Beam calcs for scenarios now work!

Next up: optimization

WiscPlanPhotonkV125/matlab_frontend/fullRO_beamCalc.m

@@ -25,9 +25,11 @@ end
 OptGoals.fullRO_beamlet_dir = beamlet_dir;
 
 %% start the modified beamlet calc
+% num_batches = helicalDosecalcSetup7_fullRO(Geometry.patient_dir, OptGoals, beamlet_dir)
+% num_batches = helicalDosecalcSetup7(Geometry.patient_dir)
+% num_batches = helicalDosecalcSetup8(Geometry.patient_dir)
 helicalDosecalcSetup7_fullRO(Geometry.patient_dir, OptGoals, beamlet_dir)
 
-
 % save the appended optGoal file
 save(path2goal, 'OptGoals');
 

WiscPlanPhotonkV125/matlab_frontend/fullRO_mergeBeams.m

@@ -0,0 +1,37 @@
+
+function fullRO_mergeBeams(Geometry)
+% this function loops through a full RO folder and merges all the beamlets
+
+    if isfield(Geometry, 'num_batches')
+        str = num2str(obj.handles.hSVPS.Geometry.num_batches);
+    else
+        str = input('Enter num of beam batches: ','s');
+    end
+    
+    % get the full RO folder
+    beamlet_dir = uigetdir([Geometry.patient_dir ], 'Select full RO folder' );
+    if beamlet_dir == 0
+       disp('no file selected, aborting')
+       return
+    end
+    
+    % loop through all scenario folders
+    files = dir(beamlet_dir);
+    % Get a logical vector that tells which is a directory.
+    dirFlags = [files.isdir];
+    % Extract only those that are directories.
+    scenarioList = files(dirFlags);
+
+    
+    idxList = [1:numel(scenarioList)];
+    for i = 3:numel(idxList);
+        scenario_i = idxList(i);
+        scenario_path = [scenarioList(scenario_i).folder, '\', scenarioList(scenario_i).name];
+        merge_beamlets(str2double(str), scenario_path);
+        
+        disp(['Scenario ' num2str(i)  ' merged!'])
+    end
+    
+    disp('All scenario beamlets merged!')
+
+end

WiscPlanPhotonkV125/matlab_frontend/helicalDosecalcSetup7_fullRO.m

@@ -55,7 +55,7 @@ ypmax = 1.25;
 % executable_path = 'C:\010-work\003_localGit\WiscPlan_v2\WiscPlanPhotonkV125\WiscPlanEXE\RyanCsphoton.x86.exe';
 
 executable_path = mfilename('fullpath');
-executable_path = [executable_path(1:end-37), 'WiscPlanEXE\RyanCsphoton.x86.exe']
+executable_path = [fileparts(fileparts(executable_path)), '\WiscPlanEXE\RyanCsphoton.x86.exe']
 
 kernel_file = 'Kernels.mat';
 geometry_file = fullfile(patient_dir, 'matlab_files\Geometry.mat');
@@ -101,142 +101,141 @@ Nphi = Nrot * N_angles;  % Grozomah
 
 phi = [0:Nphi-1]/Nphi *2*pi*Nrot;
 
