Class based Sequencing by JenHardt · Pull Request #891 · e0404/matRad

JenHardt · 2026-02-27T13:31:14Z

Implementation of a class to handle the photon sequencing with the three algorithims siochi, xia, engle as well as an ion sequencer

incorperation of the three photon sequencing algorithims and update of the base class

codecov · 2026-02-27T13:44:08Z

Codecov Report

❌ Patch coverage is 59.10596% with 494 lines in your changes missing coverage. Please review.
✅ Project coverage is 54.64%. Comparing base (adf48b0) to head (8a17097).

Files with missing lines	Patch %	Lines
matRad/gui/widgets/matRad_WorkflowWidget.m	16.51%	182 Missing ⚠️
...ring/matRad_StfGeneratorExternalRayBixelAbstract.m	38.93%	69 Missing ⚠️
matRad/sequencing/matRad_PhotonSequencerAbstract.m	70.40%	66 Missing ⚠️
matRad/sequencing/matRad_SequencerBase.m	58.33%	55 Missing ⚠️
...atRad/sequencing/matRad_SequencingPhotonsXiaLeaf.m	73.68%	20 Missing ⚠️
...ad/sequencing/matRad_SequencingPhotonsSiochiLeaf.m	86.77%	16 Missing ⚠️
...Rad/sequencing/matRad_SequencingPhotonsEngelLeaf.m	88.88%	12 Missing ⚠️
matRad/4D/matRad_acc4dDose.m	47.61%	11 Missing ⚠️
matRad/4D/matRad_calc4dDose.m	60.00%	10 Missing ⚠️
matRad/sequencing/matRad_engelLeafSequencing.m	0.00%	10 Missing ⚠️
... and 9 more

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #891      +/-   ##
==========================================
- Coverage   54.80%   54.64%   -0.16%     
==========================================
  Files         320      327       +7     
  Lines       20548    20703     +155     
==========================================
+ Hits        11261    11313      +52     
- Misses       9287     9390     +103

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github-actions · 2026-02-27T14:00:51Z

Test Results

3 files ±0 3 suites ±0 32m 53s ⏱️ + 1m 1s
357 tests ±0 353 ✅ - 4 0 💤 ±0 4 ❌ +4
1 167 runs ±0 1 158 ✅ - 4 5 💤 ±0 4 ❌ +4

For more details on these failures, see this check.

Results for commit 8a17097. ± Comparison against base commit adf48b0.

This pull request removes 5 and adds 5 tests. Note that renamed tests count towards both.

test_TopasMCEngine ‑ test_TopasMCdoseCalc4D
test_TopasMCEngine ‑ test_TopasMCdoseCalcBasic
test_TopasMCEngine ‑ test_TopasMCdoseCalcBasicRBE
test_TopasMCEngine ‑ test_TopasMCdoseCalcMultRuns
test_TopasMCEngine ‑ test_TopasMCdoseCalc_multiAlphaBeta

test_TopasMCEngine ‑ test_topasMCdoseCalc4D
test_TopasMCEngine ‑ test_topasMCdoseCalcBasic
test_TopasMCEngine ‑ test_topasMCdoseCalcBasicRBE
test_TopasMCEngine ‑ test_topasMCdoseCalcMultRuns
test_TopasMCEngine ‑ test_topasMultiAlphaBeta

♻️ This comment has been updated with latest results.

wahln · 2026-02-27T14:06:11Z

There seem to be a bunch of unhappy tests in this PR ;-)

wahln · 2026-02-27T14:10:01Z

Also I am confused about the changed 4D capabilities (that don't seem to have anything to do with sequencing in parts).
Also, we should keep downwards compatibility with the old sequencing calls for a while.

wahln

Did some preliminary rough review.

wahln · 2026-03-04T15:54:04Z

@@ -1,4 +1,4 @@
-function resultGUI = matRad_sequencing(resultGUI,stf,dij,pln,visBool)
+function resultGUI = matRad_sequencing(resultGUI,stf,pln,dij,visMode)


Is there a reason why the dij has become optional? This is a huge change without much benefit it seems.

it is just because the dij is just used to recalculate the dose based on the new sequenced weight vector, but you could run the sequencing independently

wahln · 2026-03-04T15:56:15Z

This could probably still be removed?

wahln · 2026-03-04T15:56:43Z

@@ -1,29 +1,23 @@
-function [resultGUI, timeSequence] = matRad_calc4dDose(ct, pln, dij, stf, cst, resultGUI, totalPhaseMatrix,accType)
+function resultGUI = matRad_calc4dDose(dij, pln,stf,resultGUI, totalPhaseMatrix)


why did the argument list chagne so drastically?

