silab-bonn/irrad_spectroscopy

Gamma-spectroscopy of (irradiated) samples in Python

irrad_spectroscopy's Issues

Integrate decay mode for isotope dose rate calculations

Currently, the dose rate calculations for isotopes, performed using the isotope_dose_rate function in irrad_spectroscopy.physics, do not respect the decay mode with which the given isotope decays. This results in an underestimation of the dose rate for e.g. cases where a beta plus (positron) decay generates 2 additional 511 keV photons.

This is partially related to #11, where the information on the decay mode for many isotopes is incorrect or outdated

Add to unittests

Dose rate calculation

Calculate dose rate per gamma and ultimately per isotope in air for each spectrum

Improve background - peak discrimination

Add function that returns a channel-like bool mask with peak and background positions

Add analyse_spectrum method

Add analyse_spectrum method to spectroscopy.py as convinience function in order to do full spectral analysis in one step

Add theoretical calculation of dose per isotope and activity

Add compute_dose function which takes isotope=activity keywords arguments and returns the effective dose by all given isotopes for a certain parameter set of distance etc

Code refactor

Refactor the code and remove deprecated functions / imports as well as restructure the code

API changes for version 0.1

This lists major API changes from 0.01 to 0.1:

• If bkg=None is given in spectroscopy.fit_spectrum, the method returns a tuple of (peaks, bkg). Otherwise it returns only peaks 751a73b
• Replace arguments x by channels and y by counts in spectroscopy.fit_spectrum. Don't require channels 0569349
• Replace arguments x by channels, y by counts and calibration by energy_cal in spectroscopy.interpolate_bkg. Don't require channels 0569349
• Replace arguments x by channels and y by counts in spectroscopy.fit_spectrum. Don't require channels 0569349
• Replace arguments x by channels, y by counts and calibration by energy_cal in plot_utils.plot_spectrum. Don't require channels 0569349
• Replace argument lib by table in spectroscopy.validate_isotopes 56fa1b4
• Rename isotope_lib to gamma_table, element_lib to element_table, xray_coeffs to xray_coefficients_table in irrad_spectroscopy.__init__ 56fa1b4
• Add tables folder; move table files there 56fa1b4
• Add material to xray_coefficients_table and argument material to physics.gamma_dose_rate 56fa1b4
• Rename calc_activity to get_activity in spectroscopy 566b811
• Rename spec_utils.isotopes_to_dict to spec_utils.get_isotope_info and replace arguments lib by table and fltr by iso_filter 56fa1b4
• Rename spec_utils.create_isotope_library to spec_utils.create_gamma_table 56fa1b4
• Add spec_utils.select_peaks method 44226dc
• Add functionality to do x-ray spectroscopy exclusively: add argument xray to spectroscopy.fit_spectrum in order to look only for x-ray K, L, ... lines from e.g. fluorescence 0eb5ff7

Gamma table refactor

The current gamma table is generated from this website which

1. Does not seem to be hosted anymore
2. Contains many isotopes with incorrect (outdated) information

A new gamma should be generated from a more reliable resource e.g. The Lund/LBNL Nuclear Data Search

Bugs

Remove some known bugs:

• fix IndexError for empty background for local background fit, e.g. masking entire peak surroundings, fixed in 4e480c0
• remove out-of-range gamma lines from validation procedure, fixed in 510d3fe
• correctly estimate intersection of peak fit and local background from data, fixed in 4e480c0
• multiple x peak positions for one count height possible, needs loop, fixed in 2c00f37
• finding start parameters for peak fit sometimes gives IndexError, fixed in 2c00f37
• calibrations only need to check whether the line is in the source dict, fixed in 2c00f37
• fix KeyError for local_bkg=False, fixed in 2c00f37
• fix sanity-check: higher probability of gamma should have higher activity in peak, fixed in af4773b
• fix Gaussian error propagation for spectroscopy.get_activity, fixed in 566b811