moose-spectra 0.2.0__tar.gz

moose_spectra-0.2.0/.gitignore

@@ -0,0 +1,175 @@
+# Byte-compiled / optimized / DLL files
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+*$py.class
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+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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moose_spectra-0.2.0/LICENSE

@@ -0,0 +1,7 @@
+Copyright <2022> <Antoine Salden>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

moose_spectra-0.2.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: moose-spectra
+Version: 0.2.0
+Summary: A package to simulate diatomic optical emission spectra relying on line-by-line databases compiled for MassiveOES
+Project-URL: Source, https://github.com/AntoineTUE/Moose
+Project-URL: Documentation, https://antoinetue.github.io/Moose/
+Author-email: Antoine Salden <t.p.w.salden@tue.nl>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.9
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Provides-Extra: all
+Requires-Dist: moose-spectra[docs]; extra == 'all'
+Requires-Dist: moose-spectra[examples]; extra == 'all'
+Requires-Dist: moose-spectra[fit]; extra == 'all'
+Provides-Extra: docs
+Requires-Dist: mkdocs-gen-files; extra == 'docs'
+Requires-Dist: mkdocs-git-revision-date-localized-plugin; extra == 'docs'
+Requires-Dist: mkdocs-jupyter; extra == 'docs'
+Requires-Dist: mkdocs-literate-nav; extra == 'docs'
+Requires-Dist: mkdocs-material; extra == 'docs'
+Requires-Dist: mkdocs-section-index; extra == 'docs'
+Requires-Dist: mkdocstrings; extra == 'docs'
+Requires-Dist: mkdocstrings-python; extra == 'docs'
+Provides-Extra: examples
+Requires-Dist: ipywidgets; extra == 'examples'
+Requires-Dist: matplotlib; extra == 'examples'
+Requires-Dist: moose-spectra[fit]; extra == 'examples'
+Requires-Dist: panel; extra == 'examples'
+Requires-Dist: plotly; extra == 'examples'
+Provides-Extra: fit
+Requires-Dist: lmfit; extra == 'fit'
+Description-Content-Type: text/markdown
+
+# Moose: Molecular optical emission spectroscopy for Python
+Welcome to `Moose`, a python package for simulating optical emission spectra for diatomic molecules.
+
+`Moose` was born out of a need to fit rotational and vibrational temperatures for a large set of data.
+
+For this it uses *line-by-line databases*, assuming a Boltzmann distribution for rotational and/or vibrational temperatures.
+
+On top of that `Moose` is intended to be *minimal*: it provides you some basic tools to do just that, simulate some spectra.
+
+It is up to you to read and sanitize experimental data, that you would like to fit based on these simulations, for instance.
+
+Put differently, `Moose` is aimed at helping you: you can integrate and adapt it to your workflow, rather than the reverse.
+
+To get a better grasp of how it works under the hood, see the online documentation for [code reference](https://antoinetue.github.io/Moose/reference/Moose/Simulation/) and [examples](https://antoinetue.github.io/Moose/examples/).
+
+## Supported bands
+Since `Moose` reuses the databases from [MassiveOES](https://bitbucket.org/OES_muni/massiveoes), it supports the same bands for fitting.
+Details can be found in [data_sources.txt](./Moose/data/data_sources.txt), and the [page with information on citing](https://antoinetue.github.io/Moose/citing/).
+
+| **Molecule** | **Band** |
+| --- | --- |
+| OH | A-X |
+| N2+ | B-X |
+| NH | A-X |
+| NO | B-X |
+| N2 | C-B |
+| C2 | Swan |
+| CN | B-X |
+
+
+## Dependencies
+The following packages are dependencies to be able to use `Moose`. 
+Version numbers are just indications of the package versions that were used to develop the code, your mileage may vary using either older or newer versions.
+Furthermore, even though the project does not import by default `lmfit` and contains no functions that specifically rely on it, the code contains convenience functions that were specifically written for usage with the `lmfit.Model` and `lmfit.Parameters` classes. 
+If `lmfit` is installed in the active enironment, some additional convenience function will be imported.
+
+These dependencies will be installed when you install `Moose` using `pip`.
+
+| **Package**  | **Version**  |
+|---|---|
+| Numpy  | >= 1.21.5  |
+| Pandas | >= 1.4.0 |
+| scipy | >= 1.7.3 |
+| *lmfit* (optional) | >= *1.2.0* |
+
+
+
+
+## Installation
+`Moose` can be installed by first downloading/cloning the package with `git`.
+
+Once you have a copy, you can install it using `pip` from the project directory.
