Update README with authors and license

M4I-nanoscopy · Feb 14, 2020 · 1b10e71 · 1b10e71
1 parent c0d4941
commit 1b10e71
Show file tree

Hide file tree

Showing 2 changed files with 78 additions and 66 deletions.
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 A. Schübel, David Kraphol, Erik Fröjdh, Maastricht University
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README → README.md b/README → README.md
@@ -1,32 +1,32 @@
--------------------------------------------------------------------
-
-     =========================================================
-     Geant4 - an Object-Oriented Toolkit for Simulation in HEP
-     =========================================================
-
-                         Geant4Medipix 
-                         -------------
+Geant4Medipix 
+-------------
 
  Pixel based Medipix geometry with digitiser for simulating Monte Carlo and charge transport simulation as
  well as chip electronics.
 
- 0- REFERENCES
+## REFERENCES
 
  Feel free to use and modify the code. If you intend to publish, please use these references:
 
  [1] A. Schübel, D. Krapohl, E. Fröjdh, C. Fröjdh, and G. Thungström, “A Geant4 based framework for pixel  
  detector simulation,” J. Instrum., vol. 9, no. 12, 2014.
  http://dx.doi.org/10.1088/1748-0221/9/12/C12018
 
- [2] D. Krapohl, A. Schubel, E. Frojdh, G. Thungstrom, and C. Frojdh, “Validation of Geant4 Pixel Detector  
+ [2] D. Krapohl, A. Schubel, E. Fröjdh, G. Thungstrom, and C. Fröjdh, “Validation of Geant4 Pixel Detector  
  Simulation Framework by Measurements with the Medipix Family Detectors,” IEEE Trans. Nucl. Sci., vol. 63, 
  no. 3, pp. 1874–1881, 2016.
  http://dx.doi.org/10.1109/TNS.2016.2555958
 
-
- 1- GEOMETRY DEFINITION
+## Authors
+A. Schübel, David Kraphol, Erik Fröjdh, Lucas Roussel, Paul van Schayck
+
+## License
+MIT 
+
+## GEOMETRY DEFINITION
 
 standard setup 
+```
 ╔═════════════════════════════════════════════════════════════════════════════╗
 ║                                                            ║                ║
 ║                                                         ░:█║                ║
@@ -41,38 +41,39 @@ standard setup
 ║                                                         ░:█║                ║
 ║                                                            ║                ║
 ╚═════════════════════════════════════════════════════════════════════════════╝
-
+```
 The definition of the Medipix detector is flexible in terms of pixel size
 and number of pixels
 
- 2- REQUIREMENTS
+## REQUIREMENTS
 
-    Geant4-10.00 or higher is required in order to profit from multi-threading
-    The Boost library is used to read ini-files
-    HDF5 is optional
-    CAD libraries are optional
+Geant4-10.00 or higher is required in order to profit from multi-threading
+The Boost library is used to read ini-files
+HDF5 is used to write output files
+
+CAD libraries are optional
 
 	    
- 3- PHYSICS LISTS
+## PHYSICS LISTS
 
-    Physics lists can be local (eg. in this example) or from G4 kernel
-    physics_lists subdirectory.
+Physics lists can be local (eg. in this example) or from G4 kernel
+physics_lists subdirectory.
+
+From geant4/source/physics_lists/builders:	 
+- "emstandard_opt0" recommended standard EM physics for LHC
+- "emstandard_opt1" best CPU performance standard physics for LHC
+- "emstandard_opt2"     
+- "emstandard_opt3" best current advanced EM options. 
+- "emlivermore"  low-energy EM physics using Livermore data
+- "empenelope"   low-energy EM physics implementing Penelope models
+- "dna"	     low-energe DNA physics    
+Physics lists and options can be (re)set with UI commands
 
-    From geant4/source/physics_lists/builders:	 
-    - "emstandard_opt0" recommended standard EM physics for LHC
-    - "emstandard_opt1" best CPU performance standard physics for LHC
-    - "emstandard_opt2"     
-    - "emstandard_opt3" best current advanced EM options. 
-    - "emlivermore"  low-energy EM physics using Livermore data
-    - "empenelope"   low-energy EM physics implementing Penelope models
-    - "dna"	     low-energe DNA physics    
-    Physics lists and options can be (re)set with UI commands
-
-    Please, notice that options set through G4EmProcessOPtions are global, eg
-    for all particle types. In G4 builders, it is shown how to set options per
-    particle type.
+Please, notice that options set through G4EmProcessOPtions are global, eg
+for all particle types. In G4 builders, it is shown how to set options per
+particle type.
 
- 4- VISUALIZATION
+## VISUALIZATION
 
   The Visualization Manager is set in the main().
   The initialisation of the drawing is done via the commands :
@@ -85,44 +86,34 @@ and number of pixels
   Optionaly one can choose to draw all particles, only the charged one, or none.
   This command is defined in EventActionMessenger class.
 
- 5- HOW TO START ?
+## HOW TO START ?
   - Install Geant4 and configure the environment (source pathto/geant4.sh)
   - Create a build folder and execute 
+  ```
     % cmake ..
     % make -j <nothreads>
+```
   - Execute G4Medipix in 'batch' mode from macro files
- 	% G4Medipix  -m gamma.mac -t <nothreads>
+ ```
+ % G4Medipix  -m gamma.mac -t <nothreads>
+```
 
   - Execute G4Medipix in 'interactive mode' with visualization
- 	% G4Medipix
- 	....
- 	Idle> type your commands. For instance:
- 	Idle> /control/execute gamma.mac
- 	....
- 	Idle> exit
-
-    There are example mac files in the macro folder as well as tube spectra
+ ```
+% G4Medipix
+....
+Idle> type your commands. For instance:
+Idle> /control/execute gamma.mac
+....
+Idle> exit
+ ```   
+There are example mac files in the macro folder as well as tube spectra
 
-
- 6- OUTPUT FILES
+## OUTPUT FILES
 
- G4Medipix can produce HDF5 files containing the HitCollection : 
- void Add( G4double de, G4double dl, G4ThreeVector pos, G4int column, G4int line, G4int event, G4int particleID )
-  - energy deposition
-  - track length
-  - position
-  - column
-  - line
-  - eventID
-  - particleID: 0 : gamma, 
-		1 : electron
-                2 : proton
-                3 : alpha
-               -1 : positron
-             9999 : all others if any
+G4Medipix can produce HDF5 files containing a `/g4medipix` and `/trajectories` group containing the pixel output 
+matrix and full trajectories of the incident particle.   
+
 
- The most useful output format is sparse formatted as:
- Event, X-pixel, Y-pixel, Energy, ToT, ToA
- which translates to the following python datatype:
- dt = np.dtype([('event', 'u4'), ('X', 'u4'), ('Y', 'u4'),
-               ('E', 'float64'),('ToT','float64'), ('ToA','float64')])
+
+