adding initial documentation

Author: dkazanc

docs/source/reference/methods.rst

@@ -10,8 +10,8 @@ Here we present a list of methods of the HTTomolibGPU library with more detailed
 
    methods_list/correction_methods
    methods_list/stripe_removal_methods
+   methods_list/phase_contrast_methods
    methods_list/reconstruction_methods
    methods_list/denoising_methods
    methods_list/rescale_methods
-   
-   
+

docs/source/reference/methods_list/phase_contrast_methods.rst

@@ -0,0 +1,20 @@
+.. _phase_contrast_module:
+
+Phase-contrast enhancement
+**************************
+
+Methods from the :mod:`httomolibgpu.prep.phase` module needed when the data requires phase contrast enhancement.
+
+**Description**
+
+In conventional X-ray tomography, image contrast comes mainly from absorption, i.e., how much a material attenuates X-rays.
+For some samples, especially biological, the absorption difference between structures can be insignificant and therefore the edge contrast
+can be lost. X-rays also undergo phase shifts when passing through materials with different refractive indices and
+these phase shifts carry valuable structural information that can be converted into contrast if properly reconstructed.
+
+The phase contrast enhances edges and interfaces, revealing fine internal structure that pure absorption tomography would miss.
+When we record propagation-based phase contrast images (e.g., at a certain distance from the sample), the detected intensity includes
+a mixture of absorption and phase effects. To reconstruct a clean 3D volume, we must separate phase from intensity.
+This process is called the phase retrieval. The Paganin method :cite:`Paganin02`  provides a simple, robust way to do this.
+
+:math:`n = (1 - \delta) + i \beta`

httomolibgpu/prep/phase.py

@@ -18,7 +18,7 @@
 # Created By  : Tomography Team at DLS <[email protected]>
 # 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
@@ -48,7 +48,7 @@
 
 # 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 implementation.
+# as opposed to 'alpha' in the TomoPy's implementation.
 def paganin_filter(
     tomo: cp.ndarray,
     pixel_size: float = 1.28,
@@ -71,7 +71,7 @@ def paganin_filter(
     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 :math:`n = (1 - \delta) + i \beta` and beta is the absorption.
+        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
     -------

httomolibgpu/recon/algorithm.py

@@ -18,7 +18,7 @@
 # Created By  : Tomography Team at DLS <[email protected]>
 # 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