IMPORTANT for Mac OS X Users
A CentOS 7 virtual machine image (OVA file) is now available to facilitate running Astroconda IRAF under MacOS 10.15+, which no longer supports running the necessary 32-bit binaries natively. This comes with Anaconda 2019.10, Gemini IRAF 1.14, DRAGONS 2.1.1 and other packages from Astroconda pre-installed. Users of MacOS 10.14 affected by the Tk bug that causes a desktop session logout when displaying graphics may also want to install this guest distribution as a workaround.
Please see instructions at https://gemini-iraf-vm-tutorial.readthedocs.io.
- Gemini IRAF
- Stable Version: v1.14
- Revision note: gemini_v114_rev.txt
Instructions for updating DRAGONS and Gemini IRAF
If you already have DRAGONS installed, updating to the latest version is straightforward. Replace
dragons, or whatever name you used when you first created the environment.
$ conda activate environment_name $ conda install package_name=version
$ conda activate dragons $ conda install dragons=2.1.1 $ conda activate geminiconda $ conda install iraf.gemini=1.14
conda update could be used but beware that it will likely update several other core packages. This is a conda behavior. To see all available version of a package use
conda search package_name.
Instructions for new installation of DRAGONS and Gemini IRAF
WARNING: the use of the
bash shell is required by Anaconda.
If you already have Anaconda installed, you can skip this step and go to the Install DRAGONS and Gemini IRAF section below. If not, then your first step is to get and install Anaconda. You can download it at:
Choose the version of Python that suits your other Python needs. DRAGONS is compatible with both Python 2.7 and 3.6. If you need Gemini IRAF, you will need 2.7. We recommend that you install the Python 3 version of Anaconda, the specific Python version can be adjusted later for each environment. Please note that DRAGONS will drop support of Python 2.7 soon. With everyone else dropping Python 2 support it is becoming more and more difficult to find compatible dependencies in the conda system. Also, the spectroscopy code under development is Python 3 only.
If you have downloaded the graphical installer, follow the graphical installer instructions. Install in your home directory. It should be the default.
If you have downloaded the command-line installer, type the following in a terminal, replacing the .sh file name to the name of the file you have downloaded. The /bin/bash -l line is not needed if you are already using bash. The command-line installer allows for more customization of the installation. ($ indicates the terminal prompt.)
$ /bin/bash -l $ chmod a+x Anaconda3-2019.10-MacOSX-x86_64.sh $ ./Anaconda3-2019.10-MacOSX-x86_64.sh
To prevent the Anaconda "base" environment from loading automatically, giving you back the control as to when to activate the conda environements, do:
$ conda config --set auto_activate_base false
Verify Anaconda installation
Make sure that ~/anaconda3/bin/activate is in your PATH by doing:
$ which activate
The Anaconda installer should have added conda configurations to the
~/.bash_profile for you. If activate is not found, try:
$ source ~/.bash_profile
If activate is still not found, you might have to add
export PATH=~/anaconda3/bin:$PATH to your
~/.bash_profile using your favorite text editor, and run the source command above again.
- Sometimes the Anaconda installer will install the software in ~/anaconda2 or ~/anaconda3 instead of simply ~/anaconda. Just check in your home directory which one of the three possibilities was used.
- The code Anaconda adds to the .bash_profile will automatically activate anaconda. To activate or deactivate Anaconda manually:
$ conda activate $ conda deactivate
Set up Anaconda Channels
Remember that Anaconda requires the use of the bash shell. tcsh or csh will not work. If you are using (t)csh, your first step is:
$ /bin/bash -l
Now that Anaconda is installed, we add the needed astronomy software. We add the Astroconda channel and the Gemini channel. Those channels host the conda astronomy packages. The channels need to be defined only once.
$ conda config --add channels http://ssb.stsci.edu/astroconda $ conda config --add channels http://astroconda.gemini.edu/public
Install DRAGONS and Gemini IRAF in Python 2 Environment
The next step is to create a virtual environment and install the DRAGONS software and its dependencies in it. The name of the environment can be anything you like. Here we use “geminiconda” as the name and we install Python 2.7. IMPORTANT: PyRAF does not work well in Python 3, therefore, to use Gemini IRAF we must install Python 2.7.
