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+%%
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+
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+% This version was modified by Peter Ferjancic to accept .nrrd file format
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+% for target. It was also rollbacked on some parameters back to the
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+% clinical system settings.
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+
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+% This file has been modified by Surendra Prajapati especially to run
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+% WiscPlan for KV beams. Works for running locally as well as in Server.
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+%
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+% RTF 11/4/05
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+% Sets up the run files needed for running a Condor convolution
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+% superposition dose calculation with photon beams.
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+
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+% Versions of the convolution code that run in both Windows XP, Condor, and
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+% directly through Matlab can all be created here. The only real
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+% differences between the files are in the access conventions, which just%
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+% This has to do with switching forward slashes with backslashes.
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+
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+% Surendra edits: num_batches, SAD, pitch, xpmin/max, ypmin/max, Mxp, Nphi
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+% Also edit:
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+% Kernel should always be named Kernels.mat
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+
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+function num_batches = helicalDosecalcSetup7_fullRO(patient_dir, OptGoals, beamlet_dir)
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+% -- INPUT:
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+% patient_dir: specify where kernel and [geometry] files are located
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+
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+iso = [0 0 0]; % Point about which gantry rotations begin
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+SAD = 85; % source-axis distance for the x-ray source ##
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+pitch = 0.86; % fraction of beam with couch translates per rotation
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+
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+%% --- make the figure prompt for number of angles and beamlets
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+str = inputdlg({'Enter number of calc cores', 'Enter number of angles (51 default)', ...
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+ 'Enter number of beamlets (64 default)'}, 'input', [1,35], {'1', '51', '64'});
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+num_batches = str2double(str{1}); % number of cores you want to run the beam calculation
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+% -- (3 for a 4-core comp to prevent lockdown)
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+N_angles = str2double(str{2}); % 51 for full resolution
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+Mxp = str2double(str{3}); % Mxp = 64; number of MLC leaves;
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+Nyp = 1; % always 1 for Tomo due to binary mlc
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+
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+% define the overall beam field size for each beam angle
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+% beam is 40 cm wide in transverse direction and 1-5 cm (usually 2) in y
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+% direction.
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+% isocenter is 85 cm from source, ends of jaws are 23 cm from source
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+xpmin = -20.0; % -field width / 2
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+xpmax = 20.0; % +field width / 2
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+% ypmin = -0.3125; % total jaw width is 0.625 cm
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+% ypmax = 0.3125;
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+% ypmin = -0.5; % total jaw width is 1 cm
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+% ypmax = 0.5;
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+ypmin = -1.25; % total jaw width is 2.5 cm
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+ypmax = 1.25;
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+% y-prime points in the z-direction in the CT coordinate system
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+
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+% ============================================= End of user-supplied inputs
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+% executable_path = 'C:\010-work\003_localGit\WiscPlan_v2\WiscPlanPhotonkV125\WiscPlanEXE\RyanCsphoton.x86.exe';
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+
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+executable_path = mfilename('fullpath');
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+executable_path = [executable_path(1:end-37), 'WiscPlanEXE\RyanCsphoton.x86.exe']
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+
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+kernel_file = 'Kernels.mat';
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+geometry_file = fullfile(patient_dir, 'matlab_files\Geometry.mat');
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+
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+load(geometry_file);
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+ROI_names = cellfun(@(c)c.name, Geometry.ROIS, 'UniformOutput', false);
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+[target_idx, okay] = listdlg('ListString', ROI_names, ...
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+ 'SelectionMode', 'single', 'Name', 'Target Selection', ...