+
+To simply install `Moose` itself, running the following suffices:
+
+```bash
+pip install .
+```
+
+Installing `Moose` with additional optional dependencies is described on the [documentation page on getting started](https://antoinetue.github.io/Moose/get_started/).
+
+## Basic usage
+A basic example demonstrating the usage is as follows.
+It assumes that there is a `pandas` DataFrame (called `data`) containing several spectra normalized on the interval (0,1), with the first column being a shared wavelength axis.
+It is important that the wavelength range over which we query the database (`wl_interval`), is larger than the experimental range plus the possible shift (`mu`) between simulation and experiment.
+
+Extending the fitting over multiple cores/processes can be done by using for instance the excellent [Dask](https://dask.org/) library, via i.e. `client.map`.
+More elaborate examples are available via the [online documentation](https://antoinetue.github.io/Moose/examples/).
+
+```python
+import Moose, lmfit
+
+wl_interval = (320,345) # Wavelength interval over which to simulate the spectrum
+db = Moose.query_DB('N2CB.db', wl_interval)
+
+
+# Create the lmfit.Model and lmfit.Parameters object needed for the fit.
+model = lmfit.Model(Moose.model_for_fit, sim_db=db)
+params = lmfit.create_params(**Moose.default_params)
+# Or use some default suggested parameters for thermal fitting, i.e. T_rot==T_vib
+# params = lmfit.create_params(**Moose.thermal_default_params)
+
+# Perform the fit
+fits = []
+for col in data.columns[1:]:
+    fits.append(model.Fit(data[col].values, x=data['Wavelength'].values, params=params))
+
+```
+
+
+## Copyright notice from MassiveOES
+
+The original software is massiveOES developed by the Masaryk University available from: https://bitbucket.org/OES_muni/massiveoes.
+
+### Publications
+
+VORÁČ, Jan; SYNEK, Petr; PROCHÁZKA, Vojtěch; HODER, Tomáš. State-by-state emission spectra fitting for non-equilibrium plasmas: OH spectra of surface barrier discharge at argon/water interface. Journal of Physics D: Applied Physics. 2017, 50(29), 294002. DOI: https://doi.org/10.1088/1361-6463/aa7570.
+
+
+VORÁČ, Jan; SYNEK, Petr; POTOČŇÁKOVÁ, Lucia; HNILICA, Jaroslav; KUDRLE, Vít. Batch processing of overlapping molecular spectra as a tool for spatio-temporal diagnostics of power modulated microwave plasma jet. Plasma Sources Science and Technology 26.2 (2017), 025010. DOI: https://doi.org/10.1088/1361-6595/aa51f0.
+
+
+#### Original sources for databases
+| Database | Source | DOI |
+| --- | --- | --- |
+| OHAX |J. Luque and D.R. Crosley, J. Chem. Phys., 109, 439 (1998) | https://dx.doi.org/10.1088/0022-3727/39/17/015 | 
+| OHAX | L.R. Williams and D.R. Crosley, J. Chem. Phys, 104, 6507 (1996) | https://doi.org/10.1063/1.471371 |
+| N$_2^+$BX |  J. Luque and D.R. Crosley, “LIFBASE: Database and Spectral Simulation Program (Version 1.5) ”, SRI International Report MP 99-009 (1999). |  | 
+| NHAX | Western C 2016 PGOPHER—a program for simulating rotational structure, Version 9.0.100, University of Bristol |  |
+| NHAX |  Ram R and Bernath P 2010 J. Mol. Spectrosc. 260 115–9 | https://doi.org/10.1016/j.jms.2010.01.006 |
+| NHAX | Lents J 1973 J. Quant. Spectrosc. Radiat. Transfer 13 297–310 | https://doi.org/10.1016/0022-4073(73)90061-7 |
+| NHAX  | Seong J, Park J K and Sun H 1994 Chem. Phys. Lett. 228 443–50 | https://doi.org/10.1016/j.jms.2010.01.006 |
+| NOBX | J. Luque and D.R. Crosley, “LIFBASE: Database and Spectral Simulation Program (Version 1.5) ”, SRI International Report MP 99-009 (1999). |  |
+| N$_2$CB | Nassar H, Pellerin S, Musiol K, Martinie O, Pellerin N and Cormier J 2004. Phys. D: Appl. Phys. 37 1904 | https://doi.org/10.1088/0022-3727/37/14/005 |
+| N$_2$CB | Laux C O and Kruger C H 1992 J. Quant. Spectrosc. Radiat. Transfer 48 9–24 | https://doi.org/10.1016/0022-4073(92)90003-M |
+| N$_2$CB | Faure G and Shko’nik S 1998 J. Phys. D: Appl. Phys. 31 1212 | https://doi.org/10.1088/0022-3727/31/10/013 |
+| C$_2$ Swan | James S.A. Brooke and Peter F. Bernath and Timothy W. Schmidt and George B. Bacskay; Journal of Quantitative Spectroscopy and Radiative Transfer; 2013 | https://doi.org/10.1016/j.jqsrt.2013.02.025 |
+| C$_2$ Swan | Carbone, Emile and D'Isa, Federico and Hecimovic, Ante and Fantz, Ursel; PSST; 2020; | https://doi.org/10.1088/1361-6595/ab74b4 |
+
+# License information
+This project is licensed under the MIT license.
+See [LICENSE](./LICENSE).