-condor_folder = patient_dir;
-winxp_folder = 'winxp';
-
-% create names for condor input and output folders
-input_folder = '.';
-output_folder = '.';
-
-% name of the convolution/superposition executable, which will be in the
-% 'code' folder of each respective run type folder
-condor_exectuable_name = 'convolutionCondor';  % relative path on the cluster where code will be
-winxp_executable_name = 'convolution.exe';
-matlab_executable_name = 'convolution_mex';  % name of the Matlab version of the dose calculation code
-
-% set the beam parameters, assuming a helical beam trajectory
-% folders that will be inside the 'input' folder
-beamspec_folder = 'beamspecfiles';    % directory where beam files will be stored
-beamspec_batches_folder = 'beamspecbatches';
-beamspec_batch_base_name = 'beamspecbatch';  % base name for a beamlet batch file
-kernel_folder = 'kernelfiles';  % folder where kernel information will be saved
-kernel_filenames_condor = 'kernelFilenamesCondor.txt';
-kernel_filenames_winxp = 'kernelFilenamesWinXP.txt';
-
-% output folders
-beamlet_batch_base_name = 'beamletbatch';  % base name for a dose batch file
-
-geometry_header_filename = 'geometryHeader.txt';
-geometry_density_filename = 'density.bin';  % save the density, not the Hounsfield units!
-
-% end of user-defined parameters
+%% account for beamlet shift
+for scenario_i = 1:numel(OptGoals.sss_scene_list)
+    patient_dir = [beamlet_dir '\scenario' num2str(scenario_i)];
+    mkdir(patient_dir)
+    condor_folder = patient_dir;
+    winxp_folder = 'winxp';
+
+    % create names for condor input and output folders
+    input_folder = '.';
+    output_folder = '.';
+
+    % name of the convolution/superposition executable, which will be in the
+    % 'code' folder of each respective run type folder
+    condor_exectuable_name = 'convolutionCondor';  % relative path on the cluster where code will be
+    winxp_executable_name = 'convolution.exe';
+    matlab_executable_name = 'convolution_mex';  % name of the Matlab version of the dose calculation code
+
+    % set the beam parameters, assuming a helical beam trajectory
+    % folders that will be inside the 'input' folder
+    beamspec_folder = 'beamspecfiles';    % directory where beam files will be stored
+    beamspec_batches_folder = 'beamspecbatches';
+    beamspec_batch_base_name = 'beamspecbatch';  % base name for a beamlet batch file
+    kernel_folder = 'kernelfiles';  % folder where kernel information will be saved
+    kernel_filenames_condor = 'kernelFilenamesCondor.txt';
+    kernel_filenames_winxp = 'kernelFilenamesWinXP.txt';
+
+    % output folders
+    beamlet_batch_base_name = 'beamletbatch';  % base name for a dose batch file
+
+    geometry_header_filename = 'geometryHeader.txt';
+    geometry_density_filename = 'density.bin';  % save the density, not the Hounsfield units!
+
+    % end of user-defined parameters
+
+    % check the validity of the user-defined variables
+    if xpmin >= xpmax
+        error('xpmin must be less than xpmax.');
+    end
+    if ypmin >= ypmax
+        error('ypmin must be less than ypmax.');b
+    end
 
-% check the validity of the user-defined variables
-if xpmin >= xpmax
-    error('xpmin must be less than xpmax.');
-end
-if ypmin >= ypmax
-    error('ypmin must be less than ypmax.');b
-end
+    % if phimin > phimax
+    %     error('phimin must be less than or equal to phimax.');
+    % end
 
-% if phimin > phimax
-%     error('phimin must be less than or equal to phimax.');
-% end
+    if Mxp <= 0 || Nyp <= 0 || Nphi <= 0
+        error('Mxp, Nyp, and Nphi must be greater than zero.');
+    end
 
-if Mxp <= 0 || Nyp <= 0 || Nphi <= 0
-    error('Mxp, Nyp, and Nphi must be greater than zero.');
-end
+    if SAD < 50
+        error('It is recommended that the SAD be greater than 50 cm.');
+    end
 
-if SAD < 50
-    error('It is recommended that the SAD be greater than 50 cm.');
-end
+    % the xy plane is perpendicular to the isocenter axis of the linac gantry
 
-% the xy plane is perpendicular to the isocenter axis of the linac gantry
+    % size of each beam aperture, making them vectors so extension to
+    % non-uniform aperture sizes becomes obvious
+    del_xp = (xpmax - xpmin)/Mxp;
+    del_yp = (ypmax - ypmin)/Nyp;
 
