Update on merging VMAT into dev #377

wahln · 2019-09-20T15:09:23Z

this is my updated attempt at merging dev_VMAT with dev especially concerning the new optimization interface, but also dose calculation.

What I did here, is merge dev_VMAT into a copy of the current dev branch. I think that this is better than what I did before (#376 ), because know you have a better acces to the changed files within this pull request (and see the changes i did within the merge commit).
Also @markangert should be able to close (#308 ).

It seems like it runs smoothly now with the old settings, i.e. fluence Opt & DAO opt without preconditioning. It doesn't work with VMAT yet (dose calculation works, but fluence optimization is weird and DAO/VMAT doesn't work)
But anyways, I hope you now have a better basis to continue with the merge.

Some comments:

integration worked quite well with VMAT Optimization Problem deriving from DAO. Yet I am not clear on how to do something similar with the daoVec2Aperture stuff. I am not familiar enough with the implementation, at the moment the changes are in the OptimizationProblemDAO class within the respective functions.
for me siochi leaf sequencing with fails with the matRad.m script, but only when sequencing is turned on and DAO (& of course VMAT) is turned of. Yet I like the idea of putting the number of leves into pln, so I changed all sequencers to have the pln struct in their call.
With preconditioning enabled, DAO gives worse results than directly after sequencing.
I don't like that the fluence optimization now needs the stf only because the tiny part of VMAT code. Can this be handled differently?
Should we just write a matRad_VMAToptimization that itself calls fluence optimization and dao?
Merging was at some points weird (git associated some wierd code parts with each other esp in generateStf and dosecalc). I hope I didn't mess something up there.

Let me know if you have questions. I will let you know if I forgot something in the list.

P.S.: Does someone of you have a very light test script for the VMAT?

New: Siochi leaf sequencing with more fluid number of kept apertures. Still respect constraints of min/max gantry angle spacing.

Changed the first gantry angle from 0 to non-zero. This makes things much easier.

Figured out problem with DAO: the leaf speed was defined as the difference between positions, not absolute difference. Then speed was constrained to be between 0 and 6 cm/s, which forced unidirectional motion, increasing the objective function. Temporary fix: allow negative values. Eventually, change definition of function so that it considers the absolute difference. Will also have to change the Jacobian.

Fixed leaf speed constraints and Jacobian. Siochi sequencing ready to be pilled to dev.

# Conflicts: # optimization/matRad_constFuncWrapper.m # optimization/matRad_jacobFuncWrapper.m

Testing Revert

This reverts commit 3fe0406.

Weight to MU changed from 1 to 100.

pln.bioOptimization put into options structure

This reverts commit 79e5632.

Added leaf speed constraints back in

Changed leaf speed from mm/s -> cm/s, greatly reducing treatment time. Added function helping to test planning capabilities. Fixed bug in Dij sampling, when no voxels are outside of the core.

Shifted time variable to be the time over the optimized beam's arc, rather than the time between optimized beam angles. This makes more sense when calculating e.g. dose rate. Also, this will make more sense when doing dynamic fluence calculation.

Minor tweaks and bugfixes.

Split the daoVec2ApertureInfo into 3 functions so that we didn't have to keep running if statements on VMAT, dynamic vs. static fluence calculation, etc.

Added option for dynamic fluence optimization for VMAT DAO, including support for interpolated apertures.

Support for Jacobian scaling

Added support for 4D dose calculation, including deformed CT cubes and deformation vectors.

This reverts commit de9682f.

