forked from e0404/matRad
-
Notifications
You must be signed in to change notification settings - Fork 0
/
matRad_calcLateralParticleCutOff.m
342 lines (270 loc) · 14.5 KB
/
matRad_calcLateralParticleCutOff.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
function [ machine ] = matRad_calcLateralParticleCutOff(machine,cutOffLevel,stf,visBool)
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% matRad function to calculate a depth dependend lateral cutoff for each
% pristine particle beam
%
% call
% [ machine ] = matRad_calcLateralParticleCutOff( machine,CutOffLevel,visBool )
%
% input
% machine: machine base data file
% cutOffLevel: cut off level - number between 0 and 1
% visBool: toggle visualization (optional)
%
% output
% machine: machine base data file including an additional field representing the lateral
% cutoff
%
%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% 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 cutOffLevel <= 0.98
warning('a lateral cut off below 0.98 may result in an inaccurate dose calculation')
end
conversionFactor = 1.6021766208e-02;
% function handle for calculating depth dose for APM
sumGauss = @(x,mu,SqSigma,w) ((1./sqrt(2*pi*ones(numel(x),1) * SqSigma') .* ...
exp(-bsxfun(@minus,x,mu').^2 ./ (2* ones(numel(x),1) * SqSigma' ))) * w);
if (cutOffLevel < 0 || cutOffLevel > 1)
warning('lateral cutoff is out of range - using default cut off of 0.99')
cutOffLevel = 0.99;
end
% define some variables needed for the cutoff calculation
vX = [0 logspace(-1,3,1200)]; % [mm]
% integration steps
r_mid = 0.5*(vX(1:end-1) + vX(2:end))'; % [mm]
dr = (vX(2:end) - vX(1:end-1))';
radialDist_sq = r_mid.^2;
% number of depth points for which a lateral cutoff is determined
numDepthVal = 35;
% helper function for energy selection
round2 = @(a,b)round(a*10^b)/10^b;
% extract SSD for each bixel
vSSD = ones(1,length([stf.ray(:).energy]));
cnt = 1;
for i = 1:length(stf.ray)
vSSD(cnt:cnt+numel([stf.ray(i).energy])-1) = stf.ray(i).SSD;
cnt = cnt + numel(stf.ray(i).energy);
end
% setup energy, focus index, sigma look up table - only consider unique rows
[energySigmaLUT,ixUnique] = unique([[stf.ray(:).energy]; [stf.ray(:).focusIx] ; vSSD]','rows');
rangeShifterLUT = [stf.ray(:).rangeShifter];
rangeShifterLUT = rangeShifterLUT(1,ixUnique);
% find the largest inital beam width considering focus index, SSD and range shifter for each individual energy
for i = 1:size(energySigmaLUT,1)
% find index of maximum used energy (round to keV for numerical reasons
energyIx = max(round2(energySigmaLUT(i,1),4)) == round2([machine.data.energy],4);
currFoci = energySigmaLUT(i,2);
sigmaIni = matRad_interp1(machine.data(energyIx).initFocus.dist(currFoci,:)',...
machine.data(energyIx).initFocus.sigma(currFoci,:)',...
energySigmaLUT(i,3));
sigmaIni_sq = sigmaIni^2;
% consider range shifter for protons if applicable
if strcmp(machine.meta.radiationMode,'protons') && rangeShifterLUT(i).eqThickness > 0 && ~strcmp(machine.meta.machine,'Generic')
%get max range shift
sigmaRashi = matRad_calcSigmaRashi(machine.data(energyIx).energy, ...
rangeShifterLUT(i), ...
