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petsys_analysis

Code for the analysis of data from the PETSys ASIC. Provides functions for decoding the data coming from TBPET.

Requirements

The code has the following minimum requirements:

  • python 3.10
  • scipy 1.10.0
  • numpy 1.23.5
  • matplotlib 3.7.1
  • pyyaml 6.0
  • pytest 7.1.2
  • pandas 1.5.3
  • docopt 0.6.2
  • configparser 5.0.2
  • cython 0.29.32
  • pyarrow 8.0.0

A script for environment set-up using miniconda is provided for Unix systems: source make_condaENV.sh will check if conda installed in the $HOME folder and install the environment. Running with conda already activated will also create or update the environment. If no miniconda is found the user will be prompted to either indicate a miniconda/anaconda installation or to allow the script to download and install miniconda.

For windows the file windEnv-crystal_cal.yml is provided but installation of anaconda/miniconda is left to the user at the moment.

Structure

The main code elements are structured as follows

|- pet_code
|  |- scripts/
|  |   |- cal_monitor.py -- Apply a given energy calibration and plot results.
|  |   |- checks_channels.py -- Check calibration for expected channels.
|  |   |- ctr.py -- CTR monitor script.
|  |   |- flood_maps.py -- Basic script to produce supermodule floodmaps.
|  |   |- grp_channel_specs.py -- Get energy peak position for each channel (calibration/equalization).
|  |   |- make_listmode.py -- Make a selected LM binary from a PETsys output file.
|  |   |- make_map.py -- Provides tools to generate a map file for a setup.
|  |   |- mm_hits.py -- Text output of coincidence hits per mini module.
|  |   |- negatives.py -- Checks a PETsys file for negative energies.
|  |   |- raw_channels.py -- Checks a raw ldat file for expected channels and negatives.
|  |   |- skew_calc.py -- Estimate skew iterating over reference channel data.
|  |   |- slab_spectra.py -- Make energy and time difference spectra for slabs.
|  |   |- thresholds.py -- Generate a PETsys threshold file based on relative calibration.
|  |- src/
|  |   |- filters.py -- Functions for filtering of PETsys events.
|  |   |- fits.py -- Functions for distribution fitting.
|  |   |- io.py -- Input output functions.
|  |   |- plots.py -- Plotting functions.
|  |   |- util.py -- Utilities.

Tests are provided for the functions and, assuming all requirements are met and the environment is activated, can be run with pytest -v