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+ 'PromptString', 'Please select the target ROI for beamlet calc. ');
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+if okay ~= 1
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+ msgbox('Plan creation aborted');
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+ return;
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+end
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+
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+targetMask = zeros(size(Geometry.data));
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+targetMask(Geometry.ROIS{target_idx}.ind) = 1;
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+
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+% Grozomah - targetMask needs to get a 'double' matrix with the location of
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+% the target
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+
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+targetMaskZ = sum(sum(targetMask,1),2);
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+zBow = (find(targetMaskZ>0, 1, 'first')-1)*Geometry.voxel_size(3) + Geometry.start(3) + ypmin;
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+zStern = (find(targetMaskZ>0, 1, 'last')+1)*Geometry.voxel_size(3) + Geometry.start(3) + ypmax;
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+[subi, subj, subk] = ind2sub(size(Geometry.data), Geometry.ROIS{target_idx}.ind);
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+iso = [Geometry.start(1)+Geometry.voxel_size(1)*mean(subi) ...
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+ Geometry.start(2)+Geometry.voxel_size(2)*mean(subj) 0];
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+
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+
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+% flags used to select which calculations will be set up
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+Condor_flag = 1;
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+ptvInd = target_idx; % PTV index in Geometry.ROIS
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+fieldWidth = ypmax - ypmin;
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+
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+% total number of rotations required for treatment
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+Nrot = ceil(abs(zBow - zStern)/(pitch*fieldWidth));
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+
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+% Nphi = Nrot*51; % number of angles used in the calculation
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+Nphi = Nrot * N_angles; % Grozomah
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+
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+% define the limits of the angles that will be used for the calculation
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+% ##phimin = 0; % starting angle in radians
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+% ##phimax = 2*pi*Nphi;
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+
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+phi = [0:Nphi-1]/Nphi *2*pi*Nrot;
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+
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+condor_folder = patient_dir;
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+winxp_folder = 'winxp';
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+
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+% create names for condor input and output folders
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+input_folder = '.';
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+output_folder = '.';
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+
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+% name of the convolution/superposition executable, which will be in the
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+% 'code' folder of each respective run type folder
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+condor_exectuable_name = 'convolutionCondor'; % relative path on the cluster where code will be
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+winxp_executable_name = 'convolution.exe';
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+matlab_executable_name = 'convolution_mex'; % name of the Matlab version of the dose calculation code
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+
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+% set the beam parameters, assuming a helical beam trajectory
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+% folders that will be inside the 'input' folder
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+beamspec_folder = 'beamspecfiles'; % directory where beam files will be stored
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+beamspec_batches_folder = 'beamspecbatches';
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+beamspec_batch_base_name = 'beamspecbatch'; % base name for a beamlet batch file
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+kernel_folder = 'kernelfiles'; % folder where kernel information will be saved
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+kernel_filenames_condor = 'kernelFilenamesCondor.txt';
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+kernel_filenames_winxp = 'kernelFilenamesWinXP.txt';
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+
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+% output folders
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+beamlet_batch_base_name = 'beamletbatch'; % base name for a dose batch file
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+
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+geometry_header_filename = 'geometryHeader.txt';
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+geometry_density_filename = 'density.bin'; % save the density, not the Hounsfield units!
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+
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+% end of user-defined parameters
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+
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+% check the validity of the user-defined variables
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+if xpmin >= xpmax
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+ error('xpmin must be less than xpmax.');
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+end
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+if ypmin >= ypmax
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+ error('ypmin must be less than ypmax.');b
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+end
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+
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+% if phimin > phimax
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+% error('phimin must be less than or equal to phimax.');
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+% end
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+
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+if Mxp <= 0 || Nyp <= 0 || Nphi <= 0
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+ error('Mxp, Nyp, and Nphi must be greater than zero.');
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+end
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+
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+if SAD < 50
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+ error('It is recommended that the SAD be greater than 50 cm.');
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+end
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+
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+% the xy plane is perpendicular to the isocenter axis of the linac gantry
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+
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+% size of each beam aperture, making them vectors so extension to
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+% non-uniform aperture sizes becomes obvious
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+del_xp = (xpmax - xpmin)/Mxp;
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+del_yp = (ypmax - ypmin)/Nyp;
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+
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+% Calculate the xp and yp offsets, which lie at the centers of the
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+% apertures.