-% size of each beam aperture, making them vectors so extension to
-% non-uniform aperture sizes becomes obvious
-del_xp = (xpmax - xpmin)/Mxp;
-del_yp = (ypmax - ypmin)/Nyp;
+    % Calculate the xp and yp offsets, which lie at the centers of the
+    % apertures.
+    xp = [xpmin:del_xp:xpmax-del_xp] + del_xp/2;
+    yp = [ypmin:del_yp:ypmax-del_yp] + del_yp/2;
 
-% Calculate the xp and yp offsets, which lie at the centers of the
-% apertures.
-xp = [xpmin:del_xp:xpmax-del_xp] + del_xp/2;
-yp = [ypmin:del_yp:ypmax-del_yp] + del_yp/2;
+    [M,N,Q] = size(Geometry.rhomw);
 
-[M,N,Q] = size(Geometry.rhomw);
+    START = single(Geometry.start - iso);
+    INC = single(Geometry.voxel_size);
 
-START = single(Geometry.start - iso);
-INC = single(Geometry.voxel_size);
+    % Grozomah ## 
+    % START(1) = START(1)/10;
+    % START(2) = START(2)/10;
+    % INC(1) = INC(1)/10;
+    % INC(2) = INC(2)/10;
 
-% Grozomah ## 
-% START(1) = START(1)/10;
-% START(2) = START(2)/10;
-% INC(1) = INC(1)/10;
-% INC(2) = INC(2)/10;
+    % END= START+[32,32,40].*INC
 
-% END= START+[32,32,40].*INC
+    % define the tumor mask
+    tumorMask = zeros(size(Geometry.rhomw),'single');
+    tumorMask(Geometry.ROIS{ptvInd}.ind) = 1;
 
-% define the tumor mask
-tumorMask = zeros(size(Geometry.rhomw),'single');
-tumorMask(Geometry.ROIS{ptvInd}.ind) = 1;
+    BW = bwdist(tumorMask);
+    tumorMaskExp = tumorMask;
+    tumorMaskExp(BW <= 4) = 1;
 
-BW = bwdist(tumorMask);
-tumorMaskExp = tumorMask;
-tumorMaskExp(BW <= 4) = 1;
+    P = zeros(Mxp,Nphi);
 
-P = zeros(Mxp,Nphi);
+    fprintf('Checking beam''s eye view ...\n');
+    for p=1:Nphi
+        % ir and jr form the beam's eye view (BEV)
+        ir = [-sin(phi(p)); cos(phi(p)); 0];
+        jr = [0 0 1]';
+        % kr denotes the beam direction
+        kr = [cos(phi(p)); sin(phi(p)); 0];
 
-fprintf('Checking beam''s eye view ...\n');
-for p=1:Nphi
-    % ir and jr form the beam's eye view (BEV)
-    ir = [-sin(phi(p)); cos(phi(p)); 0];
-    jr = [0 0 1]';
-    % kr denotes the beam direction
-    kr = [cos(phi(p)); sin(phi(p)); 0];
-    
-    for m=1:Mxp
-        point1 = single(-kr*SAD + [0 0 zBow + pitch*fieldWidth*phi(p)/(2*pi)]');  % source point
-        point2 = single(point1 + (SAD*kr + ir*xp(m))*10);
-        [indVisited,deffVisited] = singleRaytraceClean(tumorMaskExp,START,INC,point1,point2);
-        if ~isempty(indVisited)
-            P(m,p) = max(deffVisited);
+        for m=1:Mxp
+            point1 = single(-kr*SAD + [0 0 zBow + pitch*fieldWidth*phi(p)/(2*pi)]');  % source point
+            point2 = single(point1 + (SAD*kr + ir*xp(m))*10);
+            [indVisited,deffVisited] = singleRaytraceClean(tumorMaskExp,START,INC,point1,point2);
+            if ~isempty(indVisited)
+                P(m,p) = max(deffVisited);
+            end
         end
     end
-end
-fprintf('Finished checking BEV\n');
+    fprintf('Finished checking BEV\n');
 