moose_spectra-0.2.0/README.md

@@ -0,0 +1,122 @@
+# Moose: Molecular optical emission spectroscopy for Python
+Welcome to `Moose`, a python package for simulating optical emission spectra for diatomic molecules.
+
+`Moose` was born out of a need to fit rotational and vibrational temperatures for a large set of data.
+
+For this it uses *line-by-line databases*, assuming a Boltzmann distribution for rotational and/or vibrational temperatures.
+
+On top of that `Moose` is intended to be *minimal*: it provides you some basic tools to do just that, simulate some spectra.
+
+It is up to you to read and sanitize experimental data, that you would like to fit based on these simulations, for instance.
+
+Put differently, `Moose` is aimed at helping you: you can integrate and adapt it to your workflow, rather than the reverse.
+
+To get a better grasp of how it works under the hood, see the online documentation for [code reference](https://antoinetue.github.io/Moose/reference/Moose/Simulation/) and [examples](https://antoinetue.github.io/Moose/examples/).
+
+## Supported bands
+Since `Moose` reuses the databases from [MassiveOES](https://bitbucket.org/OES_muni/massiveoes), it supports the same bands for fitting.
+Details can be found in [data_sources.txt](./Moose/data/data_sources.txt), and the [page with information on citing](https://antoinetue.github.io/Moose/citing/).
+
+| **Molecule** | **Band** |
+| --- | --- |
+| OH | A-X |
+| N2+ | B-X |
+| NH | A-X |
+| NO | B-X |
+| N2 | C-B |
+| C2 | Swan |
+| CN | B-X |
+
+
+## Dependencies
+The following packages are dependencies to be able to use `Moose`. 
+Version numbers are just indications of the package versions that were used to develop the code, your mileage may vary using either older or newer versions.
+Furthermore, even though the project does not import by default `lmfit` and contains no functions that specifically rely on it, the code contains convenience functions that were specifically written for usage with the `lmfit.Model` and `lmfit.Parameters` classes. 
+If `lmfit` is installed in the active enironment, some additional convenience function will be imported.
+
+These dependencies will be installed when you install `Moose` using `pip`.
+
+| **Package**  | **Version**  |
+|---|---|
+| Numpy  | >= 1.21.5  |
+| Pandas | >= 1.4.0 |
+| scipy | >= 1.7.3 |
+| *lmfit* (optional) | >= *1.2.0* |
+
+
+
+
+## Installation
+`Moose` can be installed by first downloading/cloning the package with `git`.
+
+Once you have a copy, you can install it using `pip` from the project directory.
+
+To simply install `Moose` itself, running the following suffices:
+
+```bash
+pip install .
+```
+
+Installing `Moose` with additional optional dependencies is described on the [documentation page on getting started](https://antoinetue.github.io/Moose/get_started/).
+
+## Basic usage
+A basic example demonstrating the usage is as follows.
+It assumes that there is a `pandas` DataFrame (called `data`) containing several spectra normalized on the interval (0,1), with the first column being a shared wavelength axis.
+It is important that the wavelength range over which we query the database (`wl_interval`), is larger than the experimental range plus the possible shift (`mu`) between simulation and experiment.
+
+Extending the fitting over multiple cores/processes can be done by using for instance the excellent [Dask](https://dask.org/) library, via i.e. `client.map`.
+More elaborate examples are available via the [online documentation](https://antoinetue.github.io/Moose/examples/).
+
+```python
+import Moose, lmfit
+
+wl_interval = (320,345) # Wavelength interval over which to simulate the spectrum
