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QT_TestGhosting.m
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QT_TestGhosting.m
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% Copyright (C) 2013 Heidelberg University
%
% Developed at CKM (Computerunterstützte Klinische Medizin),
% Medical Faculty Mannheim, Heidelberg University, Mannheim,
% Germany
%
%
% LICENCE
%
% CKM PhM Software Library, Release 1.0 (c) 2013, Heidelberg
% University (the "Software")
%
% The Software remains the property of Heidelberg University ("the
% University").
%
% The Software is distributed "AS IS" under this Licence solely for
% non-commercial use in the hope that it will be useful, but in order
% that the University as a charitable foundation protects its assets for
% the benefit of its educational and research purposes, the University
% makes clear that no condition is made or to be implied, nor is any
% warranty given or to be implied, as to the accuracy of the Software,
% or that it will be suitable for any particular purpose or for use
% under any specific conditions. Furthermore, the University disclaims
% all responsibility for the use which is made of the Software. It
% further disclaims any liability for the outcomes arising from using
% the Software.
%
% The Licensee agrees to indemnify the University and hold the
% University harmless from and against any and all claims, damages and
% liabilities asserted by third parties (including claims for
% negligence) which arise directly or indirectly from the use of the
% Software or the sale of any products based on the Software.
%
% No part of the Software may be reproduced, modified, transmitted or
% transferred in any form or by any means, electronic or mechanical,
% without the express permission of the University. The permission of
% the University is not required if the said reproduction, modification,
% transmission or transference is done without financial return, the
% conditions of this Licence are imposed upon the receiver of the
% product, and all original and amended source code is included in any
% transmitted product. You may be held legally responsible for any
% copyright infringement that is caused or encouraged by your failure to
% abide by these terms and conditions.
%
% You are not permitted under this Licence to use this Software
% commercially. Use for which any financial return is received shall be
% defined as commercial use, and includes (1) integration of all or part
% of the source code or the Software into a product for sale or license
% by or on behalf of Licensee to third parties or (2) use of the
% Software or any derivative of it for research with the final aim of
% developing software products for sale or license to a third party or
% (3) use of the Software or any derivative of it for research with the
% final aim of developing non-software products for sale or license to a
% third party, or (4) use of the Software to provide any service to an
% external organisation for which payment is received. If you are
% interested in using the Software commercially, please contact
% Prof. Dr. Lothar Schad (lothar.schad@medma.uni-heidelberg.de).
%
%Method Description:
%-------------------
%Run final Ghosting evaluation, store and plot results
Pref.AimResolution = 256;
Pref.AimBitDepth = 12;
Pref.DoPlotVisible = 1;
Pref.ImageIntensity = 0.8;
%Distortions
Pref.Perform_NonUniformity = 0;
Pref.Dist_NonUniNVec = [1 4 -1]';
Pref.Perform_ChemicalShift = 0;
Pref.Dist_ChemShiftX = 0;
Pref.Dist_ChemShiftY = 0;
%In this test routine, the rotation and translation is disabled. This is
%done to be able to predefine the desired ghosting ratio as determined by
%the equation (cf. paper). The central ROI is a mixture of both the normal
%image intensity and an area overlayed with a ghost, yielding an increased
%averaged of the full ROI.
Pref.Perform_Rotation = 0;
Pref.Dist_RotAngleDeg = 5.0;
Pref.Perform_Translation = 0;
Pref.Dist_ShiftXpx = 0.0;
Pref.Dist_ShiftYpx = 0.0;
Pref.Perform_Ghosting = 1;
Pref.Dist_GhostingLevel = 0.1;
Pref.Perform_Blur = 0;
Pref.Dist_BlurSigma = 1.0;
Pref.Perform_Noise = 0;
Pref.Dist_NoiseSTD = 15;
Pref.Dist_NoiseMean = 30;
Pref.Perform_ProjectiveDeformation = 0;
Pref.Dist_ProjectiveT = [ 1 0 0; ...
0 1 0.0001; ...
0.01 0 1];
Pref.Perform_BarrelDeformation = 0;
Pref.Dist_BarrelLambda = 0.005;
Pref.Perform_PolynomialDeformation = 0;
Pref.Dist_PolynomialT = [ 0 0; ...
1 0; ...
0 1; ...