…e if possible!

wahln · 2019-09-27T13:31:36Z

So now VMAT optimization also runs, i.e. the example runs trhough at least, but the result doesn't make sense. After fluence optimization, I get a really nice and conformal dose distirbution, but after the VMAT-DAO I get this:

Mabyer I introduced a sign error somewhere in the optimization, because it seems only to upregulate beamlets that to not hit the target:

Seems like I messed something up in the merge... might be tricky to find...

wahln · 2019-09-27T14:11:19Z

matRad_visApertureInfo.m

-    % loop over all shapes of the beam 
-    for j = 1:apertureInfo.beam(i).numOfShapes
+    % loop over all shapes of the beam
+    for j = 1:numOfShapes


I am a little confused here about "numOfShapes". Because above, the numOfShapes is queried by counting the shape structs, which can be different from the "numOfShapes" property in apertureInfo.beam(i).numOfShapes. Was this always this way? @markbangert can you clarify?

wahln · 2019-09-27T14:16:55Z

matRad_fluenceOptimization.m


+if pln.propOpt.runVMAT


This if branch is the only reason we require the stf in the fluenceOptimization call.
The only thing it does is to set a start weight of 0 to beamlets of certain sub-beams. I don't completely get it, because the comment says it should avoid optimization there, but I don't think that setting certain wOnes to zero stops them from being used/changed during the optimization.

…erge # Conflicts: # matRad_calcPhotonDose.m # matRad_directApertureOptimization.m # matRad_engelLeafSequencing.m # matRad_fluenceOptimization.m # matRad_generateStf.m # matRad_sequencing2ApertureInfo.m # matRad_siochiLeafSequencing.m # matRad_xiaLeafSequencing.m # optimization/matRad_collapseDij.m # photons_Generic.mat

…4/matrad into dev_VMAT_merge # Conflicts: # matRad_calcPhotonDose.m # optimization/@matRad_OptimizationProblemDAO/matRad_constraintFunctions.m # optimization/@matRad_OptimizationProblemDAO/matRad_getJacobianStructure.m

…4/matrad into dev_VMAT_merge

wahln · 2021-05-06T14:56:26Z

The most recent updates fixed the jacobian computation and ensured that we always use the newest shape/bixel information (see #506 ), so now it is possible to use dose constraints again.
Something seems to be off when using preconditioning still.

wahln · 2021-05-08T17:14:36Z

Fixed the bug of the missing dij.scaleFactor in matRad_DoseProjection. I don't think that's the best solution, and we should look at it further berfore merging, but at least we should be back with a working default VMAT setting with the new structure.
So now, tasks remaining for me include

figure out the best and least intrusive way to include the preconditioning factor
integrate all other VMAT-Optimization-specific code into the VMAT Optimization Problem class
make sure standard DAO & VMAT are nicely separated in the new structure and VMAT reuses DAO code
check all new parameter definitions
integrate the preconditioner into standard DAO as part of the merge (bonus)

…erge # Conflicts: # matRad_calcCubes.m # matRad_fluenceOptimization.m # matRad_generateStf.m

wahln · 2023-01-27T09:49:27Z

examples/matRad_example8_photonsVMAT.m

+pln.propOpt.VMAToptions.maxGantryAngleSpacing    = 2;      % Max gantry angle spacing for dose calculation
+pln.propOpt.VMAToptions.maxDAOGantryAngleSpacing = 4;      % Max gantry angle spacing for DAO
+pln.propOpt.VMAToptions.maxFMOGantryAngleSpacing = 28;     % Max gantry angle spacing for FMO


These parameters only seem to work for certain combinations of parameters.
Using the following comination throws an error:
pln.propOpt.VMAToptions.maxGantryAngleSpacing = 8; % Max gantry angle spacing for dose calculation pln.propOpt.VMAToptions.maxDAOGantryAngleSpacing = 16; % Max gantry angle spacing for DAO pln.propOpt.VMAToptions.maxFMOGantryAngleSpacing = 28; % Max gantry angle spacing for FMO
If this is intended behavior, the conditions should be tested for and a sensible error message should appear. I don't know if I induced this or it was already there before.

github-actions · 2024-07-07T01:09:31Z

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

eric11210 added 30 commits October 27, 2016 17:53

Test

7f207c0

another test

88708ae

another

9b10669

Added lots of old stuff, some new

951d101

New: Siochi leaf sequencing with more fluid number of kept apertures. Still respect constraints of min/max gantry angle spacing.

Modifying leaf spread

a3e4443

Changed the first gantry angle from 0 to non-zero. This makes things much easier.

