Add demo for loading data.

MATLAB/Demos/d21_ScannerDataLoader.m

@@ -0,0 +1,118 @@
+%% Demo 21: Loading scanner data to TIGRE. 
+%
+% This demo will demostrate the options for loading scanner data into
+% TIGRE.
+%
+%   Supported Manufacturers:
+%
+%       Varian
+%
+%       Nikon
+%
+%       Xradia (Zeiss)
+%
+%
+% Currently we have instructions for generic, Nikon (micro-CT) and Varian
+% scanners. 
+%
+% We are always looking to expand this, if you have code for a scanner that
+% is not supported by TIGRE and are allowed to share it, please do, we'd
+% like to have as many as possible. 
+
+%--------------------------------------------------------------------------
+%--------------------------------------------------------------------------
+% This file is part of the TIGRE Toolbox
+% 
+% Copyright (c) 2015, University of Bath and 
+%                     CERN-European Organization for Nuclear Research
+%                     All rights reserved.
+%
+% License:            Open Source under BSD. 
+%                     See the full license at
+%                     https://github.com/CERN/TIGRE/blob/master/LICENSE
+%
+% Contact:            [email protected]
+% Codes:              https://github.com/CERN/TIGRE/
+% Coded by:           Ander Biguri 
+%--------------------------------------------------------------------------
+%%
+
+%% Varan onboard CBCT.
+
+% If you have a Varian scanner that saves data in XIM format, the following
+% code will be able to load your dataset. 
+%
+% If you have a recosntructed image, it will take the geometry from there,
+% but if you don't, it will estimate appropiate geometry. You can always
+% change the image parameters, but the detector parameters should stay the
+% same unless you change the projections. 
+
+directory='~/your_data_path/varian/2020-01-01_123456/';
+[proj,geo, angles ] = VarianDataLoader(datafolder);
+[proj,geo, angles ] = VarianDataLoader(datafolder, false); %remove motion lag correction.
+
+% You can directly call reconstruction code now:
+
+img=OS_SART(proj,geo,angles,100);
+img=FDK(proj,geo,angles);
+
+%% Nikon micro-CT
+
+% Similarly, a Nikon dataset can be loaded with the following code:
+
+directory='~/your_data_path/Nikon/Sample_name/';
+[proj,geo, angles ] = NikonDataLoader(datafolder);
+
+% as micro-CT datasets are large, optional arguments for loading partial
+% amount of data is available:
+
+% load equidistant angles, but only few:
+[proj,geo, angles ] = NikonDataLoader(datafolder,'sampling','equidistant','num_angles',150);
+% load every X angles (10)
+[proj,geo, angles ] = NikonDataLoader(datafolder,'sampling','step','sampling_step',10);
+% load first X angles (1000)
+[proj,geo, angles ] = NikonDataLoader(datafolder,'sampling','continuous','num_angles',1000);
+
+% You can directly call reconstruction code now:
+
+img=OS_SART(proj,geo,angles,100);
+img=FDK(proj,geo,angles);
+
+%% Generic
+
+% It is possible that your scanner is not currently supported, or that it
+% simply does not have any way of storing the information (Zeiss Xradia
+% does not store anything but the projecions)
+
+% if this is the case, the general way of tackling the problem is:
+
+% Step 1: define your geometry and angles
+
+% Step 2: Load projections:
+[num_files, filenames] % Figure out a way of finding this. Often dir([path,'/*.extension'])
+% prealocate
+proj = single(zeros(geo.nDetector(1),geo.nDetector(2),length(angles)));
+% load files
+for ii=1:num_files
+    proj(:,:,ii)=single(imread(filenames(ii)));
+end
+
+% Step 3: validate
+
+plotProj(proj,angles)
+% you need to make sure that:
+%     1) white=metal/bone/high density and black=air.
+%         If this is not the case
+proj=-log(proj/(max(proj(:))+1)); % Beer-Lanbert law
+%     2) rotation happens left-right instead of top-bottom.
+%        If its top bottom:
+proj=permute(proj,[2,1,3]);
+
+% Step 4: test
+imgfdk=FDK(proj,geo,angles);
+plotImg(imgFDK,'dim','z');
+% If this does not look good, possible things to check:
+% - Are the angles in the right direction? maybe they need to be inverted. 
+% - Is your geometry properly defined? mistake on geometry will be
+%   detrimental to image quality
+% - if microCT: halos around the features? COR correction needed. 

MATLAB/Utilities/IO/VarianCBCT/VarianDataLoader.m

@@ -1,4 +1,8 @@
-function [proj, angles, geo] = VarianDataLoader(datafolder, varargin)
+function [proj,geo, angles ] = VarianDataLoader(datafolder, varargin)
+% VarianDataLoader   Loads Varian CBCT projection, geomtry and angles data
+%
+%   Optional parameter: Motion lag correction. Default True. 
+%
 % Load all dataset that are needed for reconstruction
 % Date: 2020-04-16
 % Author: Yi Du ([email protected])