Implementation of LET modifying objectives by lisaseckler · Pull Request #706 · e0404/matRad

lisaseckler · 2024-03-27T14:49:51Z

What's new:

Dirty Dose (dose delivered by high-LET) objectives and its projection and functions (calcDirtyDose and calcLETmask)
LETxDose objectives and its projection (coming from dij.mLETDose)
LETd objectives and its projection (dose weighted LET, but only LETd SquaredUnderdosing is working nicely)
Examples for all those three new objectives, mainly SquaredOverdosing and SquaredUnderdosing are shown
Test Functions to create plots/histograms for the dirty dose share

For all new Objectives there are changes in objectiveFunction, objectiveGradient, OptimizationProblem and so on.

Dirty dose is calculated test wise in matRad_returnDirtyandCleanDose To implement dirty dose in matRad there are matRad_calcLETmask and matRad_calcDirtyDose otherwise there are new dirty dose objectives in an extra DirtyDoseObjectives folder

Changes in dirty dose objectives and two more Objectives: mLETDose and LETd

…to dev_varRBErobOpt

changes in LETd Objectives

cluster variance for dirty dose, dose and LETd + changes in LETd Projection

…ion.asv

…ent.asv

removing all the unnecessary parts

…rdosingTesting.m

into dev_varRBErobOpt

matRad_calcDirtyDose.m

amitantony · 2024-04-10T09:39:30Z

matRad_plotDirtynCleanDoseShare.m

@@ -0,0 +1,72 @@
+function [stackedbarDose,physDoseInDepth,RBExDcurve,RBEcurve,h,d] = matRad_plotDirtynCleanDoseShare(definedEnd,index,ct,ctCube,dij,resultGUI,add,LET_thres,k,displayComparison)
+%


small description on the kind of plot generated here

amitantony · 2024-04-10T09:40:47Z

matRad_plotLETbeamletSpectrumInVoxel.m

@@ -0,0 +1,53 @@
+function [wPhysDose,LET] = matRad_plotLETbeamletSpectrumInVoxel(index, ct, ctCube, dij, resultGUI, bins, displayfigures)


could we remove the ctCube in the arguments and just directly use the ct ?

amitantony · 2024-04-10T09:41:12Z

matRad_returnDirtyandCleanDose.m

@@ -0,0 +1,83 @@
+function [highLETphysDose,lowLETphysDose,totalphysDose] = matRad_returnDirtyandCleanDose(index,ct,ctCube,dij,resultGUI,LET_thres,displayfigures,maxDirtyDose,bins)


same here with the ctCube?

amitantony · 2024-04-22T07:54:04Z

matRad_calcLETmask.m

+%   dij:       matRad dij struct
+%
+% output
+%   LETmask:   logical matrix for dirty dose


have to change the documentation for the output variables

Amits Commits

# Conflicts: # matRad/optimization/+DoseObjectives/matRad_DoseVariance.m # matRad/optimization/projections/matRad_DirtyDoseProjection.m # matRad/optimization/projections/matRad_LETdProjection.m # matRad/optimization/projections/matRad_LETxDoseProjection.m # matRad_calcParticleDose.m # test/matRad_runTests.m

wahln · 2024-06-28T12:14:17Z

I just updated with the new folder structure and dose engines.
Will make a quick review for @amitantony and @lisaseckler to consider.

wahln

Looks already quite good.

Some things remain with respect to the projections, (not) exchanging LET for LETd throughout the code, the calcDirtyDose and calcLETmasks functions, the necessity to keep mLETd as a matrix.

Consistent naming of LETxDose should also be checked.

wahln · 2024-06-28T12:16:58Z

examples/matRad_example12_simpleParticleMonteCarlo.m

@@ -108,7 +108,7 @@

 %% Compare LET
 if isfield(resultGUI,'LET') && isfield(resultGUI_MC,'LET')


If we change LET to LETd, then this need to really be done rigorously. Also here the isfield checks need to do this.

I am not entirely sure if I want to have that change, probably just using LET is better.

wahln · 2024-06-28T12:17:40Z

examples/matRad_example16_LETd.m

Could we merge examples 16,17,18 into one example comparing the different objectives?

wahln · 2024-06-28T12:18:23Z

examples/matRad_example7_carbon.m

 % Let's plot the transversal iso-center LET slice
 slice = round(pln.propStf.isoCenter(3)./ct.resolution.z);
 figure;
-imagesc(resultGUI.LET(:,:,slice)),colorbar, colormap(jet);


Similar considerations about changing LET to LETd as above.. I start to more and more dislike it, as we want to stay flexible.

wahln · 2024-06-28T12:19:11Z

matRad/doseCalc/matRad_calcDirtyDose.m

+dij.dirtyDoseThreshold                       = LET_thres;
+[dij.LETmaskDirty,dij.LETmaskClean,dij.mLET] = matRad_calcLETmask(dij);
+
+dij.dirtyDose = cellfun(@times,dij.LETmaskDirty, dij.physicalDose,'UniformOutput',false);


Did some changes here to consider scenarios.

wahln · 2024-06-28T12:19:51Z

matRad/doseCalc/matRad_calcDirtyDose.m

+% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+dij.dirtyDoseThreshold                       = LET_thres;
+[dij.LETmaskDirty,dij.LETmaskClean,dij.mLET] = matRad_calcLETmask(dij);


Is there any reason to separate matRad_calcLETmask(dij) out o fthe dirty dose function? Do we need it anywhere else?

