Merge pull request #763 from Gattowski/dev

Stf Generators Refactor

Author: wahln

examples/matRad_example12_simpleParticleMonteCarlo.m

@@ -65,6 +65,7 @@
 %Enable/Disable use of range shifter (has effect only when we need to fill 
 %up the low-range region)
 pln.propStf.useRangeShifter = false;  
+pln.propStf.generator = 'ParticleSingleSpot'; 
 
 %Enable LET calculation
 pln.propDoseCalc.calcLET = true;
@@ -74,8 +75,7 @@
 % pln.propMC.externalCalculation = true;
 
 %% generate steering file
-%stf = matRad_generateStf(ct,cst,pln);
-stf = matRad_generateSingleBixelStf(ct,cst,pln); %Example to create a single beamlet stf
+stf = matRad_generateStf(ct,cst,pln);
 
 %% analytical dose calculation
 pln.propDoseCalc.engine = 'MCsquare';

examples/matRad_example15_brachy.m

@@ -121,32 +121,34 @@
 
 
 pln.propStf.bixelWidth   = 5; % [mm] template grid distance
-pln.propStf.templateRoot = matRad_getTemplateRoot(ct,cst); % mass center of
-% target in x and y and bottom in z
+
+%Template Type
+pln.propStf.template.type = 'checkerboard'; %  'checkerboard' if template is created automatically 
+                                            %  'manual' if template is  needed as preset manually (see below)
+
+%Template Root - mass center of target in x and y and bottom in z
+pln.propStf.template.root = matRad_getTemplateRoot(ct,cst); 
 
 % Here, we define active needles as 1 and inactive needles
 % as 0. This is the x-y plane and needles point in z direction. 
 % A checkerboard pattern is frequantly used. The whole geometry will become
 % clearer when it is displayed in 3D view in the next section.
-
-pln.propStf.template.activeNeedles = [0 0 0 1 0 1 0 1 0 1 0 0 0;... % 7.0
-                                      0 0 1 0 1 0 0 0 1 0 1 0 0;... % 6.5
-                                      0 1 0 1 0 1 0 1 0 1 0 1 0;... % 6.0
-                                      1 0 1 0 1 0 0 0 1 0 1 0 1;... % 5.5
-                                      0 1 0 1 0 1 0 1 0 1 0 1 0;... % 5.0
-                                      1 0 1 0 1 0 0 0 1 0 1 0 1;... % 4.5
-                                      0 1 0 1 0 1 0 1 0 1 0 1 0;... % 4.0
-                                      1 0 1 0 1 0 0 0 1 0 1 0 1;... % 4.5
-                                      0 1 0 1 0 1 0 1 0 1 0 1 0;... % 3.0
-                                      1 0 1 0 1 0 1 0 1 0 1 0 1;... % 2.5
-                                      0 1 0 1 0 1 0 1 0 1 0 1 0;... % 2.0
-                                      1 0 1 0 1 0 0 0 0 0 1 0 1;... % 1.5
-                                      0 0 0 0 0 0 0 0 0 0 0 0 0];   % 1.0
-                                     %A a B b C c D d E e F f G
-
-pln.propStf.isoCenter    = matRad_getIsoCenter(cst,ct,0); %  target center
-
-
+if strcmp(pln.propStf.template.type,'manual')
+    pln.propStf.template.activeNeedles = [0 0 0 1 0 1 0 1 0 1 0 0 0;... % 7.0
+        0 0 1 0 1 0 0 0 1 0 1 0 0;... % 6.5
+        0 1 0 1 0 1 0 1 0 1 0 1 0;... % 6.0
+        1 0 1 0 1 0 0 0 1 0 1 0 1;... % 5.5
+        0 1 0 1 0 1 0 1 0 1 0 1 0;... % 5.0
+        1 0 1 0 1 0 0 0 1 0 1 0 1;... % 4.5
+        0 1 0 1 0 1 0 1 0 1 0 1 0;... % 4.0
+        1 0 1 0 1 0 0 0 1 0 1 0 1;... % 4.5
+        0 1 0 1 0 1 0 1 0 1 0 1 0;... % 3.0
+        1 0 1 0 1 0 1 0 1 0 1 0 1;... % 2.5
+        0 1 0 1 0 1 0 1 0 1 0 1 0;... % 2.0
+        1 0 1 0 1 0 0 0 0 0 1 0 1;... % 1.5
+        0 0 0 0 0 0 0 0 0 0 0 0 0];   % 1.0
+       %A a B b C c D d E e F f G
+end
 
