Update - #12
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Merge remote-tracking branch 'upstream/develop' into develop
Upstream Update try v2
Improved the way traces and doses are saved to files using multithreading.
* develop tests
* Create mdbook.yml * Update * Branch to documentation selected * Update mdbook.yml --------- Co-authored-by: Bartek Rachwał <brachwal@agh.edu.pl>
* Positiopning from CAD model.
Almost isocentre where it should be...
Almost.
* Positioning, renaming and if iba then X and Z in cell positioning are multiplied by -1
* put iba rotaion check directly in layer
* remove redundant code and tune naming
* WIP -> Iba update and naming in code.
TODO!
Change All Plans (Positioning from CSV move to to D3DDetector_Detector)
TopPositionInenv rename to TranslationInLocalFrame
TranslationInLocalFrame moved to Cell
Uptade fobs to incorporate that.
* WIP
* There were a doubled shift of the phantom. Partialy resolved.
TODO - update cell positioning to work properly...
* iba positioning - done!
* Updated - Positioning for IbaImRT Phantom
* Proper box positioning and plan.
Proper table rotation.
Proper box rotation.
* Static radiotherapy-ready setup for Iba ImRT Just Box.
* Updated - enable proper simplified MLC positioning.
* renamings
* Proper MLC positioning and orientation.
* fix d3dtray issue
* WIP.
TODO:
Incorporate it to word construction.
* works for StlDetectorWithPositioningFromCsv
* works for PositioningFromCsv
* WIP ComputeCellsPositioning
* Modular Detector should inherit from IPhysicalVolume and not VPatent
Todo - fix it
* Uptade - Geo creation from 3mf format (saved to db with vertexes in csv) is working almost properly.
Todo:
Deal with the problem in which some walls are “too small” to be considered valid.
fCarTolerance = myMaxExtent * 1e-11 * mm
This depends on the size of the world.
The larger the world, the larger you must have geometric elements in the simulation.
* Phantom Explosion state fixed.
* make it working for regular positioning
* remove Layer Pads export
* cleanup
* rm layer context from d3ddetector
* rmD3DMLayer from project
* WIP - for propouse of merging changes.
* Added tool to change Surface tolerance size.
TODO:
Check in ModularPhantom.cc ModularPhantom::Construct if the triangles are to small or degenerate - if they are - do not create them.
TODO: V2: During exporting meshes to DB -> simplifie meshes in trimesh.
* Code that works well enough. I am careful not to overcomplicate things.
Temporaly - fewer errors
when prouking geometry.
During simulation, more chance that a particle will get stuck because the few remaining damaged elements are more damaged.
* WIP - refac.
* temp data added
* GeometryBuilder and GeometryParser have been refactoured.
The directory structure has been revised.
TODO:
A lot of
* Wip - almost there...
* // TODO: Filtrowanie elementów, które chcemy usunąć z IbaImRT
// TODO: Musi zostać stworzony jakiś modół który pozwoli pobrać ścieżkę do DB i do CSV z z PhantomWorld
Bouth - project them as generic mechanizm and then - implement them in IBA and ModularWP
* TODO:
- Rename Geometry Parser to GeometryDBReader.
- Inside GeometryDBReader -> build list of scintilator cells.
- if path to DB exist -> then then do stuff.
- read materials from DB && translate them to geant materials.
- move and rotate all nev elements inside patient world.
- set minimal patient world size based on GetExtent():
// Get extents
G4VisExtent ve = solid->GetExtent();
G4double xmin = ve.GetXmin(), xmax = ve.GetXmax();
G4double ymin = ve.GetYmin(), ymax = ve.GetYmax();
G4double zmin = ve.GetZmin(), zmax = ve.GetZmax();
* WIP
* Cleaning - Bug:
label = D3DDetector_Cell_ON245 position: (58.7,47.95,59.45)
[INFO]:: IPhysicalVolume::Construct: No direct pv to link...
[INFO]:: Link logical D3DDetector_Cell_ON245 with G4PV: phmWorldPV
transformPosition: (58.7,47.95,59.45)...
no physical volume found.
no rotation.
no rotation.
Looking for source of bug and wgy it was working elier...
* Almost done...
* Working code.
Python intrerpreter finalized properly.
* TODO def.
* Unnecessary double finalization of GeometryDBReader
* Working code.
* Add d3df-patients as submodule under submodules/g4rtd3df-patients
* Patient update
* Capping updated
* Submodule update.
* Submodule update
* Modular Water Phantom updated.
* WIP
* Excluding components from Toml -> Done.
* TODO:
- Update README.md here and in the submodule.
- Implement rotation of 3mf parts.
