The project contains scripts/data/results only for measurements with the alpha source for now. Most of the code has been written by Geng-Yuan Jeng.

.
└── AlphaSource                 # Main directory
    ├── Data                    # Here you put your .txt files
    ├── Results                 # Plots and results go here
    │   ├── 20181027
    │   └── ...                 # Various date named folders
    ├── root                    # Here you put your .root files
    ├── RunLists                # You don't need to edit this place with the newer versions
    ├── DoseConstants
    └── Plotter                 # Routines for plotting, fitting and style configuration

In order to able to run this code you should have already installed Python 2 and ROOT. Warning: Do not use Python 3! You need Python 2 and Root installed in your system. Python is really easy to install on all machines: https://www.python.org/downloads/release/python-2715/ Then you need ROOT. I suppose most people use macOS so I will give instructions for that:

1. install xcode tools: xcode-select --install
2. install homebrew: /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
3. install dependencies: brew install dpkg cmake binutils
4. export PATH="/Applications/CMake.app/Contents/bin":"$PATH"
5. Download root source: https://root.cern/download/root_v6.18.04.source.tar.gz and extract it: cd Downloads && tar -xf root_v6.18.04.source.tar.gz
6. mkdir buildroot && cd buildroot
7. configure: cmake ../root_v6.18.04 -DCMAKE_INSTALL_PREFIX=/Applications/ROOT.app -DPYTHON_EXECUTABLE=/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 -DPYTHON_LIBRARY=/Library/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib -DPYTHON_INCLUDE_DIR=/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
8. build cmake --build . -- -j4
9. install cmake --build . --target install
10. set environment source /Applications/ROOT.app/bin/thisroot.sh
11. open root root
12. optionally add root directory to path permanently

cat >> ~/.bashrc << "EOF"
source /Applications/ROOT.app/bin/thisroot.sh
EOF

Installation in Linux is not that different. Just install all dependecies using a packet manager i.e.

sudo apt-get install git dpkg-dev cmake g++ gcc binutils libx11-dev libxpm-dev \
libxft-dev libxext-dev gfortran libssl-dev libpcre3-dev \
xlibmesa-glu-dev libglew1.5-dev libftgl-dev \
libmysqlclient-dev libfftw3-dev libcfitsio-dev \
graphviz-dev libavahi-compat-libdnssd-dev \
libldap2-dev python-dev libxml2-dev libkrb5-dev \
libgsl0-dev libqt4-dev

and then proceed with compiling and installing normally using the apropriate directory names.

In order to run any of the scripts, you can issue

python scriptName.py

You can fit a single measurement by issuing

python compareSimpleAlpha_fitRoutine.py -i root/AlphaSource/<Filename>.root

This is going to output the fit results on the command line and also create a PDF file with a plot under Results/<Date of Execution>/<Filename>.pdf.

In order to create .root files for your measurements, just place the .txt files under AlphaSource/Data/AlphaSource and then run the txt2root.sh script from the alphaSource directory:

sh txt2root.sh <date>

where stands for the measurements' date eg. 20181024

You can calculate the dose constant by issuing

python doseConstantCalculator.py -i someConfiguration.txt

where the someConfiguration.txt file contains all the filenames and info that should be passed to the calculator. To create a simple configuration file you can do

cat >> someConfiguration.txt << "EOF"
EJ200PS-1X1P
root/AlphaSource/Pu239new_EJ200PS-1X1P_1_Default_Nofoil_FaceA_FastFrame_20181129.root
root/AlphaSource/Pu239new_EJ200PS-1X1P_4_Default_Nofoil_FaceA_FastFrame_20181115.root
root/AlphaSource/DarkCurrent_HV1700_trigger_101mV_amp50p5mVpDiv_20181121.root
root/AlphaSource/DarkCurrent_HV1700_trigger_101mV_amp50p5mVpDiv_20181121.root
root/AlphaSource/Pu239new_EJ200-2X_3_Default_Nofoil_FaceA_FastFrame_20181129.root
root/AlphaSource/Pu239new_EJ200-2X_3_Default_Nofoil_FaceA_FastFrame_20181115.root
1.32
0.132
EOF

The structure of the file is

rod name
pre irr. measurement file
post irr. measurement file
dark current for pre irr. file
dark current for post irr. file
EJ200-2X_3 rod measurement on pre irr. measurement day
EJ200-2X_3 rod measurement on post irr. measurement day
total dose in Mrad
dose uncertainty in Mrad

Now follows a brief description of the scripts:

Plots a number of measurements under the same histogram. You have to put manually the measurements inside the plot.

The same as the oldRoutine, but this time things are being handled automatically. You just need to put the filenames that you want to plot inside a list.

Takes just one measurement, fits a gaussian curve and outputs its peak with the systematic error.

This script needs some work. It fits many measurements and and overlays their histograms with their fits. It also outputs a simple .dat file with 2 rows, the first being the peak of each curve and the second being the peak error.

Takes a .txt file with raw measurement numbers and converts that into a histogram stored under a TTree inside a .root file.

Just a newer version of the previous script which is not yet compatible with our code yet.

Takes as input the .dat file from compareSimpleAlpha_fitDrawRoutine.py and plots the peaks numbers vs the operator name. The vertical axis has alphanumeric bins corresponding to the operator name.

Legacy version of the previous routine. Might be reserved for future use.

Script that calculates the Dose constant. You need to just give a list of the files and a lists containing the material types and the irradiation details.

Warning: The Instructions below are outdated. You don't need to use them. Just use the txt2root.sh script! (This is how to create the ROOT files) Save your data txt files in alphaSource/data.

First, make a txt file that lists all the data txt files that you want to process. Usually you take all your measurements for a set of samples on the same day; in the example command below, the date is 20180223, but you should replace that with the date of your measurements of interest. Then, from alphaSource directory run

ls -l Data/AlphaSource | grep -ir 20180223 | awk '{print substr($10,0,length($10))}' > RunLists/List-AlphaSource-20180223.txt

At this point you should check if the list file has been created correctly. issue

cat RunLists/List-AlphaSource-20180223.txt

You should see a list containing all the filenames of measurements done on 20180223. If you don't see that then you might want to check if $10 is the correct number in the previous command. (Sometimes you need to set it to $9 or $11.)

Then, you want to run makeTree.py on this list of files to convert them into ROOT histograms. So, you do the following with your list file from the scripts directory:

python makeTree.py - -i RunLists/List-AlphaSource-20180223.txt -d Data/AlphaSource

The files are being written inside the root/alphaSource directory. You might want to check if they were created properly.

Finally, choose one of the more recent compareSimpleAlpha_????.py files in scripts directory and edit it to run over your new root files, which will be saved in alphaSource/data In this python script, create an alias for each root file that you want to run over. Decide which histograms you want to compare on the same canvas, and then create a vector of canvases "plotSets" (at the end of the script); for each canvas, specify the set of histograms (the aliases you defined earlier) that you want to plot together for comparison. Then, run it:

python compareSimpleAlpha_????.py