energySigmaLUT(i,3));
% add to initial sigma in quadrature
sigmaIni_sq = sigmaIni_sq + sigmaRashi.^2;
end
energySigmaLUT(i,4) = sigmaIni_sq;
end
% find for each individual energy the broadest inital beam width
uniqueEnergies = unique(energySigmaLUT(:,1));
largestSigmaSq4uniqueEnergies = NaN * ones(numel(uniqueEnergies),1);
ix_Max = NaN * ones(numel(uniqueEnergies),1);
for i = 1:numel(uniqueEnergies)
[largestSigmaSq4uniqueEnergies(i), ix_Max(i)] = max(energySigmaLUT(uniqueEnergies(i) == energySigmaLUT(:,1),4));
end
% get energy indices for looping
vEnergiesIx = find(ismember([machine.data(:).energy],uniqueEnergies(:,1)));
cnt = 0;
% loop over all entries in the machine.data struct
for energyIx = vEnergiesIx
% set default depth cut off - finite value will be set during first iteration
depthDoseCutOff = inf;
% get the current integrated depth dose profile
if isstruct(machine.data(energyIx).Z)
idd_org = sumGauss(machine.data(energyIx).depths,machine.data(energyIx).Z.mean,...
machine.data(energyIx).Z.width.^2,...
machine.data(energyIx).Z.weight) * conversionFactor;
else
idd_org = machine.data(energyIx).Z * conversionFactor;
end
[~,peakIxOrg] = max(idd_org);
% get indices for which a lateral cutoff should be calculated
cumIntEnergy = cumtrapz(machine.data(energyIx).depths,idd_org);
peakTailRelation = 0.5;
numDepthValToPeak = ceil(numDepthVal*peakTailRelation); % number of depth values from 0 to peak position
numDepthValTail = ceil(numDepthVal*(1-peakTailRelation)); % number of depth values behind peak position
energyStepsToPeak = cumIntEnergy(peakIxOrg)/numDepthValToPeak;
energyStepsTail = (cumIntEnergy(end)-cumIntEnergy(peakIxOrg))/numDepthValTail;
% make sure to include 0, peak position and end position
vEnergySteps = unique([0:energyStepsToPeak:cumIntEnergy(peakIxOrg) cumIntEnergy(peakIxOrg) ...
cumIntEnergy(peakIxOrg+1):energyStepsTail:cumIntEnergy(end) cumIntEnergy(end)]);
[cumIntEnergy,ix] = unique(cumIntEnergy);
depthValues = matRad_interp1(cumIntEnergy,machine.data(energyIx).depths(ix),vEnergySteps);
if isstruct(machine.data(energyIx).Z)
idd = sumGauss(depthValues,machine.data(energyIx).Z.mean,...
machine.data(energyIx).Z.width.^2,...
machine.data(energyIx).Z.weight) * conversionFactor;
else
idd = matRad_interp1(machine.data(energyIx).depths,machine.data(energyIx).Z,depthValues) * conversionFactor;
end
cnt = cnt +1 ;
% % calculate dose in spot
baseData = machine.data(energyIx);
baseData.LatCutOff.CompFac = 1;
for j = 1:numel(depthValues)
% save depth value
machine.data(energyIx).LatCutOff.depths(j) = depthValues(j);
if cutOffLevel == 1
machine.data(energyIx).LatCutOff.CompFac = 1;
machine.data(energyIx).LatCutOff.CutOff(j) = Inf;
else
% calculate dose
dose_r = matRad_calcParticleDoseBixel(depthValues(j) + baseData.offset, radialDist_sq, largestSigmaSq4uniqueEnergies(cnt), baseData);
cumArea = cumsum(2*pi.*r_mid.*dose_r.*dr);
relativeTolerance = 0.5; %in [%]
if abs((cumArea(end)./(idd(j)))-1)*100 > relativeTolerance
warning('LateralParticleCutOff: shell integration is wrong !')
end
IX = find(cumArea >= idd(j) * cutOffLevel,1, 'first');
machine.data(energyIx).LatCutOff.CompFac = cutOffLevel^-1;
if isempty(IX)
depthDoseCutOff = Inf;
warning('LateralParticleCutOff: Couldnt find lateral cut off !')
