# PyThea: A software package to reconstruct the 3D structure of CMEs and shock waves
[](https://www.python.org/)
[](https://github.com/AthKouloumvakos/PyThea/releases)
[](https://github.com/AthKouloumvakos/PyThea/releases)
[](https://www.gnu.org/licenses/gpl-3.0)
_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO) and Solar Terrestrial Relations Observatory (STEREO).
## 💾 Installation
We recommend, creating a virtual environment for _PyThea_ and installing the package from PyPI using ```pip```.
If you use Anaconda or Miniconda (which we also recommend) you can create a virtual environment using ```conda``` and then install _PyThea_ using from PyPI using ```pip```. In the terminal do the following:
```python
# Create a virtual environment. Use python=3.8 or 3.9
conda create --name PyThea python=3.9
# Activate the environment
conda activate PyThea
# install the required packages using pip3
pip3 install PyThea
# Run locally the application with streamlit (see also the section "Run locally the PyThea application" )
PyThea streamlit
# When you are done you can deactivate the virtual environment
conda deactivate
```
If ```conda``` is not your favorite way of creating a virtual environment in python, then you can manually create it and install _PyThea_ with ```pip``` as previously shown. For example, you can do the following:
```python
# Create a virtual environment.
python3 -m venv PyThea
# Activate the environment
source PyThea/bin/activate
# install the required packages using pip3
pip3 install PyThea
# Run locally the application with streamlit (see also the section "Run locally the PyThea application" )
PyThea streamlit
# When you are done you can deactivate the virtual environment
deactivate
```
At the directory where the terminal is open, this method will create a folder named ```/PyThea``` and install _PyThea_ and all the required packages inside.
### ⬆️ Update
To update the package to the latest version activate the environment first and then:
```python
# Update _PyThea_ using pip3
pip3 install PyThea -U
```
One way to see witch version is installed in your environment is to open a python session and do:
```python
import PyThea
PyThea.__version__
```
You can also see the verion used and the latest version on the main page of the application.
## 🐾 Run locally the _PyThea_ application
After installing _PyThea_ software package you can run the application using the terminal.
If the environment is not active then use ```conda activate PyThea``` or ```source PyThea/bin/activate``` to activate this and then run _PyThea_ with
```
PyThea streamlit
```
The application should now open in the default browser!
Deactivate the environment when you finish.
If there is an error when running ```PyThea streamlit``` then you can manually run PyThea following these steps:
1) Locate where PyThea_app.py have been instaled. This is usually inside the anaconda3 enviroment folder. For example here ```~/opt/anaconda3/envs/PyThea/lib/python3.9/site-packages/PyThea```
2) Then run the PyThea_app.py using: ```streamlit run <PyTheaRootDir>/PyThea_app.py``` replacing \<PyTheaRootDir\> with your path first.
## 📙 Usage
Complete documentation of the _PyThea_ is under construction.
## 📦 Useful Python packages
- [SunPy](https://sunpy.org/): The community-developed, free and open-source solar data analysis environment for Python.
- [AstroPy](https://www.astropy.org/): The Astropy Project is a community effort to develop a single core package for Astronomy in Python.
- [gcs_python](https://github.com/johan12345/gcs_python/): An implementation of the Graduated Cylindrical Shell model in python.
## 📜 Acknowledging or Citing PyThea [](https://www.frontiersin.org/articles/10.3389/fspas.2022.974137/) [](https://doi.org/10.5281/zenodo.5713659)
If you use _PyThea_ for scientific work or research presented in a publication, please mention it in the main text and cite _PyThea_ paper (see [Paper](https://www.frontiersin.org/articles/10.3389/fspas.2022.974137/) or ADS). Additionally, add in the methods or acknowledgements section the following: "This research has made use of PyThea v?.?.?, an open-source and free Python package to reconstruct the 3D structure of CMEs and shock waves (Zenodo: [https://doi.org/10.5281/zenodo.5713659](https://doi.org/10.5281/zenodo.5713659))." and changing the v?.?.? to the version you have used. To acknowledge _PyThea_ in posters or talks include the project [logo](https://github.com/AthKouloumvakos/PyThea/blob/master/docs/logo/pythea_logo.png) or [icon](https://github.com/AthKouloumvakos/PyThea/blob/master/docs/logo/pythea_icon.png). _PyThea_ has a strong dependency on SunPy and AstroPy Python packages, consider citing these packages as well.
## ⓘ The mythology of Thea:
In Greek mythology, Thea, also called Euryphaessa "wide-shining", is the Titaness of sight and the shining light of the clear blue sky. Her brother/consort is Hyperion, a Titan and god of the sun, and together they are the parents of Helios (the Sun), Selene (the Moon), and Eos (the Dawn).
