%%%%% Master thesis attachment %%%%

Author: Markéta Tkadlecová
Noise reduction in high resolution CT data

Precise mechanics and optics, Faculty of Mechanical Engineering, Brno University of Technology

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The code contained in this attachment requires the Matlab version of the ASTRA toolbox, version 2.1.0. to run.
You can download the ASTRA toolbox here:https://www.astra-toolbox.com/downloads/index.html

This version of ASTRA requires an nVidia GPU with CUDA 9.0+ capability.

All code was created using Matlab R2022a. Functionality in other Matlab versions has not been tested.
The image processing toolbox and parallel computing toolbox are required.

This folder contains essential codes and methods used in the thesis, or some support functions. 

+io .. a folder containing functions for reading the data, checking of directory, or writing outcomes to .xsl 

+metrics .. there are codes for evaluation of result, FR_metrics calculates the output of full-reference metrics SSIM, PSNR, MSE and otsu_dice_coeff evaluate the segmentation using Otis method

+proc .. there are some support function, also the function noise_estimation is included in the folder. This function estimates the snadard deviation of the noise. It is used in the denoising of tomograms and measured datasets.

+recon .. functions for tomographic reconstruction using FBP/FDK.


Datagen.ipynb .. Jupyter script for generation of foam phantom 
 
Methods .. folder containing every evaluated denoising method, with their licenses etc.

Statistical analysis .. functions and scripts for performing statistical analysis of bright field images captured using Riga nano3DX