finishing methods restructuring

dkazanc · dkazanc · commit f9b35c621102 · 2025-08-27T14:06:19.000+01:00
diff --git a/docs/source/api/httomolibgpu.cuda_kernels.rst b/docs/source/api/httomolibgpu.cuda_kernels.rst
@@ -6,5 +6,5 @@ Module contents
 
 .. automodule:: httomolibgpu.cuda_kernels
    :members:
-   :show-inheritance:
    :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.cupywrapper.rst b/docs/source/api/httomolibgpu.cupywrapper.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.cupywrapper
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.misc.corr.rst b/docs/source/api/httomolibgpu.misc.corr.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.misc.corr
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.misc.denoise.rst b/docs/source/api/httomolibgpu.misc.denoise.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.misc.denoise
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.misc.morph.rst b/docs/source/api/httomolibgpu.misc.morph.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.misc.morph
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.misc.rescale.rst b/docs/source/api/httomolibgpu.misc.rescale.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.misc.rescale
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.misc.rst b/docs/source/api/httomolibgpu.misc.rst
@@ -18,5 +18,5 @@ Module contents
 
 .. automodule:: httomolibgpu.misc
    :members:
-   :show-inheritance:
    :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.prep.alignment.rst b/docs/source/api/httomolibgpu.prep.alignment.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.prep.alignment
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.prep.normalize.rst b/docs/source/api/httomolibgpu.prep.normalize.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.prep.normalize
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.prep.phase.rst b/docs/source/api/httomolibgpu.prep.phase.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.prep.phase
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.prep.rst b/docs/source/api/httomolibgpu.prep.rst
@@ -17,5 +17,5 @@ Module contents
 
 .. automodule:: httomolibgpu.prep
    :members:
-   :show-inheritance:
    :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.prep.stripe.rst b/docs/source/api/httomolibgpu.prep.stripe.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.prep.stripe
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.recon.algorithm.rst b/docs/source/api/httomolibgpu.recon.algorithm.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.recon.algorithm
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.recon.rotation.rst b/docs/source/api/httomolibgpu.recon.rotation.rst
@@ -2,5 +2,5 @@
 ============================================
 .. automodule:: httomolibgpu.recon.rotation
    :members:
-   :show-inheritance:
-   :undoc-members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.recon.rst b/docs/source/api/httomolibgpu.recon.rst
@@ -15,5 +15,5 @@ Module contents
 
 .. automodule:: httomolibgpu.recon
    :members:
-   :show-inheritance:
    :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/api/httomolibgpu.rst b/docs/source/api/httomolibgpu.rst
@@ -25,5 +25,5 @@ Module contents
 
 .. automodule:: httomolibgpu
    :members:
-   :show-inheritance:
    :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/reference/methods.rst b/docs/source/reference/methods.rst
@@ -8,4 +8,10 @@ Here we present a list of methods of the HTTomolibGPU library with more detailed
 .. toctree::
    :glob:
 
-   methods_list/stripe_removal_methods
+   methods_list/correction_methods
+   methods_list/stripe_removal_methods
+   methods_list/reconstruction_methods
+   methods_list/denoising_methods
+   methods_list/rescale_methods
+   
+   
diff --git a/docs/source/reference/methods_list/correction/median_filter.rst b/docs/source/reference/methods_list/correction/median_filter.rst
@@ -5,8 +5,7 @@ Median filter
 
 **Description**
 
-Median filter is a part of the module :doc:`../../api/httomolibgpu.misc.corr` for data correction. Median filter is a non-linear noise removing technique with 
-edge-preserving properties, see more on it `here <https://en.wikipedia.org/wiki/Median_filter>`_.  Mathematically, one can express the median filter as: 
+Median filter is a non-linear noise removing technique with edge-preserving properties, see more on it `here <https://en.wikipedia.org/wiki/Median_filter>`_.  Mathematically, one can express the median filter as: 
 
 .. math::
 
@@ -23,7 +22,7 @@ Where :math:`\mathrm{N}_{i}` is the symmetric neighbourhood (e.g. 3 x 3) of the
 **Where and how to use it:**
 
 Median filter can be used in post-processing, e.g., after the reconstruction to remove the noise and prepare the image for further analysis. Applying edge-preserving noise correction
-can simplify segmentation. 
+can simplify segmentation. It is recommended, however, to use more advanced :ref:`data_denoising_module` in order to achieve a better quality of denoising.
 
