpha * (cp.add.outer(cp.square(indx), cp.square(indy))))
+    )
 
-    # Build filter in the Fourier space.
-    phase_filter = fftshift(_paganin_filter_factor2(energy, dist, alpha, w2))
     phase_filter = phase_filter / phase_filter.max()  # normalisation
 
     # Filter projections
@@ -132,6 +140,12 @@ def paganin_filter_tomopy(
     return _log_kernel(tomo)
 
 
+def _calculate_alpha(energy, distance_micron, ratio_delta_beta):
+    return (
+        _wavelength_micron(energy) * distance_micron / (4 * math.pi)
+    ) * ratio_delta_beta
+
+
 def _shift_bit_length(x: int) -> int:
     return 1 << (x - 1).bit_length()
 
@@ -192,42 +206,12 @@ def _pad_projections_to_second_power(
     return padded_tomo, tuple(pad_list)
 
 
-def _paganin_filter_factor2(energy, dist, alpha, w2):
-    # Alpha represents the ratio of delta/beta.
-    return 1 / (_wavelength(energy) * dist * w2 / (4 * math.pi) + alpha)
-
-
-def _wavelength(energy: float) -> float:
-    SPEED_OF_LIGHT = 299792458e2  # [cm/s]
+def _wavelength_micron(energy: float) -> float:
+    SPEED_OF_LIGHT = 299792458e2 * 10000.0  # [microns/s]
     PLANCK_CONSTANT = 6.58211928e-19  # [keV*s]
     return 2 * math.pi * PLANCK_CONSTANT * SPEED_OF_LIGHT / energy
 
 
-def _reciprocal_grid(pixel_size: float, shape_proj: tuple) -> cp.ndarray:
-    """
-    Calculate reciprocal grid.
-
-    Parameters
-    ----------
-    pixel_size : float
-        Detector pixel size in cm.
-    shape_proj : tuple
-        Shape of the reciprocal grid along x and y axes.
-
-    Returns
-    -------
-    ndarray
-        Grid coordinates.
-    """
-    # Sampling in reciprocal space.
-    indx = _reciprocal_coord(pixel_size, shape_proj[0])
-    indy = _reciprocal_coord(pixel_size, shape_proj[1])
-    indx_sq = cp.square(indx)
-    indy_sq = cp.square(indy)
-
-    return cp.add.outer(indx_sq, indy_sq)
-
-
 def _reciprocal_coord(pixel_size: float, num_grid: int) -> cp.ndarray:
     """
     Calculate reciprocal grid coordinates for a given pixel size
@@ -236,7 +220,7 @@ def _reciprocal_coord(pixel_size: float, num_grid: int) -> cp.ndarray:
     Parameters
     ----------
     pixel_size : float
-        Detector pixel size in cm.
+        Detector pixel size in microns.
     num_grid : int
         Size of the reciprocal grid.
 

httomolibgpu/recon/algorithm.py

@@ -18,7 +18,7 @@
 # Created By  : Tomography Team at DLS <scientificsoftware@diamond.ac.uk>
 # Changes relative to ToMoBAR 2024.01 version
 # ---------------------------------------------------------------------------
-"""Module for tomographic reconstruction. For more detailed information see :ref:`image_reconstruction_module`"""
+"""Module for tomographic reconstruction. For more detailed information, see :ref:`image_reconstruction_module`"""
 
 import numpy as np
 from httomolibgpu import cupywrapper
@@ -215,9 +215,9 @@ def LPRec3d_tomobar(
     recon_size: Optional[int] = None,
     recon_mask_radius: float = 0.95,
     power_of_2_oversampling: Optional[bool] = True,
-    power_of_2_cropping: Optional[bool] = True,
-    min_mem_usage_filter: Optional[bool] = False,
-    min_mem_usage_ifft2: Optional[bool] = False,
+    power_of_2_cropping: Optional[bool] = False,
+    min_mem_usage_filter: Optional[bool] = True,
+    min_mem_usage_ifft2: Optional[bool] = True,
     neglog: bool = False,
 ) -> cp.ndarray:
     """
@@ -680,5 +680,5 @@ def _take_neg_log_np(data: np.ndarray) -> np.ndarray:
 def __estimate_detectorHoriz_padding(detX_size) -> int:
     det_half = detX_size // 2
     padded_value_exact = int(np.sqrt(2 * (det_half**2))) - det_half
-    padded_add_margin = int(0.1 * padded_value_exact)
+    padded_add_margin = padded_value_exact // 2
     return padded_value_exact + padded_add_margin

