Warning, /geant4/examples/advanced/exp_microdosimetry/README is written in an unsupported language. File is not indexed.
0001 ========================================================
0002 Geant4 - exp_microdosimetry example
0003 =========================================================
0004
0005 README
0006 ---------------------
0007
0008
0009 The exp_microdosimetry example, originally named "Radioprotection", is currently developed and mantained by Susanna Guatelli (Centre For Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia) Giuliana Milluzzo and Francesco Romano (INFN - Sezione di Catania, Catania, Italy)
0010
0011 ------------------------------------------------------------------------
0012
0013 Contact: susanna@uow.edu.au
0014 giuliana.milluzzo@ct.infn.it
0015 francesco.romano@ct.infn.it
0016 geant4-advanced-examples@cern.ch
0017
0018 ------------------------------------------------------------------------
0019
0020 List of external collaborators:
0021 J. Magini and G. Parisi - University of Surrey, United Kingdom
0022 J. Davis and D. Bolst - University of Wollongong, NSW, Australia
0023 V. Conte, A. Bianchi, A. Selva- INFN-Laboratori Nazionali di Legnaro, Italy
0024
0025 -----------------------------------------------------------------
0026 ----> Introduction.
0027
0028 The exp_microdosimetry example models different detectors for microdosimetry in space applications. The example lets the user
0029 choose between the models of a simplified diamond (1), a micro-diamond (2), a simplified silicon (3), a silicon microdosimeter (4), a two-stage diamond detector (5) a SiC microdosimeter (6) and a mini TEPC:
0030
0031 1) A semplified diamond microdosimeter is based on the detector developed by Prof. Anatoly Rosenfeld and his team at the Centre For Medical Radiation Physics, CMRP, University of Wollongong, NSW, Australia. The design of the device is documented in J. Davis, et al., "Characterisation of a novel diamond-based microdosimeter prototype
0032 for radioprotection applications in space environments",IEEE Transactions on Nuclear Science,
0033 Vol. 59, pp. 3110-3116, 2012.
0034
0035 2) The microdiamond detector is based on the detectors developed by the Research Group of The University of Rome "Tor Vergata". The design and performances of the detector are documented in C. Verona et al., "Spectroscopic properties and radiation damage investigation of a diamond based Schottky diode for ion-beam therapy microdosimetry", Journal of Applied Physics, vol. 118, 2015, and in C. Verona et al., "Toward the use of single crystal diamond based detector for ion-beam therapy microdosimetry", Radiation Measurements, vol. 110, 2018.
0036
0037 3-4) Both silicon microdosimeters are based on the "Bridge" microdosimeter, developed by the Centre For Medical Radiation physics, University of Wollongong, documented in chapter 7 of the PhD Thesis of D. Bolst “Silicon microdosimetry in hadron therapy using Geant4”, https://ro.uow.edu.au/theses1/619/ . (3) contains a simplified geometry with only four sensitive volumes, while (4) includes the complete design.
0038
0039 5) The diamond telescope is based on the detector developed by University of Rome "Tor Vergata". Its design and characterisation are documented in Cesaroni et al., "", Nucl. Instrum. Methods. Phys. Res. A, vol.947, 2019, DOI:https://doi.org/10.1016/j.nima.2019.162744 , and in C. Verona et al., "Characterisation of a monolithic ΔE-E diamond telescope detector using low energy ion microbeams", Radiation Measurements, vol. 159, 2022, DOI:https://doi.org/10.1016/j.radmeas.2022.106875 .
0040 6) A sempliefied version of a Silicon Carbide (SiC) based microdosimeter developed at INFN-CT, including the 370 um thick substrate. The default size are the following: 100x100x22 um.
0041
0042 7) The mini tissue equivalent proportional counter (mini TEPC) developed by the INFN Laboratori Nazionali di Legnaro (A. Bianchi et al., Radiation Physics and Chemistry 202 (2023) 110567) is implemented in the code. In particular, TEPC are considered as the reference detectors employed in experimental microdosimetry according to ICRU, 1983. In the code a preliminary geometry of a mini TEPC with 0.5 mm radius, 1 mm height cylindrical propane sensitive volume at 408 mbar pressure is included. Validation of of the calculated microdosimetric spectra with the experimental data is in progress and will be completed soon. Therefore the implemented current geometry has to be considered as a demonstrative example of a typical mini TEPC used in microdosimetry.
