restructuring methods 1

Author: dkazanc

docs/source/reference/methods.rst

@@ -3,78 +3,9 @@
 Methods Description
 -------------------
 
-Here we present a list of methods that exist in the HTTomolibGPU library with more detailed information in places compared to :ref:`reference_api`.
-
-.. _data_correction_module:
-
-Data correction module
-^^^^^^^^^^^^^^^^^^^^^^
-
-Modules from `Data correction` can be used as pre-processing (e.g. apply :ref:`method_outlier_removal` to raw projection data) or in some
-cases as post-processing (e.g. apply :ref:`method_median_filter` to the result of the reconstruction) tools.
-
-.. toctree::
-   :glob:
-
-   methods_list/median_filter
-   methods_list/outlier_removal
-
-
-.. _data_denoising_module:
-
-Data denoising module
-^^^^^^^^^^^^^^^^^^^^^^
-
-Modules from `Data denoising` can be used as post-processing tools. For instance, denoising procedures can be applied to the results of the reconstruction.
+Here we present a list of methods of the HTTomolibGPU library with more detailed information compared to :ref:`reference_api`.
 
 .. toctree::
    :glob:
 
-   methods_list/total_variation_ROF
-   methods_list/total_variation_PD
-
-.. _stripes_removal_module:
-
-Stripes removal module
-^^^^^^^^^^^^^^^^^^^^^^
-
-Modules from `Stripes removal` are normally used as a pre-processing tool. Stripes removal is equivalent to removing ring artefacts in the reconstructed images.
-
-
-.. toctree::
-   :glob:
-
-   methods_list/remove_stripe_based_sorting
-   methods_list/remove_all_stripe
-   methods_list/remove_stripe_ti
-   methods_list/raven_filter
-
-
-.. _image_reconstruction_module:
-
-Image reconstruction module
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Modules from `Image reconstruction` are needed in order to reconstruct data from 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 when the data is erroneuos or/and undersampled. 
-
-.. toctree::
-   :glob:
-
-   methods_list/LPRec3d_tomobar
-   methods_list/FBP3d_tomobar
-   methods_list/FBP2d_astra
-   
-
-.. _data_rescale_module:
-
-Data rescale module
-^^^^^^^^^^^^^^^^^^^
-
-Modules from `Data rescale` is usually needed when the data needs to be rescaled to be saved in different bit-type as images.
-
-.. toctree::
-   :glob:
-
-   methods_list/rescale_to_int
-
+   methods_list/stripe_removal_methods

…/reference/methods_list/raven_filter.rst …ods_list/stripe_removal/raven_filter.rstdocs/source/reference/methods_list/raven_filter.rst renamed to docs/source/reference/methods_list/stripe_removal/raven_filter.rst docs/source/reference/methods_list/raven_filter.rst renamed to docs/source/reference/methods_list/stripe_removal/raven_filter.rst

@@ -5,7 +5,7 @@ Remove stripes by sorting
 
 **Description**
 
-This stripe removal algorithm is developed by Dr. Nghia Vo and is a part of the module :doc:`../../api/httomolibgpu.prep.stripe` for data correction.
+This stripe removal algorithm is developed by Dr. Nghia Vo and is a part of the module :doc:`../../../api/httomolibgpu.prep.stripe` for data correction.
 This filter works in the sinogram space to minimise stripes leading to `Ring Artifacts <https://radiopaedia.org/articles/ring-artifact-2?lang=gb>`_ in the reconstruction. See more about the filter in the original publication :cite:`vo2018superior`.
 Also more information about the method can be found on the author's software `Sarepy <https://sarepy.readthedocs.io/>`_.
 
@@ -26,27 +26,27 @@ In this example we demonstrate how to apply the stripe removal algorithm to the
 .. list-table::
 
 
-    * - .. figure:: ../../_static/auto_images_methods/data_stripes_added_sino.png
+    * - .. figure:: ../../../_static/auto_images_methods/data_stripes_added_sino.png
 
            Input (sinogram view) with the stripes added
 
-      - .. figure:: ../../_static/auto_images_methods/data_stripes_added_proj.png
+      - .. figure:: ../../../_static/auto_images_methods/data_stripes_added_proj.png
 
            Input (projection view) with the stripes added
 
-    * - .. figure:: ../../_static/auto_images_methods/remove_stripe_based_sorting_sino.png
+    * - .. figure:: ../../../_static/auto_images_methods/remove_stripe_based_sorting_sino.png
 
            After applying remove stripes by sorting (sinogram)
 
-      - .. figure:: ../../_static/auto_images_methods/remove_stripe_based_sorting_proj.png
+      - .. figure:: ../../../_static/auto_images_methods/remove_stripe_based_sorting_proj.png
 
            After applying remove stripes by sorting (projection)
 
-    * - .. figure:: ../../_static/auto_images_methods/remove_stripe_based_sorting_res_sino.png
+    * - .. figure:: ../../../_static/auto_images_methods/remove_stripe_based_sorting_res_sino.png
 
            Sinogram view of absolute residual between input and output
 
-      - .. figure:: ../../_static/auto_images_methods/remove_stripe_based_sorting_res_proj.png
+      - .. figure:: ../../../_static/auto_images_methods/remove_stripe_based_sorting_res_proj.png
 
            Projection view of absolute residual between input and output
 

…rence/methods_list/remove_all_stripe.rst …ist/stripe_removal/remove_all_stripe.rstdocs/source/reference/methods_list/remove_all_stripe.rst renamed to docs/source/reference/methods_list/stripe_removal/remove_all_stripe.rst docs/source/reference/methods_list/remove_all_stripe.rst renamed to docs/source/reference/methods_list/stripe_removal/remove_all_stripe.rst

@@ -0,0 +1,16 @@
+.. _stripes_removal_module:
+
+Stripe Removal methods
+**********************
+
+Methods from `Stripes removal` module are normally used as a pre-processing tool to be applied to sinograms to remove ring artefacts in the reconstructed images.
+
+.. toctree::
+   :maxdepth: 2
+
+   stripe_removal/remove_stripe_based_sorting
+   stripe_removal/remove_all_stripe
+   stripe_removal/raven_filter
+   stripe_removal/remove_stripe_ti
+
+