-% load data required for the dose calculator
-load(kernel_file);
+    % load data required for the dose calculator
+    load(kernel_file);
 
-Geometry.rhomw(Geometry.rhomw < 0) = 0;
-Geometry.rhomw(Geometry.rhomw < 0.0013) = 0.0013;  % fill blank voxels with air
+    Geometry.rhomw(Geometry.rhomw < 0) = 0;
+    Geometry.rhomw(Geometry.rhomw < 0.0013) = 0.0013;  % fill blank voxels with air
 
-% convert Geometry and kernels to single
-f = fieldnames(Kernels);
-for k=1:length(f)
-    if isnumeric(getfield(Kernels,f{k}))
-        Kernels = setfield(Kernels,f{k},single(getfield(Kernels,f{k})));    
+    % convert Geometry and kernels to single
+    f = fieldnames(Kernels);
+    for k=1:length(f)
+        if isnumeric(getfield(Kernels,f{k}))
+            Kernels = setfield(Kernels,f{k},single(getfield(Kernels,f{k})));    
+        end
     end
-end
 
-f = fieldnames(Geometry);
-for k=1:length(f)
-    if isnumeric(getfield(Geometry,f{k}))
-        Geometry = setfield(Geometry,f{k},single(getfield(Geometry,f{k})));    
+    f = fieldnames(Geometry);
+    for k=1:length(f)
+        if isnumeric(getfield(Geometry,f{k}))
+            Geometry = setfield(Geometry,f{k},single(getfield(Geometry,f{k})));    
+        end
     end
-end
-
-% account for isocenter
-Geometry.start_nominal = single(Geometry.start - iso);
 
-%% account for beamlet shift
-for scenario_i = 1  % :numel(OptGoals.sss_scene_list)
-    disp(OptGoals.sss_scene_list{scenario_i});
+    % account for isocenter
+    Geometry.start_nominal = single(Geometry.start - iso);
 
     % change Condor folder names as appropriate
-    condor_folder_scenario = [beamlet_dir '\scenario' num2str(scenario_i)];
-    mkdir(condor_folder_scenario)
-    patient_dir_scenario = condor_folder_scenario
+    
+    
     
     % do the isocenter shift
     shift = OptGoals.sss_scene_list{scenario_i}; % Y X Z
@@ -307,97 +306,97 @@ for scenario_i = 1  % :numel(OptGoals.sss_scene_list)
     % useable form.
     if Condor_flag == 1
         % delete the old submission file
-        err = rmdir(fullfile(condor_folder_scenario,beamspec_batches_folder),'s');
-        err = rmdir(fullfile(condor_folder_scenario,kernel_folder),'s');
+        err = rmdir(fullfile(condor_folder,beamspec_batches_folder),'s');
+        err = rmdir(fullfile(condor_folder,kernel_folder),'s');
 
         % create folders where batch information will be sent
-        mkdir([condor_folder_scenario '/' input_folder '/' beamspec_batches_folder]);
+        mkdir([condor_folder '/' input_folder '/' beamspec_batches_folder]);
 
         % save the kernels
-        save_kernels(Kernels,[condor_folder_scenario '/' input_folder '/' kernel_folder]);
+        save_kernels(Kernels,[condor_folder '/' input_folder '/' kernel_folder]);
         fprintf(['Successfully saved Condor kernels to ' input_folder '/' kernel_folder '\n']);
 
