axes order in image/label show method

[Artur-man]

before

class:  SpatialDataLabel (MultiScale)
Scales (3): (3,2,512,512 3,2,256,256 3,2,128,128)

after

class:  SpatialDataLabel (t,z,y,x)
Scales (3): (3,2,512,512 3,2,256,256 3,2,128,128)

[Bisaloo]

I was also thinking about a colour scheme, where each dimension would get a different colour in the show method. I would make it easier to match dimensions across elements in the case of high-dimension spatialdata objects, such as the one in your example.

[HelenaLC]

I love the idea in principle, but worry because if the multiscales. We'd get repeated patterns that might look messy.

I was also thinking to add the scales (pixel to physical)? There's a new internal accessor for this that I might turn into a proper accessor.

[HelenaLC]

Q: spatial dimensions will always have the same scale factor, right? This is too many numbers and commas for me... not sure if useful or not.

class: SpatialDataImage (c,z,y,x) 
level(5): (1,2,2160,5120 1,2,1080,2560 1,2,540,1280 1,2,270,640 1,2,135,320)
scale(5): (1,1,0.1625,0.1625 1,1,0.325,0.325 1,1,0.65,0.65 1,1,1.3,1.3 1,1,2.6,2.6)
color(1): (DAPI)

[HelenaLC]

this seems cleaner... let me know if we like it?

class: SpatialDataImage (4d: czyx) 
level(5): (1,2,2160,5120) (1,2,1080,2560) (1,2,540,1280) (1,2,270,640) (1,2,135,320)
scale(5): (1,1,0.1625,0.1625) (1,1,0.325,0.325) (1,1,0.65,0.65) (1,1,1.3,1.3) (1,1,2.6,2.6)
channels(1): (DAPI)

[HelenaLC]

Btw, I am also wondering whether we should include the coordTrans available for each element? This would affect all element show methods = image/label/point/shape; e.g.,

class: SpatialDataImage (3d: cyx) 
coords(1): global
levels(1): (3,64,64)
scales(1): (1,1,1)
channels(3): (0,1,2) 

class: SpatialDataLabel (2d: yx) 
coords(5): global scale translation affine sequence
levels(1): (64,64)
scales(1): (1,1)

class: SpatialDataPoint (200)
names(4): genes instance_id __null_dask_index__ geometry
trans(1): global

It might make more sense to consolidate levels and scale factors into one line per level... that's how they are stored. Eg dash list like the SpatialData show? 1st = index/pixel/dimension, 2nd = map to physical

class: SpatialDataImage (3d: cyx) 
coords(1): global
levels(3):
- (3,64,64) x (1,1,1)
- (3,32,32) x (1,2,2)
- (3,16,16) x (1,4,4)
channels(3): (0,1,2)