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"description": "# PyThea: A software package to reconstruct the 3D structure of CMEs and shock waves\n\n[](https://www.python.org/)\n[](https://github.com/AthKouloumvakos/PyThea/releases)\n[](https://github.com/AthKouloumvakos/PyThea/releases)\n[](https://www.gnu.org/licenses/gpl-3.0)\n\n\n\n_PyThea_ is an open-source software package that can be used to reconstruct the 3D structure of Coronal Mass Ejections (CMEs) and shock waves and determine their kinematics using remote-sensing observations. The tool implements the Graduated Cylindrical Shell (GCS) model that can be used to reconstruct CMEs and two geometrical models, namely a spheroid and ellipsoid model to reconstruct shock waves. It also implements remote-sensing observations from multiple viewpoints such as the Solar and Heliospheric Observatory (SoHO) and Solar Terrestrial Relations Observatory (STEREO).\n\n## \ud83d\udcbe Installation\n\nWe recommend, creating a virtual environment for _PyThea_ and installing the package from PyPI using ```pip```.\n\nIf you use Anaconda or Miniconda (which we also recommend) you can create a virtual environment using ```conda``` and then install _PyThea_ using from PyPI using ```pip```. In the terminal do the following:\n\n```python\n# Create a virtual environment. Use python=3.8 or 3.9\nconda create --name PyThea python=3.9\n\n# Activate the environment\nconda activate PyThea\n\n# install the required packages using pip3\npip3 install PyThea\n\n# Run locally the application with streamlit (see also the section \"Run locally the PyThea application\" )\nPyThea streamlit\n\n# When you are done you can deactivate the virtual environment\nconda deactivate\n```\n\nIf ```conda``` is not your favorite way of creating a virtual environment in python, then you can manually create it and install _PyThea_ with ```pip``` as previously shown. For example, you can do the following:\n\n```python\n# Create a virtual environment.\npython3 -m venv PyThea\n\n# Activate the environment\nsource PyThea/bin/activate\n\n# install the required packages using pip3\npip3 install PyThea\n\n# Run locally the application with streamlit (see also the section \"Run locally the PyThea application\" )\nPyThea streamlit\n\n# When you are done you can deactivate the virtual environment\ndeactivate\n```\n\nAt the directory where the terminal is open, this method will create a folder named ```/PyThea``` and install _PyThea_ and all the required packages inside.\n\n### \u2b06\ufe0f Update\n\nTo update the package to the latest version activate the environment first and then:\n\n```python\n# Update _PyThea_ using pip3\npip3 install PyThea -U\n```\n\nOne way to see witch version is installed in your environment is to open a python session and do:\n```python\nimport PyThea\nPyThea.__version__\n```\nYou can also see the verion used and the latest version on the main page of the application.\n\n## \ud83d\udc3e Run locally the _PyThea_ application\n\nAfter installing _PyThea_ software package you can run the application using the terminal.\n\nIf the environment is not active then use ```conda activate PyThea``` or ```source PyThea/bin/activate``` to activate this and then run _PyThea_ with\n\n```\nPyThea streamlit\n```\n\nThe application should now open in the default browser!\n\nDeactivate the environment when you finish.\n\nIf there is an error when running ```PyThea streamlit``` then you can manually run PyThea following these steps:\n\n1) Locate where PyThea_app.py have been instaled. This is usually inside the anaconda3 enviroment folder. For example here ```~/opt/anaconda3/envs/PyThea/lib/python3.9/site-packages/PyThea```\n\n2) Then run the PyThea_app.py using: ```streamlit run <PyTheaRootDir>/PyThea_app.py``` replacing \\<PyTheaRootDir\\> with your path first.\n\n## \ud83d\udcd9 Usage\n\nComplete documentation of the _PyThea_ is under construction.\n\n## \ud83d\udce6 Useful Python packages\n\n- [SunPy](https://sunpy.org/): The community-developed, free and open-source solar data analysis environment for Python.\n- [AstroPy](https://www.astropy.org/): The Astropy Project is a community effort to develop a single core package for Astronomy in Python.\n- [gcs_python](https://github.com/johan12345/gcs_python/): An implementation of the Graduated Cylindrical Shell model in python.\n\n## \ud83d\udcdc Acknowledging or Citing PyThea [](https://www.frontiersin.org/articles/10.3389/fspas.2022.974137/) [](https://doi.org/10.5281/zenodo.5713659)\n\nIf you use _PyThea_ for scientific work or research presented in a publication, please mention it in the main text and cite _PyThea_ paper (see [Paper](https://www.frontiersin.org/articles/10.3389/fspas.2022.974137/) or ADS). Additionally, add in the methods or acknowledgements section the following: \"This research has made use of PyThea v?.?.?, an open-source and free Python package to reconstruct the 3D structure of CMEs and shock waves (Zenodo: [https://doi.org/10.5281/zenodo.5713659](https://doi.org/10.5281/zenodo.5713659)).\" and changing the v?.?.? to the version you have used. To acknowledge _PyThea_ in posters or talks include the project [logo](https://github.com/AthKouloumvakos/PyThea/blob/master/docs/logo/pythea_logo.png) or [icon](https://github.com/AthKouloumvakos/PyThea/blob/master/docs/logo/pythea_icon.png). _PyThea_ has a strong dependency on SunPy and AstroPy Python packages, consider citing these packages as well.\n\n## \u24d8 The mythology of Thea:\n\nIn Greek mythology, Thea, also called Euryphaessa \"wide-shining\", is the Titaness of sight and the shining light of the clear blue sky. 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