0043
0044 The type of detectors, its shape, and its position can be set via the included "geometry.mac" macro.
0045 This macro is called in both the vis.mac and run.mac macro files, and include the following options:
0046 - a macro command to choose the type of detector between the above (/geometrySetup/selectDetector "...")
0047 - two macro commands to customise the width and thickness of the sensitive volumes (/geometrySetup/detectorDimension/setWidth "...", /geometrySetup/detectorDimension/setThinckness "..."). It won't take effect when using (1) and (4), as these are finalised designs
0048 - two equivalent macro commands (/geometrySetup/detectorDimension/secondStage/...) to customise the second stage of the detector, if (5) is used
0049 - a macro command to choose whether to place the detector in vacuum or inside a water phantom (/geometrySetup/enableWaterPhantom "true/false")
0050 - a macro command for use with the water phantom to set the detector's width in water (/geometrySetup/detectorPosition/setDepth "...")
0051 The above only take effect only if the macro command /geometrySetup/applyChanges is applied. If the user forgets to run this last command a warning is issued at runtime.
0052
0053 A parallel 1 mm radius circular proton beam at 60 MeV (gaussian) is simulated as default of the simulation (protonBeam.mac).
0054 Moreover, an isotropic field of Galactic Cosmic Rays (GCR) protons is available to the users.
0055
0056 NOTE: To maximise efficiency the field has been modelled with a limiting angle to reduce redundant events.
0057
0058 This macro contains a proton field of Galactic Cosmic Rays (GCR)
0059 The energy deposition of each primary and secondary particles traversing the detectors is calculated within the defined sensitive volume.
0060
0061 In particular in this example it is shown how to:
0062 - model realistic experimental microdosimeters in Geant4
0063 - customise the detector's geometry and its position at runtime via macros
0064 - retrieve the information of secondary particles originated in the SV
0065 - define the physics by means of a Geant4 Modular Physics List
0066 - characterise the response of a realistic detector
0067 - save results in an analysis ROOT or or plaintext csv file using the Geant4 analysis component.
0068 - model a realistic isotropic field of GCRs by means of the General Particle Source
0069 The example can be executed in multithreading mode
0070
0071 ------------------------------------------------------------------------
0072 ----> 1.Experimental set-up.
0073
0074 The diamond microdosimeter can be set either in vacuum (for space radioprotection applications) or at a user-defined depth within a water phantom (for clinical applications).
0075 - if placing the detector in a vacuum, its centre coincides with the centre of the world volume. The world is a box with size 10 cm, filled with vacuum.
0076 - if placing the detector in a water phantom, its centre coincides with the chosen depth inside the water phantom. The water phantom is a water box of width 5 cm and length equal to the detector depth + 2 cm. It's placed in a world volume filled with air having twice its size, located so that a depth equal to 0 cm corresponds to the centre of the world.
0077
0078 All SV structures are active.
0079
0080 The default radiation field is defined by means of the GeneralParticleSource in the file
0081 protonBeam.mac
0082
0083 -------------------------------------------------------------------------
0084 ----> 2.SET-UP
0085
0086 A standard Geant4 example CMakeLists.txt is provided.
0087
0088 Setup for analysis:
0089 By default, the example has no analysis component.
0090
0091 To compile and use the application with the analysis on, build the example with the following command:
0092 cmake -DWITH_ANALYSIS_USE=ON -DGeant4_DIR=/path/to/Geant4_installation /path/to/exp_microdosimetry example
0093
0094 When the analysis is enables, the default output format is one compatible with ROOT
0095 The user can switch to a plaintext csv by uncommenting the corresponding macro command in output.mac (/analysis/useRoot false)
0096
0097 Two data analysis scripts are provided for use with each output format:
0098 - for ROOT output (exp_microdosimetry.root), plot.C is provided. If the user intends to use this macro, ROOT must be installed (http://root.cern/drupal/)
0099 - for csv output (exp_microdosimetry_*.csv), 1_plot_distributions.py and 2_calculate_means_rbe.py (in this order). If the user intends to use these macros, Python 3 must be installed (https://www.python.org/)
0100 Both scripts plot the microdosimetric spectrum resulting from the simulation, calculate the microdosimetric means, and provide one or more RBE estimates (this is just provided as an example, and the user is encouraged to look into RBE modelling himself)
0101
0102 ------------------------------------------------------------------------
0103 ----> 3.How to run the example.
