Update on merging VMAT into dev

examples/matRad_example8_photonsVMAT.m

@@ -0,0 +1,125 @@
+%% Example Photon Treatment Plan with VMAT direct aperture optimization
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% Copyright 2017 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.
+%
+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%
+% In this example we will show 
+% (i) how to load patient data into matRad
+% (ii) how to input necessary parameters in the pln structure
+% (iii) how to setup a photon dose calculation
+% (iv) how to inversely optimize fluence directly from command window in MatLab.
+% (v) how to apply a sequencing algorithm
+% (vi) how to run a VMAT direct aperture optimization
+% (vii) how to visually and quantitatively evaluate the result
+
+%% Patient Data Import
+% Let's begin with a clear Matlab environment and import the TG119 patient
+% into your workspace
+matRad_rc
+
+load TG119.mat
+
+%% Treatment Plan
+% The next step is to define your treatment plan labeled as 'pln'. This 
+% structure requires input from the treatment planner and defines 
+% the most important cornerstones of your treatment plan.
+
+% meta information for treatment plan
+pln.numOfFractions  = 30;
+pln.radiationMode   = 'photons';            % either photons / protons / helium / carbon / brachy
+pln.machine         = 'Generic';            % generic for RT / LDR or HDR for BT
+
+pln.bioModel = 'none';      % none: for photons, protons, carbon, brachy    % constRBE: constant RBE for photons and protons 
+                            % MCN: McNamara-variable RBE model for protons  % WED: Wedenberg-variable RBE model for protons 
+                            % LEM: Local Effect Model for carbon ions       % HEL: data-driven RBE parametrization for helium
+
+pln.multScen = 'nomScen';   % scenario creation type 'nomScen'  'wcScen' 'impScen' 'rndScen'         
+
+% beam geometry settings
+pln.propStf.bixelWidth      = 5;            % [mm] / also corresponds to lateral spot spacing for particles
+pln.propStf.maxGantryAngleSpacing    = 30;   % [°] / max gantry angle spacing for dose calculation
+pln.propStf.maxDAOGantryAngleSpacing = 60;  % [°] / max gantry angle spacing for DAO
+pln.propStf.maxFMOGantryAngleSpacing = 180;  % [°] / max gantry angle spacing for FMO
+pln.propStf.startingAngle = -180;           % [°] / starting angle for VMAT
+pln.propStf.finishingAngle = 180;           % [°] / finishing angle for VMAT
+pln.propStf.couchAngle      = 0;            % [°]
+pln.propStf.isoCenter       = matRad_getIsoCenter(cst,ct,0);
+pln.propStf.generator       = 'PhotonVMAT';
+pln.propStf.continuousAperture  = false;
+
+% dose calculation settings
+pln.propDoseCalc.doseGrid.resolution.x = 5; % [mm]
+pln.propDoseCalc.doseGrid.resolution.y = 5; % [mm]
+pln.propDoseCalc.doseGrid.resolution.z = 5; % [mm]
+
+% sequencing settings
+pln.propSeq.runSequencing   = true;  % true: run sequencing, false: don't / will be ignored for particles and also triggered by runDAO below
+pln.propSeq.sequencer       = 'siochi';
+pln.propSeq.numLevels       = 7;
+
+% optimization settings
+pln.propOpt.quantityOpt         = 'physicalDose';   % Quantity to optimizer (could also be RBExDose, BED, effect)
+pln.propOpt.optimizer           = 'IPOPT';          % We can also utilize 'fmincon' from Matlab's optimization toolbox
+pln.propOpt.runDAO              = true;             % 1/true: run DAO, 0/false: don't / will be ignored for particles
+pln.propOpt.runVMAT             = true;
+pln.propOpt.preconditioner      = true;
+
+%pln.propOpt.VMAToptions.machineConstraintFile = [pln.radiationMode '_' pln.machine];
+
+%% Generate Beam Geometry STF
+stf = matRad_generateStf(ct,cst,pln);
+
+%% Dose Calculation
+% Lets generate dosimetric information by pre-computing dose influence 
+% matrices for unit beamlet intensities. Having dose influences available 
+% allows for subsequent inverse optimization.
+dij = matRad_calcDoseInfluence(ct, cst, stf, pln);
+
+%% Inverse Planning for IMRT
+% The goal of the fluence optimization is to find a set of beamlet weights 
+% which yield the best possible dose distribution according to the 
+% predefined clinical objectives and constraints underlying the radiation 
+% treatment. In VMAT, FMO is done only at the angles in the
+% FMOGantryAngles set. Once the optimization has finished, trigger once the GUI to
+% visualize the optimized dose cubes.
+resultGUI = matRad_fluenceOptimization(dij,cst,pln,stf);
+matRadGUI;
+
+%% Sequencing
+% This is a multileaf collimator leaf sequencing algorithm that is used in 
+% order to modulate the intensity of the beams with multiple static 
+% segments, so that translates each intensity map into a set of deliverable 
+% aperture shapes. The fluence map at each angle in the initGantryAngles
+% set is sequenced, with the resulting apertures spread to neighbouring
+% angles from the optGantryAngles set.
+resultGUI = matRad_sequencing(resultGUI,stf,dij,pln);
+
+%% DAO - Direct Aperture Optimization
+% The Direct Aperture Optimization is an optimization approach where we 
+% directly optimize aperture shapes and weights at the angles in the
+% optGantryAngles set.  The gantry angle speed, leaf speed, and MU rate are
+% constrained by the min and max values specified by the user.
+resultGUI = matRad_directApertureOptimization(dij,cst,resultGUI.apertureInfo,resultGUI,pln);
+
+%% Aperture visualization
+% Use a matrad function to visualize the resulting aperture shapes
+matRad_visApertureInfo(resultGUI.apertureInfo);
+
+%% Indicator Calculation and display of DVH and QI
+resultGUI = matRad_planAnalysis(resultGUI,ct,cst,stf,pln);
+
+%% Calculate delivery metrics
+
+resultGUI = matRad_calcDeliveryMetrics(resultGUI,pln,stf);
+

