https://github.com/dpscience/dcontinpals
pyDCONTINPALS - A Python program for running the historical FORTRAN code CONTIN-PALS which solves Fredholm integral equations with convoluted exponential decays as kernels of the type that occur in the analysis of Positron Annihilation Lifetime Spectra (PALS).
https://github.com/dpscience/dcontinpals
analysis contin datareduction exponential-decay exponential-distributions flm fredholm-integral-equation ill-posed inverse-problems laplace-inversion lifetime-spectroscopy linear-algebraic-equations multi-exponential-decay nonnegativity-constraints pals positron-annihilation-lifetime positron-lifetime-spectra regularization tikhonov tikhonov-regularization
Last synced: 5 months ago
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pyDCONTINPALS - A Python program for running the historical FORTRAN code CONTIN-PALS which solves Fredholm integral equations with convoluted exponential decays as kernels of the type that occur in the analysis of Positron Annihilation Lifetime Spectra (PALS).
- Host: GitHub
- URL: https://github.com/dpscience/dcontinpals
- Owner: dpscience
- License: other
- Created: 2019-12-25T15:08:29.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2023-09-27T20:38:38.000Z (over 2 years ago)
- Last Synced: 2025-03-09T16:35:59.558Z (11 months ago)
- Topics: analysis, contin, datareduction, exponential-decay, exponential-distributions, flm, fredholm-integral-equation, ill-posed, inverse-problems, laplace-inversion, lifetime-spectroscopy, linear-algebraic-equations, multi-exponential-decay, nonnegativity-constraints, pals, positron-annihilation-lifetime, positron-lifetime-spectra, regularization, tikhonov, tikhonov-regularization
- Language: Fortran
- Homepage:
- Size: 4.42 MB
- Stars: 4
- Watchers: 2
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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# pyDCONTINPALS
Copyright (c) 2020-2023 Dr. Danny Petschke (danny.petschke@uni-wuerzburg.de). All rights reserved.
pyDCONTINPALS - A program in Python for running the historical FORTRAN code CONTIN-PALS initially provided by [Provencher (1982)](https://www.sciencedirect.com/science/article/abs/pii/0010465582901746) and [Gregory et al. (1990/](https://www.sciencedirect.com/science/article/abs/pii/016890029090358D)[1991)](https://www.sciencedirect.com/science/article/abs/pii/016890029190367Y). CONTIN-PALS program solves Fredholm integral equations with convoluted exponential decays as kernels of the type that occur in the analysis of Positron Annihilation Lifetime Spectra (PALS).
# Quickstart Guide
`pyDCONTINPALS` consists of 3 files ...
`pyDCONTINPALS.py`
`pyDCONTINPALSInput.py`
`pyDCONTINPALSSpecSimulator.py`
* edit the input file `pyDCONTINPALSInput.py`:
```python
__demoMode = True # disable if running from real data
# NOTE: SPECTRUM and IRF (or mono-exponential decay spectrum) data vectors require equal length!
__roi_start = 0
__roi_end = 7400 # Note: number of channels is internally limited by CONTIN to <= 4000, so adjust the '__binFactor' in order to fit the given number of channels into this range
# file path (and name) to the SPECTRUM data:
__usingRefSpectrum = True # if set to FALSE the '__irfXXX' related parameters are considered
__filePathSpec = 'testData/spectrum_10ps.dat'
__specDataDelimiter = '\t'
# file path (and name) to the IRF data:
__filePathRefOrIRFSpec = 'testData/ref_10ps.dat'
__refDataDelimiter = '\t'
# define the number of rows to be skipped during the import of the data (e.g. for ignoring the header entries):
__skipRows = 5;
# fixed mono-decay component in units of picoseconds [ps] (1/lambda = tau):
# Note: set to values below 1E-6 if you are providing numerical IRF data as input otherwise the decay rate in [ps]:
__tau_monoDecaySpec_in_ps = 182. # [ps]
# used to model the IRF data in case '__usingRefSpectrum' = False:
__t_zero = 2000 # channel number
__irf_fwhm = [270.04,498.63] # [ps]
__irf_intensity = [0.9382,0.0618] # [ps]
__irf_t0 = [0.,6.6] # [ps]
# grid of characteristic lifetimes with equally distributed grid points defining the resulting intensity spectrum to be expected as output:
__gridTau_start = 10.0 # [ps]
__gridTau_stop = 3000.0 # [ps]
__gridPoints = 100 # 10 ... 100 Note: this value is internally limited by CONTIN
# channel/bin resolution [ps]:
__channelResolutionInPs = 10. # >= 10 ... Note: this value is internally limited by CONTIN. If lower, increase '__binFactor' to fit into this range
__binFactor = 2 # Note: number of channels is internally limited by CONTIN to <= 4000, so adjust the '__binFactor' in order to fit the given number of channels into this range
# background estimation/calculation region:
__bkgrd_startIndex = 6500;
__bkgrd_count = 900; # number of channels with respect to the 'startIndex''
```
* execute `pyDCONTINPALS.py`
* finished. You should see the results as shown above in the figures when running in the demo mode (__demoMode = True).
# How to cite this Program?
* Before citing this program pyDCONTINPALS you need at least to cite the initial publication of the FORTRAN program [CONTIN-PALS provided by Gregory et al. (1990)](https://www.sciencedirect.com/science/article/abs/pii/016890029090358D).
[90358--D-yellowgreen)](https://www.sciencedirect.com/science/article/abs/pii/016890029090358D)
[R.B. Gregory, Y. Zhu, Analysis of positron annihilation lifetime data by numerical laplace inversion with the program CONTIN, Nucl. Instruments Methods Phys. Res. Sect. A Accel. Spectrometers, Detect. Assoc. Equip. 290 (1990) 172–182. doi:10.1016/0168-9002(90)90358-D.](https://doi.org/10.1016/0168-9002(90)90358-D).
* Additionally, you should cite the applied version of this program in your study.
You can cite all released software versions by using the DOI 10.5281/zenodo.3665474. This DOI represents all versions, and will always resolve to the latest one.
[](https://doi.org/10.5281/zenodo.3665475)
## ``v1.x``
pyDCONTINPALS v1.04
[](https://doi.org/10.5281/zenodo.8384544)
pyDCONTINPALS v1.03
[](https://doi.org/10.5281/zenodo.7023157)
pyDCONTINPALS v1.02
[](https://doi.org/10.5281/zenodo.4630108)
pyDCONTINPALS v1.01
[](https://doi.org/10.5281/zenodo.4452238)
pyDCONTINPALS v1.0
[](https://doi.org/10.5281/zenodo.3665475)
# License of (py)DCONTINPALS (GNU General Public License)
Copyright (c) 2020-2023 Dr. Danny Petschke (danny.petschke@uni-wuerzburg.de) All rights reserved.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details see [GNU General Public License v3](https://www.gnu.org/licenses/gpl-3.0)