Software for design optimization - Revision history

Hpe090: /* Creating the full simulations files for a range-energy look-up-table */

2017-04-05T10:46:13Z

Creating the full simulations files for a range-energy look-up-table

← Older revision		Revision as of 10:46, 5 April 2017
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	=== Creating the full simulations files for a range-energy look-up-table ===		=== Creating the full simulations files for a range-energy look-up-table ===
	~~First, enable the full scoring of all volumes by commenting / uncommenting in ''Main.mac'':~~		It is not critical to have a high number of primaries in this part. 5000-10000 is enough for this step.
	~~#/control/execute readout.mac~~
	~~/control/execute readout_full.mac~~
	~~Then, in the same file, save to the correct ROOT file:~~
	~~/gate/output/root/setFileName ../../DTCToolkit/Data/MonteCarlo/DTC_Full_Aluminium_Absorber{absorberthickness}mm_Degrader{degraderthickness}mm_{energy}MeV~~
	~~#/gate/output/root/setFileName ../../DTCToolkit/Data/MonteCarlo/DTC_Aluminium_Absorber{absorberthickness}mm_{energy}MeV~~
	It is not critical to have a high number of primaries in this part. 10000 is enough for this step. ~~Change this in the ''Main.mac'' file!~~
	To loop through different energy degrader thicknesses, run the script ''runDegrader.sh'':		To loop through different energy degrader thicknesses, run the script ''runDegrader.sh'':
	[gate/python] $ ./runDegraderFull.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>		[gate/python] $ ./runDegraderFull.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>

Hpe090: /* Creating the chip-readout simulations files for resolution calculation */

2017-04-05T10:45:52Z

Creating the chip-readout simulations files for resolution calculation

← Older revision		Revision as of 10:45, 5 April 2017
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	=== Creating the chip-readout simulations files for resolution calculation ===		=== Creating the chip-readout simulations files for resolution calculation ===
	~~First, undo the changes to Main.mac:~~		A sub 1-mm step size will really tell us if we manage to detect such small changes in a beam energy.
	~~/control/execute readout.mac~~		Loop through the different absorber thicknesses:
	~~#/control/execute readout_full.mac~~		[gate/python] $ ./runDegrader.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>
	~~Then, in the same file, save to the correct ROOT file:~~
	~~#/gate/output/root/setFileName ../../DTCToolkit/Data/MonteCarlo/DTC_Full_Aluminium_Absorber{absorberthickness}mm_Degrader{degraderthickness}mm_{energy}MeV~~
	~~/gate/output/root/setFileName ../../DTCToolkit/Data/MonteCarlo/DTC_Aluminium_Absorber{absorberthickness}mm_{energy}MeV~~
	~~In this step a higher number of particles is desired. I usually use 25000 since we need O(100) simulations.~~ A sub 1-mm step size will really tell us if we manage to detect such small changes in a beam energy.

	~~And loop~~ through the different absorber thicknesses:
	[gate/python] $ sh runDegrader.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>
	The same parallel-in-sequential run mode has been configured here.		The same parallel-in-sequential run mode has been configured here.

Hpe090: /* Creating the full simulations files for a range-energy look-up-table */

2017-04-05T10:45:25Z

Creating the full simulations files for a range-energy look-up-table

← Older revision		Revision as of 10:45, 5 April 2017
Line 25:		Line 25:
	It is not critical to have a high number of primaries in this part. 10000 is enough for this step. Change this in the ''Main.mac'' file!		It is not critical to have a high number of primaries in this part. 10000 is enough for this step. Change this in the ''Main.mac'' file!
	To loop through different energy degrader thicknesses, run the script ''runDegrader.sh'':		To loop through different energy degrader thicknesses, run the script ''runDegrader.sh'':
	[gate/python] $ sh runDegraderFull.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>		[gate/python] $ ./runDegraderFull.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>
	The brackets indicate the folder in the Github repository to run the code from.		The brackets indicate the folder in the Github repository to run the code from. Please note that the program should not be executed using the <code>sh</code> command, as this refers do different shells in different Linux distribtions, and not all shells support the conditional bash expressions used in the script.

