Pareto navigation #669

tobiasbecher · 2023-11-02T09:59:05Z

Added support for Pareto optimization and Pareto navigation

Objectives and constraints are now stored as variables of the optimization problem. This takes away a lot of the redundant operations in the optimization function that loop over the cst otherwise. Also changed the objective function to now calculate all objective function values in a separate function and then sum them up afterwards. First changes for Pareto optimization were also added with the normalization options

Readded function head to getConstraintBounds and more documentation.

- Added plan navigation functionality - Fixed bug with normals in higher dimensions - Added test scripts - Option to calculate voxels on dose Grid

Fixed some changes mentioned in the pull request regarding normalization

- Renamed type to scheme for normalization - Moved normalization to optimation problem for Gradient (not entirely happy) - Some cleanup

wahln · 2023-11-02T10:28:16Z

Thanks for that PR.
Please make sure that standard parameters are not affected, if possible. Then I will review.

Changed converge criteria and added warnings to Pareto function

ferdymercury · 2023-11-27T17:58:55Z

Is this similar to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8526351/ ? Thanks!

tobiasbecher · 2023-11-28T15:32:50Z

No, this uses a different algorithm that generates a set of Pareto optimal plans (https://papers.ssrn.com/sol3/papers.cfm?abstract_id=1427721) and allows for interactive exploration of the Pareto surface after computation.

wahln

Did a rough first review. I think that the pareto stuff can be more directly integrated.
This means you should not have a "Pareto" folder on the top level. The UI should follow the Widget classes (look in the gui folder). the optimization functions as well as the functions for generating points etc. can go into the optimization folder (you can make a pareto subfolder there).

optimization/+DoseConstraints/matRad_MinMaxDose.m

optimization/+DoseObjectives/matRad_EUDMin.m

wahln · 2023-12-12T14:53:15Z

optimization/@matRad_OptimizationProblem/matRad_OptimizationProblem.m

@@ -24,17 +24,27 @@

    properties
        BP
+        normalizationScheme = struct('scheme','none'); % used in pareto optimization


why is this a struct?

For the normalization I need to set upper and lower bounds that I store as further fields of the structure.

Then they should probably be initialized to NaN or some default value as well here.

optimization/@matRad_OptimizationProblem/matRad_OptimizationProblem.m

wahln · 2023-12-12T14:58:35Z

Pareto/tests/matRad_ParetoExample.m

Function names / script names should not start with a capital letter

Also, isn't this an exampkle and not a test?

wahln · 2023-12-12T14:59:22Z

Pareto/tools/matRad_ParetoSurfFromFacets.m

@@ -0,0 +1,74 @@
+function [k,facets] = matRad_ParetoSurfFromFacets(fVals)


see comment on capitalization

wahln · 2023-12-12T15:00:28Z

README.md

It seems weird, that this file is changed in your PR. But the change is correct.

Not entirely sure myself, why this was changed. I think this is already present on the main branch and it was updated when I synced my fork.

wahln · 2023-12-12T15:02:29Z

matRad_fluenceOptimization.m

@@ -263,7 +263,7 @@
 backProjection.scenarioProb = pln.multScen.scenProb;
 backProjection.nominalCtScenarios = linIxDIJ_nominalCT;

-optiProb = matRad_OptimizationProblem(backProjection);
+optiProb = matRad_OptimizationProblem(backProjection,cst);


Maybe I would change this to have the cst first, because in the future it will be possible to have multiple projections (multiple quantities)

I chose this approach since I was not sure if there are cases where the matRad_OptimizationProblem is called in other places than matRad_fluenceOptimization (and my Pareto optimization). So the idea was to allow "backwards" compatibility for now

wahln · 2023-12-12T15:09:01Z

Pareto/NavigationUI/matRad_UIInterpolation.m

This should follow the Widget mechanism (check the gui folder). Create a widget derived from matRad_Widget here, you may ask @amitantony for help with that.

- Changed naming conventions - Some first moving of files

- Created a preProcessing function that is called at the start of fluenceOptimization and lexicographicOptimization to unify the process - Updated objectives to allow for change to lexicographic objective _ Added support for priority lists

# Conflicts: # MatRad_Config.m # matRad_calcCubes.m # matRad_fluenceOptimization.m # optimization/optimizer/matRad_OptimizerIPOPT.m

wahln

Now I gave it a thorough review, see the individual comments.

Pareto/NavigationUI/matRad_navigationProblem.m

wahln · 2024-05-13T10:54:16Z

Pareto/NavigationUI/matRad_navigationProblem.m

+    options = optimoptions('linprog','Display','iter');
+    %options = optimoptions('linprog','Algorithm','interior-point','Display','iter');
+    v = linprog(f,A,b,Aeq,beq,lb,ub,options); 


Looks like this requires the Optimization Toolbox. Is there a way to solve it (maybe slower) with standard Matlab tools? Then we could have an if / else setup. Anyway, you should check for a license using license('test',...) and throw a descriptive error if not available.

