Known Issues

On MacOS versions 10.13 and older, install fails due to scikit-image

This can be fixed by reinstalling scikit-image:

pip uninstall scikit-image
conda install scikit-image

The reason for this issue is that prebuilt binaries for scikit-image don’t work on Mac versions of 10.13 or older and conda installs an older version of scikit-image that works with those versions. Another way to get the up-to-date scikit-image version is:

pip install -U --no-binary scikit-image scikit-image.

Although this solution takes much longer (~5 minutes) to install than the first solution.

On some platforms, install fails due to vispy

The 0.6.4 version of vispy fails to build for some combinations of platform/OS and Python versions. vispy 0.6.5 has resolved this, but a workaround if you have an older version of vispy is to ensure you have a compatible version:

% conda create -n jdaviz python=3.8 % conda activate jdaviz % pip install vispy>=0.6.5 % pip install jdaviz –no-cache-dir

See Issue #305 for updates on this topic.

On some platforms, install fails due to bottleneck

In a conda environment, where numpy was installed using conda, installing jdaviz using pip will attempt to pull bottleneck from PyPI. This might result in bottleneck trying to build numpy from source and crash, stalling the installation altogether. When this happens, exit the installation, install bottleneck with conda, and try to install jdaviz again.

Collapse Plugin spectral bounds don’t match selected region

Spectral bounds are off in the plugin compared to the spectrum viewer.

Ghost subsets and models in spectrum viewer

Mysterious extra subsets and models appear in the Specviz spectrum viewer after fitting a model. Pan/zoom and resize were also used, but it is unclear if they play a role or not in this bug.

Cubeviz Collapse and Moment Maps: Spectral bounds do not match Region selection

When trying to do a second collapse with the same spectral region, but with resized bounds: change to Region=None, resize the region, then reselect Region 1, the region bounds are correct. However, applying Collapse again, it errors out and the image viewer that contained the intial collapse goes blank.

Cubeviz cube viewer colormap printed out

When changing the colormap in the Cubeviz cube viewer–>Layer–>colormap, the colormap name is printed in the cell output.

Cubeviz cube viewer contrast changes when collapsing jupyter scroll window

In order to see the full Cubeviz app in a Jupyter notebook, one can click on the side of the cell output to collapse or expand the scrollable window. This has the unintended consequence of changing the contrast of the image displayed in the Cubeviz cube viewer.

Reporting a bug

You can report a bug in the Jdaviz GitHub issues: