In this code example we define a 3D object in Matlab which we then forward project using CONRAD. Afterwards a comparison is done between a backprojection only and a backprojection that includes the ramp filtering step. The ground truth object, the created projections, the backprojection and the full FDK reconstruction including filtering are visualized in ImageJ windows.
Exported from Notepad++
clear variables
close all
clc
% Example for the forward and backward projection using CONRAD
% (1) import java packages
import ij.*
import edu.stanford.rsl.conrad.utils.*
import edu.stanford.rsl.conrad.data.*
% (2) Load the CONRAD settings xml file
try
% default config file as provided
% (just replace path to your own config file if needed)
config = Configuration.loadConfiguration(fullfile(fileparts(mfilename('fullpath')),'Conrad.xml'));
Configuration.setGlobalConfiguration(config);
catch err
error('Could not load valid CONRAD config file!');
end
% (3) open ImageJ / if already open, close all images
if (isempty(IJ.getInstance()))
ImageJ();
else
while(WindowManager.getImageCount()>0)
openImg = IJ.getImage();
openImg.close();
end
end
% (4) define a matlab volume (two spheres with high and low density)
volDim = [512,512,512];
[x,y,z]=meshgrid(1:volDim(1),1:volDim(2),1:volDim(3));
vol=zeros(volDim);
% sphere 1
vol(sqrt((x-(volDim(1)+1)/2).^2+(y-(volDim(2)+1)/2).^2+(z-(volDim(3)+1)/2).^2) < min(volDim)*0.5/2)=1;
% sphere 2
vol(sqrt((x-(volDim(1)+1)/2).^2+(y-(volDim(2)+1)/2).^2+(z-(volDim(3)+1)/2).^2) < min(volDim)*0.3/2)=4;
% (5) OpenCL forward projection
projections=OpenCLForwardProjection(vol);
projections.show('Forward Projected Matlab Object');
% (6) OpenCL backprojection without filtering
volRec1=OpenCLBackProjection(projections);
volRec1.show('Backprojection without filtering');
% (7) A full reconstruction with filtering
volRec2=reconstructionHelper(projections);
volRec2.show('Full reconstruction with filtering');
% (8) Show also the Ground Truth in ImageJ
gT = mat2Grid3D(vol);
gT.show('Ground Truth');
% If the outcome of the forward or backward projections are needed in
% Matlab format use the following (This copies the whole volume --> slow):
% mProjections = grid3D2mat(projections);
% However, you can also access the Grid3D directly (much faster) by using
% for example "projections.setAtIndex(x,y,z,value)".
here. Please follow the instructions in the Readme-file that is provided with the code examples for installation.