the ct was only used to save the number of ct scenarios and the motion period , this should now be in the pln scenario model and the cst was used for the ax and bx vectors this is taken directly from the dij

okay let's approach it from the other way: can we avoid the pln struct when using the ct?
I would like to keep pln out of lower-level functions as much as possible, and only pass it to top-level workflow functions (as the pln can, for example, be easily changed in the GUI and lead to inconsistent inputs).

i think this can be done, but then i need the ct again,

no acctually i need it to selecect the sequencer and calculate the phaseMatrix if not given, although right now the phaseMatrix is only calculated for ions not photons

wahln · 2026-03-04T15:57:25Z

Isn#t this a function that should actually be moved into the IonSequencer?

it is this was one of the files i deleted, where i just now reverted the delition to make it backwards compatible, i haved pushed the update to this file jet

wahln · 2026-03-04T16:00:53Z

Change in the interface destroys downwards compatibility.. Is this necessary?

i removed it because it was never used in the function

wahln · 2026-03-04T16:02:06Z

Naming the file sequencingOld and the function still sequencing will create problems. I suggest to not change the interface of the sequencing call (with the optional dij at the end) but just keep the old interface (resultGUI,stf,dij,pln,visBool) -> visBool can become visMode, this is still OK just selecting the visMode 1 if it is true.

similar to above this is an issue of the delition and reverting of the delition that is not completet yet

wahln · 2026-03-04T16:02:35Z

What is changed in the submodule? Is this intentional?

…ate of test data

github-actions · 2026-04-20T02:37:30Z

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

wahln · 2026-05-05T15:30:53Z

I think this needs an update from the dev branch

read-the-docs-community · 2026-05-11T09:29:04Z

Documentation build overview

📚 matRad | 🛠️ Build #32632799 | 📁 Comparing 8a17097 against latest (c014dc8)

🔍 Preview build

38 files changed · + 1 added · ± 37 modified

+ Added

datastructures/userfolder.html

± Modified

JenHardt added 15 commits June 27, 2025 17:27

first very rough draft of sequecing class with SiochiLeaf Implementation

e867f80

Merge branch 'dev' into dev_Sequencing

c4a105a

Merge branch 'dev' into dev_Sequencing

87ddbe3

updates to sequencing

3c43496

incorperation of the three photon sequencing algorithims and update of the base class

continuationof sequencing

dcb8749

Merge branch 'dev' into dev_Sequencing

9331425

Update ompMC

bb931d3

delete old files

4bbfe0f

updated 3d conformal

b777135

part of class now

68ea49a

part of ion sequencer class

cb40953

removed unused opt result

f4e74e4

updated DAO example

460f8ba

remove unnecessary update ResultGUi

5bdd747

set fill empty Bixels to true to fix DAO issue with empty bixels

dd36310

JenHardt added 3 commits March 4, 2026 13:36

restore Files

6e7ca5b

revert files

a307a62

revert files

dc96b20

wahln mentioned this pull request Mar 4, 2026

Update on merging VMAT into dev #377

Open

wahln requested changes Mar 4, 2026

View reviewed changes

JenHardt added 6 commits March 6, 2026 15:13

updates test

f28cf64

fill empty bixels only for photons so not to interfer so much and upd…

2a138b5

…ate of test data

changing of names

f1fca5a

updates of old functions

d511408

merge dev branch

cbbed97

merge dev

aaea936

octave6fix

5b6e8a8

github-actions Bot added the stale Automatic label for stale issues label Apr 20, 2026

github-actions Bot removed the stale Automatic label for stale issues label May 6, 2026

merge dev

8a17097

		@@ -1,4 +1,4 @@
		function resultGUI = matRad_sequencing(resultGUI,stf,dij,pln,visBool)
		function resultGUI = matRad_sequencing(resultGUI,stf,pln,dij,visMode)

		@@ -1,29 +1,23 @@
		function [resultGUI, timeSequence] = matRad_calc4dDose(ct, pln, dij, stf, cst, resultGUI, totalPhaseMatrix,accType)
		function resultGUI = matRad_calc4dDose(dij, pln,stf,resultGUI, totalPhaseMatrix)

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JenHardt commented Feb 27, 2026

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wahln commented Feb 27, 2026

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github-actions Bot commented Apr 20, 2026

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read-the-docs-community Bot commented May 11, 2026

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