         % create kernel filenames files
         kernel_filenames_CHTC = 'kernelFilenamesCHTC.txt';
         kernel_filenames_condor = 'kernelFilenamesCondor.txt';
-        fid = fopen([condor_folder_scenario '/' input_folder '/' kernel_filenames_condor],'w');
-        fid2 = fopen([condor_folder_scenario '/' input_folder '/' kernel_filenames_CHTC],'w');
+        fid = fopen([condor_folder '/' input_folder '/' kernel_filenames_condor],'w');
+        fid2 = fopen([condor_folder '/' input_folder '/' kernel_filenames_CHTC],'w');
 
         fprintf(fid,'kernel_header\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/kernel_header.txt\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'kernel_header.txt'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'kernel_header.txt'));
         fprintf(fid2,'kernel_header\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'kernel_header.txt');
 
         fprintf(fid,'kernel_radii\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/radii.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'radii.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'radii.bin'));
         fprintf(fid2,'kernel_radii\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'radii.bin');
 
         fprintf(fid,'kernel_angles\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/angles.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'angles.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'angles.bin'));
         fprintf(fid2,'kernel_angles\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'angles.bin');
 
         fprintf(fid,'kernel_energies\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/energies.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'energies.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'energies.bin'));
         fprintf(fid2,'kernel_energies\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'energies.bin');
 
         fprintf(fid,'kernel_primary\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/primary.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'primary.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'primary.bin'));
         fprintf(fid2,'kernel_primary\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'primary.bin');  
 
         fprintf(fid,'kernel_first_scatter\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/first_scatter.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'first_scatter.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'first_scatter.bin'));
         fprintf(fid2,'kernel_first_scatter\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'first_scatter.bin');
 
         fprintf(fid,'kernel_second_scatter\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/second_scatter.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'second_scatter.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'second_scatter.bin'));
         fprintf(fid2,'kernel_second_scatter\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'second_scatter.bin');
 
         fprintf(fid,'kernel_multiple_scatter\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/multiple_scatter.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'multiple_scatter.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'multiple_scatter.bin'));
         fprintf(fid2,'kernel_multiple_scatter\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'multiple_scatter.bin');
 
         fprintf(fid,'kernel_brem_annih\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/brem_annih.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'brem_annih.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'brem_annih.bin'));
         fprintf(fid2,'kernel_brem_annih\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'brem_annih.bin');
 
         fprintf(fid,'kernel_total\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/total.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'total.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'total.bin'));
         fprintf(fid2,'kernel_total\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'total.bin');
 
         fprintf(fid,'kernel_fluence\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/fluence.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'fluence.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'fluence.bin'));
         fprintf(fid2,'kernel_fluence\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'fluence.bin');
 
         fprintf(fid,'kernel_mu\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/mu.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'mu.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'mu.bin'));
         fprintf(fid2,'kernel_mu\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'mu.bin');
 
         fprintf(fid,'kernel_mu_en\n');
         % fprintf(fid,['./' input_folder '/' kernel_folder '/mu_en.bin\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'mu_en.bin'));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,kernel_folder,'mu_en.bin'));
         fprintf(fid2,'kernel_mu_en\n');
         fprintf(fid2, '%s/%s\n', kernel_folder,'mu_en.bin');
 
@@ -420,25 +419,25 @@ for scenario_i = 1  % :numel(OptGoals.sss_scene_list)
     beamlet_batches_folder = 'beamletbatches';  % folder where resulting beamlet batches will be stored
 
     if Condor_flag == 1
-        mkdir([condor_folder_scenario '/' output_folder '/' beamlet_batches_folder]);
-        mkdir([condor_folder_scenario '/' output_folder '/' batch_output_folder]);
+        mkdir([condor_folder '/' output_folder '/' beamlet_batches_folder]);
+        mkdir([condor_folder '/' output_folder '/' batch_output_folder]);
 
-        save_geometry(Geometry,[condor_folder_scenario '/' input_folder '/' geometry_folder],geometry_header_filename,geometry_density_filename);
+        save_geometry(Geometry,[condor_folder '/' input_folder '/' geometry_folder],geometry_header_filename,geometry_density_filename);
         fprintf(['Successfully saved Condor geometry to ' input_folder '/' geometry_folder '\n']);
 
