Clatterbridge/TOPAS - Revision history

JacintaYap at 11:09, 1 April 2021

2021-04-01T11:09:59Z

← Older revision		Revision as of 11:09, 1 April 2021
Line 1:		Line 1:
	This simulation is a model of the 62.5 MeV ocular proton therapy beamline at the [http://www.clatterbridgecc.nhs.uk/patients/treatment-and-support/proton-therapy Clatterbridge Cancer Centre] built using TOPAS, a wrap around of the Geant4 code specifically developed for proton therapy applications. This model was redeveloped in TOPAS to incorporate geometry updates and general progress made from the previous [http://www.hep.ucl.ac.uk/pbt/wiki/Clatterbridge/Geant4 Geant4 model].		This simulation is a model of the 62.5 MeV ocular proton therapy beamline at the [http://www.clatterbridgecc.nhs.uk/patients/treatment-and-support/proton-therapy Clatterbridge Cancer Centre] built using [https://topas.readthedocs.io/en/latest/index.html TOPAS], a wrap around of the Geant4 code specifically developed for proton therapy applications. This model was redeveloped in TOPAS to incorporate geometry updates and general progress made from the previous [http://www.hep.ucl.ac.uk/pbt/wiki/Clatterbridge/Geant4 Geant4 model].

	= Parameter system =		= Parameter system =
Line 129:		Line 129:
	= Running the simulation =		= Running the simulation =

	The simulation has been updated for compatibility with TOPAS v3.6.1 and can be cloned from this [https://github.com/jacyap/ClatterbridgeTreatmentLine.git Github repository].		The simulation has been updated for compatibility with TOPAS v3.6.1 and can be cloned from this [https://github.com/jacyap/ClatterbridgeTreatmentLine.git Github repository]. It is not necessary to install Geant4 to run TOPAS, instructions are listed on the readme.

	== Parameter files ==		== Parameter files ==

JacintaYap: /* File chain structure */

2021-04-01T06:46:25Z

File chain structure

← Older revision		Revision as of 06:46, 1 April 2021
Line 19:		Line 19:
	</pre>		</pre>

	It can be useful to ~~also~~ call another file from within the secondary parameter file where it then becomes a parameter file chain. This allows the application to be organised and managed as essentially separate modules: a supportive feature for collaborative work or developing different aspects of a simulation model. Parameter file chains can span horizontally as well as vertically, however the hierarchy structure must be considered as the order is important in this case. Parameter lines higher up in the chain will take precedence over the same commands further down. Moreover, to handle all the different parameters, TOPAS does not allow settings belonging to the same object to be changed in a separate chain~~. Two~~ different files are not able to modify the same parameter. Similarly, all components which are given the same geometry or the same scorer must be contained in the same vertical chain. Fundamentally, the main or default parameters should be defined in the initial file and then everything else that utilises these conditions should be written into adjoining files. A mostly linear hierarchical structure was adopted with interchangeable files for the scoring, this is illustrated in the diagram below.		It can be useful to call another file from within the secondary parameter file where it then becomes a parameter file chain. These can span horizontally as well as vertically however the hierarchy structure must be considered as the order is important in this case. Parameter lines higher up in the chain will take precedence over the same commands further down. Moreover, to handle all the different parameters, TOPAS does not allow settings belonging to the same object to be changed in a separate chain: two different files are not able to modify the same parameter. Similarly, all components which are given the same geometry or the same scorer must be contained in the same vertical chain. Fundamentally, the main or default parameters should be defined in the initial file and then everything else that utilises these conditions should be written into adjoining files. A mostly linear hierarchical structure was adopted with interchangeable files for the scoring, this is illustrated in the diagram below.