 **What are the adjustable parameters:**
 
@@ -38,27 +37,27 @@ In this example we demonstrate how to apply median filter to projection data to
 .. list-table:: 
 
 
-    * - .. figure:: ../../_static/auto_images_methods/normalisation_sino.png
+    * - .. figure:: ../../../_static/auto_images_methods/normalisation_sino.png
 
            Input (sinogram view)
 
-      - .. figure:: ../../_static/auto_images_methods/normalisation_proj.png
+      - .. figure:: ../../../_static/auto_images_methods/normalisation_proj.png
 
            Input (projection view)
 
-    * - .. figure:: ../../_static/auto_images_methods/median_filter_sino.png
+    * - .. figure:: ../../../_static/auto_images_methods/median_filter_sino.png
 
            After applying median filter (sinogram)
 
-      - .. figure:: ../../_static/auto_images_methods/median_filter_proj.png
+      - .. figure:: ../../../_static/auto_images_methods/median_filter_proj.png
 
            After applying median filter (projection)
 
-    * - .. figure:: ../../_static/auto_images_methods/median_filter_res_sino.png
+    * - .. figure:: ../../../_static/auto_images_methods/median_filter_res_sino.png
 
            Sinogram view of absolute residual between input and output
 
-      - .. figure:: ../../_static/auto_images_methods/median_filter_res_proj.png
+      - .. figure:: ../../../_static/auto_images_methods/median_filter_res_proj.png
 
            Projection view of absolute residual between input and output
 
diff --git a/docs/source/reference/methods_list/correction/outlier_removal.rst b/docs/source/reference/methods_list/correction/outlier_removal.rst
@@ -5,8 +5,7 @@ Outliers removal filter
 
 **Description**
 
-Also called as a **dezinger**. Outliers removal filter is a part of the module :doc:`../../api/httomolibgpu.misc.corr` for data correction. 
-This method seeks the pixels/voxels that do not fit normally distributed data and replace them by using the :ref:`method_median_filter`. Essentially, dezinger is 
+Outliers removal filter is also called as a **dezinger**. This method seeks the pixels/voxels that do not fit normally distributed data and replace them by using the :ref:`method_median_filter`. Essentially, dezinger is 
 a spatially variant median filter. The user needs to set the threshold parameter, based on which the filter will remove the outliers that are **above** 
 the chosen threshold. See the :code:`dif` parameter of the :code:`remove_outlier` method. 
 Mathematically, one can express the dezinger as: 
@@ -46,26 +45,26 @@ In this example we demonstrate how the outliers, visible in sinogram and project
 .. list-table:: 
 
 
-    * - .. figure:: ../../_static/auto_images_methods/remove_outlier_input_sino.png
+    * - .. figure:: ../../../_static/auto_images_methods/remove_outlier_input_sino.png
 
            Input (sinogram view) with a stripe of outliers in the middle of the image. 
 
-      - .. figure:: ../../_static/auto_images_methods/remove_outlier_input_proj.png
+      - .. figure:: ../../../_static/auto_images_methods/remove_outlier_input_proj.png
 
            Input (projection view) with some outliers in the left part of the image.
 
-    * - .. figure:: ../../_static/auto_images_methods/remove_outlier_sino.png
+    * - .. figure:: ../../../_static/auto_images_methods/remove_outlier_sino.png
 
            After applying outliers removal (sinogram)
 
-      - .. figure:: ../../_static/auto_images_methods/remove_outlier_proj.png
+      - .. figure:: ../../../_static/auto_images_methods/remove_outlier_proj.png
 
            After applying outliers removal (projection)
 
-    * - .. figure:: ../../_static/auto_images_methods/remove_outlier_res_sino.png
+    * - .. figure:: ../../../_static/auto_images_methods/remove_outlier_res_sino.png
 
            Sinogram view of absolute residual between input and output. Note that the residual contains only removed outliers, we want to avoid smoothing the data.
 