         % create geometry filenames files
-        fid = fopen([condor_folder_scenario '/' input_folder '/' geometry_filenames_condor],'w');
-        fid2 = fopen([condor_folder_scenario '/' input_folder '/' geometry_filenames_CHTC],'w');
+        fid = fopen([condor_folder '/' input_folder '/' geometry_filenames_condor],'w');
+        fid2 = fopen([condor_folder '/' input_folder '/' geometry_filenames_CHTC],'w');
 
         fprintf(fid,'geometry_header\n');
         % fprintf(fid,['./' input_folder '/' geometry_folder '/' geometry_header_filename '\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,geometry_folder,geometry_header_filename));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,geometry_folder,geometry_header_filename));
         fprintf(fid2,'geometry_header\n');
         fprintf(fid2, '%s/%s\n', geometry_folder,'geometryHeader.txt');
 
         fprintf(fid,'geometry_density\n');
         % fprintf(fid,['./' input_folder '/' geometry_folder '/' geometry_density_filename '\n']);
-        fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,geometry_folder,geometry_density_filename));
+        fprintf(fid,'%s\n',fullfile(patient_dir,input_folder,geometry_folder,geometry_density_filename));
         fprintf(fid2,'geometry_density\n');
         fprintf(fid2, '%s/%s\n', geometry_folder,'density.bin');
         fclose(fid);
@@ -446,12 +445,12 @@ for scenario_i = 1  % :numel(OptGoals.sss_scene_list)
         % write command file
         % TODO consistent naming throughout script
         for k = 1:numel(batches)
-            fid = fopen(fullfile(condor_folder_scenario,sprintf('run%d.cmd',k-1)), 'w');
+            fid = fopen(fullfile(condor_folder,sprintf('run%d.cmd',k-1)), 'w');
             fprintf(fid, '"%s" "%s" "%s" "%s" "%s"', executable_path,...
-                fullfile(patient_dir_scenario, kernel_filenames_condor),...
-                fullfile(patient_dir_scenario, geometry_filenames_condor),...
-                fullfile(patient_dir_scenario, 'beamspecbatches', sprintf('beamspecbatch%d.txt',k-1)),...
-                fullfile(patient_dir_scenario, sprintf('batch_dose%d_S%d.bin',k-1, scenario_i)));
+                fullfile(patient_dir, kernel_filenames_condor),...
+                fullfile(patient_dir, geometry_filenames_condor),...
+                fullfile(patient_dir, 'beamspecbatches', sprintf('beamspecbatch%d.txt',k-1)),...
+                fullfile(patient_dir, sprintf('batch_dose%d.bin',k-1)));
             fclose(fid);
         end
 
@@ -475,7 +474,7 @@ for scenario_i = 1  % :numel(OptGoals.sss_scene_list)
     % % write the condor submit file
     %      beamspec_batch_filename = ['./' input_folder '/' beamspec_batches_folder '/' beamspec_batch_base_name '$(Process).txt'];
     %      beamlet_batch_filename = ['./' output_folder '/' beamlet_batches_folder '/' beamlet_batch_base_name '$(Process).bin'];
-         fid = fopen([condor_folder_scenario '/' condor_submit_file],'w');
+         fid = fopen([condor_folder '/' condor_submit_file],'w');
          fprintf(fid,'###############################################################\n');
          fprintf(fid,'# Condor submission script for convolution/superposition code\n');
          fprintf(fid,'###############################################################\n\n');
@@ -498,7 +497,7 @@ for scenario_i = 1  % :numel(OptGoals.sss_scene_list)
         batch = batches{n};  % current batch
 
         if Condor_flag == 1
-            save_beamspec_batch(batch,[condor_folder_scenario '/' input_folder '/' beamspec_batches_folder],[beamspec_batch_base_name num2str(n-1) '.txt']);
+            save_beamspec_batch(batch,[condor_folder '/' input_folder '/' beamspec_batches_folder],[beamspec_batch_base_name num2str(n-1) '.txt']);
         end
     end
 
