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https://github.com/adonath/snakemake-workflow-fermi-lat
A Snakemake workflow for Fermi-LAT data reduction
https://github.com/adonath/snakemake-workflow-fermi-lat
data-reduction fermi-lat fermitools gammapy snakemake
Last synced: 2 months ago
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A Snakemake workflow for Fermi-LAT data reduction
- Host: GitHub
- URL: https://github.com/adonath/snakemake-workflow-fermi-lat
- Owner: adonath
- License: other
- Created: 2023-02-10T23:24:06.000Z (almost 2 years ago)
- Default Branch: main
- Last Pushed: 2023-10-19T01:52:10.000Z (about 1 year ago)
- Last Synced: 2024-10-03T17:45:09.830Z (3 months ago)
- Topics: data-reduction, fermi-lat, fermitools, gammapy, snakemake
- Language: Python
- Homepage:
- Size: 79.1 KB
- Stars: 11
- Watchers: 3
- Forks: 0
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
- Citation: CITATION.cff
Awesome Lists containing this project
README
# Snakemake Workflow for Fermi-LAT Data Reduction
This is an example snakemake workflow for data reduction of Fermi-LAT data.
The workflow will run the standard `fermitools` for a given configuration
and produce FITS files in a format that Gammapy can read.
Thereby it will handle the reduction of counts, exposure and point
spread function (PSF) for multiple PSF classes.
## Getting Started
### Use as Snakemake Module (recommended)
If you would like use this as Snakmake module you should add e.g. the following to your `Snakefile`:
```python3
module fermi_lat_data_workflow:
snakefile:
# here, plain paths, URLs and the special markers for code hosting providers (see below) are possible.
github("adonath/snakemake-workflow-fermi-lat", path="workflow/Snakefile", branch="main")
config: config["fermi-lat-data"]
use rule * from fermi_lat_data_workflow as fermi_lat_data_*
```
### Use as Repository
Alternatively you could also just clone this repository to your local machine:
```bash
git clone https://github.com/adonath/snakemake-workflow-fermi-lat.git
```
If you havn't done yet, please install [conda](https://www.anaconda.com/products/distribution)
or [mamba](https://mamba.readthedocs.io/en/latest/installation.html).
Now change to the directory of the repository:
```bash
cd snakemake-workflow-fermi-lat/
```
And create the conda environment using:
```bash
mamba env create -f environment.yaml
```
Once the process is done you can activate the environment:
```bash
conda activate snakemake-workflow-fermi-lat
```
### Download Data
Go to https://fermi.gsfc.nasa.gov/cgi-bin/ssc/LAT/LATDataQuery.cgi and download the data
you are interested in. The data should be downloaded to the `./data` folder.
### Configure and Run the Workflow
Now you should adapt the configuration in [config/config.yaml](config/config.yaml)
to match your data.
Then you are ready to run the workflow, like:
```bash
snakemake --cores 8
```
You can also create a report to see previews of the counts, exposure and PSF images:
```bash
snakemake --report report.html
open report.html
```
Finally you can read and print the datasets as well as models using Gammapy:
```python3
from gammapy.datasets import Datasets
from gammapy.modeling.models import Models
datasets = Datasets.read("results//datasets/-datasets-all.yaml")
models = Models.read("results//model/-model.yaml")
print(datasets)
print(models)
```