yeah we dont really use it for any other functions, so we could include it into the function

wahln · 2024-06-28T12:26:57Z

matRad/optimization/projections/matRad_BackProjection.m

            wGrad = cell(size(dij.physicalDose));
            wGrad(obj.scenarios) = arrayfun(@(scen) projectSingleScenarioGradient(obj,dij,doseGrad,scen,w),obj.scenarios,'UniformOutput',false);         
-        end
+        end 


unneccessary whitespace

wahln · 2024-06-28T12:28:52Z

matRad/optimization/projections/matRad_LETdProjection.m

@@ -0,0 +1,96 @@
+classdef matRad_LETdProjection < matRad_BackProjection


The LETdProjection could probably derive from the LETDose projection (and maybe the pyhsicalDose projection) and then just call the superclass methods to obtain their intermediate results?)

wahln · 2024-06-28T12:29:38Z

tempFile.m

This should go? Maybe I added it by accident...

wahln · 2024-06-28T12:30:10Z

test/autoExampleTest/test_examples.m

+    'examples/matRad_example16_LETd.m',...
+    'examples/matRad_example17_LETxDose.m',...
+    'examples/matRad_example18_DirtyDose.m',...


See comment about merging into one example!

wahln · 2024-06-28T12:30:36Z

matRad/util/matRad_calcCubes.m

Did some streamlining on this file

github-actions · 2025-02-14T01:14:17Z

This PR was automatically marked as stale it has been open 30 days with no activity. Please review/update/merge this PR.

lisaseckler added 30 commits November 21, 2023 11:16

Dirty dose calculation and objectives

a2f3241

Dirty dose is calculated test wise in matRad_returnDirtyandCleanDose To implement dirty dose in matRad there are matRad_calcLETmask and matRad_calcDirtyDose otherwise there are new dirty dose objectives in an extra DirtyDoseObjectives folder

LET Objectives

a3b1f91

Changes in dirty dose objectives and two more Objectives: mLETDose and LETd

Merge branch 'dev_varRBErobOpt' of https://github.com/e0404/matRad in…

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…to dev_varRBErobOpt

Test change

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LETd Objective

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changes in LETd Objectives

Objective Variance Implementation

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cluster variance for dirty dose, dose and LETd + changes in LETd Projection

LET experiments for PTCOG

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Cleaning branch

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Function Test

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Test DD

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test change

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Delete matRad_Beam2DirtyDose.asv

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Delete matRad_DoseComparison.asv

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Delete optimization/+DoseObjectives/matRad_LETDirtyDose.asv

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Delete optimization/@matRad_OptimizationProblem/matRad_objectiveFunct…

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…ion.asv

Delete optimization/@matRad_OptimizationProblem/matRad_objectiveGradi…

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…ent.asv

Delete optimization/projections/matRad_DirtyDoseProjection.asv

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Delete optimization/projections/matRad_LETdProjection.asv

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Update matRad_Beam2DirtyDose.m

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removing all the unnecessary parts

Delete matRad_Beam2DirtyDoseMCN_WED.m

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Delete matRad_Beam2mLETDoseMCN.m

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Update matRad_Beam2DirtyDose.m

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Delete matRad_UnderdosingTesting.asv

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Update and rename matRad_UnderdosingTesting.m to matRad_DirtyDoseUnde…

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…rdosingTesting.m

Delete matRad_calcLETmask.asv

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Delete matRad_fluenceOptimization.asv

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Cleaning LET Optimization

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Merge branch 'dev_varRBErobOpt' of https://github.com/lisaseckler/matRad

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into dev_varRBErobOpt

Clean up

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Testing examples and deleting scripts

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lisaseckler added 10 commits March 27, 2024 14:35

Merge branch 'e0404:dev_varRBErobOpt' into dev_varRBErobOpt

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Merge branch 'dev_varRBErobOpt' of https://github.com/lisaseckler/matRad

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into dev_varRBErobOpt

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amitantony self-assigned this Mar 27, 2024

amitantony self-requested a review April 9, 2024 16:11

amitantony reviewed Apr 10, 2024

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amitantony reviewed Apr 22, 2024

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lisaseckler and others added 4 commits April 22, 2024 21:01

Examples

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Amits Commits

Description of LETmask

c3b26c1

some streamlining of the calculation of dirty dose and the LET masks

2d05c9b

wahln self-requested a review June 28, 2024 12:15

wahln requested changes Jun 28, 2024

View reviewed changes

wahln added 3 commits June 28, 2024 15:35

Merge branch 'dev_varRBErobOpt' into pr/706

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remove the tempfile

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Merge branch 'dev_varRBErobOpt' into pr/706

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github-actions bot added the stale Automatic label for stale issues label Feb 14, 2025

		@@ -0,0 +1,72 @@
		function [stackedbarDose,physDoseInDepth,RBExDcurve,RBEcurve,h,d] = matRad_plotDirtynCleanDoseShare(definedEnd,index,ct,ctCube,dij,resultGUI,add,LET_thres,k,displayComparison)
		%

		@@ -0,0 +1,53 @@
		function [wPhysDose,LET] = matRad_plotLETbeamletSpectrumInVoxel(index, ct, ctCube, dij, resultGUI, bins, displayfigures)

		@@ -0,0 +1,83 @@
		function [highLETphysDose,lowLETphysDose,totalphysDose] = matRad_returnDirtyandCleanDose(index,ct,ctCube,dij,resultGUI,LET_thres,displayfigures,maxDirtyDose,bins)

		@@ -108,7 +108,7 @@

		%% Compare LET
		if isfield(resultGUI,'LET') && isfield(resultGUI_MC,'LET')

		@@ -0,0 +1,96 @@
		classdef matRad_LETdProjection < matRad_BackProjection

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