Leaf speed fix

d6746b1

Fixed leaf speed constraints and Jacobian. Siochi sequencing ready to be pilled to dev.

Merge remote-tracking branch 'refs/remotes/e0404/dev' into eric

3ca258f

# Conflicts: # optimization/matRad_constFuncWrapper.m # optimization/matRad_jacobFuncWrapper.m

Merge remote-tracking branch 'refs/remotes/e0404/dev' into eric

7085692

Update from dev

3fe0406

Revert Test

db26593

Testing Revert

Revert "Update from dev"

5d24f17

This reverts commit 3fe0406.

Changed MU Conversion

a278043

Weight to MU changed from 1 to 100.

Cleaning up DAO

50b79ff

pln.bioOptimization put into options structure

Revert to old

79f1fa9

Again

79e5632

Revert "Again"

bc71c7d

This reverts commit 79e5632.

Up to date

a794fb1

Added leaf speed constraints back in

Cleanup

9c13746

VMAT Ready?

2f443a7

Changed leaf speed from mm/s -> cm/s, greatly reducing treatment time. Added function helping to test planning capabilities. Fixed bug in Dij sampling, when no voxels are outside of the core.

Had to

b322dca

Had to

79ee967

VMAT - new time variable

ce545ed

Shifted time variable to be the time over the optimized beam's arc, rather than the time between optimized beam angles. This makes more sense when calculating e.g. dose rate. Also, this will make more sense when doing dynamic fluence calculation.

Tweaks

1406582

Minor tweaks and bugfixes.

Split daoVec2ApertureInfo

56d3073

Split the daoVec2ApertureInfo into 3 functions so that we didn't have to keep running if statements on VMAT, dynamic vs. static fluence calculation, etc.

Dynamic fluence optimization

e50abad

Added option for dynamic fluence optimization for VMAT DAO, including support for interpolated apertures.

Jacobi Scaling

c896b4e

Support for Jacobian scaling

4D Dose Calc

de9682f

Added support for 4D dose calculation, including deformed CT cubes and deformation vectors.

Revert "4D Dose Calc"

3148472

This reverts commit de9682f.

More

40fa6e8

wahln added 3 commits September 27, 2019 15:13

Fix display at the end of VMAT example

525cc14

fix display of apertures - please check

c46df5c

readd stf to fluence optimization call... should be removed from ther…

446d163

…e if possible!

wahln commented Sep 27, 2019

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stale bot added the stale Automatic label for stale issues label Nov 3, 2020

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stale bot removed the stale Automatic label for stale issues label Nov 3, 2020

wahln added 2 commits December 3, 2020 22:13

fix basedata

e3d3c1e

wahln mentioned this pull request Mar 31, 2021

Question about VMAT branches #499

Open

wahln added 4 commits May 3, 2021 14:22

Fix correct sequence of precondition factors and dose cube computation

9a59db3

Merge branch 'hotfixes/daoWithConstraints' of https://github.com/e040…

58e3067

…4/matrad into dev_VMAT_merge

fix some issues, mainly with the jacobian in VMAT

a789828

wahln added 2 commits May 8, 2021 19:08

adding the scale factor to the DoseProjection

bcb0a59

Making sure the right aperturevector conversion is used

2b79fb7

wahln and others added 6 commits May 10, 2021 00:27

fix the bixelWeight vector usage in DAO constraint jacobian

a879d71

correct gradient for jacobiScale in DAO

165a017

fix issue with assigning isocenter for VMAT plans in dicom import

98bafb6

fix error in example script

ef7cbd8

Merge branch 'dev' of https://github.com/e0404/matRad into dev_VMAT_m…

e398da2

…erge # Conflicts: # matRad_calcCubes.m # matRad_fluenceOptimization.m # matRad_generateStf.m

turn off diagnostics for fmincon because of error in R2022b

463ca2a

wahln commented Jan 27, 2023

View reviewed changes

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Update on merging VMAT into dev #377

Update on merging VMAT into dev #377

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