* README Uptade
* Submodule update
* Submodule uptaded
* Jobs for testbeam
* HDF5 old dependencies remopved, Annoying "make" warning about visability removed, UPdated - g4rt_env.yml to working wersion (also with tools to visualize phantom by trimesh).
* Pyglet and fretype update.
* Properly rotated 3mf geometry.
* PDD update
* update patient reference
* add some improvements
* fix and patient update
* update patient sumbmodule
* Cmake uptades - python path issue.
* Last needed changes.
(missing collon, GDML language (on polisk systems))
* 55 refactor volume calc for the analysis (Dose3D-Future#60)
* add volume for vpatient
* add extra cell volume logic
* fix CellInfo ctr issue
* remove ::SIZE usage
* refactor ::SIZE type
* rm obsolete scoring func
* touch gtest
* add cad export issue fix
* GeometryBuilder cleanup
---------
Co-authored-by: Bartek Rachwal <brachwal@agh.edu.pl>
* add tps test job and data * add fsf test files * add custom beam masks * tuning the fsf definition * exporting of metrics work * add mterics calc * add modified plans * add srunet production data * beam fix * remove redundant method * add merge fixes for new logic
* init app structure (wip)
* sim without final tld obj
* add tld creation (cubic)
* add vtk tweaks
* cleanup fsf
* asf pipeline added
* make asf working with ct data
* add production jobs
* update jobs names
* fix rotation for beam
* fix rotation issue
* tune priorities in TOML job config
* fix hashed scoring mapping
* tld cell scoring added
* voxel scoring added, fixed centre calc in ScoringVolume
* sync
* merge and fix issues with updated develop
* dev sync
* sync
* sync
* Material update.
GPS production in progress.
* GPS Updated and tuned.
* Showstoper - problem z kodowaniem STL... ;_; Again.
* Log massage removel and
* Naprawa meergowania developa into branch 19.
* Update. Incomporate changes from develop to branch 19.
* Add some example data to branch
* Rename ast to stl.
* The method of positioning TLD pastilles in the tray has been changed.
* GPS update
* GPS positioning update
* Updated STL files list
* add new material LiF:Cu,Mg,P
* Positiopning from CAD model.
Almost isocentre where it should be...
Almost.
* Positioning, renaming and if iba then X and Z in cell positioning are multiplied by -1
* remove redundant code and tune naming
* WIP -> Iba update and naming in code.
TODO!
Change All Plans (Positioning from CSV move to to D3DDetector_Detector)
TopPositionInenv rename to TranslationInLocalFrame
TranslationInLocalFrame moved to Cell
Uptade fobs to incorporate that.
* WIP
* There were a doubled shift of the phantom. Partialy resolved.
TODO - update cell positioning to work properly...
* iba positioning - done!
* Updated - Positioning for IbaImRT Phantom
* Proper box positioning and plan.
Proper table rotation.
Proper box rotation.
* Static radiotherapy-ready setup for Iba ImRT Just Box.
* Updated - enable proper simplified MLC positioning.
* Proper MLC positioning and orientation.
* renamings
* WIP.
TODO:
Incorporate it to word construction.
* Modular Detector should inherit from IPhysicalVolume and not VPatent
Todo - fix it
* Uptade - Geo creation from 3mf format (saved to db with vertexes in csv) is working almost properly.
Todo:
Deal with the problem in which some walls are “too small” to be considered valid.
fCarTolerance = myMaxExtent * 1e-11 * mm
This depends on the size of the world.
The larger the world, the larger you must have geometric elements in the simulation.
* Phantom Explosion state fixed.
* WIP - for propouse of merging changes.
* fix d3dtray issue
* works for StlDetectorWithPositioningFromCsv
* works for PositioningFromCsv
* WIP ComputeCellsPositioning
* make it working for regular positioning
* remove Layer Pads export
* cleanup
* rm layer context from d3ddetector
* Added tool to change Surface tolerance size.
TODO:
Check in ModularPhantom.cc ModularPhantom::Construct if the triangles are to small or degenerate - if they are - do not create them.
TODO: V2: During exporting meshes to DB -> simplifie meshes in trimesh.
* Code that works well enough. I am careful not to overcomplicate things.
Temporaly - fewer errors
when prouking geometry.
During simulation, more chance that a particle will get stuck because the few remaining damaged elements are more damaged.
* WIP - refac.
* temp data added
* GeometryBuilder and GeometryParser have been refactoured.
The directory structure has been revised.
TODO:
A lot of
* Wip - almost there...
* // TODO: Filtrowanie elementów, które chcemy usunąć z IbaImRT
// TODO: Musi zostać stworzony jakiś modół który pozwoli pobrać ścieżkę do DB i do CSV z z PhantomWorld
Bouth - project them as generic mechanizm and then - implement them in IBA and ModularWP
* TODO:
- Rename Geometry Parser to GeometryDBReader.