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+xp = [xpmin:del_xp:xpmax-del_xp] + del_xp/2;
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+yp = [ypmin:del_yp:ypmax-del_yp] + del_yp/2;
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+
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+[M,N,Q] = size(Geometry.rhomw);
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+
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+START = single(Geometry.start - iso);
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+INC = single(Geometry.voxel_size);
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+
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+% Grozomah ##
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+% START(1) = START(1)/10;
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+% START(2) = START(2)/10;
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+% INC(1) = INC(1)/10;
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+% INC(2) = INC(2)/10;
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+
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+% END= START+[32,32,40].*INC
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+
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+% define the tumor mask
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+tumorMask = zeros(size(Geometry.rhomw),'single');
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+tumorMask(Geometry.ROIS{ptvInd}.ind) = 1;
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+
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+BW = bwdist(tumorMask);
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+tumorMaskExp = tumorMask;
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+tumorMaskExp(BW <= 4) = 1;
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+
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+P = zeros(Mxp,Nphi);
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+
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+fprintf('Checking beam''s eye view ...\n');
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+for p=1:Nphi
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+ % ir and jr form the beam's eye view (BEV)
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+ ir = [-sin(phi(p)); cos(phi(p)); 0];
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+ jr = [0 0 1]';
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+ % kr denotes the beam direction
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+ kr = [cos(phi(p)); sin(phi(p)); 0];
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+
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+ for m=1:Mxp
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+ point1 = single(-kr*SAD + [0 0 zBow + pitch*fieldWidth*phi(p)/(2*pi)]'); % source point
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+ point2 = single(point1 + (SAD*kr + ir*xp(m))*10);
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+ [indVisited,deffVisited] = singleRaytraceClean(tumorMaskExp,START,INC,point1,point2);
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+ if ~isempty(indVisited)
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+ P(m,p) = max(deffVisited);
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+ end
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+ end
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+end
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+fprintf('Finished checking BEV\n');
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+
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+% load data required for the dose calculator
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+load(kernel_file);
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+
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+Geometry.rhomw(Geometry.rhomw < 0) = 0;
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+Geometry.rhomw(Geometry.rhomw < 0.0013) = 0.0013; % fill blank voxels with air
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+
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+% convert Geometry and kernels to single
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+f = fieldnames(Kernels);
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+for k=1:length(f)
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+ if isnumeric(getfield(Kernels,f{k}))
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+ Kernels = setfield(Kernels,f{k},single(getfield(Kernels,f{k})));
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+ end
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+end
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+
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+f = fieldnames(Geometry);
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+for k=1:length(f)
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+ if isnumeric(getfield(Geometry,f{k}))
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+ Geometry = setfield(Geometry,f{k},single(getfield(Geometry,f{k})));
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+ end
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+end
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+
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+% account for isocenter
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+Geometry.start_nominal = single(Geometry.start - iso);
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+
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+%% account for beamlet shift
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+for scenario_i = 1 % :numel(OptGoals.sss_scene_list)
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+ disp(OptGoals.sss_scene_list{scenario_i});
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+
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+ % change Condor folder names as appropriate
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+ condor_folder_scenario = [beamlet_dir '\scenario' num2str(scenario_i)];
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+ mkdir(condor_folder_scenario)
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+ patient_dir_scenario = condor_folder_scenario
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+
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+ % do the isocenter shift
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+ shift = OptGoals.sss_scene_list{scenario_i}; % Y X Z
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+ iso = [iso(1)+Geometry.voxel_size(1)*shift(1) ...
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+ iso(2)+Geometry.voxel_size(2)*shift(2) ...
