fitlistreader

A package for reading and evaluating fitlist.xml files as generated by hdtv.

Installation

$ pip install fitlistreader

Requirements

python 3.8.14 or newer
numpy 1.19.4 or newer
scipy 1.5.4 or newer (for interpolation background models)

All requirements will automatically install with the pip command above, given you have a supported python version.

Usage

For basic usage in a terminal, CLI integration is available with the command

$ fitlistreader [-h] [-I] [-C] [--noheader] [-l args] path/to/fitlist.xml

The output is of a form that can be used directly or imported into excel or similar.

Options

Flag	Description
`-I` `--Integrals`	Switches to integral mode. Only the recorded integrals are listed. This is different from the int_* options for -l, as all integrals are listed and not only the ones belonging to peaks.
`-C` `--Calibrations`	Switches to read out the calibrations of respective spectra contained in the fitlist
`-h` `--help`	Displays this help text and exits.
`--noheader`	Ommit printing the header line
`-l [args]` `--labels`	Change printed values to those specified in labels arg (see below). By default, `pos`, `dpos`, `vol`, `dvol`, `width`, `dwidth`, `bg`, `dbg` and `bg_model` are used.

Labels:

With the -l/–labels option, the values which are extracted from the fitlist.xml file can be changed. The values will be printed in order of specification. Available labels are:

Label	Description
pos	Peak position
dpos	Uncertainty in peak position
vol	Peak volume
dvol	Uncertainty in peak volume
width	Peak width
dwidth	Uncertainty in peak width
bg	Background volume under the peak
dbg	Uncertainty in background volume under peak
bg_model	Background model used in fitting
spc	Spectrum name from which the peaks were fitted
cal	Calibration coefficients (polynomial, 0 order first) of the spectrum
int_id	ID of corresponding Integral
int_pos	Position of corresponding Integral
int_dpos	Uncertainty in position of corresponding Integral
int_vol	Volume of corresponding Integral
int_dvol	Uncertainty in volume of corresponding Integral
int_width	Width of corresponding Integral
int_dwidth	Uncertainty in width of corresponding Integral
int_skew	Skew of corresponding Integral
int_dskew	Uncertainty in skew of corresponding Integral

Usage as a package

If you want to programatically interact with the data stored in a fitlist.xml file without parsing the datastructure yourself, filistreader offers full access to all stored data with a quick, iterable and freely addressable datastructure called a fitlist.

from fitlistreader.fitlist import fitlist

fl = fitlist('path/to/fitlist.xml')
for peak in fl:
    print(peak.pos)

The fitlist object parses the supplied xml file and determines the basic structure of the fitlist like its length. The actual data, however, is only read on demand and then cached, improving reading times. For further details on the included objects, consult the documentation.

License

fitlistreader was created by Markus Muellenmeister. It is licensed under the terms of the GNU General Public License v3.0 license.

Credits

fitlistreader was created with cookiecutter and the py-pkgs-cookiecutter template.