+db = Moose.query_DB('N2CB.db', wl_interval)
+
+
+# Create the lmfit.Model and lmfit.Parameters object needed for the fit.
+model = lmfit.Model(Moose.model_for_fit, sim_db=db)
+params = lmfit.create_params(**Moose.default_params)
+# Or use some default suggested parameters for thermal fitting, i.e. T_rot==T_vib
+# params = lmfit.create_params(**Moose.thermal_default_params)
+
+# Perform the fit
+fits = []
+for col in data.columns[1:]:
+    fits.append(model.Fit(data[col].values, x=data['Wavelength'].values, params=params))
+
+```
+
+
+## Copyright notice from MassiveOES
+
+The original software is massiveOES developed by the Masaryk University available from: https://bitbucket.org/OES_muni/massiveoes.
+
+### Publications
+
+VORÁČ, Jan; SYNEK, Petr; PROCHÁZKA, Vojtěch; HODER, Tomáš. State-by-state emission spectra fitting for non-equilibrium plasmas: OH spectra of surface barrier discharge at argon/water interface. Journal of Physics D: Applied Physics. 2017, 50(29), 294002. DOI: https://doi.org/10.1088/1361-6463/aa7570.
+
+
+VORÁČ, Jan; SYNEK, Petr; POTOČŇÁKOVÁ, Lucia; HNILICA, Jaroslav; KUDRLE, Vít. Batch processing of overlapping molecular spectra as a tool for spatio-temporal diagnostics of power modulated microwave plasma jet. Plasma Sources Science and Technology 26.2 (2017), 025010. DOI: https://doi.org/10.1088/1361-6595/aa51f0.
+
+
+#### Original sources for databases
+| Database | Source | DOI |
+| --- | --- | --- |
+| OHAX |J. Luque and D.R. Crosley, J. Chem. Phys., 109, 439 (1998) | https://dx.doi.org/10.1088/0022-3727/39/17/015 | 
+| OHAX | L.R. Williams and D.R. Crosley, J. Chem. Phys, 104, 6507 (1996) | https://doi.org/10.1063/1.471371 |
+| N$_2^+$BX |  J. Luque and D.R. Crosley, “LIFBASE: Database and Spectral Simulation Program (Version 1.5) ”, SRI International Report MP 99-009 (1999). |  | 
+| NHAX | Western C 2016 PGOPHER—a program for simulating rotational structure, Version 9.0.100, University of Bristol |  |
+| NHAX |  Ram R and Bernath P 2010 J. Mol. Spectrosc. 260 115–9 | https://doi.org/10.1016/j.jms.2010.01.006 |
+| NHAX | Lents J 1973 J. Quant. Spectrosc. Radiat. Transfer 13 297–310 | https://doi.org/10.1016/0022-4073(73)90061-7 |
+| NHAX  | Seong J, Park J K and Sun H 1994 Chem. Phys. Lett. 228 443–50 | https://doi.org/10.1016/j.jms.2010.01.006 |
+| NOBX | J. Luque and D.R. Crosley, “LIFBASE: Database and Spectral Simulation Program (Version 1.5) ”, SRI International Report MP 99-009 (1999). |  |
+| N$_2$CB | Nassar H, Pellerin S, Musiol K, Martinie O, Pellerin N and Cormier J 2004. Phys. D: Appl. Phys. 37 1904 | https://doi.org/10.1088/0022-3727/37/14/005 |
+| N$_2$CB | Laux C O and Kruger C H 1992 J. Quant. Spectrosc. Radiat. Transfer 48 9–24 | https://doi.org/10.1016/0022-4073(92)90003-M |
+| N$_2$CB | Faure G and Shko’nik S 1998 J. Phys. D: Appl. Phys. 31 1212 | https://doi.org/10.1088/0022-3727/31/10/013 |
+| C$_2$ Swan | James S.A. Brooke and Peter F. Bernath and Timothy W. Schmidt and George B. Bacskay; Journal of Quantitative Spectroscopy and Radiative Transfer; 2013 | https://doi.org/10.1016/j.jqsrt.2013.02.025 |
+| C$_2$ Swan | Carbone, Emile and D'Isa, Federico and Hecimovic, Ante and Fantz, Ursel; PSST; 2020; | https://doi.org/10.1088/1361-6595/ab74b4 |
+
+# License information
+This project is licensed under the MIT license.
+See [LICENSE](./LICENSE).

moose_spectra-0.2.0/_version.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
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+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.2.0'
+__version_tuple__ = version_tuple = (0, 2, 0)

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moose_spectra-0.2.0/docs/citing.md