elseif isnumeric(IX)
depthDoseCutOff = r_mid(IX);
end
machine.data(energyIx).LatCutOff.CutOff(j) = depthDoseCutOff;
end
end
end
%% visualization
if visBool
% determine which pencil beam should be plotted
subIx = ceil(numel(vEnergiesIx)/2);
energyIx = vEnergiesIx(subIx);
baseData = machine.data(energyIx);
focusIx = energySigmaLUT(ix_Max(subIx),2);
maxSSD = energySigmaLUT(ix_Max(subIx),3);
rangeShifter = rangeShifterLUT(ix_Max(subIx));
TmpCompFac = baseData.LatCutOff.CompFac;
baseData.LatCutOff.CompFac = 1;
% plot 3D cutoff at one specific depth on a rather sparse grid
sStep = 0.5;
vLatX = -100 : sStep : 100; % [mm]
dimX = numel(vLatX);
midPos = round(length(vLatX)/2);
[X,Y] = meshgrid(vLatX,vLatX);
radDepths = [0:sStep:machine.data(energyIx).depths(end)] + machine.data(energyIx).offset;
radialDist_sq = (X.^2 + Y.^2);
radialDist_sq = radialDist_sq(:);
mDose = zeros(dimX,dimX,numel(radDepths));
vDoseInt = zeros(numel(radDepths),1);
for kk = 1:numel(radDepths)
% calculate initial focus sigma
sigmaIni = matRad_interp1(machine.data(energyIx).initFocus.dist(focusIx,:)', ...
machine.data(energyIx).initFocus.sigma(focusIx,:)',maxSSD);
sigmaIni_sq = sigmaIni^2;
% consider range shifter for protons if applicable
if rangeShifter.eqThickness > 0 && strcmp(pln.radiationMode,'protons')
% compute!
sigmaRashi = matRad_calcSigmaRashi(machine.data(energyIx).energy,rangeShifter,maxSSD);
% add to initial sigma in quadrature
sigmaIni_sq = sigmaIni_sq + sigmaRashi^2;
end
mDose(:,:,kk) = reshape(matRad_calcParticleDoseBixel(radDepths(kk), radialDist_sq, sigmaIni_sq,baseData),[dimX dimX]);
[~,IX] = min(abs((machine.data(energyIx).LatCutOff.depths + machine.data(energyIx).offset) - radDepths(kk)));
TmpCutOff = machine.data(energyIx).LatCutOff.CutOff(IX);
vXCut = vX(vX<=TmpCutOff);
% integration steps
r_mid_Cut = (0.5*(vXCut(1:end-1) + vXCut(2:end)))'; % [mm]
dr_Cut = (vXCut(2:end) - vXCut(1:end-1))';
radialDist_sqCut = r_mid_Cut.^2;
dose_r_Cut = matRad_calcParticleDoseBixel(radDepths(kk), radialDist_sqCut(:), sigmaIni_sq,baseData);
cumAreaCut = cumsum(2*pi.*r_mid_Cut.*dose_r_Cut.*dr_Cut);
if ~isempty(cumAreaCut)
vDoseInt(kk) = cumAreaCut(end);
end
end
% obtain maximum dose
if isstruct(machine.data(energyIx).Z)
idd = sumGauss(depthValues,machine.data(energyIx).Z.mean,...
machine.data(energyIx).Z.width.^2,...
machine.data(energyIx).Z.weight) * conversionFactor;
else
idd = matRad_interp1(machine.data(energyIx).depths,machine.data(energyIx).Z,depthValues) * conversionFactor;
end
[~,peakixDepth] = max(idd);
dosePeakPos = matRad_calcParticleDoseBixel(machine.data(energyIx).depths(peakixDepth), 0, sigmaIni_sq, baseData);
vLevelsDose = dosePeakPos.*[0.01 0.05 0.1 0.9];
doseSlice = squeeze(mDose(midPos,:,:));
figure,set(gcf,'Color',[1 1 1]);
subplot(311),h=imagesc(squeeze(mDose(midPos,:,:)));hold on;
set(h,'AlphaData', .8*double(doseSlice>0));
contour(doseSlice,vLevelsDose,'LevelListMode','manual','LineWidth',2);hold on
ax = gca;
ax.XTickLabelMode = 'manual';
ax.XTickLabel = strsplit(num2str(ax.XTick*sStep + machine.data(energyIx).offset),' ')';
ax.YTickLabelMode = 'manual';
ax.YTickLabel = strsplit(num2str(ax.YTick*sStep + machine.data(energyIx).offset),' ')';
plot(1+(machine.data(energyIx).LatCutOff.depths)*sStep^-1,...