	[[File:F_parameterfilechain.png\|border\|center\|600px]]		[[File:F_parameterfilechain.png\|border\|center\|600px]]


	= Geometry =		= Geometry =

JacintaYap: General model overview, more details to be added

2021-04-01T06:40:53Z

General model overview, more details to be added

← Older revision		Revision as of 06:40, 1 April 2021
Line 1:		Line 1:
	This simulation is a model of the 62.5 MeV ocular proton ~~beam~~ at the [http://www.clatterbridgecc.nhs.uk/patients/treatment-and-support/proton-therapy Clatterbridge Cancer Centre] built using TOPAS, a wrap around of the Geant4 code specifically developed for proton therapy applications. This model was redeveloped in TOPAS to incorporate geometry updates and general progress made from the previous [http://www.hep.ucl.ac.uk/pbt/wiki/Clatterbridge/Geant4 Geant4 model].		This simulation is a model of the 62.5 MeV ocular proton therapy beamline at the [http://www.clatterbridgecc.nhs.uk/patients/treatment-and-support/proton-therapy Clatterbridge Cancer Centre] built using TOPAS, a wrap around of the Geant4 code specifically developed for proton therapy applications. This model was redeveloped in TOPAS to incorporate geometry updates and general progress made from the previous [http://www.hep.ucl.ac.uk/pbt/wiki/Clatterbridge/Geant4 Geant4 model].

	= Parameter system =		= Parameter system =

JacintaYap: /* Particle Source */

2021-04-01T06:34:58Z

Particle Source

← Older revision		Revision as of 06:34, 1 April 2021
Line 75:		Line 75:
	Three options are written for the CCC beam. The geometrical parameters of the beam (size and angular divergence) were determined by optical modelling of the beam transport line and implemented as a Gaussian distribution for the first option. The second option, defines the beam by the obtained Twiss parameters. The third option enables a particle source to be generated from a phase space file (PhaseSpaceSource_100k.phsp is provided to generate a beam of 100k protons at the origin).		Three options are written for the CCC beam. The geometrical parameters of the beam (size and angular divergence) were determined by optical modelling of the beam transport line and implemented as a Gaussian distribution for the first option. The second option, defines the beam by the obtained Twiss parameters. The third option enables a particle source to be generated from a phase space file (PhaseSpaceSource_100k.phsp is provided to generate a beam of 100k protons at the origin).

	#BeamSource (default, standard monoenergetic beam)		#''BeamSource'' (default, standard monoenergetic beam)
	#BeamSourceTwiss (Gaussian beam defined by Twiss parameters)		#''BeamSourceTwiss'' (Gaussian beam defined by Twiss parameters)
	#BeamSourcePhase (input beam from phase space file)		#''BeamSourcePhase'' (input beam from phase space file)

	== Phase space inputs ==		== Phase space inputs ==

JacintaYap: /* Additional capabilities */

2021-04-01T06:32:56Z

Additional capabilities

← Older revision		Revision as of 06:32, 1 April 2021
Line 165:		Line 165:

	= Additional capabilities =		= Additional capabilities =

			*Incorporation of information from particle transport codes
			*TOPAS-nBIO extensions

JacintaYap at 06:29, 1 April 2021

2021-04-01T06:29:04Z

@@ Line 27: / Line 27: @@
 = Geometry =
 In general, TOPAS geometry can be described in different ways: essentially the dimensions and position must be specified with respect to the centre of their parent volume. The component name is included in each line with the stated type (shape), parent volume and material. Translational and rotational ''X, Y, Z'' parameters are assigned for positioning of the component within its mother in ''x'', ''y'' and ''z''. The orientation however will depend on the type of component and additional parameters may be required.
 == Treatment beamline ==
@@ Line 68: / Line 68: @@
 d:Ph/Default/CutForPositron = 0.1 mm
 </pre>
 = Particle Source =
@@ Line 133: / Line 131: @@
 The simulation has been updated for compatibility with TOPAS v3.6.1 and can be cloned from this [https://github.com/jacyap/ClatterbridgeTreatmentLine.git Github repository].
 = Output =

JacintaYap: /* Analysis */

2021-04-01T06:18:31Z

Analysis

← Older revision		Revision as of 06:18, 1 April 2021
Line 136:		Line 136:
	= Output =		= Output =
	== Analysis ==		== Analysis ==

			Matlab scripts to plot the BP and LETd alongside CCC data as well as the transverse beam profile as shown below, are included in the /data/analysis directory.

