The check for required parameters now takes precedence over displaying help information. I had to run relion_mask_create --i nonsense --help to display the help information.

Need to check dimensional reshaping

TypeError Traceback (most recent call last)
in ()
1 step_chan = 'DC_Offset'
----> 2 px.be_viz_utils.jupyter_visualize_beps_sho(h5_sho_fit, step_chan)

~\Documents\GitHub\pycroscopy\pycroscopy\viz\be_v

Introduced when merging #226

https://github.com/neuropoly/axondeepseg/blob/dae4a1dcd90539cfcc7347d38cb8264395de8a66/AxonDeepSeg/models/download_model.py#L12-L13

Should probably used the Path() function as well as relative paths to the main repo location.

Currently not all command line options are in the documentation. This should be improved.

Maybe, we can add a linting rule which checks that all functions in the api file have docstrings? At least, importNmlAsString is missing a docstring.

It would be great to add Doxygen or similar for auto-generation of documentation and start a push towards standardisation of the style and comment/description data as to work with such a system.

Use Case

Please provide a use case to help us understand your request in context
Related to #104

Monitor image read performance on every commit to master to watch for performance hits introduced with each patch.

Solution

Please describe your ideal solution
Look into asv which is used by pandas for benchmarking whi

Currently the focus of the navcam is hard coded. If you're lucky, the focus is correct, but in most of the time you're not lucky.

So instead of using a hard coded position, we should either:

• Run the autofocus (starting from this hard coded position)
• Run the autofocus at calibration and reuse this value (= one value per Phenom/sample holder)