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matRad_engelLeafSequencing.m
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matRad_engelLeafSequencing.m
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function resultGUI = matRad_engelLeafSequencing(resultGUI,stf,dij,numOfLevels,visBool)
% multileaf collimator leaf sequencing algorithm
% for intensity modulated beams with multiple static segments accroding
% to Engel et al. 2005 Discrete Applied Mathematics
%
% call
% resultGUI = matRad_engelLeafSequencing(resultGUI,stf,dij,numOfLevels,visBool)
%
% input
% resultGUI: resultGUI struct to which the output data will be added, if
% this field is empty resultGUI struct will be created
% stf: matRad steering information struct
% dij: matRad's dij matrix
% numOfLevels: number of stratification levels
% visBool: toggle on/off visualization (optional)
%
% output
% resultGUI: matRad result struct containing the new dose cube
% as well as the corresponding weights
%
% References
% [1] http://www.sciencedirect.com/science/article/pii/S0166218X05001411
%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2015 the matRad development team.
%
% This file is part of the matRad project. It is subject to the license
% terms in the LICENSE file found in the top-level directory of this
% distribution and at https://github.com/e0404/matRad/LICENSES.txt. No part
% of the matRad project, including this file, may be copied, modified,
% propagated, or distributed except according to the terms contained in the
% LICENSE file.
%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% if visBool not set toogle off visualization
if nargin < 5
visBool = 0;
end
numOfBeams = numel(stf);
if visBool
% create the sequencing figure
sz = [800 1000]; % figure size
screensize = get(0,'ScreenSize');
xpos = ceil((screensize(3)-sz(2))/2); % center the figure on the screen horizontally
ypos = ceil((screensize(4)-sz(1))/2); % center the figure on the screen vertically
seqFig = figure('position',[xpos,ypos,sz(2),sz(1)]);
end
offset = 0;
for i = 1:numOfBeams
numOfRaysPerBeam = stf(i).numOfRays;
% get relevant weights for current beam
wOfCurrBeams = resultGUI.w(1+offset:numOfRaysPerBeam+offset);
X = ones(numOfRaysPerBeam,1)*NaN;
Z = ones(numOfRaysPerBeam,1)*NaN;
for j=1:stf(i).numOfRays
X(j) = stf(i).ray(j).rayPos_bev(:,1);
Z(j) = stf(i).ray(j).rayPos_bev(:,3);
end
% sort bixels into matrix
minX = min(X);
maxX = max(X);
minZ = min(Z);
maxZ = max(Z);
dimOfFluenceMxX = (maxX-minX)/stf(i).bixelWidth + 1;
dimOfFluenceMxZ = (maxZ-minZ)/stf(i).bixelWidth + 1;
%Create the fluence matrix.
fluenceMx = zeros(dimOfFluenceMxZ,dimOfFluenceMxX);
% Calculate X and Z position of every fluence's matrix spot
% z axis = axis of leaf movement!
xPos = (X-minX)/stf(i).bixelWidth+1;
zPos = (Z-minZ)/stf(i).bixelWidth+1;
% Make subscripts for fluence matrix
indInFluenceMx = zPos + (xPos-1)*dimOfFluenceMxZ;
%Save weights in fluence matrix.
fluenceMx(indInFluenceMx) = wOfCurrBeams;
% Stratification
calFac = max(fluenceMx(:));
D_k = round(fluenceMx/calFac*numOfLevels);
% Save the stratification in the initial intensity matrix D_0.
D_0 = D_k;
% container to remember generated shapes; allocate space for 10000 shapes
shapes = NaN*ones(dimOfFluenceMxZ,dimOfFluenceMxX,10000);
k = 0;
if visBool
clf(seqFig);
colormap(seqFig,'jet');
seqSubPlots(1) = subplot(2,2,1,'parent',seqFig);
imagesc(D_k,'parent',seqSubPlots(1));
set(seqSubPlots(1),'CLim',[0 numOfLevels],'YDir','normal');
title(seqSubPlots(1),['Beam # ' num2str(i) ': max(D_0) = ' num2str(max(D_0(:))) ' - ' num2str(numel(unique(D_0))) ' intensity levels']);
xlabel(seqSubPlots(1),'x - direction parallel to leaf motion ')
ylabel(seqSubPlots(1),'z - direction perpendicular to leaf motion ')
colorbar;
drawnow
end
% start sequencer
while max(D_k(:) > 0)
%calculate the difference matrix diffMat
diffMat = diff([zeros(size(D_k,1),1) D_k zeros(size(D_k,1),1)],[],2);
%calculate complexities
c = sum(max(0,diffMat),2); %TNMU-row-complexity
com = max(c); %TNMU complexity
g = com - c; %row complexity gap
%initialize segment
segment = zeros(size(D_k));
k = k + 1;
%Plot residual intensity matrix.