	== Dose profiles ==		== Dose profiles ==

JacintaYap at 06:15, 1 April 2021

2021-04-01T06:15:11Z

@@ Line 30: / Line 30: @@
 == Treatment beamline ==
 [[File:F_TOPASbeamline.png]]
@@ Line 35: / Line 44: @@
 [[File:F_TOPAS_topview_labelled.png]]
 == CAD model ==
@@ Line 41: / Line 53: @@
-The geometries were built in CAD according to their exact physical dimensions which are displayed in this [[Media:A_CCC_treatmentline_drawing.pdf|complete schematic]]. Components are exported as Stereolithography binary (STL) files which describe geometry only by their surfaces (a tessellation of triangular and quadrangular faces which approximate the volume). Although other file formats (i.e. GDML) may intrinsically include different properties such as materials or colour attributes, TOPAS does not interpret this information and each component (with their elements grouped by material) exists as an individual STL file. Furthermore, components may have their own respective axis within the world coordinate system retained during export and additional rotation or translation using parameter lines may be required. To avoid overlaps, a 0.05 mm tolerance was built betwee adjacents surface and components. The positions of every single element within the treatment line coordinate system are displayed in this [[Media:A_CCC_dim_spreadsheet_topas.png|listing]].
+The geometries were built in CAD according to their exact physical dimensions which are displayed in this [[Media:A_CCC_treatmentline_drawing.pdf|complete schematic]]. Components are exported as Stereolithography binary (STL) files which describe geometry only by their surfaces (a tessellation of triangular and quadrangular faces which approximate the volume). Although other file formats (i.e. GDML) may intrinsically include different properties such as materials or colour attributes, TOPAS does not interpret this information and each component (with their elements grouped by material) exists as an individual STL file. Furthermore, components may have their own respective axis within the world coordinate system retained during export and additional rotation or translation using parameter lines may be required. To avoid overlaps, a 0.05 mm tolerance was built between adjacents surface and components. The positions of every single element within the treatment line coordinate system are displayed in this [[Media:A_CCC_dim_spreadsheet_topas.png|listing]]. Additionally, schematics were obtained and used to model the components which were not able to be physically measured (i.e. dose monitors). These can be found with numerous photos of every component from the [http://www.hep.ucl.ac.uk/pbt/wikiData/clatterbridge/ImageMaps/treatmentbeamline/treatmentbeamline.html Clatterbridge Treatment Beamline Image Maps].
 = Physics settings =
 = Visualisation =
 = Particle Source =
 == Phase space inputs ==
-=== BDSIM ===
 = Scoring =
 == Volume scorers ==
 === Dose deposition ===
 === Linear energy transfer ===
 == Surface scorers ==
 === Transverse beam profiles ===
 = Running the simulation =
 The simulation has been updated for compatibility with TOPAS v3.6.1 and can be cloned from this [https://github.com/jacyap/ClatterbridgeTreatmentLine.git Github repository].
@@ Line 68: / Line 138: @@
 == Dose profiles ==
 [[File:F_TOPAS_matchBP.png|700px]]

JacintaYap at 05:20, 1 April 2021

2021-04-01T05:20:53Z

← Older revision		Revision as of 05:20, 1 April 2021
Line 41:		Line 41:


	The geometries were built in CAD according to their exact physical dimensions which are displayed in this [[Media:A_CCC_treatmentline_drawing.pdf\|complete schematic]]. Components are exported as Stereolithography binary (STL) files which describe geometry only by their surfaces (a tessellation of triangular and quadrangular faces which approximate the volume). Although other file formats (i.e. GDML) may intrinsically include different properties such as materials or colour attributes, TOPAS does not interpret this information~~. Therefore~~ each component (with their elements grouped by material) exists as an individual STL file. ~~However~~, ~~each component~~ may have ~~its~~ own respective axis within the world coordinate system retained during export and additional rotation or translation using parameter lines may be required. To avoid overlaps, a 0.05 mm tolerance was built betwee adjacents surface and components. The positions of every single element within the treatment line coordinate system are displayed in this [[Media:A_CCC_dim_spreadsheet_topas.png\|listing]].		The geometries were built in CAD according to their exact physical dimensions which are displayed in this [[Media:A_CCC_treatmentline_drawing.pdf\|complete schematic]]. Components are exported as Stereolithography binary (STL) files which describe geometry only by their surfaces (a tessellation of triangular and quadrangular faces which approximate the volume). Although other file formats (i.e. GDML) may intrinsically include different properties such as materials or colour attributes, TOPAS does not interpret this information and each component (with their elements grouped by material) exists as an individual STL file. Furthermore, components may have their own respective axis within the world coordinate system retained during export and additional rotation or translation using parameter lines may be required. To avoid overlaps, a 0.05 mm tolerance was built betwee adjacents surface and components. The positions of every single element within the treatment line coordinate system are displayed in this [[Media:A_CCC_dim_spreadsheet_topas.png\|listing]].


	= Physics settings =		= Physics settings =

JacintaYap at 05:18, 1 April 2021

2021-04-01T05:18:57Z

← Older revision		Revision as of 05:18, 1 April 2021
Line 1:		Line 1:
	This simulation is a model of the 62.5 MeV ocular proton beam at the [http://www.clatterbridgecc.nhs.uk/patients/treatment-and-support/proton-therapy Clatterbridge Cancer Centre] built using TOPAS, a wrap around of the Geant4 code specifically developed for proton therapy applications. This model was redeveloped in TOPAS to incorporate geometry updates and general progress made from the previous [http://www.hep.ucl.ac.uk/pbt/wiki/Clatterbridge/Geant4 Geant4 model].		This simulation is a model of the 62.5 MeV ocular proton beam at the [http://www.clatterbridgecc.nhs.uk/patients/treatment-and-support/proton-therapy Clatterbridge Cancer Centre] built using TOPAS, a wrap around of the Geant4 code specifically developed for proton therapy applications. This model was redeveloped in TOPAS to incorporate geometry updates and general progress made from the previous [http://www.hep.ucl.ac.uk/pbt/wiki/Clatterbridge/Geant4 Geant4 model].


	= Parameter system =		= Parameter system =
Line 20:		Line 19:
	</pre>		</pre>

	It can be useful to also call another file from within the secondary parameter file where it then becomes a parameter file chain. This allows the application to be organised and managed as essentially separate modules: a supportive feature for collaborative work or developing different aspects of a simulation model. Parameter file chains can span horizontally as well as vertically, however the hierarchy structure must be considered as the order is important in this case. Parameter lines higher up in the chain will take precedence over the same commands further down. Moreover, to handle all the different parameters, TOPAS does not allow settings belonging to the same object to be changed in a separate chain. Two different files are not able to modify the same parameter. Similarly, all components which are given the same geometry or the same scorer must be contained in the same vertical chain. Fundamentally, the main or default parameters should be defined in the initial file and then everything else that utilises these conditions should be written into adjoining files. A mostly linear hierarchical structure was adopted ~~for the CCC model~~ with interchangeable files for the scoring ~~and~~ this is illustrated in the diagram below.		It can be useful to also call another file from within the secondary parameter file where it then becomes a parameter file chain. This allows the application to be organised and managed as essentially separate modules: a supportive feature for collaborative work or developing different aspects of a simulation model. Parameter file chains can span horizontally as well as vertically, however the hierarchy structure must be considered as the order is important in this case. Parameter lines higher up in the chain will take precedence over the same commands further down. Moreover, to handle all the different parameters, TOPAS does not allow settings belonging to the same object to be changed in a separate chain. Two different files are not able to modify the same parameter. Similarly, all components which are given the same geometry or the same scorer must be contained in the same vertical chain. Fundamentally, the main or default parameters should be defined in the initial file and then everything else that utilises these conditions should be written into adjoining files. A mostly linear hierarchical structure was adopted with interchangeable files for the scoring, this is illustrated in the diagram below.