-      - .. figure:: ../../_static/auto_images_methods/remove_outlier_res_proj.png
+      - .. figure:: ../../../_static/auto_images_methods/remove_outlier_res_proj.png
 
            Projection view of absolute residual between input and output. Note that the residual contains only removed outliers, we want to avoid smoothing the data.
diff --git a/docs/source/reference/methods_list/correction_methods.rst b/docs/source/reference/methods_list/correction_methods.rst
@@ -0,0 +1,14 @@
+.. _data_correction_module:
+
+Data correction methods
+***********************
+
+Methods from the :mod:`httomolibgpu.misc.corr` module can be used as a pre-processing tool. Some of them can be applied to raw projection data, as :ref:`method_outlier_removal`.
+
+.. toctree::
+   :maxdepth: 2
+
+   correction/median_filter
+   correction/outlier_removal
+
+
diff --git a/docs/source/reference/methods_list/denoising/total_variation_PD.rst b/docs/source/reference/methods_list/denoising/total_variation_PD.rst
@@ -13,15 +13,15 @@ From the user perspective this model usually leads to true piecewise-constant im
 .. list-table::
 
 
-    * - .. figure:: ../../_static/figures/FBP.png
+    * - .. figure:: ../../../_static/figures/FBP.png
 
            The noisy image
 
-      - .. figure:: ../../_static/figures/SB.png
+      - .. figure:: ../../../_static/figures/SB.png
 
            Recovery using PD-TV denoising
 
-      - .. figure:: ../../_static/figures/SB_zoom.png
+      - .. figure:: ../../../_static/figures/SB_zoom.png
 
            Zoomed to PD-TV denoised image
 
diff --git a/docs/source/reference/methods_list/denoising/total_variation_ROF.rst b/docs/source/reference/methods_list/denoising/total_variation_ROF.rst
@@ -13,15 +13,15 @@ The resulting denoised images are piecewise-constant or cartoon-like.
 .. list-table::
 
 
-    * - .. figure:: ../../_static/figures/FBP.png
+    * - .. figure:: ../../../_static/figures/FBP.png
 
            The noisy image
 
-      - .. figure:: ../../_static/figures/ROF.png
+      - .. figure:: ../../../_static/figures/ROF.png
 
            Recovery using ROF-TV denoising
 
-      - .. figure:: ../../_static/figures/ROF_zoom.png
+      - .. figure:: ../../../_static/figures/ROF_zoom.png
 
            Zoomed to ROF-TV denoised image
 
diff --git a/docs/source/reference/methods_list/denoising_methods.rst b/docs/source/reference/methods_list/denoising_methods.rst
@@ -0,0 +1,14 @@
+.. _data_denoising_module:
+
+Denoising methods
+*****************
+
+Methods from the :mod:`httomolibgpu.misc.denoise` module are normally used as a post-processing tool, applied to the results of the reconstruction.
+
+.. toctree::
+   :maxdepth: 2
+
+   denoising/total_variation_ROF
+   denoising/total_variation_PD
+
+
diff --git a/docs/source/reference/methods_list/reconstruction/FBP2d_astra.rst b/docs/source/reference/methods_list/reconstruction/FBP2d_astra.rst
diff --git a/docs/source/reference/methods_list/reconstruction/FBP3d_tomobar.rst b/docs/source/reference/methods_list/reconstruction/FBP3d_tomobar.rst
diff --git a/docs/source/reference/methods_list/reconstruction/LPRec3d_tomobar.rst b/docs/source/reference/methods_list/reconstruction/LPRec3d_tomobar.rst
diff --git a/docs/source/reference/methods_list/reconstruction_methods.rst b/docs/source/reference/methods_list/reconstruction_methods.rst
@@ -0,0 +1,18 @@
+.. _image_reconstruction_module:
+
+Image reconstruction methods
+****************************
+
+Methods from :mod:`httomolibgpu.recon.algorithm` module are required to reconstruct the projection data, i.e., converting the set of sinograms into a reconstructed volume.
+The reconstruction methods can be divided into two groups: Direct methods and Iterative methods. 
+The former are faster and suitable for the majority of well-sampled and well-exposed data. 
+The latter are more complex and slower methods suitable for erroneuos or/and undersampled data. 
+
+.. toctree::
+   :maxdepth: 2
+
+   reconstruction/LPRec3d_tomobar
+   reconstruction/FBP3d_tomobar
+   reconstruction/FBP2d_astra
+
+
diff --git a/docs/source/reference/methods_list/rescale/rescale_to_int.rst b/docs/source/reference/methods_list/rescale/rescale_to_int.rst
@@ -34,24 +34,24 @@ In this example we demonstrate how to use the rescaling when saving the data fro
 .. list-table::
 