	For example, with a 3 mm degrader, and simulating a 250 MeV beam passing through a phantom of 50, 55, 60, 65 and 70 mm water:		For example, with a 3 mm degrader, and simulating a 250 MeV beam passing through a phantom of 50, 55, 60, 65 and 70 mm water:
	[gate/python] $ sh runDegraderFull.sh 3 50 5 70		[gate/python] $ ./runDegraderFull.sh 3 50 5 70
	Please note that there is a variable NCORES in this script, which ensures that NCORES versions of the Gate executable are run in parallel, and then waits for the last background process to complete before a new set of NCORES executables are run. So if you set NCORES=8, and run <code>sh runDegraderFull.sh 3 50 1 70</code>, first 50-57 will run in parallel, and when they're done, 58-65 will start, etc. The default value is NCORES=4.		Please note that there is a variable NCORES in this script, which ensures that NCORES versions of the Gate executable are run in parallel, and then waits for the last background process to complete before a new set of NCORES executables are run. So if you set NCORES=8, and run <code>sh runDegraderFull.sh 3 50 1 70</code>, first 50-57 will run in parallel, and when they're done, 58-65 will start, etc. The default value is NCORES=4.

Jars: /* Creating the full simulations files for a range-energy look-up-table */

2017-04-03T09:38:15Z

Creating the full simulations files for a range-energy look-up-table

← Older revision		Revision as of 09:38, 3 April 2017
Line 25:		Line 25:
	It is not critical to have a high number of primaries in this part. 10000 is enough for this step. Change this in the ''Main.mac'' file!		It is not critical to have a high number of primaries in this part. 10000 is enough for this step. Change this in the ''Main.mac'' file!
	To loop through different energy degrader thicknesses, run the script ''runDegrader.sh'':		To loop through different energy degrader thicknesses, run the script ''runDegrader.sh'':
	[gate/python] $ sh ~~runDegrader~~.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>		[gate/python] $ sh runDegraderFull.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>
	The brackets indicate the folder in the Github repository to run the code from.		The brackets indicate the folder in the Github repository to run the code from.

	For example, with a 3 mm degrader, and simulating a 250 MeV beam passing through a phantom of 50, 55, 60, 65 and 70 mm water:		For example, with a 3 mm degrader, and simulating a 250 MeV beam passing through a phantom of 50, 55, 60, 65 and 70 mm water:
	[gate/python] $ sh ~~runDegrader~~.sh 3 50 5 70		[gate/python] $ sh runDegraderFull.sh 3 50 5 70
	Please note that there is a variable NCORES in this script, which ensures that NCORES versions of the Gate executable are run in parallel, and then waits for the last background process to complete before a new set of NCORES executables are run. So if you set NCORES=8, and run <code>sh runDegraderFull.sh 3 50 1 70</code>, first 50-57 will run in parallel, and when they're done, 58-65 will start, etc. The default value is NCORES=4.		Please note that there is a variable NCORES in this script, which ensures that NCORES versions of the Gate executable are run in parallel, and then waits for the last background process to complete before a new set of NCORES executables are run. So if you set NCORES=8, and run <code>sh runDegraderFull.sh 3 50 1 70</code>, first 50-57 will run in parallel, and when they're done, 58-65 will start, etc. The default value is NCORES=4.

Hpe090: /* Creating the chip-readout simulations files for resolution calculation */

2017-04-02T18:00:52Z

Creating the chip-readout simulations files for resolution calculation

← Older revision		Revision as of 18:00, 2 April 2017
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	And loop through the different absorber thicknesses:		And loop through the different absorber thicknesses:
	[gate/python] $ sh runDegrader.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>		[gate/python] $ sh runDegrader.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>
			The same parallel-in-sequential run mode has been configured here.

	== Creating the basis for range-energy calculations ==		== Creating the basis for range-energy calculations ==

Hpe090: /* Creating the full simulations files for a range-energy look-up-table */

2017-04-02T18:00:20Z

Creating the full simulations files for a range-energy look-up-table

← Older revision		Revision as of 18:00, 2 April 2017
Line 30:		Line 30:
	For example, with a 3 mm degrader, and simulating a 250 MeV beam passing through a phantom of 50, 55, 60, 65 and 70 mm water:		For example, with a 3 mm degrader, and simulating a 250 MeV beam passing through a phantom of 50, 55, 60, 65 and 70 mm water:
	[gate/python] $ sh runDegrader.sh 3 50 5 70		[gate/python] $ sh runDegrader.sh 3 50 5 70
	~~This~~ is a parallel process, ~~so don't do too much together~~. ~~I've found that on my 4 core i5~~, ~~100~~ parallel ~~simulations are OK (of course~~ they ~~only get a few % CPU each)~~, ~~but with >200 the virtual machine stops working.~~.. ~~So turn on overnight, but know your limits!~~		Please note that there is a variable NCORES in this script, which ensures that NCORES versions of the Gate executable are run in parallel, and then waits for the last background process to complete before a new set of NCORES executables are run. So if you set NCORES=8, and run <code>sh runDegraderFull.sh 3 50 1 70</code>, first 50-57 will run in parallel, and when they're done, 58-65 will start, etc. The default value is NCORES=4.