if visBool
seqSubPlots(2) = subplot(2,2,2,'parent',seqFig);
imagesc(D_k,'parent',seqSubPlots(2));
set(seqSubPlots(2),'CLim',[0 numOfLevels],'YDir','normal');
title(seqSubPlots(2),['k = ' num2str(k)]);
colorbar
drawnow
end
%loop over all rows
for j=1:size(D_0,1)
%determine essential intervals
data(j).left(1) = 0; %left interval limit, actual for an empty interval
data(j).right(1) = 0; %right interal limit, actual for an empty interval
data(j).v(1) = g(j); %greatest number such that the inequalities (6) resp. (7) is satisfied with u=v
data(j).w(1) = inf; %smallest number in the interval
data(j).u(1) = data(j).v(1); %min(v,w)
[~, pos, ~] = find(diffMat(j,:) > 0); % indices of all positive elements in the j. row of diffmat
[~, neg, ~] = find(diffMat(j,:) < 0); % indices of all negative elements in the j. row of diffMat
n=2;
%loop over the positive elements in the j. row of diffmat ->
%possible left interval limits
for m=1:size(pos,2)
%loop over the negative elements in the j. row of diffMat ->
%possible right interval limit
for l=1:size(neg,2)
%take only intervals I=[l,r] with l<=r
if pos(m) <= neg(l)-1
%set interval limits
data(j).left(n) = pos(m);
data(j).right(n) = neg(l)-1;
%calculate v according to Lemma 8
if g(j) <= abs( diffMat(j,pos(m)) + diffMat(j,neg(l)) )
data(j).v(n) = min( diffMat(j,pos(m)), -diffMat(j,neg(l)) ) + g(j);
else
data(j).v(n) = ( diffMat(j, pos(m)) - diffMat(j, neg(l)) + g(j)) / 2;
end
%calculate w and u according to equality (11) and
%(12)
data(j).w(n) = min(D_k(j,pos(m):(neg(l)-1)));
data(j).u(n) = min(data(j).v(n), data(j).w(n));
n = n+1;
end
end
end
u(j) = max(data(j).u);
end
%calculate u_max from theorem 9
d_k = min(u);
%loop over all rows
for j=1:size(D_0,1)
%find all possible (and essential) intervals
candidate = find(data(j).u >= d_k);
%calculate the potential of the possible intervals
%initialize p as -Inf
data(j).p(1:length(data(j).left)) = -Inf;
%loop over all possible intervals
for s=1:size(candidate,2)
if (s==1 && data(j).left(candidate(s)) == 0)
data(j).p(candidate(1)) = 0;
else
%calculate p1 according to equality (17)
if (d_k == diffMat(j, data(j).left(candidate(s))) && d_k ~= D_k(j, data(j).left(candidate(s))))
p1 = 1;
else
p1 = 0;
end
%calculate p2 according to equalitiy (18)
% if data(j).right(candidate(s)) < size(D_0, 2)
if (d_k == -diffMat(j, data(j).right(candidate(s))+1) && d_k ~= D_k(j, data(j).right(candidate(s))))
p2 = 1;
else
p2 = 0;
end
% else
%
% if d_k == -diffMat(j, data(j).right(candidate(s))+1)
% p2 = 1;
% else
% p2 = 0;
% end
%
% end
%calculate p3 according to equality (19)
p3 = size(find(D_k(j, data(j).left(candidate(s)):data(j).right(candidate(s))) == d_k),2);
data(j).p(candidate(s)) = p1 + p2+ p3;
end
end
%determinate intervals with maximum potential
maxPot = find(data(j).p == max(data(j).p));
%if several intervals have maximum potential, select
%the interval which has maximum length
if size(maxPot,2) > 1
for t=1:size(maxPot,2)
if t==1 && data(j).left(maxPot(t)) == 0
data(j).l(1) = 0;
else
data(j).l(maxPot(t)) = data(j).right(maxPot(t)) - data(j).left(maxPot(t)) + 1;
end
end
%data(j).l(maxPot) = data(j).right(maxPot) - data(j).left(maxPot) + 1;