 
-    * - .. figure:: ../../_static/auto_images_methods/rescale_to_int_proj_0_to_100.png
+    * - .. figure:: ../../../_static/auto_images_methods/rescale_to_int_proj_0_to_100.png
 
            Projection data saved into 8-bit image with :code:`perc_range_min = 0` and :code:`perc_range_max = 100` scaling.
 
-      - .. figure:: ../../_static/auto_images_methods/rescale_to_int_histo_0_to_100.png
+      - .. figure:: ../../../_static/auto_images_methods/rescale_to_int_histo_0_to_100.png
 
            The corresponding histogram of the image to the left. Note that the background contains high values (250-255) and they dominate the image which is what reflected in the histogram.
 
-    * - .. figure:: ../../_static/auto_images_methods/rescale_to_int_proj_10_to_90.png
+    * - .. figure:: ../../../_static/auto_images_methods/rescale_to_int_proj_10_to_90.png
 
            Projection data saved into 8-bit image with :code:`perc_range_min = 10` and :code:`perc_range_max = 90` scaling. Note that the contrast appears to be better with this scaling.
-      - .. figure:: ../../_static/auto_images_methods/rescale_to_int_histo_10_to_90.png
+      - .. figure:: ../../../_static/auto_images_methods/rescale_to_int_histo_10_to_90.png
 
            The corresponding histogram of the image to the left. Note that the background is now outside the range and the histogram shows a good distribution of values withing the [0,128] range. If possible, however, it is better to aim for a wider histogram which represents the image well within the given range.
 
-    * - .. figure:: ../../_static/auto_images_methods/rescale_to_int_proj_30_to_70.png
+    * - .. figure:: ../../../_static/auto_images_methods/rescale_to_int_proj_30_to_70.png
 
            Projection data saved into 8-bit image with :code:`perc_range_min = 30` and :code:`perc_range_max = 70` scaling. This is en example of a poorer scaling when the loss of the information is clearly visible through poorer contrast.
-      - .. figure:: ../../_static/auto_images_methods/rescale_to_int_histo_30_to_70.png
+      - .. figure:: ../../../_static/auto_images_methods/rescale_to_int_histo_30_to_70.png
 
            The corresponding histogram of the image to the left. Note that the histogram has been significantly flattened with this scaling. Meaning that there is less values that represent the image in the selected range. And the histogram also has got less variation of values compared to the histogram without percentage scaling. Such flat histograms is best to avoid.
diff --git a/docs/source/reference/methods_list/rescale_methods.rst b/docs/source/reference/methods_list/rescale_methods.rst
@@ -0,0 +1,14 @@
+.. _data_rescale_module:
+
+Data rescale methods
+********************
+
+Methods from the :mod:`httomolibgpu.misc.rescale` module needed when the data needs to be rescaled to be saved in different bit-type as an image.
+
+.. toctree::
+   :maxdepth: 2
+
+   rescale/rescale_to_int
+
+
+
diff --git a/docs/source/reference/methods_list/stripe_removal/raven_filter.rst b/docs/source/reference/methods_list/stripe_removal/raven_filter.rst
diff --git a/docs/source/reference/methods_list/stripe_removal/remove_all_stripe.rst b/docs/source/reference/methods_list/stripe_removal/remove_all_stripe.rst
diff --git a/docs/source/reference/methods_list/stripe_removal/remove_stripe_based_sorting.rst b/docs/source/reference/methods_list/stripe_removal/remove_stripe_based_sorting.rst
diff --git a/docs/source/reference/methods_list/stripe_removal/remove_stripe_ti.rst b/docs/source/reference/methods_list/stripe_removal/remove_stripe_ti.rst
diff --git a/docs/source/reference/methods_list/stripe_removal_methods.rst b/docs/source/reference/methods_list/stripe_removal_methods.rst
