Updated for prostate data reading and calculating

WiscPlanPhotonkV125/matlab_frontend/NLP_getFullDose.m

@@ -7,7 +7,8 @@ function NLP_getFullDose(NLP_path, NLP_file)
 load([NLP_path '\' NLP_file]);
 
 path2 = NLP_path(1:end-14);
-D = read_ryan_beamlets([path2 '\beamlet_batch_files\beamletbatch0.bin'],'ryan sum', NLP_result.weights);
+D = read_ryan_beamlets([path2 '\batch_dose.bin'],'ryan sum', NLP_result.weights);
+% D = read_ryan_beamlets([path2 '\beamlet_batch_files\beamletbatch0.bin'],'ryan sum', NLP_result.weights);
 
 % orthoslice(D-NLP_result.dose, [0,90])
 

WiscPlanPhotonkV125/matlab_frontend/NLP_optimizer_v3.m

@@ -39,7 +39,7 @@ else
     [Goal_path,Goal_file,ext] = fileparts(path2goal);
 end
 
-dialogue_box = 'no'
+dialogue_box = 'yes'
 switch dialogue_box
     case 'yes'
         str = inputdlg({'N of iterations for initial calc', 'N of iterations for full calc', ...
@@ -50,7 +50,7 @@ switch dialogue_box
     case 'no'
         disp('dialogue box skipped')
         N_fcallback1 = 100000;
-        N_fcallback2 = 500000;
+        N_fcallback2 = 1e6; % 500000;
         pre_beamWeights = 'n';
 end
 

WiscPlanPhotonkV125/matlab_frontend/dicomrt/dicomrt2geometry.m

@@ -123,7 +123,7 @@ if downsample_flag == true
         ct_xmesh = linspace(ct_xmesh(1)+dx/2, ct_xmesh(end)-dx/2, numel(ct_xmesh)*downsample_factor);
         ct_ymesh = linspace(ct_ymesh(1)+dy/2, ct_ymesh(end)-dy/2, numel(ct_ymesh)*downsample_factor);
     else
-        downsample_factor = 0.25;
+        downsample_factor = 0.5;
         downsample_factor = 1/2;
         dx = ct_xmesh(2)-ct_xmesh(1);
         dy = ct_ymesh(2)-ct_ymesh(1);

WiscPlanPhotonkV125/matlab_frontend/helicalDosecalcSetup7.m

@@ -83,6 +83,11 @@ zStern = (find(targetMaskZ>0, 1, 'last')+1)*Geometry.voxel_size(3) + Geometry.st
 iso = [Geometry.start(1)+Geometry.voxel_size(1)*mean(subi) ...
     Geometry.start(2)+Geometry.voxel_size(2)*mean(subj) 0];
 
+% shift = [0 8 0] % Y X Z
+% iso = [iso(1)+Geometry.voxel_size(1)*shift(1) ...
+%     iso(2)+Geometry.voxel_size(2)*shift(2) ...
+%     iso(3)+Geometry.voxel_size(3)*shift(3)];
+
 % flags used to select which calculations will be set up
 Condor_flag = 1;