maxLength = find(data(j).l == max(data(j).l));
%left and right interval limits of the selected
%interval
leftIntLimit(j) = data(j).left(maxLength(1));
rightIntLimit(j) = data(j).right(maxLength(1));
else
%left and right interval limits of the selected
%interval
leftIntLimit(j) = data(j).left(maxPot);
rightIntLimit(j) = data(j).right(maxPot);
end
%create segment associated by the selected interval
if leftIntLimit(j) ~= 0
segment(j,leftIntLimit(j):rightIntLimit(j)) = 1;
end
end
%write the segment in shape_k
shape_k = segment;
%show the leaf positions
if visBool
seqSubPlots(4) = subplot(2,2,3.5,'parent',seqFig);
imagesc(shape_k,'parent',seqSubPlots(4));
hold(seqSubPlots(4),'on');
set(seqSubPlots(4),'YDir','normal')
xlabel(seqSubPlots(4),'x - direction parallel to leaf motion ')
ylabel(seqSubPlots(4),'z - direction perpendicular to leaf motion ')
title(seqSubPlots(4),['beam # ' num2str(i) ' shape # ' num2str(k) ' d_k = ' num2str(d_k)]);
for j = 1:dimOfFluenceMxZ
leftLeafIx = find(shape_k(j,:)>0,1,'first');
rightLeafIx = find(shape_k(j,:)>0,1,'last');
if leftLeafIx > 1
plot(seqSubPlots(4),[.5 leftLeafIx-.5],j-[.5 .5] ,'w','LineWidth',2)
plot(seqSubPlots(4),[.5 leftLeafIx-.5],j+[.5 .5] ,'w','LineWidth',2)
plot(seqSubPlots(4),[ leftLeafIx-.5 leftLeafIx-.5],j+[.5 -.5] ,'w','LineWidth',2)
end
if rightLeafIx<dimOfFluenceMxX
plot(seqSubPlots(4),[dimOfFluenceMxX+.5 rightLeafIx+.5],j-[.5 .5] ,'w','LineWidth',2)
plot(seqSubPlots(4),[dimOfFluenceMxX+.5 rightLeafIx+.5],j+[.5 .5] ,'w','LineWidth',2)
plot(seqSubPlots(4),[ rightLeafIx+.5 rightLeafIx+.5],j+[.5 -.5] ,'w','LineWidth',2)
end
if isempty(rightLeafIx) && isempty (leftLeafIx)
plot(seqSubPlots(4),[dimOfFluenceMxX+.5 .5],j-[.5 .5] ,'w','LineWidth',2)
plot(seqSubPlots(4),[dimOfFluenceMxX+.5 .5],j+[.5 .5] ,'w','LineWidth',2)
plot(seqSubPlots(4),.5*dimOfFluenceMxX*[1 1]+[0.5],j+[.5 -.5] ,'w','LineWidth',2)
end
end
axis tight
drawnow
pause(1);
end
%save shape_k in container
shapes(:,:,k) = shape_k;
%save the calculated MU
shapesWeight(k) = d_k;
%calculate new matrix, the diference matrix and complexities
D_k = D_k - d_k*shape_k;
%delete variables
clear data;
clear segment;
clear u;
clear leftIntLimit;
clear rightIntLimit;
end
sequencing.beam(i).numOfShapes = k;
sequencing.beam(i).shapes = shapes(:,:,1:k);
sequencing.beam(i).shapesWeight = shapesWeight(1:k)/numOfLevels*calFac;
sequencing.beam(i).bixelIx = 1+offset:numOfRaysPerBeam+offset;
sequencing.beam(i).fluence = D_0;
sequencing.w(1+offset:numOfRaysPerBeam+offset,1) = D_0(indInFluenceMx)/numOfLevels*calFac;
offset = offset + numOfRaysPerBeam;
end
resultGUI.w = sequencing.w;
resultGUI.wSequenced = sequencing.w;
resultGUI.sequencing = sequencing;
resultGUI.apertureInfo = matRad_sequencing2ApertureInfo(sequencing,stf);
doseSequencedDoseGrid = reshape(dij.physicalDose{1} * sequencing.w,dij.doseGrid.dimensions);
% interpolate to ct grid for visualiation & analysis
resultGUI.physicalDose = matRad_interp3(dij.doseGrid.x,dij.doseGrid.y',dij.doseGrid.z, ...
doseSequencedDoseGrid, ...
dij.ctGrid.x,dij.ctGrid.y',dij.ctGrid.z);
% if weights exists from an former DAO remove it
if isfield(resultGUI,'wDao')
resultGUI = rmfield(resultGUI,'wDao');
end
end