 %% II.1 - dose calculation options
 % for dose calculation we use eather the 2D or the 1D formalism proposed by
@@ -176,6 +178,8 @@
 else
     pln.propOpt.optimizer = 'IPOPT';
 end
+
+pln.propOpt.optimizer = 'IPOPT';
 %% II.1 - book keeping
 % Some field names have to be kept although they don't have a direct
 % relevance for brachy therapy.
@@ -189,21 +193,21 @@
 
 %% II.1 - view plan
 % Et voila! Our treatment plan structure is ready. Lets have a look:
-display(pln);
+disp(pln);
 
 
 %% II.2 Steering Seed Positions From STF
 % The steering file struct contains all needls/catheter geometry with the
 % target volume, number of needles, seeds and the positions of all needles
 % The one in the end enables visualization.
 
-stf = matRad_generateStf(ct,cst,pln,1);
+stf = matRad_generateStf(ct,cst,pln);
+
 
 %% II.2 - view stf
 % The 3D view is interesting, but we also want to know how the stf struct
 % looks like.
-
-display(stf)
+disp(stf);
 
 %% II.3 - Dose Calculation
 % Let's generate dosimetric information by pre-computing a dose influence 
@@ -226,7 +230,7 @@
 %% IV.1 Plot the Resulting Dose Slice
 % Let's plot the transversal iso-center dose slice
 
-slice = matRad_world2cubeIndex(pln.propStf.isoCenter(1,:),ct);
+slice = matRad_world2cubeIndex(matRad_getIsoCenter(cst,ct),ct);
 slice = slice(3);
 figure
 imagesc(resultGUI.physicalDose(:,:,slice)),colorbar, colormap(jet);

examples/matRad_example2_photons.m

@@ -122,7 +122,7 @@
 % calculate the iso-center which is per default the center of gravity of 
 % all target voxels.
 pln.propStf.numOfBeams      = numel(pln.propStf.gantryAngles);
-pln.propStf.isoCenter       = ones(pln.propStf.numOfBeams,1) * matRad_getIsoCenter(cst,ct,0);
+pln.propStf.isoCenter       = matRad_getIsoCenter(cst,ct,0);
 
 %% dose calculation settings
 % set resolution of dose calculation and optimization
@@ -150,6 +150,7 @@
 %% Generate Beam Geometry STF
 % The steering file struct comprises the complete beam geometry along with 
 % ray position, pencil beam positions and energies, source to axis distance (SAD) etc.
+
 stf = matRad_generateStf(ct,cst,pln);
 
 %%
@@ -184,6 +185,8 @@
 pln.propStf.couchAngles  = zeros(1,numel(pln.propStf.gantryAngles));
 pln.propStf.numOfBeams   = numel(pln.propStf.gantryAngles);
 
+
+
 stf                      = matRad_generateStf(ct,cst,pln);
 pln.propStf.isoCenter    = vertcat(stf.isoCenter);
 dij                      = matRad_calcDoseInfluence(ct,cst,stf,pln);

matRad/MatRad_Config.m

@@ -197,6 +197,7 @@ function setDefaultProperties(obj)
             %  input
 
             %Default Steering/Geometry Properties
+            obj.defaults.propStf.generator = {'PhotonIMRT','ParticleIMPT','SimpleBrachy'};
             obj.defaults.propStf.longitudinalSpotSpacing = 2;
             obj.defaults.propStf.addMargin = true; %expand target for beamlet finding
             obj.defaults.propStf.bixelWidth = 5;