machine.data(energyIx).LatCutOff.CutOff * sStep^-1 + midPos,'rx');
legend({'isodose 1%,5%,10% 90%','calculated cutoff'}) ,colorbar,set(gca,'FontSize',12),xlabel('z [mm]'),ylabel('x [mm]');
entry = machine.data(energyIx);
if isstruct(entry.Z)
idd = sumGauss(entry.depths,entry.Z.mean,entry.Z.width.^2,entry.Z.weight);
else
idd = machine.data(energyIx).Z;
end
subplot(312),plot(machine.data(energyIx).depths,idd*conversionFactor,'k','LineWidth',2),grid on,hold on
plot(radDepths - machine.data(energyIx).offset,vDoseInt,'r--','LineWidth',2),hold on,
plot(radDepths - machine.data(energyIx).offset,vDoseInt * TmpCompFac,'bx','LineWidth',1),hold on,
legend({'original IDD',['cut off IDD at ' num2str(cutOffLevel) '%'],'cut off IDD with compensation'},'Location','northwest'),
xlabel('z [mm]'),ylabel('[MeV cm^2 /(g * primary)]'),set(gca,'FontSize',12)
totEnergy = trapz(machine.data(energyIx).depths,idd*conversionFactor) ;
totEnergyCutOff = trapz(radDepths,vDoseInt * TmpCompFac) ;
relDiff = ((totEnergy/totEnergyCutOff)-1)*100;
title(['rel diff of integral dose ' num2str(relDiff) '%']);
baseData.LatCutOff.CompFac = TmpCompFac;
subplot(313),
if isfield(machine.data(energyIx),'sigma1')
yyaxis left;
plot(machine.data(energyIx).LatCutOff.depths,machine.data(energyIx).LatCutOff.CutOff,'LineWidth',2),hold on
plot(machine.data(energyIx).depths,(machine.data(energyIx).sigma1),':','LineWidth',2),grid on,hold on,ylabel('mm')
yyaxis right;
plot(machine.data(energyIx).depths,(machine.data(energyIx).sigma2),'-.','LineWidth',2),grid on,hold on,ylabel('mm')
legend({'Cutoff','sigma1','sigma2'});
else
yyaxis left;plot(machine.data(energyIx).LatCutOff.depths,machine.data(energyIx).LatCutOff.CutOff,'LineWidth',2),hold on,ylabel('mm')
yyaxis right;subplot(313),plot(machine.data(energyIx).depths,machine.data(energyIx).sigma,'LineWidth',2),grid on,hold on
legend({'Cutoff','sigma'});ylabel('mm')
end
set(gca,'FontSize',12),xlabel('z [mm]'), ylabel('mm')
% plot cutoff of different energies
figure,set(gcf,'Color',[1 1 1]);
cnt = 1;
for i = vEnergiesIx
plot(machine.data(i).LatCutOff.depths,machine.data(i).LatCutOff.CutOff,'LineWidth',1.5),hold on
cellLegend{cnt} = [num2str(machine.data(i).energy) ' MeV'];
cnt = cnt + 1;
end
grid on, grid minor,xlabel('depth in [mm]'),ylabel('lateral cutoff in [mm]')
title(['cutoff level = ' num2str(cutOffLevel)]),
ylim = get(gca,'Ylim'); set(gca,'Ylim',[0 ylim(2)+3]), legend(cellLegend)
end
end