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+ iso(3)+Geometry.voxel_size(3)*shift(3)];
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+ Geometry.start = Geometry.start_nominal- iso;
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+
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+ % find the total number of beams
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+ Nbeam = Nphi*Mxp*Nyp;
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+
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+ batch_num = 0; % start the count for the number of total batches
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+
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+ % fill up a cell array of beam structures, grouped by batch
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+ clear batches;
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+ batch_num = 0;
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+
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+ batches = cell(1,Nrot); % start the batches cell array (cell array of beam batches)
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+ rotNum = 0;
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+
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+ % calculate beams for all source directions and apertures
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+ for k=1:Nphi % loop through all gantry angles
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+ % calculate the source location for a helical trajectory
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+ beam.SAD = single(SAD);
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+
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+ % the kp vector is the beam direction, ip and jp span the beam's eye view
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+ beam.ip = single([-sin(phi(k)) cos(phi(k)) 0]);
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+ beam.jp = single([0 0 1]);
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+ beam.kp = single([cos(phi(k)) sin(phi(k)) 0]);
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+ beam.y_vec = single(-beam.kp*SAD + [0 0 zBow + pitch*fieldWidth*phi(k)/(2*pi)]);
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+
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+ rotNumOld = rotNum;
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+ rotNum = floor(k/51) + 1; % current rotation number
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+ if rotNum - rotNumOld > 0
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+ beam_num = 0; % if the rotation number has changed, start the beam count over
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+ end
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+
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+ for m=1:Mxp % loop through all apertures in the xp-direction
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+ % calculate the beam if the tomotherapy fluence value is non-zero
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+ if P(m,k) > 0
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+ num = m + (k-1)*Mxp - 1; % beamlet number (overall)
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+ beam_num = beam_num + 1;
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+
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+ % set the beam aperture parameters
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+ beam.del_xp = single(del_xp);
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+ beam.del_yp = single(del_yp);
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+ beam.xp = single(xp(m));
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+ beam.yp = single(0);
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+ beam.num = single(num); % record the beam number to avoid any later ambiguity
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+
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+ batches{rotNum}{beam_num} = beam;
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+ end
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+ end
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+ end
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+ % merge/split batches
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+ all_beams = horzcat(batches{:});
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+ num_beams_per_batch = ceil(numel(all_beams)/num_batches);
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+ batches = cell(num_batches,1);
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+ for k = 1:(num_batches)
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+ beams_idx = 1+num_beams_per_batch*(k-1):num_beams_per_batch*k;
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+ beams_idx (beams_idx>numel(all_beams)) = [];
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+ batches{k} = all_beams(beams_idx);
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+ end
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+ % batches{num_batches} = all_beams(1+num_beams_per_batch*(k):end);