0104
0105 - Batch mode:
0106 ./exp_microdosimetry run.mac
0107
0108 - Interative mode:
0109 ./exp_microdosimetry
0110 vis.mac is the default macro, executed in interactive mode.
0111
0112 ---------------------------------------------------------------------------------
0113 ----> 4. Primary radiation Field
0114
0115 The radiation field is defined with the General Particle Source.
0116 Look at the macro protonBeam.mac .
0117
0118 If this example is used for medical applications (with a water phantom) the user is encouraged to replace this macro with one that might simulate a therapeutic beam of interest
0119
0120 ------------------------------------------------------------------------
0121 ----> 5. Simulation output
0122
0123 **** SEQUENTIAL MODE
0124 The output is radioprotection.root, containing
0125 - an ntuple with the A, Z, and energy of the secondary particles originated in the diamond microdosimeters.
0126 - an ntuple withe the energy spectrum (in MeV) of primary particles.
0127 - an ntuple with the energy deposition per event(in keV) in the SV.
0128
0129 When outputting to plaintext csv a separate file is used for each ntuple, following the naming scheme:
0130 radioprotection_nt_10?.csv
0131
0132 where ? is the number of the ntuple
0133
0134
0135 **** MULTITHREAD mode
0136 output files:
0137 exp_microdosimetry.root_t0
0138 ..
0139 ..
0140 exp_microdosimetry.root_t#
0141
0142 where # is the number of threads
0143
0144 When outputting to plaintext csv a separate file is used for each ntuple, following the naming scheme:
0145 exp_microdosimetry_nt_10?_t#.csv
0146
0147 where ? is the number of the ntuple
0148
0149
0150 when using ROOT type: source MergeFiles to merge the output of each thread in a single one
0151 when using Python, the first script takes care of parsing and merging the ntuples
0152
0153 -------------------------------------------------------------------------------
0154 ----> 6.Visualisation
0155
0156 a macro is provided ad example of visualisation: vis.mac
0157
0158 For any problem or question please contact Susanna Guatelli, susanna@uow.edu.au
0159
0160 -------------------------------------------------------------------------------
0161 ----> 7. Analysis
0162 Two sets of macro:
0163 - ProcessMicro.C for ROOT output
0164 - 1_plot_distributions.py and 2_calculate_means_rbe.py (to be executed in this order) for csv output
0165
0166 Each macro performs analysis of the energy deposition stored in the ntuple and performs the following microdosimetry operations:
0167 -Bins the event by event energy deposition stored in the ntuple into a histogram (both with linear and logarithmic binning) and converts to lineal energy
0168 -Calculates the quantities: mean lineal energy (yF), the dose mean lineal energy (yD), the quality factor (Q) using the weighting factors from the ICRP 60 report
0169 -In addition to these quantities the macro also calculates an estimate for the RBE using the modified MK model. This model is not generally used for shielding/radiation proction but in hadron therapy, but is provided for interest.
0170 -The Python macro also includes an RBE estimate via weight function. For more info about this RBE model, see T. Loncol et al, “Radiobiological Effectiveness of Radiation Beams with Broad
0171 LET Spectra: Microdosimetric Analysis Using Biological Weighting Functions”, Radiation Protection Dosimetry 52.1-4, pp. 347–352, 1994
0172 -The macro also generates the common "microdosimetric spectra" or yd(y) in a semi-log plot
0173
0174 When using the two-stage detector (5), no analysis script is currently included for the second stage
0175
0176 ------------------------------------------------------------------------------
0177 -----> Future developments
0178
0179 1) Further macros will be included for placing a variable number of sensitive volumes
0180 2) A new macro messenger will be included to allow the user to stop the simulation after a given number of recorded events, in order to have more control over the statistics of the simulation
0181 3) A new script will be added to provide a dE-E plot for use with the telescope detector (5)
