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Pyplis is a Python toolbox originally developed for the analysis of UV SO2 camera data. The software includes a comprehensive and flexible collection of algorithms for the analysis of atmospheric imaging data and is tested for all major operating systems and python 3 as well as python 2.7 (which is not recommended to use anymore).
Contact: Jonas Gliß (jonasgliss@gmail.com)
Since I have to maintain pyplis during my free time and since I am not working in the field of volcano remote sensing anymore, I would be very grateful for contributions from users / developers closer to the application of UV SO2 cameras. If you are interested, feel free to get in touch with me (jonasgliss@gmail.com) or go ahead and send a PR via a fork, or by creating issues (best if you tag me with @jgliss in issues and PRs).
Cheers, Jonas
The code documentation of pyplis and more information is hosted on Read the Docs <http://pyplis.readthedocs.io/>
_.
Gliss et al., 2018, AMT <https://www.atmos-meas-tech.net/11/781/2018/>
_).FITS format <https://de.wikipedia.org/wiki/Flexible_Image_Transport_System>
_.A detailed description of pyplis and its features (including analysis examples) can be found in Gliss et al., 2017, MDPI Geosciences <http://www.mdpi.com/2076-3263/7/4/134>
_.
We recommend using the Anaconda Python distribution <https://www.anaconda.com/distribution/>
(or Miniconda <https://docs.conda.io/en/latest/miniconda.html>
, if you want to save disk space) and to use the conda package manager. Why? See, e.g. here for some good reasons <https://www.opensourceanswers.com/blog/best-practices-with-conda.html>
_.
Below it is assumed that you made yourself familiar with the conda package manager and that it is installed on your system. It is recommended to have a look at the guidelines related to conda virtual environments <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html>
_.
We highly recommend to work in individual conda environments for your different projects and not to install everything into your Anaconda root environment (base), which is usually activated by default. In other words: please do not install pyplis into your root environment but create a new one using::
conda create -n my_awesome_conda_environment
Why? <https://www.opensourceanswers.com/blog/best-practices-with-conda.html>
_
Pyplis is available via the conda-forge channel <https://anaconda.org/conda-forge/pyplis>
_ and can be easily installed via::
conda install -c conda-forge pyplis
This will install all requirements as well. This is the recommended (and by far easiest) way to get pyplis running on your system.
Before installing pyplis, make sure you have all requirements installed (which is done automatically if you install pyplis via conda as described in previous section).
A list of all mandatory requirements can be found in the provided conda environment file pyplis_env.yml <https://github.com/jgliss/pyplis/blob/master/pyplis_env.yml>
_, which can also directly be used to install the requirements, as described below.
Optional dependencies (to use extra features) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Pillow (PIL fork) >= 3.3.0
this example <https://pyplis.readthedocs.io/en/latest/api.html#pyplis.custom_image_import.load_hd_new>
_pip install pillow
rather than conda install pillow
due tohere <https://github.com/python-pillow/Pillow/issues/2945>
_pydoas >= 1.0.0 (comes with conda installation and provided environment file)
Before installing Pyplis, you need to install all requirements. To do so, you may either use the provided conda environment file or install all requirements manually, as described in the following two sections. All instructions below assume that you use Anaconda <https://www.anaconda.com/>
_ as package manager.
Installation of requirements using provided conda environment file ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You can install all mandatory requirements using the provided environment file pyplis_env.yml (or pyplis_env_py27.yml if you still use python 2.7). You can install the environment file into a new environment (here, named pyplis) using::
conda env create -n pyplis_env_test -f pyplis_env.yml
Or you may install it into an existing environment by activating the environment and then::
conda env update -f=pyplis_env.yml
Manual installation of requirements ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You may also install all requirements from scratch as described in the following step-by-step guide::
conda create --name pyplis # creates new conda environment with name pyplis (optional) conda activate pyplis # activates new environment (optional) conda install -c conda-forge scipy pandas astropy basemap opencv geonum pydoas
Here, you have 3 options.
Via conda ^^^^^^^^^ From the command line, call::
conda install -c conda-forge pyplis
This option installs pyplis and all requirements automatically.
Via pip ^^^^^^^^ From the command line, call::
pip install pyplis
This option only installs pyplis, you have to install all requirements yourself (for details, see previous sections).
From Source
^^^^^^^^^^^
In order to install from source, please download or clone the repo <https://github.com/jgliss/pyplis>
(or one of the pyplis releases <https://github.com/jgliss/pyplis/releases>
) into a local directory of your choice. Then, unzip and from the project root directory (the one that contains setup.py file) call::
python setup.py install
This option only installs pyplis, you have to install all requirements yourself (for details, see previous sections).
Note ^^^^ Use Option 2 if you want to run the tests and / or example scripts (since these are not shipped with the PyPi installation that uses a binary wheel of Pyplis).
If you work on a Windows machine and run into problems with installation of one of the requirements (e.g. if you already had Python 2.7 installed and want to upgrade dependencies such as numpy or scipy), check out the pre-compiled binary wheels on Christoph Gohlke's webpage <http://www.lfd.uci.edu/~gohlke/pythonlibs/>
_
Sometimes it is helpful, to reinstall your whole Python environment (or, if you use Anaconda, create a new one <https://conda.io/docs/user-guide/tasks/manage-environments.html>
_) rather than trying to upgrade all dependencies to the required version
If you find a bug or detect a specific problem with one of the requirements (e.g. due to future releases) please let us know or raise an issue <https://github.com/jgliss/pyplis/issues>
_.
Do not hesitate to contact us (or raise an issue), if you have problems installing pyplis.
The Pyplis example scripts <https://github.com/jgliss/pyplis/tree/master/scripts>
(see previous point) are a good starting point to get familiar with the features of Pyplis and for writing customised analysis scripts. The scripts require downloading the Etna example dataset (see following section for instructions). If you require more thorough testing, refer to this wiki entry <https://github.com/jgliss/pyplis/wiki/Contribution-to-pyplis-and-testing>
The pyplis example data (required to run example scripts) is not part of the installation. It can be downloaded from here <https://folk.nilu.no/~arve/pyplis/pyplis_etna_testdata.zip>
_ or automatically downloaded in a Python shell (after installation) using::
import pyplis
pyplis.inout.download_test_data(
which downloads the data into the my_pyplis directory if
pyplis.inout.find_test_data()
The latter searches all paths provided in the file _paths.txt whenever access to the test data is required. It raises an Exception, if the data cannot be found.
If the data is downloaded manually (e.g. using the link provided above), please make sure to unzip it into a local directory
import pyplis
pyplis.inout.set_test_data_path(
The article:
Pyplis - A Python Software Toolbox for the Analysis of SO2 Camera Images for Emission Rate Retrievals from Point Sources, Gliß, J., Stebel, K., Kylling, A., Dinger, A. S., Sihler, H., and Sudbø, A., Geosciences, 2017
introduces Pyplis and implementation details. Furthermore, the article provides a comprehensive review of the technique of SO2 cameras with a focus on the required image analysis. The paper was published in December 2017 as part of a special issue on Volcanic plumes <http://www.mdpi.com/journal/geosciences/special_issues/volcanic_processes>
of the Journal Geosciences (MDPI).
Download paper <http://www.mdpi.com/2076-3263/7/4/134>
.
If you find Pyplis useful for your data analysis, we would highly appreciate if you acknowledge our work by citing the paper. Citing details can be found here <http://www.mdpi.com/2076-3263/7/4/134>
__.
Copyright (C) 2017 Jonas Gliss (jonasgliss@gmail.com)
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License a 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. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see here <http://www.gnu.org/licenses/>
_.
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