Introduction

ORB is the kernel module for the whole suite of data reduction and analysis tools for SITELLE: ORBS, ORCS.

It provides basic access to the data cubes as long as the fitting engine of ORCS and numerous utilitary functions for the analysis of interferometric and spectral data, imaging data, astrometry, photometry.

You can find the up-to-date documentation here:

https://orb.readthedocs.io

installation instructions with Anaconda (should work on Linux, Mac OSX, Windows)

1. download Miniconda for your OS and python 2.7.

If you already have Anaconda installed go to step 2

instructions are here: Miniconda — Conda

1. place the downloaded file on your home directory
2. install it (use the real file name instead of Miniconda*.sh)

bash Miniconda*.sh

2. install conda-build tools

conda install conda-build

3. create orb environment

automatic procedure if you have a *.yml* file:

create an environment automatically

conda env create -f orb-env.yml

manual installation of the librairies

create an environment and install needed modules manually

conda create -n orb python=2.7 
conda install -n orb numpy scipy bottleneck matplotlib astropy cython h5py dill pandas
conda install -n orb -c conda-forge pyregion
conda install -n orb -c astropy photutils

if your shell is bash, which is now generally the case for OSX and most linux distributions please do

conda init bash

If you have a different shell replace bash with the name of your shell.

Now if you have Scisoft installed (which does not goes well with Anaconda/Python... but still you may want to have it) then please add export PYTHONPATH='' at the end of your profile file where some environment variables are defined (e.g. .bashrc, .profile, .bash_profile).

You may then activate your environment with

conda activate orb

now your prompt should be something like (orb) $. If conda activate orb does not work. Please do the following conda init bash (if bash is your shell

note: you may now have to install gcc on Mac OSX if you want to be able to execute the following with no error (see https://discussions.apple.com/thread/8336714). To check that you have gcc installed type gcc --help in a terminal. You should see the usage informations displayed.

pip install gvar --no-deps
pip install lsqfit --no-deps
pip install pp --no-deps

4. add orb module

clone ORB

mkdir orb-stable # do it where you want to put orb files
cd orb-stable
git clone https://github.com/thomasorb/orb.git

in the downloaded folder

conda activate orb # you don't need to do it if you are already in the orb environment
cd path/to/orb-stable/orb
python setup.py build_ext --inplace
python setup.py install

Test it:

conda activate orb # you don't need to do it if you are already in the orb environment
python -c 'import orb.core'

5. Install jupyter

conda install -n orb -c conda-forge jupyterlab

Run it

conda activate orb # you don't need to do it if you are already in the orb environment
jupyter lab

You should now have your web browser opened and showing the jupyter lab interface !