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+
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+
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+ % Everything else in this file is related to saving the batches in a
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+ % useable form.
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+ if Condor_flag == 1
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+ % delete the old submission file
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+ err = rmdir(fullfile(condor_folder_scenario,beamspec_batches_folder),'s');
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+ err = rmdir(fullfile(condor_folder_scenario,kernel_folder),'s');
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+
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+ % create folders where batch information will be sent
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+ mkdir([condor_folder_scenario '/' input_folder '/' beamspec_batches_folder]);
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+
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+ % save the kernels
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+ save_kernels(Kernels,[condor_folder_scenario '/' input_folder '/' kernel_folder]);
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+ fprintf(['Successfully saved Condor kernels to ' input_folder '/' kernel_folder '\n']);
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+
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+ % create kernel filenames files
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+ kernel_filenames_CHTC = 'kernelFilenamesCHTC.txt';
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+ kernel_filenames_condor = 'kernelFilenamesCondor.txt';
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+ fid = fopen([condor_folder_scenario '/' input_folder '/' kernel_filenames_condor],'w');
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+ fid2 = fopen([condor_folder_scenario '/' input_folder '/' kernel_filenames_CHTC],'w');
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+
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+ fprintf(fid,'kernel_header\n');
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+ % fprintf(fid,['./' input_folder '/' kernel_folder '/kernel_header.txt\n']);
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+ fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'kernel_header.txt'));
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+ fprintf(fid2,'kernel_header\n');
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+ fprintf(fid2, '%s/%s\n', kernel_folder,'kernel_header.txt');
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+
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+ fprintf(fid,'kernel_radii\n');
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+ % fprintf(fid,['./' input_folder '/' kernel_folder '/radii.bin\n']);
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+ fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'radii.bin'));
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+ fprintf(fid2,'kernel_radii\n');
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+ fprintf(fid2, '%s/%s\n', kernel_folder,'radii.bin');
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+
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+ fprintf(fid,'kernel_angles\n');
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+ % fprintf(fid,['./' input_folder '/' kernel_folder '/angles.bin\n']);
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+ fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'angles.bin'));
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+ fprintf(fid2,'kernel_angles\n');
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+ fprintf(fid2, '%s/%s\n', kernel_folder,'angles.bin');
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+
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+ fprintf(fid,'kernel_energies\n');
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+ % fprintf(fid,['./' input_folder '/' kernel_folder '/energies.bin\n']);
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+ fprintf(fid,'%s\n',fullfile(patient_dir_scenario,input_folder,kernel_folder,'energies.bin'));
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+ fprintf(fid2,'kernel_energies\n');
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+ 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(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(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(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(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(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(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(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(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(fid2,'kernel_mu_en\n');
|
|
|
+ fprintf(fid2, '%s/%s\n', kernel_folder,'mu_en.bin');
|
|
|
+
|
|
|
+ fclose(fid);
|
|
|
+ end
|
|
|
+
|
|
|
+ % name for the condor submit file that will be used