Don't really see how this should be solvable without it since it is a linear programming problem:

Option might be to check for the optimization toolbox when starting the Pareto GUI and if it is not available only allow to navigate the pre-calculated plans

Pareto/NavigationUI/matRad_plotPS.m

ParetoGUI/matRad_ButtonWidget.m

ParetoGUI/matRad_ParetoDVHWidget.m

optimization/ParetoOptimization/tools/matRad_generateDummyPoints.m

optimization/ParetoOptimization/tools/matRad_normalFromFacet.m

optimization/ParetoOptimization/tools/matRad_paretoCheck.m

optimization/ParetoOptimization/matRad_paretoOptimization.m

Pareto optimization now supports the preprocessing function and renamed to initOptimization

Actually required for plotting functions! (Forgot to include in commit)

Updates remove some errors I had with using them in the Pareto GUI. Do not interfere with the actual functionality as far as I can tell

Added calc for variable RBE. No scenario support though

# Conflicts: # matRad/MatRad_Config.m # matRad/matRad_fluenceOptimization.m # matRad/optimization/@matRad_OptimizationProblem/matRad_objectiveFunctions.m # matRad/plotting/matRad_plotPenaltyPoints.m # matRad/util/matRad_calcCubes.m

…into dev_ParetoNav

github-actions · 2024-08-04T01:10:41Z

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

tobiasbecher added 16 commits May 31, 2023 13:45

Merge branch 'dev_Pareto' into dev_ParetoObj

823794f

Merge branch 'dev_Pareto' into dev_ParetoObj

4cba6b2

Merge branch 'dev_varRBErobOpt' into dev_ParetoObj

2e806a9

Fixed bug with constraints and added some comments

bc7f21d

Readded function head to getConstraintBounds and more documentation.

Added Pareto Sandwich support

0faf883

Added navigation functionality

6b8aa22

- Added plan navigation functionality - Fixed bug with normals in higher dimensions - Added test scripts - Option to calculate voxels on dose Grid

Merge branch 'e0404:master' into dev_ParetoNavigation

21347fe

Changed naming convention

22bb7e6

Merge branch 'dev_varRBErobOpt' into dev_ParetoNavigation

fed3c63

Incorporate scenario change

778b4cc

Small fixes

8cb4398

Fixed some changes mentioned in the pull request regarding normalization

Final updates

d134d85

- Renamed type to scheme for normalization - Moved normalization to optimation problem for Gradient (not entirely happy) - Some cleanup

File cleanup

23eee6a

Delete testRun.mat

b9009b1

Updated documentation

46ec9b3

tobiasbecher changed the title ~~Dev pareto nav~~ Pareto navigation Nov 2, 2023

Reverted to default values

267d2b8

Changed converge criteria and added warnings to Pareto function

wahln requested changes Dec 12, 2023

View reviewed changes

tobiasbecher added 5 commits January 11, 2024 16:50

First changes based on pull request comments

823f44d

- Changed naming conventions - Some first moving of files

Moved some files and updated GUI

5ddce71

Small bug fix

e8c6218

Added lexicographic optimization

b38a859

- Created a preProcessing function that is called at the start of fluenceOptimization and lexicographicOptimization to unify the process - Updated objectives to allow for change to lexicographic objective _ Added support for priority lists

Update matRad_MinMaxDose.m

f19635f

wahln requested review from amitantony and remocristoforetti April 4, 2024 12:44

Merge branch 'dev_varRBErobOpt' into pr/669

8004b74

# Conflicts: # MatRad_Config.m # matRad_calcCubes.m # matRad_fluenceOptimization.m # optimization/optimizer/matRad_OptimizerIPOPT.m

wahln added 3 commits May 13, 2024 11:47

fix documentation

13e4615

fix missing ct scenario index in calcCubesDoseGrid

ece7b7f

Merge branch 'dev_varRBErobOpt' into pr/669

75f7513

wahln requested changes May 13, 2024

View reviewed changes

tobiasbecher added 8 commits June 18, 2024 17:41

First fixes

c7dc07e

Optimization Preprocessing changes

74ae379

Pareto optimization now supports the preprocessing function and renamed to initOptimization

Plotting support for Pareto optimization

4ceb2bf

Updates to the GUI

db5d715

Readded option to calculate Pareto surface from the given facets

b8df93d

Actually required for plotting functions! (Forgot to include in commit)

Delete matRad_plotPS.m

5baac7a

Delete matRad_ButtonWidget.m

41234fe

Small updates to plotting functions

94d2d46

Updates remove some errors I had with using them in the Pareto GUI. Do not interfere with the actual functionality as far as I can tell

wahln assigned wahln, amitantony, tobiasbecher and remocristoforetti Jun 20, 2024

wahln added the enhancement label Jun 20, 2024

tobiasbecher and others added 8 commits June 21, 2024 12:05

Removed some unnecessary functions

a0336fe

Temporary calcCubes fix for RBExD

130bcc7

Added calc for variable RBE. No scenario support though

changed default linestyle

f0fd213

Changed linewidth for VOIContours

2210d7f

Merge branch 'dev_varRBErobOpt' into pr/669

e93381b

# Conflicts: # matRad/MatRad_Config.m # matRad/matRad_fluenceOptimization.m # matRad/optimization/@matRad_OptimizationProblem/matRad_objectiveFunctions.m # matRad/plotting/matRad_plotPenaltyPoints.m # matRad/util/matRad_calcCubes.m

Merge branch 'dev' into pr/669

aa90d6a

Small GUI updates

c0b9594

Merge branch 'dev_ParetoNav' of https://github.com/tobiasbecher/matRad …

7e1653f

…into dev_ParetoNav

github-actions bot added the stale Automatic label for stale issues label Aug 4, 2024

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Pareto navigation #669

Pareto navigation #669

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github-actions bot commented Aug 4, 2024

		@@ -0,0 +1,74 @@
		function [k,facets] = matRad_ParetoSurfFromFacets(fVals)

Pareto navigation #669

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Pareto navigation #669

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