.. test_page documentation master file, created by
   sphinx-quickstart on Wed Mar 18 17:03:45 2015.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Structure-oriented smoothing of 2D & 3D images on the GPU
=========================================================

.. toctree::
   :maxdepth: 3

*March 20, 2015*

This page describes the code I wrote for my undergraduate thesis while in my final year
at Colorado School of Mines. The code is found in two different git repositories
on |location_link|. The final working code and demo
is found within my fork of the Mines Java Tool Kit created by |dhale| (my advisor for this 
project). This is the `jtk` repository and  my test and other code is found within the 
`Senior_Design` repository.

.. |location_link| raw:: html

   <a href="https://github.com/ke0m" target="_blank">my GitHub page</a> 

.. |dhale| raw:: html

   <a href="https://inside.mines.edu/~dhale/" target="_blank">Professor Dave Hale</a>


Installation
------------
 
The instructions for installing the working code and demo
can be found in the README file on this |webpage|.

.. |webpage| raw:: html

   <a href="https://github.com/ke0m/jtk#structure-oriented-smoothing-of-2d-images-on-the-gpu" target="_blank">web page</a>

Introduction
------------

Geoscientists use seismic images to better understand the subsurface geology of a given region. The proper 
interpretation of these images is key in creating an accurate geologic model to make predictions on the location
of hydrocarbon reservoirs. This interpretation can be time-consuming and a major bottleneck in the process of 
creating geologic models [Fehmers-Hocker]_. 
Applying image processing algorithms can aid in speeding up this interpretation as they
can remove unwanted noise and help delineate subtle yet important geologic features. One of these algorithms is 
known as structure-oriented smoothing [Fehmers-Hocker]_. The application of this filter to a seismic image will smooth
along the geologic structure in the image rather than across it in order to enhance the structural features. By clicking Figure 1 
below, you can see the results of structure-oriented smoothing of a 2D seismic image.

.. raw:: html

  <div style="text-align: center;">
  <img id="sos_click" onclick="changeImage()"
  src="_images/input.png" width="60%" height="60%">
  </div>

  <p style="text-align: center"><b>Figure 1:</b> Click the figure above to toggle between the input and smoothed image.</p>

  <script>
  function changeImage() {
    var image = document.getElementById("sos_click");
    if(image.src.match("smoothed")) {
      image.src = "_images/input.png";
    }
    else {
      image.src = "_images/smoothed.png"
    }
  }
  </script>


Structure-oriented smoothing
----------------------------

The underlying algorithm that performs this adaptive smoothing is known as anisotropic diffusion filtering and has been used 
extensively in image processing applications [Weickert]_.  By solving the anisotropic diffusion equation using the input seismic
image as an initial condition, we simulate the anistropic diffusion process which diffuses the seismic amplitudes of the input image
[Fehmers-Hocker]_. This diffusion is guided along the structure present in the image by computed structure tensors that serve as 
input parameters in the anisotropic diffusion process. [Hale]_, describes an implementation of this algorithm by implicitly solving
a modified version of the diffusion equation via conjugate gradient iterations. 

The software that implements this conjugate gradient method for solving the anisotropic
diffsuion equation can be found within the `solve` method in the |LocalSmoothingFilter| class
of the Mines JTK. This method, written by Hale, is shown in the listing below:

.. literalinclude:: _codes/solve.java
  :language: java
  :linenos:


.. |LocalSmoothingFilter| raw:: html

   <a href="https://github.com/dhale/jtk/blob/master/src/main/java/edu/mines/jtk/dsp/LocalSmoothingFilter.java" target="_blank">LocalSmoothingFilter</a>


GPU Implementation
------------------