@@ -0,0 +1,52 @@
+# Citing Moose
+`Moose` is made publicly available via it's `git` repository.
+
+To make it easier to cite and reference, it also has a `DOI`, provided via [Zenodo](https://zenodo.org).
+
+Whenever a new version is released, this will be automatically updated to Zenodo.
+
+Therefore, the recommended way of citing it is as follows:
+
+```bibtex
+@software{
+    author = {Salden, Antoine},
+    title = {Moose: Molecular Optical Emission Simulation in python},
+    url = {https://doi.org/xxx-xxx},
+    version = {}
+}
+```
+
+
+## Copyright notice from MassiveOES
+
+The original software is massiveOES developed by the Masaryk University available from: [https://bitbucket.org/OES_muni/massiveoes](https://bitbucket.org/OES_muni/massiveoes).
+
+
+### Publications introducing MassiveOES
+
+!!! info
+    VORÁČ, Jan; SYNEK, Petr; PROCHÁZKA, Vojtěch; HODER, Tomáš. State-by-state emission spectra fitting for non-equilibrium plasmas: OH spectra of surface barrier discharge at argon/water interface. Journal of Physics D: Applied Physics. 2017, 50(29), 294002. DOI: [10.1088/1361-6463/aa7570](https://doi.org/10.1088/1361-6463/aa7570).
+
+!!! info
+    VORÁČ, Jan; SYNEK, Petr; POTOČŇÁKOVÁ, Lucia; HNILICA, Jaroslav; KUDRLE, Vít. Batch processing of overlapping molecular spectra as a tool for spatio-temporal diagnostics of power modulated microwave plasma jet. Plasma Sources Science and Technology 26.2 (2017), 025010. DOI: [10.1088/1361-6595/aa51f0](https://doi.org/10.1088/1361-6595/aa51f0).
+
+
+# Original sources for databases
+| Database | Source | DOI |
+| --- | --- | --- |
+| OHAX |J. Luque and D.R. Crosley, J. Chem. Phys., 109, 439 (1998) | <https://doi.org/10.1063/1.476582> |
+| OHAX | L.R. Williams and D.R. Crosley, J. Chem. Phys, 104, 6507 (1996) | <https://doi.org/10.1063/1.471371> |
+| OHAX | Kristen L. Steffens, Jorge Luque, Jay B. Jeffries, David R. Crosley;  J. Chem. Phys. 15 April 1997; 106 (15): 6262–6267.  | <https://doi.org/10.1063/1.473644> |
+| N$_2^+$BX |  J. Luque and D.R. Crosley, “LIFBASE: Database and Spectral Simulation Program (Version 1.5) ”, SRI International Report MP 99-009 (1999). |  | 
+| NHAX | Western C 2016 PGOPHER—a program for simulating rotational structure, Version 9.0.100, University of Bristol |  |
+| NHAX |  Ram R and Bernath P 2010 J. Mol. Spectrosc. 260 115–9 | <https://doi.org/10.1016/j.jms.2010.01.006> |
+| NHAX | Lents J 1973 J. Quant. Spectrosc. Radiat. Transfer 13 297–310 | <https://doi.org/10.1016/0022-4073(73)90061-7> |
+| NHAX  | Seong J, Park J K and Sun H 1994 Chem. Phys. Lett. 228 443–50 | <https://doi.org/10.1016/j.jms.2010.01.006> |
+| NOBX | J. Luque and D.R. Crosley, “LIFBASE: Database and Spectral Simulation Program (Version 1.5) ”, SRI International Report MP 99-009 (1999). |  |
+| N$_2$CB | Nassar H, Pellerin S, Musiol K, Martinie O, Pellerin N and Cormier J 2004. Phys. D: Appl. Phys. 37 1904 | <https://doi.org/10.1088/0022-3727/37/14/005> |
+| N$_2$CB | Laux C O and Kruger C H 1992 J. Quant. Spectrosc. Radiat. Transfer 48 9–24 | <https://doi.org/10.1016/0022-4073(92)90003-M> |
+| N$_2$CB | Faure G and Shko’nik S 1998 J. Phys. D: Appl. Phys. 31 1212 | <https://doi.org/10.1088/0022-3727/31/10/013> |
+| C$_2$ Swan | James S.A. Brooke and Peter F. Bernath and Timothy W. Schmidt and George B. Bacskay; Journal of Quantitative Spectroscopy and Radiative Transfer; 2013 | <https://doi.org/10.1016/j.jqsrt.2013.02.025> |
+| C$_2$ Swan | Carbone, Emile and D'Isa, Federico and Hecimovic, Ante and Fantz, Ursel; PSST; 2020; | <https://doi.org/10.1088/1361-6595/ab74b4> |
+| CNBX | Carbone, Emile and D'Isa, Federico and Hecimovic, Ante and Fantz, Ursel; PSST; 2020; | <https://doi.org/10.1088/1361-6595/ab74b4> |
+