add axis labels to display()

[kevinyamauchi]

Description

This PR adds axis labels to starfish.display() using the recently-added labeled axis support in napari (thanks, @HagaiHargil !).

Approach

I added the axis_labels keyword argument to the Viewer constructor in _display.py.

Question

Currently, I just create a list of the Axes Enum values. Is there a better way to do this? Maybe get the axes from the stack?

Testing:

I downloaded and viewed the test data from the ISS example notebook.

[ttung]

Do we need to upgrade the napari version pin?

[kevinyamauchi]

@ttung, yeah we would need to bump to napari 0.2.6. I changed the constant in _display(). Where is the version pinned for pip install starfish[napari]? I am in the process of updating the docstrings.

[codecov-io]

Codecov Report

Merging #1682 into master will decrease coverage by 0.09%.
The diff coverage is 16.66%.

@@            Coverage Diff            @@
##           master    #1682     +/-   ##
=========================================
- Coverage   90.24%   90.15%   -0.1%     
=========================================
  Files         230      230             
  Lines        8745     8755     +10     
=========================================
+ Hits         7892     7893      +1     
- Misses        853      862      +9

Impacted Files	Coverage Δ
starfish/core/_display.py	21.35% <16.66%> (-1.23%)	⬇️

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 0324fbd...7aba7a7. Read the comment docs.

[kevinyamauchi]

@ttung, if I read setup.py correctly, the napari version comes from the _display.py, so I think we are good there. I just updated the display() docstring.

[ttung]

I would grab these three from starfish/core/imagestack/dataorder.py

[kevinyamauchi]

Will do!

[kevinyamauchi]

@ttung , it looks like AXES_DATA contains names and orders for round, channel, and z, but not x and y. Should I just assume (y, 3) and (x, 4)? Or is the axis ordering for y and x stored elsewhere?

[kevinyamauchi]

(you can rotate views in napari, so the y and x axis names may get displayed)

[ttung]

Unfortunately, Y and X are not stored anywhere. It has always been assumed Y then X.

[kevinyamauchi]

Sounds good!

[kevinyamauchi]

@ttung, I changed it such that the axis order comes from starfish.core.imagestack.dataorder.