	=== Creating the chip-readout simulations files for resolution calculation ===		=== Creating the chip-readout simulations files for resolution calculation ===

Jars: Added findRange.C usage

2017-03-03T11:27:15Z

Added findRange.C usage

← Older revision		Revision as of 11:27, 3 March 2017
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	# The mean value and straggling is calculated correctly		# The mean value and straggling is calculated correctly
	# The energy loss is calculated correctly		# The energy loss is calculated correctly
			You can run <code>findRange.C</code> in root by compiling and giving it three arguments; Energy of the protons, absorber thickness, and the degrader thickness you wish to inspect.
			[DTCToolkit/Scripts] $ root
			ROOT [1] .L findRange.C+
			// void findRange(Int_t energy, Int_t absorberThickness, Int_t degraderThickness)
			ROOT [2] findRange f(250, 3, 50); f.Run();

	The output should look like this: Correctly places Gaussian fits is a good sign.		The output should look like this: Correctly places Gaussian fits is a good sign.

Hpe090: /* Creating the full simulations files for a range-energy look-up-table */

2017-03-03T08:00:29Z

Creating the full simulations files for a range-energy look-up-table

← Older revision		Revision as of 08:00, 3 March 2017
Line 27:		Line 27:
	[gate/python] $ sh runDegrader.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>		[gate/python] $ sh runDegrader.sh <absorber thickness> <degraderthickness from> <degraderthickness stepsize> <degraderthickness to>
	The brackets indicate the folder in the Github repository to run the code from.		The brackets indicate the folder in the Github repository to run the code from.

	For example, with a 3 mm degrader, and simulating a 250 MeV beam passing through a phantom of 50, 55, 60, 65 and 70 mm water:		For example, with a 3 mm degrader, and simulating a 250 MeV beam passing through a phantom of 50, 55, 60, 65 and 70 mm water:
	[gate/python] $ sh runDegrader.sh 3 50 5 70		[gate/python] $ sh runDegrader.sh 3 50 5 70

Hpe090: /* Displaying the results */

2017-03-02T11:23:03Z

Displaying the results

← Older revision		Revision as of 11:23, 2 March 2017
Line 179:		Line 179:
	If there are no problems, use the script <code>DTCToolkit/Scripts/makePlots.C</code> to plot the contents of the file <code>DTCToolkit/OutputFiles/results_makebraggpeakfit.csv</code>:		If there are no problems, use the script <code>DTCToolkit/Scripts/makePlots.C</code> to plot the contents of the file <code>DTCToolkit/OutputFiles/results_makebraggpeakfit.csv</code>:
	[DTCToolkit] $ root Scripts/makePlots.C		[DTCToolkit] $ root Scripts/makePlots.C
	The output ~~should be something like this~~:		The output is a map of the accuracy of the range determination, and a comparison between the range resolution (#sigma of the range determination) and its lower limit, the range straggling.

			[[File:makePlots_accuracy.JPG\|800px]]

			[[File:makePlots_resolution.JPG\|800px]]

Hpe090: /* Finding the resolution */

2017-03-02T10:47:32Z

Finding the resolution

← Older revision		Revision as of 10:47, 2 March 2017
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	// drawBraggPeakGraphFit(Int_t Runs, Int_t dataType = kMC, Bool_t recreate = 0, Float_t energy = 188, Float_t degraderThickness = 0)		// drawBraggPeakGraphFit(Int_t Runs, Int_t dataType = kMC, Bool_t recreate = 0, Float_t energy = 188, Float_t degraderThickness = 0)
	ROOT [0] drawBraggPeakGraphFit(1, 0, 1, 250, 34)		ROOT [0] drawBraggPeakGraphFit(1, 0, 1, 250, 34)
			This is a serial process, so don't worry about your CPU when analysing all ROOT files in one go.
	With the result		With the result