|
|
|
+ condor_submit_file = 'convolutionSubmit.txt';
|
|
|
+
|
|
|
+ geometry_filenames_condor = 'geometryFilenamesCondor.txt';
|
|
|
+ geometry_filenames_CHTC = 'geometryFilenamesCHTC.txt';
|
|
|
+
|
|
|
+ % check the geometry file to ensure that it's not in Hounsfield units
|
|
|
+ if length(find(Geometry.rhomw > 20)) || length(find(Geometry.rhomw < 0))
|
|
|
+ error('Double check the Geometry structure, it may still be in Hounsfield units!');
|
|
|
+ end
|
|
|
+
|
|
|
+ geometry_folder = 'geometryfiles';
|
|
|
+ batch_output_folder = 'batchoutput'; % folder to which stdout will be printed
|
|
|
+ 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]);
|
|
|
+
|
|
|
+ save_geometry(Geometry,[condor_folder_scenario '/' 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');
|
|
|
+
|
|
|
+ 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(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(fid2,'geometry_density\n');
|
|
|
+ fprintf(fid2, '%s/%s\n', geometry_folder,'density.bin');
|
|
|
+ fclose(fid);
|
|
|
+
|
|
|
+ % 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');
|
|
|
+ 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)));
|
|
|
+ fclose(fid);
|
|
|
+ end
|
|
|
+
|
|
|
+ % 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 '/' condor_submit_file],'w');
|
|
|
+ % fprintf(fid,'###############################################################\n');
|
|
|
+ % fprintf(fid,'# Condor submission script for convolution/superposition code\n');
|
|
|
+ % fprintf(fid,'###############################################################\n\n');
|
|
|
+ % fprintf(fid,'copy_to_spool = false\n');
|
|
|
+ % fprintf(fid,['Executable = ' code_folder '/' condor_exectuable_name '\n']);
|
|
|
+ % fprintf(fid,['arguments = ' input_folder '/' kernel_filenames_condor ' ' input_folder '/' geometry_filenames_condor ' ' beamspec_batch_filename ' ' beamlet_batch_filename '\n']);
|
|
|
+ % fprintf(fid,['Output = ./' output_folder '/' batch_output_folder '/batchout$(Process).txt\n']);
|
|
|
+ % fprintf(fid,['Log = ./' output_folder '/' batch_output_folder '/log.txt\n']);
|
|
|
+ % fprintf(fid,['Queue ' num2str(Nrot)]);
|
|
|
+ % fclose(fid);
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+ % % write the condor submit file
|
|
|
+ % beamspec_batch_filename = ['./' input_folder '/' beamspec_batches_folder '/' beamspec_batch_base_name '$(Process).txt'];
|
|
|
+ % beamlet_batch_filename = ['./' output_folder '/' beamlet_batches_folder '/' beamlet_batch_base_name '$(Process).bin'];
|
|
|
+ fid = fopen([condor_folder_scenario '/' condor_submit_file],'w');
|
|
|
+ fprintf(fid,'###############################################################\n');
|
|
|
+ fprintf(fid,'# Condor submission script for convolution/superposition code\n');
|
|
|
+ fprintf(fid,'###############################################################\n\n');
|
|
|
+ fprintf(fid,'copy_to_spool = false\n');
|
|
|
+ fprintf(fid,['Executable = ' condor_exectuable_name '\n']);
|
|
|
+ fprintf(fid,['Arguments = ' kernel_filenames_CHTC ' ' geometry_filenames_CHTC ' ' beamspec_batch_base_name '$(Process).txt ' 'batch_dose$(Process).bin\n']);
|
|
|
+ fprintf(fid,['Transfer_input_files = ' kernel_folder ',' geometry_folder ',' beamspec_batches_folder '/' beamspec_batch_base_name '$(Process).txt' ',' kernel_filenames_CHTC ',' geometry_filenames_CHTC '\n']);
|
|
|
+ fprintf(fid,['Request_memory = 1000' '\n']);
|
|
|
+ fprintf(fid,['Request_disk = 500000' '\n']);
|
|
|
+ fprintf(fid,['Output = $(Cluster).out' '\n']);
|
|
|
+ fprintf(fid,['Log = $(Cluster).log' '\n']);
|
|
|
+ fprintf(fid,['Error = $(Cluster).err' '\n']);
|
|
|
+ fprintf(fid,['Queue ' num2str(num_batches) '\n']);
|
|
|
+ % fclose(fid);
|
|
|
+ end
|
|
|
+
|
|
|
+
|
|
|
+ % write the batches to files
|
|
|
+ for n=1:numel(batches)
|
|
|
+ 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']);
|
|
|
+ end
|
|
|
+ end
|
|
|
+
|
|
|
+
|
|
|
+ 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');
|
|
|
+ % for k = 1:numel(batches)
|
|
|
+ % system([fullfile(patient_dir,sprintf('run%d.cmd',k-1)) ' &']);
|
|
|
+ % end
|
|
|
+
|
|
|
+ % Ask for User option to run the dose calculation locally on the computer
|
|
|
+ % or just to get necessary files for CHTC server
|
|
|
+ % 'y' means run locally, 'n' means not to run locally on the computer
|
|
|
+
|
|
|
+ strBeamlet = '';
|
|
|
+ while(1)
|
|
|
+ if strcmpi('y',strBeamlet)
|
|
|
+ break;
|
|
|
+ elseif strcmpi('n',strBeamlet)
|
|
|
+ break;
|
|
|
+ end
|
|
|
+
|
|
|
+% strBeamlet = input('Run beamlet batches dose calculation locally? y/n \n','s');
|
|
|
+ strBeamlet = 'y'; %bypass question
|
|
|
+ end
|
|
|
+
|
|
|
+ t = datetime('now');
|
|
|
+ disp(['Calculating ' num2str(size(all_beams, 2)) ' beamlets in ' num2str(size(batches, 1))...
|
|
|
+ ' batches. Start: ' datestr(t)])
|
|
|
+
|
|
|
+ if(strcmpi('y',strBeamlet))
|
|
|
+ for k = 1:numel(batches)
|
|
|
+ system([fullfile(patient_dir_scenario,sprintf('run%d.cmd',k-1)) ' &']);
|
|
|
+ end
|
|
|
+ end
|
|
|
+
|
|
|
+end % end of scenario loop
|
|
|
+
|
|
|
+end
|
|
|
+
|
MEDPHYSICS\pferjancic