The best way to learn about Gammapy is to read and play with the examples in the Gammapy Tutorial notebooks.
This section explains the steps to get set up for the Gammapy tutorials on your machine:
- Install Anaconda and the Gammapy environment
- Download tutorial notebooks and example datasets
- Check your setup and Gammapy environment
- Use Gammapy with Python, IPython or Jupyter
If you have used conda, Python, IPython and Jupyter before, you can just skim this page, and quickly copy & paste the commands to get set up.
If you have any questions or issues, please ask for help on the Gammapy Slack, mailing list or on Github (whatever is easiest for you, see Gammapy contact)
To install Gammapy we recommend that you install the Anaconda distribution from https://www.anaconda.com/download/. The following instructions and commands below need to have Anaconda installed.
Anaconda it’s free, works on Linux, MacOS and Windows. It installs in your home directory, no system privileges needed, and you can just delete it without problems if you don’t need or want it any more.
Besides the software included in the Anaconda distribution, it gives you the conda tool, which is a package and environment manager. We will use it to create a dedicated environment for the latest stable Gammapy version and a known good set of Gammapy dependencies (e.g. Python, Numpy and Astropy).
Once Anaconda has been installed, use the following commands to install and activate
gammapy-0.12 conda environment:
curl -O https://gammapy.org/download/install/gammapy-0.12-environment.yml conda env create -f gammapy-0.12-environment.yml conda activate gammapy-0.12
On Windows, comment out the lines for
healpy in the
environment YAML file. These are optional dependencies that we are currently
using that aren’t supported on Windows. You will be able to do most analyses
with Gammapy, but you will not be able to work with HEALPix data or fit
with Sherpa (the default fitting backend currently is Minuit).
Congratulations! You are all set to start using Gammapy!
Every time you open a new terminal window, you will have to activate the Gammapy conda environment again before you can use it.
conda activate gammapy-0.12
You can now proceed to download the Gammapy tutorial notebooks and the example datasets used there (at the moment from CTA, H.E.S.S. and Fermi-LAT). The total size to download is about 100 MB.
gammapy download tutorials --release 0.12 cd gammapy-tutorials export GAMMAPY_DATA=$PWD/datasets-0.12
You might want to put the definition of the
variable in your shell profile setup file that is executed when you open a new
terminal (for example
If you are not using the
bash shell, handling of shell environment variables
might be different, e.g. in some shells the command to use is
set or something
else instead of
export, and also the profile setup file will be different.
On Windows, you should set the
GAMMAPY_DATA environment variable in the
“Environment Variables” settings dialog, as explained e.g.
The datasets are curated and stable, the notebooks are still under development just like Gammapy itself, and thus stored in a sub-folder that contains the Gammapy version number.
gammapy download command and versioning of the notebooks is new. If
there are issues, note that you can just delete the folder any time using
-r gammapy-tutorials and start over.
Also note that it’s of course possible to download just the notebooks, just the datasets, a single notebook or dataset, or a specific tutorial with the datasets it uses. See the help:
gammapy download --help
Check your setup¶
You might want to display some info about Gammapy installed. You can execute the following command, and it should print detailed information about your installation to the terminal:
If there is some issue, the following commands could help you to figure out your setup:
conda info which python which ipython which jupyter which gammapy env | grep PATH python -c 'import gammapy; print(gammapy); print(gammapy.__version__)'
You can also use the following commands to check which conda environment is active and which ones you have set up:
conda info conda env list
If you’re new to conda, you could also print out the conda cheat sheet, which lists the common commands to install packages and work with environments.
Gammapy is a Python package, so you can of course import and use it from Python:
$ python Python 3.6.0 | packaged by conda-forge | (default, Feb 10 2017, 07:08:35) [GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from gammapy.stats import significance >>> significance(n_on=10, mu_bkg=4.2, method='lima') array([2.39791813])
IPython is nicer to use for interactive analysis:
$ ipython Python 3.6.0 | packaged by conda-forge | (default, Feb 10 2017, 07:08:35) Type 'copyright', 'credits' or 'license' for more information IPython 6.5.0 -- An enhanced Interactive Python. Type '?' for help. In : from gammapy.stats import significance In : significance(n_on=10, mu_bkg=4.2, method='lima') Out: array([2.39791813])
For example you can use
? to look up help for any Gammapy function, class or
method from IPython:
In : significance?
Of course, you can also use the Gammapy online docs if you prefer, clicking in links
gammapy.stats.significance) or using search docs field in the upper left.
>>> from gammapy.data import DataStore >>> data_store = DataStore.from_dir('$GAMMAPY_DATA/hess-dl3-dr1/') >>> events = data_store.obs(obs_id=23523).events >>> print(events) EventList info: - Number of events: 7613 - Median energy: 0.953 TeV - OBS_ID = 23523 >>> events.energy.mean() <Quantity 4.418008 TeV>
Try to make your first plot using the
peek helper method:
>>> events.peek() >>> plt.savefig("events.png")
Another common way to use Gammapy is to write a Python script.
Try it and put the following code into a file called
"""Example Python script using Gammapy""" from gammapy.data import DataStore data_store = DataStore.from_dir('$GAMMAPY_DATA/hess-dl3-dr1/') events = data_store.obs(obs_id=23523).events print(events.energy.mean())
You can run it with Python:
$ python example.py 4.418007850646973 TeV
If you want to continue with interactive data or results analysis after running some Python code, use IPython like this:
$ ipython -i example.py
As you have already seen, installing Gammapy gives you a
gammapy command line
tool with subcommands such as
gammapy info or
We plan to add a high-level interface to Gammapy soon that will let you run Gammapy analyses via the command line interface, probably driven by a config file. This is not available yet, for now you have to use Gammapy as a Python package.
To learn more about Gammapy, and also for interactive data analysis in general, we recommend you use Jupyter notebooks. Assuming you have followed the steps above to install Gammapy and activate the conda environment, you can start JupyterLab like this:
$ jupyter lab
This should open up JupyterLab app in your web browser, where you can
create new Jupyter notebooks or open up existing ones. If you have downloaded the
gammapy download tutorials, you can browse your
folder with Jupyterlab and execute them there.
If you haven’t used Jupyter before, try typing
print("Hello Jupyter") in the
first input cell, and use the keyboard shortcut
SHIFT + ENTER to execute it.
If you have problems and think you might not be using the right Python or importing Gammapy isn’t working or giving you the right version, checking your Python executable and import path might help you find the issue:
import sys print(sys.executable) print(sys.path)
To check which Gammapy you are using you can use this:
import gammapy print(gammapy) print(gammapy.__version__)
Now you should be all set and to use Gammapy. Let’s move on to the Tutorial notebooks.