Software tutorial at IFT - Revision history

Hpe090: /* Configuring the DTC Toolkit to run with correct geometry */

2017-06-02T11:37:21Z

Configuring the DTC Toolkit to run with correct geometry

@@ Line 465: / Line 465: @@
 === Configuring the DTC Toolkit to run with correct geometry ===
-The values from <code>findManyRanges.C</code> should already be in <code>DTCToolkit/Data/Ranges/3mm_Al.csv</code> (or the corresponding material / thickness). Check that the file is correctly loaded in the file <code>DTCToolkit/GlobalConstants/MaterialConstants.C</code>. The values from <code>findAPAndStraggling.C</code> are put into the same file <code>DTCToolkit/GlobalConstants/MaterialConstants.C</code>:
+The values from <code>findManyRanges.C</code> should already be in <code>DTCToolkit/Data/Ranges/3mm_Al.csv</code> (or the corresponding material / thickness).
-Or in the corresponding material (alpha_pmma, alpha_carbon, etc.) and absorbatorthickness lines.
+Look in the file <code>DTCToolkit/GlobalConstants/Constants.h</code> and check that the correct absorber thickness values etc. are set:
     ...
 Bool_t useDegrader = true;
@@ Line 499: / Line 478: @@
 Since we don't use tracking but only MC truth in the optimization, the number kEventsPerRun (<math>n_p</math> in the NIMA article) should be higher than the number of primaries per energy.
 == Running the DTC Toolkit ==

Hpe090: /* Range straggling parameterization and R_0 = \alpha E^p */

2017-06-02T11:35:35Z

Range straggling parameterization and R_0 = \alpha E^p

← Older revision		Revision as of 11:35, 2 June 2017
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	=== Range straggling parameterization and <math>R_0 = \alpha E^p</math> ===		=== Range straggling parameterization and <math>R_0 = \alpha E^p</math> ===
	It is important to know the amount of range straggling in the detector, and the amount of energy straggling after the degrader. In addition, to calculate the parameters <math>\alpha, p</math> from the somewhat inaccurate Bragg-Kleeman equation <math>R_0 = \alpha E ^ p</math>, in order to correctly model the "depth-dose curve" <math>dE / dz = p^{-1} \alpha^{-1/p} (R_0 - z)^{1/p-1}</math>. This is ~~done~~ by ~~fitting~~ the ~~Bragg-Kleeman equation to~~ the ~~range-energy look up tables found~~ by using <code>~~DTCToolkit/Scripts/findManyRangesDegrader~~.C</code>.		It is important to know the amount of range straggling in the detector, and the amount of energy straggling after the degrader. In addition, to calculate the parameters <math>\alpha, p</math> from the somewhat inaccurate Bragg-Kleeman equation <math>R_0 = \alpha E ^ p</math>, in order to correctly model the "depth-dose curve" <math>dE / dz = p^{-1} \alpha^{-1/p} (R_0 - z)^{1/p-1}</math>. This happens automatically in <code>DTCToolkit/GlobalConstants/MaterialConstants.C</code>, so there is no need to do this by hand. This step should be followed anyhow, since it is a check of the data produced in the last step: Outliers should be removed or "fixed", eg. by manually fitting the conflicting datapoints using <code>findRange.C</code>.

	To find all this, run the script <code>DTCToolkit/Scripts/findAPAndStraggling.C</code>. This script will loop through all available data lines in the <code>DTCToolkit/OutputFiles/findManyRangesDegrader.csv</code> file that has the correct absorber thickness, so you need to clean the file first (or just delete it before running <code>findManyRangesDegrader.C</code>).		To find all this, run the script <code>DTCToolkit/Scripts/findAPAndStraggling.C</code>. This script will loop through all available data lines in the <code>DTCToolkit/OutputFiles/findManyRangesDegrader.csv</code> file that has the correct absorber thickness, so you need to clean the file first (or just delete it before running <code>findManyRangesDegrader.C</code>).
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	[[File:findAPAndStraggling.JPG\|700px]]		[[File:findAPAndStraggling.JPG\|700px]]

	~~In addition, the following parameters should be extracted:~~

	~~Bragg-Kleeman parameters: R = 0.011626 E ^ 1.743151~~
	~~Straggling = 1.8568 + 0.000856 R~~

	=== Configuring the DTC Toolkit to run with correct geometry ===		=== Configuring the DTC Toolkit to run with correct geometry ===