0 0; ...
0 0; ...
0.00001 0];
%read images
if ~exist('I_res_raw','var')
I_res_raw = double(imread('Quality Tests\PhantomDummy_Resolution.tif'));
I_imuni_raw = double(imread('Quality Tests\PhantomDummy_Uniformity.tif'));
% I_spatlin_raw = double(imread('Quality Tests\PhantomDummy_SpatialLinearity.tif'));
end
%% QT Preferences
% General
%Parameter.GEN.SaveFolder = DatasetList{DatasetIndex}{2}(1 : end - 4);
%Parameter.GEN.SavePath = ['Phantom Results/', DatasetList{DatasetIndex}{2}(1 : end - 4) ];
Parameter.GEN.Threshold = 1000; %DEFAULT, will be changed
Parameter.GEN.Angle = 0; %DEFAULT, will be changed
switch Pref.DoPlotVisible
case 1
Parameter.GEN.PlotVisible = 'on';
case 0
Parameter.GEN.PlotVisible = 'off';
end
%Start Values for Center
Parameter.GEN.CenterX = nan;
Parameter.GEN.CenterY = nan;
Parameter.GEN.Radius = nan;
% =================================
% ======== Signal-To-Noise ========
% =================================
%Relative size of SNR-ROI for Mean Calculation (based on Radius)
Parameter.SNR.RelInnerROIRadius = 0.8;
%if set to one, all four STD-ROIs are set to have equal size
Parameter.SNR.EqualSTDAreas = 1;
%if set to one, STD-ROIs are set to be positioned in the corners of the
%image, otherwise the are right next to the phantoms border
Parameter.SNR.BorderROIinCorner = 0;
%relative space between edge of Phantom and Ghost-ROIs based on Radius
Parameter.SNR.BorderROIMargin = 0.025;
%Relative Minimum Margin Size at each Edge based on Phantom Radius
Parameter.SNR.MinEdgeMargin = 0.06;
Parameter.SNR.MaxEdgeMargin = 0.1;
%Relative Size of ROI based on real MinEdgeMargin of Dataset
%(Size perpendicular to circle)
Parameter.SNR.ROISizePerp = 0.9;
%Relative Size of ROI based on Diameter (!!!) of Phantom
%(Size tangential to circle)
Parameter.SNR.ROISizeTang = 0.75;
% Image Uniformity
Parameter.IU.RadialSection = 0.8;
% =================================
% ======= Spatial Linearity =======
% =================================
% Range of valid areas based
Parameter.SL.AreaRange = [0.5, 1.5];
Parameter.SL.RelExpObjectSize = 0.14;
Parameter.SL.BiSinFit = 0;
Parameter.SL.PixelSpacing = 0.4688;
Parameter.RES.PixelSpacing = Parameter.SL.PixelSpacing;
%Resolution
Parameter.RES.AdjustPeak = 2;
% = 0: none
% = 1: by max
% = 2: by fit
Parameter.RES.RemoveGrayValueGradient = 1;
Parameter.RES.RelRegionSizeRadius = 0.1314;
Parameter.RES.RelGradientAreaRadius = 0.0395;
Parameter.RES.RelProfileRegionRadius = 0.0075;
Parameter.RES.PeakFitArea = [0.0074, 0.0056, 0.0037];
Parameter.RES.GrayvalueVisibilityThreshold = 200;
%% Final calculations
% Shift 0 to 70, overall 8 steps
% Angle 0 to 10 degree, overall 8 steps
GhostingLevel = linspace(0.0,0.20,10);
EstGhost = nan(size(GhostingLevel));
RealGhost = nan(size(GhostingLevel));
for p = 1 : numel(GhostingLevel)
%we want to reach a ghosting ratio of Dist_GhostingLevel(p)
%the ratio is caluclated by
%
% R = | (M_top + M_bottom) - (M_left + M_right)| / (2 * M_center)
% M_top = M_bottom = Noise_mean
% M_left = M_right = Pref.Dist_GhostingLevel * M_center
% M_center = OriginalSignal + RelAreaGhost * Pref.Dist_GhostingLevel * OriginalSignal
%However, the central ROI is a sum of areas of original image intensity
%and overlays by the ghost, the amounts are defined as follows:
%
RelAreaGhost = 3623/15437;
RelAreaOriginal = 11814/15437;
M_center = Pref.ImageIntensity * (2^Pref.AimBitDepth - 1);
%with adjusted central mean:
%M_center := (M_center * (1 + RelAreaGhost * Pref.Dist_GhostingLevel))
GL1 = (-GhostingLevel(p) * (M_center * (1 + RelAreaGhost * Pref.Dist_GhostingLevel)) + Pref.Dist_NoiseMean * Pref.Perform_Noise )/(M_center * (1 + RelAreaGhost * Pref.Dist_GhostingLevel));
GL2 = (+GhostingLevel(p) * (M_center * (1 + RelAreaGhost * Pref.Dist_GhostingLevel)) + Pref.Dist_NoiseMean * Pref.Perform_Noise )/(M_center * (1 + RelAreaGhost * Pref.Dist_GhostingLevel));
GL = max([GL1, GL2]);
if GL < 0
warning('GL < 0')
end
Pref.Dist_GhostingLevel = GL;
I_res = QT_DistortImage( I_res_raw, Pref );
I_imuni = QT_DistortImage( I_imuni_raw, Pref );
RawImSize = size(I_res_raw);
ImSize = size(I_res);
%First of all, estimate the Threshold
Parameter = DetermineThreshold( I_imuni, Parameter ); %.GEN.Threshold
%All position parameters such as center, radius and angle are determined
%using the start values from the "raw" data given by the
%DetermineThreshold-function; afterwards these startvalues will be replaced
%by the accurate results which will be further used as startvalues
[CenterX, CenterY, Radius, AngleEst, ~] = GetPhantomCenter( I_res, Parameter, 1, 0, 1 );
%Save the position paramters to be used as start values for upcoming
%calculations, if needed
Parameter.GEN.CenterX = CenterX;
Parameter.GEN.CenterY = CenterY;
Parameter.GEN.Radius = Radius;
Parameter.GEN.Angle = AngleEst;
% SNR
[Result_SNR, Parameter] = MeasureSNR( I_imuni, Parameter );
fprintf(' ********************************* \n')
fprintf(' **** L O C A L I Z A T I O N **** \n')
fprintf(' ********************************* \n')
fprintf(' CenterX: Real = %.2f | Estim. = %.2f\n', Pref.AimResolution/2 + Pref.Dist_ShiftXpx, CenterX)
fprintf(' CenterY: Real = %.2f | Estim. = %.2f\n', Pref.AimResolution/2 + Pref.Dist_ShiftYpx, CenterY)
fprintf(' Radius: Real = %.2f | Estim. = %.2f\n', 0.5 * 2834 * Pref.AimResolution/RawImSize(1), Radius)
fprintf(' Angle: Real = %.2f | Estim. = %.2f\n', Pref.Dist_RotAngleDeg, AngleEst / pi * 180.0)
fprintf(' ********************************* \n')
fprintf(' ******* G H O S T I N G ******** \n')
fprintf(' ********************************* \n')
fprintf(' Level: Real = %.2f | Estim. = %.2f\n', GhostingLevel(p), Result_SNR.GhostingRatio)
% %Save the position paramters to be used as start values for upcoming
% %calculations, if needed
% Parameter.GEN.CenterX = CenterX;
% Parameter.GEN.CenterY = CenterY;
% Parameter.GEN.Radius = Radius;
% Parameter.GEN.Angle = Angle;
EstGhost(p) = Result_SNR.GhostingRatio;
RealGhost(p) = GhostingLevel(p);
end
save('QA Results\QA_Ghosting.mat','EstGhost','RealGhost')
LH = QT_PlotEstimatesAgainstReal( EstGhost, RealGhost );
title('\textbf{Ghosting Artifacts}','Interpreter','latex','Fontsize',12)
set(LH,'String',{'Identity','Estimated vs. Synthetic'});
set(LH,'Interpreter','latex','Location','NorthWest')
set(LH,'OuterPosition', [0.1303 0.7038 0.5085 0.1779])
set(LH,'Position', [0.1389 0.7115 0.4957 0.1702])
xlabel('Synthetic Ghosting $[w.E.]$','Interpreter','latex')
ylabel('Estimated Ghosting $[w.E.]$','Interpreter','latex')
grid on
ylim([-0.02 0.22])