- Inside GeometryDBReader -> build list of scintilator cells.
- if path to DB exist -> then then do stuff.
- read materials from DB && translate them to geant materials.
- move and rotate all nev elements inside patient world.
- set minimal patient world size based on GetExtent():
// Get extents
G4VisExtent ve = solid->GetExtent();
G4double xmin = ve.GetXmin(), xmax = ve.GetXmax();
G4double ymin = ve.GetYmin(), ymax = ve.GetYmax();
G4double zmin = ve.GetZmin(), zmax = ve.GetZmax();
* WIP
* Cleaning - Bug:
label = D3DDetector_Cell_ON245 position: (58.7,47.95,59.45)
[INFO]:: IPhysicalVolume::Construct: No direct pv to link...
[INFO]:: Link logical D3DDetector_Cell_ON245 with G4PV: phmWorldPV
transformPosition: (58.7,47.95,59.45)...
no physical volume found.
no rotation.
no rotation.
Looking for source of bug and wgy it was working elier...
* Almost done...
* Working code.
Python intrerpreter finalized properly.
* TODO def.
* Unnecessary double finalization of GeometryDBReader
* Working code.
* Add d3df-patients as submodule under submodules/g4rtd3df-patients
* Patient update
* Capping updated
* Submodule update.
* Submodule update
* Modular Water Phantom updated.
* WIP
* Excluding components from Toml -> Done.
* TODO:
- Update README.md here and in the submodule.
- Implement rotation of 3mf parts.
* Submodule update
* Jobs for testbeam
* HDF5 old dependencies remopved, Annoying "make" warning about visability removed, UPdated - g4rt_env.yml to working wersion (also with tools to visualize phantom by trimesh).
* Pyglet and fretype update.
* Properly rotated 3mf geometry.
* PDD update
* add some improvements
* fix and patient update
* Cmake uptades - python path issue.
* Last needed changes.
(missing collon, GDML language (on polisk systems))
* 55 refactor volume calc for the analysis (Dose3D-Future#60)
* add volume for vpatient
* add extra cell volume logic
* fix CellInfo ctr issue
* remove ::SIZE usage
* refactor ::SIZE type
* update CMakeLists with extra flags
* Al changes requested by Maja and Aleksandra are done.
* Finalizing rebase.
* Last improvements.
---------
Co-authored-by: Bartek Rachwal <brachwal@agh.edu.pl>
…s and reactions taking place inside the scintillator.
…izm tej ifologi gotowe -> zostało tylko wprowadzić te ify odpowiednio i wprowadzić zmiany proponowane przez bartka.
Analysis flag redoo. Proposed changes implemented. TODO: - Usage of flags in "Scoring" eg: TracksAnalysis = true -> StoreTracks=true MinimalMode=true Itp. - Rename func name in VoxelHit.
TODO: - Rename methods in Voxel Hit. - Enable/Disable flags on basic of job definition.
TODO's for future defined. Before merge TODO: - Enable/Disable flags on basic of job definition.
In new jobs U need to add flags StoreTracks= true StorePositions= true StoreEnergies = true StorePrimaries = true StoreRunInfo= true MinimalMode= false In RunSvc to run full NtupleAnalisys
…ording-the-type-of-physical-event-in-g4 51 the process of recording the type of physical event in g4
…to matrix format with CSV, pickle, and PNG output options.
* The old LogService has been removed. The logg macros have temporarily been replaced by the std::cout << "Temp" << "\n" expression; Todo: - Introduce new logService. - Introduce G4cout and G4err message capture - Introduce callback triggers. * Working Logger. * Probably ready to merge. For the future - update readme (slightly). And add logs whereever U want. * Setting the log level from the CLI -> Done * TODO List Uptaded * TODO english * Update TODO.md * TODO extended * Fix D3DDetector config parsing and update RunSvc geometry initialization order * Refactor main function: reorganize logger initialization In order to capture G4cout and G4err before the kernel launch G4UImanager i need to initialize logSession. (Otherwise, G4cout is only captured from the start of the simulation) * SRUNET -> Działa. TEASTBEAM -> Działa. 95% zmian proponowanych w review - wprowadzono. * Działa na Testbeam, na SRUNET i na WaterPhantom. Wszystkie (poza submodułem) proponowane zmiany zostały wprowadzone. * Job Update
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jhajduga
merged commit Jul 22, 2025
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Doccumentation-Update-for-Propouse-of-PhD
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…se-of-PhD Merge pull request #12 from jhajduga/develop
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