matRad/MatRad_Config.m

@@ -249,6 +249,7 @@ function setDefaultProperties(obj)
 
             %Sequencing Options
             obj.defaults.propSeq.sequencer = 'siochi';
+            obj.defaults.propSeq.numLevels = 5;
 
 
 
@@ -324,12 +325,12 @@ function setDefaultGUIProperties(obj)
                 if ispc
                     light = logical(winqueryreg('HKEY_CURRENT_USER','Software\\Microsoft\\Windows\\CurrentVersion\\Themes\\Personalize','AppsUseLightTheme'));
                 elseif ismac
-                    out = system('defaults read -g AppleInterfaceStyle');
-                    if ~strcmp(out,'Dark')
+                    [~,out] = system('defaults read -g AppleInterfaceStyle');
+                    if ~strcmp(out(1:end-1),'Dark')
                         light = true;
                     end
                 else
-                    out = system('gsettings get org.gnome.desktop.interface color-scheme');
+                    [~,out] = system('gsettings get org.gnome.desktop.interface color-scheme');
                     if strcmp(out,'prefer-light')
                         light = true;
                     end

matRad/dicom/@matRad_DicomImporter/matRad_importDicomSteeringPhotons.m

@@ -47,7 +47,16 @@
     % set necessary steering information 
     obj.stf(i).gantryAngle  = UniqueComb(i,1);
     obj.stf(i).couchAngle   = UniqueComb(i,2);
-    obj.stf(i).isoCenter    = obj.pln.propStf.isoCenter(i,:);
+
+    %Handle possibility of multiple isocenters
+    if size(obj.pln.propStf.isoCenter,1) == 1
+        obj.stf(i).isoCenter    = obj.pln.propStf.isoCenter;
+    elseif size(pln.propStf.isoCenter,1) == obj.pln.propStf.numOfBeams
+        obj.stf(i).isoCenter = obj.pln.propStf.isoCenter(i,:);
+    else
+        matRad_cfg = MatRad_Config.instance();
+        matRad_cfg.dispError('Invalid number of isocenters - should either be one or as many as beams!');
+    end
 
     % bixelWidth = 'field' as keyword for whole field dose calc
     obj.stf(i).bixelWidth    = 'field';

matRad/doseCalc/+DoseEngines/matRad_PhotonPencilBeamSVDEngine.m

@@ -159,6 +159,17 @@ function setDefaults(this)
                 matRad_cfg.dispWarning('Kernel Cut-Off ''%f mm'' cannot be smaller than geometric lateral cutoff ''%f mm''. Using ''%f mm''!',this.kernelCutOff,this.geometricLateralCutOff,this.geometricLateralCutOff);
                 this.kernelCutOff = this.geometricLateralCutOff;
             end
+
+            % TODO: calculate and add weightToMU for the generic photon
+            % machine. Typical calibration: 100 cGy/100 MU in a 10x10 cm^2
+            % field, 100 cm SSD, depth of dose maximum for the given beam
+            % quality.
+            if isfield(this.machine.data,'weightToMU')
+                dij.weightToMU = this.machine.data.weightToMU;
+            else
+                dij.weightToMU = 100;
+                matRad_cfg.dispWarning('photon machine file does not contain weight to MU scaling factor. Assuming %.1f.',dij.weightToMU);
+            end
 
             %% kernel convolution
             % set up convolution grid