Hpe090: /* GATE simulations */

2017-06-02T11:32:39Z

GATE simulations

← Older revision		Revision as of 11:32, 2 June 2017
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	The simplified simulation geometry for the future DTC simulations has been proposed as:		The simplified simulation geometry for the future DTC simulations has been proposed as:

	[[File:Layer schematics.PNG\|~~600px~~]]		[[File:Layer schematics.PNG\|700px]]

	It is partly based on the ALPIDE design, and the FoCal design. The GATE geometry corresponding to this scheme is based on the following hierarchy:		It is partly based on the ALPIDE design, and the FoCal design. The GATE geometry corresponding to this scheme is based on the following hierarchy:

Hpe090: /* Geometry scheme */

2017-06-02T11:32:30Z

Geometry scheme

← Older revision		Revision as of 11:32, 2 June 2017
Line 373:		Line 373:
	The simplified simulation geometry for the future DTC simulations has been proposed as:		The simplified simulation geometry for the future DTC simulations has been proposed as:

	[[File:~~geometry~~.PNG\|600px]]		[[File:Layer schematics.PNG\|600px]]

	It is partly based on the ALPIDE design, and the FoCal design. The GATE geometry corresponding to this scheme is based on the following hierarchy:		It is partly based on the ALPIDE design, and the FoCal design. The GATE geometry corresponding to this scheme is based on the following hierarchy:

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

2017-04-05T10:47:09Z

Creating the chip-readout simulations files for resolution calculation

← Older revision		Revision as of 10:47, 5 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] $ ./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 */

2017-04-05T10:47:02Z

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

← Older revision		Revision as of 10:47, 5 April 2017
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	In this step, 5000-10000 particles are usually sufficient in order to get accurate results.		In this step, 5000-10000 particles are usually sufficient in order to get accurate results.
	To loop through different energy degrader thicknesses, run the script ''runDegraderFull.sh'':		To loop through different energy degrader thicknesses, run the script ''runDegraderFull.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. 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.		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.

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

2017-04-05T10:46:51Z

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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	To loop through different energy degrader thicknesses, run the script ''runDegraderFull.sh'':		To loop through different energy degrader thicknesses, run the script ''runDegraderFull.sh'':
	[gate/python] $ sh runDegraderFull.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. 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:

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

2017-04-02T18:01:22Z

Creating the chip-readout simulations files for resolution calculation

← Older revision		Revision as of 18:01, 2 April 2017
Line 406:		Line 406:
	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 */

2017-04-02T18:01:03Z

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

← Older revision		Revision as of 18:01, 2 April 2017
Line 399:		Line 399:
	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] $ sh runDegraderFull.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 ===

Mri083: /Troubleshooting / adding new section

2017-03-22T20:34:55Z

Troubleshooting: adding new section

← Older revision		Revision as of 20:34, 22 March 2017
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	'''DISCLAIMER: Some of the materials have been copied from the GATE v7.2 User's guide: http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.2'''		'''DISCLAIMER: Some of the materials have been copied from the GATE v7.2 User's guide: http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.2'''

			== Troubleshooting ==
			=== makeGeometryDTC.py - python ImportError: cannot import name _tkagg ===
			The makeGeometryDTC.py scripts requires specific functionality in the python '''matplotlib'''. The following error can be solved by rebuilding '''matplotlib''' after installing the '''tk-dev''' package.

			Traceback (most recent call last):
			File "test.py", line 7, in <module>
			from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg, NavigationToolbar2TkAgg
			File "/home/fieldsofgold/new/env/local/lib/python2.7/site-packages/matplotlib/backends/backend_tkagg.py", line 13, in <module>
			import matplotlib.backends.tkagg as tkagg
			File "/home/fieldsofgold/new/env/local/lib/python2.7/site-packages/matplotlib/backends/tkagg.py", line 7, in <module>
			from matplotlib.backends import _tkagg
			ImportError: cannot import name _tkagg

			Rebuild '''matplotlib''':
			sudo apt-get install tk-dev
			pip uninstall -y matplotlib
			pip --no-cache-dir install -U matplotlib

Software tutorial at IFT - Revision history

Hpe090: /* Configuring the DTC Toolkit to run with correct geometry */

Hpe090: /* Range straggling parameterization and R_0 = \alpha E^p */

Hpe090: /* GATE simulations */

Hpe090: /* Geometry scheme */

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

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

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

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

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

Mri083: /*Troubleshooting */ adding new section

Mri083: /Troubleshooting / adding new section