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snakemake-workflow-fermi-lat

A Snakemake workflow for Fermi-LAT data reduction

https://github.com/adonath/snakemake-workflow-fermi-lat

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
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    Scientific vocabulary similarity
    Low similarity (14.1%) to scientific vocabulary

Keywords

data-reduction fermi-lat fermitools gammapy snakemake
Last synced: 6 months ago · JSON representation ·

Repository

A Snakemake workflow for Fermi-LAT data reduction

Basic Info
  • Host: GitHub
  • Owner: adonath
  • License: other
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 90.8 KB
Statistics
  • Stars: 12
  • Watchers: 3
  • Forks: 1
  • Open Issues: 5
  • Releases: 1
Topics
data-reduction fermi-lat fermitools gammapy snakemake
Created about 3 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

DOI

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 fermilatdata_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 fermilatdataworkflow as fermilatdata* ```

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 or mamba.

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 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) ```

Owner

  • Name: Axel Donath
  • Login: adonath
  • Kind: user
  • Location: Cambridge, MA
  • Company: Center for Astrophysics | Havard & Smithonian

I'm a Postdoc researcher at Center for Astrophysics. I work on statistical methods for analysis of low counts astronomical data.

Citation (CITATION.cff) 

title: A Snakemake Workflow for Fermi-LAT data reduction for Gammapy
repository-code: https://github.com/adonath/snakemake-workflow-fermi-lat
version: v0.1
date-released: 2023-10-17
authors:
  - given-names: Axel
    family-names: Donath
    affiliation: Center for Astrophysics | Harvard & Smithsonian
    orcid: https://orcid.org/0000-0003-4568-7005
cff-version: 1.2.0

GitHub Events

Total
  • Create event: 1
  • Release event: 1
  • Issues event: 4
  • Watch event: 3
  • Issue comment event: 6
  • Push event: 8
  • Fork event: 1
Last Year
  • Create event: 1
  • Release event: 1
  • Issues event: 4
  • Watch event: 3
  • Issue comment event: 6
  • Push event: 8
  • Fork event: 1

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 60
  • Total Committers: 2
  • Avg Commits per committer: 30.0
  • Development Distribution Score (DDS): 0.133
Past Year
  • Commits: 60
  • Committers: 2
  • Avg Commits per committer: 30.0
  • Development Distribution Score (DDS): 0.133
Top Committers
Name Email Commits
Axel Donath a****h@c****u 52
Axel Donath a****h 8
Committer Domains (Top 20 + Academic)
cfa.harvard.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 8
  • Total pull requests: 0
  • Average time to close issues: about 1 year
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.88
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: 2 days
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 2.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • adonath (7)
  • AtreyeeS (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/ci.yml actions
  • actions/cache v2 composite
  • actions/checkout v3 composite
  • conda-incubator/setup-miniconda v2 composite
environment.yaml conda
  • astropy >=5.2
  • fermitools >=2.2.0
  • gammapy >=v1.0
  • pydantic <2.0
  • python 3.9.*
  • snakemake >=6.4.1