Installation
Qubefit has been tested on both macOS as well as Linux (Red Hat 7). To install the code clone or download the latest version from github: qubefit. After downloading the code (and unzipping if necessary), open up a terminal window, navigate to the directory where the code lives, which contains the setup.py file, and type:
python setup.py install
If everything goes correctly, this installs the code. To test if the installation was
successful, see if the GUI loads. Use the command line to put yourself Inside the examples folder qubefit/examples
and then type:
qubemom WolfeDiskCube.fits
and
qfgui WolfeDiskSetup.py
If this brings up the two GUIs such as shown in the section Graphical User Interfaces, the code was installed correctly.
Dependencies
Qubefit has been tested on python 3.8 and depends heavily on the following packages, where the version numbers are the version used for testing the code:
numpy (v1.19.2)
scipy (v1.5.2)
astropy (v4.0.2)
matplotlib (v3.3.2)
h5py (2.10.0)
scikit-image (v0.17.2)
tqdm (v4.50.2)
emcee (v3.0.2)
corner (v2.1.0)
The first four packages are standard packages that you probably
already have installed on your computer. For these the version number
is probably not particularly important except for numpy
, which pre
v.1.15 will throw an error because of certain missing functions.
The following four packages can simply be installed using conda e.g.,:
conda install h5py
conda install scikit-image
conda install tqdm
conda install -c conda-forge emcee
It should be noted that the top three packages are normally installed in the full installation of conda (v4.9.2). Alternatively, these programs can also be installed using pip. See the repsective websites for each program: h5py, scikit image, tqdm,
emcee.
scikit-image
package is only needed to generate masks, and if you
want to make your own masks, it does not need to be installed. The
tqdm
package provides the progress bar used in the MCMC chain.
Warning
It is very important to use version 3.X or higher for
emcee
, because version 2.X or earlier of this code will result
in errors. Further details are given in the
documentation for emcee v3.0.
Although the corner
package is not required to run the fitting
routine, it is recommended for displaying the output of the fitting
routine, and is necessary to create the diagnostic plots. It can be installed using pip, see the documentation for corner.