@@ -506,7 +505,7 @@ for scenario_i = 1  % :numel(OptGoals.sss_scene_list)
     all_beams{1}.Mxp = Mxp;
     all_beams{1}.N_angles = N_angles;
     all_beams{1}.num_batches = num_batches;
-    save([condor_folder_scenario '\all_beams.mat'], 'all_beams');
+    save([condor_folder '\all_beams.mat'], 'all_beams');
     % for k = 1:numel(batches)
     %         system([fullfile(patient_dir,sprintf('run%d.cmd',k-1)) ' &']);
     %     end 
@@ -533,7 +532,7 @@ for scenario_i = 1  % :numel(OptGoals.sss_scene_list)
 
     if(strcmpi('y',strBeamlet)) 
         for k = 1:numel(batches)
-            system([fullfile(patient_dir_scenario,sprintf('run%d.cmd',k-1)) ' &']);
+            system([fullfile(patient_dir,sprintf('run%d.cmd',k-1)) ' &']);
         end 
     end
 

WiscPlanPhotonkV125/matlab_frontend/lab/XTPS.m

@@ -74,12 +74,17 @@ classdef XTPS < handle
             
             obj.handles.hExportPinnacleMenu   = uimenu(obj.handles.hFileMenu, 'Label', 'Export Pinnacle Files', 'Separator','on');
             
+            % Full RO menu
+            obj.handles.hFullROMenu   = uimenu(obj.handles.hMainFigure, 'Label', 'Full RO');     
+            obj.handles.hFullRO_beamCalc = uimenu(obj.handles.hFullROMenu,  'Label', 'Full RO beam calc');
+            obj.handles.hFullRO_mergeBeams = uimenu(obj.handles.hFullROMenu,  'Label', 'mergeBeams');
+            obj.handles.hFullRO_Opt = uimenu(obj.handles.hFullROMenu,  'Label', 'Full RO optimization');
+            
             % Tools menu
             obj.handles.hToolsMenu   = uimenu(obj.handles.hMainFigure, 'Label', 'Tools');            
             obj.handles.hPlotDVHMenu = uimenu(obj.handles.hToolsMenu,  'Label', 'Plot DVH');
             obj.handles.hResampleGeometry = uimenu(obj.handles.hToolsMenu,  'Label', 'Resample Geometry');
-            obj.handles.hFullRO_beamCalc = uimenu(obj.handles.hToolsMenu,  'Label', 'Full RO beam calc');
-            obj.handles.hFullRO_Opt = uimenu(obj.handles.hToolsMenu,  'Label', 'Full RO optimization');
+            
             
 
             % Associate callbacks
@@ -113,6 +118,7 @@ classdef XTPS < handle
             set(obj.handles.hPlotDVHMenu, 'Callback',               @obj.PlotDVHMenu_Callback);
             set(obj.handles.hResampleGeometry, 'Callback',          @obj.ResampleGeometry_Callback);
             set(obj.handles.hFullRO_beamCalc, 'Callback',           @obj.FullRO_beamCalc_Callback);
+            set(obj.handles.hFullRO_mergeBeams, 'Callback',         @obj.hFullRO_mergeBeams_Callback);
             set(obj.handles.hFullRO_Opt, 'Callback',                @obj.FullRO_Opt_Callback);
             set(obj.handles.hDoseModeDropdown, 'Callback',          @obj.DoseModeDropdown_Callback);
             set(obj.handles.hWWSlider, 'Callback',                  @obj.WWSlider_Callback);
@@ -693,6 +699,11 @@ classdef XTPS < handle
             disp('Full RO beamcalc called!')
             fullRO_beamCalc(obj.handles.hSVPS.Geometry)
         end
+%-------------------------------------------------------------------------------    
+        function hFullRO_mergeBeams_Callback(obj, src, evt)
+            disp('Merging full RO beamlets')
+            fullRO_mergeBeams(obj.handles.hSVPS.Geometry)
+        end
 %-------------------------------------------------------------------------------
         function FullRO_Opt_Callback(obj, src, evt)
             % call function to do full RO optimization based on multiple