$ conda create -n geminiconda2 python=2.7 gemini stsci iraf-all pyraf-all
To use this environment, activate it:
$ conda activate geminiconda2
You will need to activate the environment whenever you start a new shell. If you are planning to use it all the time, you might want to add the command to your .bash_profile, after the “conda init” block.
Python 3 and DRAGONS
DRAGONS is fully compatible with Python 3. It was tested with Python 3.6, specifically. To install the Gemini suite on Python 3:
$ conda create -n geminiconda python=3.6 gemini stsci iraf-all pyraf-all
PyRAF and Gemini IRAF do not work well under Python 3. If you are going to reduce data with Gemini IRAF, eg, spectroscopy data, please install the Python 2 environment (see previous section).
If you are not planning to use IRAF, you can install an IRAF-free version of DRAGONS that will use Python 3. Create the environment as follow:
$ conda create -n dragons python=3.6 dragons stsci
Depending on your needs, it could be a good idea to have multiple environments installed, eg. geminiconda2 and dragons. They will not interfere with each other and you can switch from one the other by doing
conda activate dragons or
conda activate geminiconda2.
Configuration and Testing
If you have installed IRAF and PyRAF and need to use Gemini IRAF, make sure that there is a configured
iraf directory in your home directory. If you have used IRAF before it might already be there, it might still be wise to re-run the
mkiraf step. To set up a new IRAF directory:
$ cd ~ $ mkdir iraf $ cd iraf $ mkiraf
mkiraf step, choose xterm or xgterm for the terminal, and re-initialize the
uparm when/if asked.
Your computer might require 32-bit compatibility libraries. See this Astroconda FAQ for details and how to install those libraries on Linux: http://astroconda.readthedocs.io/en/latest/faq.html#why-is-iraf-32-bit-instead-of-64-bit
DRAGONS requires a configuration file located in
$ cd ~ $ mkdir .geminidr $ cd .geminidr $ touch rsys.cfg
rsys.cfg with you favorite editor and add these lines:
[calibs] standalone = True database_dir = ~/.geminidr/
Configure buffers for ds9:
$ cd ~ $ cp $CONDA_PREFIX/lib/python3.6/site-packages/gempy/numdisplay/imtoolrc ~/.imtoolrc $ vi .bash_profile (or use you favorite editor) Add this line to the .bash_profile: export IMTOOLRC=~/.imtoolrc
Test the installation
- Test Gemini IRAF
$ conda activate geminiconda $ pyraf --> gemini
You should be seeing the Gemini IRAF packages for each instruments.
- Test DRAGONS
$ conda activate dragons (or geminiconda) $ python >>> import astrodata >>> import gemini_instruments
If the imports are successful, i.e. no errors show up, exit Python (Ctrl-D).
Now test that
reduceruns. There may be some delay initially as packages and modules are compiled and loaded.
$ reduce --help
This will print the reduce help to the screen.
If you have Gemini FITS files available, you can test that the Recipe System is functioning as expected as follow (replace the file name with the name of your file):
$ reduce N20180106S0700.fits -r prepare
If all is well, you will see something like:
--- reduce, v2.0.8 --- All submitted files appear valid Found 'prepare' as a primitive. ================================================================================ RECIPE: prepare ================================================================================ PRIMITIVE: prepare ------------------ PRIMITIVE: validateData ----------------------- . PRIMITIVE: standardizeStructure ------------------------------- . PRIMITIVE: standardizeHeaders ----------------------------- PRIMITIVE: standardizeObservatoryHeaders ---------------------------------------- Updating keywords that are common to all Gemini data . PRIMITIVE: standardizeInstrumentHeaders --------------------------------------- Updating keywords that are specific to NIRI . . . Wrote N20180106S0700_prepared.fits in output directory reduce completed successfully.