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EM27 Retrieval Pipeline

Quick Start

1. Ensure system requirements

Section titled “1. Ensure system requirements”

The pipeline was developed and is tested on Unix-based operating systems. You need to have the following dependencies installed on your system:

You can check whether they are installed using:

Terminal window
python3.11 --version
git-lfs --version
unzip --version
gfortran --version

2. Clone or download the pipeline’s code

Section titled “2. Clone or download the pipeline’s code”

Links: repository | all releases

Using git clone (ssh):

Terminal window
git clone git@github.com:tum-esm/em27-retrieval-pipeline.git
cd em27-retrieval-pipeline
git switch --detach v1.11.1

… or git clone (https):

Terminal window
git clone https://github.com/tum-esm/em27-retrieval-pipeline.git
cd em27-retrieval-pipeline
git switch --detach v1.11.1

… or wget:

Terminal window
wget https://github.com/tum-esm/em27-retrieval-pipeline/archive/refs/tags/v1.11.1.tar.gz
tar -xzf em27-retrieval-pipeline-1.11.1.tar.gz && rm em27-retrieval-pipeline-1.11.1.tar.gz
cd em27-retrieval-pipeline-1.11.1

3. Create a virtual environment

Section titled “3. Create a virtual environment”
Terminal window
python3.11 -m venv .venv
source .venv/bin/activate

You can of course use any other way to manage your Python environments.

4. Install the dependencies using

Section titled “4. Install the dependencies using”

Using pip:

Terminal window
pip install ".[dev]"

… or uv:

Terminal window
uv sync --extra=dev

5. Explore and run the example

Section titled “5. Explore and run the example”

Contents:

  • The example/config folder contains all configuration files required to run this example from raw interferograms to bundled retrieval outputs and GEOMS exports.
  • The example/data/inputs directory contains some EM27/SUN interferograms, pressure observations recorded next the EM27/SUN and atmospheric profiles at the observation locations. When running your own retrievals, you only need to bring the interferograms and the pressure observations - the atmospheric profiles can be downloaded automatically using the pipelines GGG Profiles Downloader.
  • The example/data/outputs directory will be empty after you clone the repository but will be filled with the different outputs after running the example.
  • The example/data/logs directory will be empty after you clone the repository but will contain the log files of the pipeline produced during the example run.

Run it:

Terminal window
source .venv/bin/activate
cd example
bash run.sh

Have some patience on the retrieval process - the full example run should take around 2-5 minutes.

6. Run your own retrievals

Section titled “6. Run your own retrievals”

Next steps to run your own retrievals:

  • The Configuration Guide explains how to configure the pipeline.
  • The EM27 Metadata Guide explains how to create the required metadata files.
  • The Data Directories Guide explains how the different input and output directories used by the pipeline are structured.
  • The Full Usage Guide explains how to run each step of the pipeline.
  • The FAQ answers some frequently asked questions about the pipeline.

The following sections contain a full API reference for the CLI and all configuration files used by the pipeline:

You can use this documentation’s search function (top navigation bar) to find what you are looking for, open an issue on GitHub or ask Moritz Oliveira Makowski (moritz.makowski@tum.de) if you are stuck on something.