{httomolibgpu-3.1.1.dist-info → httomolibgpu-4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: httomolibgpu
-Version: 3.1.1
+Version: 4.0
 Summary: Commonly used tomography data processing methods at DLS.
 Author-email: Daniil Kazantsev <daniil.kazantsev@diamond.ac.uk>, Yousef Moazzam <yousef.moazzam@diamond.ac.uk>, Naman Gera <naman.gera@diamond.ac.uk>
 License: BSD-3-Clause

{httomolibgpu-3.1.1.dist-info → httomolibgpu-4.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-httomolibgpu/__init__.py,sha256=sz3ia5rSjC4lj6Xw4VZekh3OxmeVB2E2747bzyHqQdY,838
+httomolibgpu/__init__.py,sha256=j9BuoVz3kfxtUY8zDExpZOnM05eHuwNrua9zNZq1Zqw,831
 httomolibgpu/cupywrapper.py,sha256=6ITGJ2Jw5I5kVmKEL5LlsnLRniEqqBLsHiAjvLtk0Xk,493
 httomolibgpu/cuda_kernels/__init__.py,sha256=VQNMaGcVDwiE-C64FfLtubHpLriLG0Y3_QnjHBSHrN0,884
 httomolibgpu/cuda_kernels/calc_metrics.cu,sha256=oV7ZPcwjWafmZjbNsUkBYPvOViJ_nX3zBoOAuPCmIrA,11335
@@ -16,13 +16,13 @@ httomolibgpu/misc/supp_func.py,sha256=yDzNmRlIlIikQ4sKd2y9trQ9yQtblECmQ2JM5vmIY5
 httomolibgpu/prep/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 httomolibgpu/prep/alignment.py,sha256=BuFTfLZD5_THQAKP_ikQ3fRE8JpN-JItGllZgrHRU5s,5657
 httomolibgpu/prep/normalize.py,sha256=ozVUAs4UY2DY7MQtJKllUgahp_4wRFKPuc_3iQl6bCE,4879
-httomolibgpu/prep/phase.py,sha256=zIuAVqlnHVqcDUBtj40NRBoHaO7O2KqGZ5CCUABRXBQ,7282
+httomolibgpu/prep/phase.py,sha256=X4RsIEux7DP9O6BXgNiOO2nEwGsphh2BtaUHiOm5onc,7200
 httomolibgpu/prep/stripe.py,sha256=YgOVb7Z5H7NFM3d2Y1jfNNwwj7ZMDv9nMZMMCvdBnVM,15150
 httomolibgpu/recon/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-httomolibgpu/recon/algorithm.py,sha256=pCByNRby-6SUdH8QfC1z1BXVazTGcErLAyRgOPlm37o,28075
+httomolibgpu/recon/algorithm.py,sha256=6IbczYAikyXyqZbLjjBHOFE7Kir0OGHgJtnjUI8IJWk,28069
 httomolibgpu/recon/rotation.py,sha256=k_E0lBRprJz6AGclagIkrzk_9dipADxPtL5BxrggSwM,27729
-httomolibgpu-3.1.1.dist-info/licenses/LICENSE,sha256=bXeLsgelPUUXw8HCIYiVC97Dpjhm2nB54m7TACdH8ng,48032
-httomolibgpu-3.1.1.dist-info/METADATA,sha256=W0UoO0iumuI9Hs5WmIa3Q0Pxyf0v69yF4LLRq_D_g34,3341
-httomolibgpu-3.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-httomolibgpu-3.1.1.dist-info/top_level.txt,sha256=nV0Ty_YvSPVd1O6MNWuIplD0w1nwk5hT76YgBZ-bzUw,13
-httomolibgpu-3.1.1.dist-info/RECORD,,
+httomolibgpu-4.0.dist-info/licenses/LICENSE,sha256=bXeLsgelPUUXw8HCIYiVC97Dpjhm2nB54m7TACdH8ng,48032
+httomolibgpu-4.0.dist-info/METADATA,sha256=Y1elgzNtqV5cTbTs_AqFyCF9QAawUujRGaspi3bfeDY,3339
+httomolibgpu-4.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+httomolibgpu-4.0.dist-info/top_level.txt,sha256=nV0Ty_YvSPVd1O6MNWuIplD0w1nwk5hT76YgBZ-bzUw,13
+httomolibgpu-4.0.dist-info/RECORD,,