Fix slicer pre-transforming the planes' center

[carlocastoldi]

The Slicer automatically set the centre x positioning to its negative value.
This, however, is not something whose responsibility is of the constructor, but rather of the renderer.
As a consequence, it required some weird problems when messing with slicers' planes.

Additionally, it adds the parameter both to plan.show().

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

How has this PR been tested?

from brainrender import Atlas, settings

import brainglobe_heatmap as bgh
import numpy as np

settings.SHOW_AXES = True

atlas = Atlas(atlas_name="allen_mouse_25um")
center = np.array([100, 100, 100])
slicer = bgh.slicer.Slicer(center, "frontal", 10, atlas.get_region("root"))
assert all(slicer.plane0.center == center)

Is this a breaking change?

no

Does this PR require an update to the documentation?

no

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[codecov]

Codecov Report

Attention: Patch coverage is 0% with 2 lines in your changes missing coverage. Please review.

Project coverage is 0.00%. Comparing base (aa723a8) to head (756680f).

Files with missing lines	Patch %	Lines
brainglobe_heatmap/planner.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@          Coverage Diff          @@
##            main     #71   +/-   ##
=====================================
  Coverage   0.00%   0.00%           
=====================================
  Files          5       5           
  Lines        284     283    -1     
=====================================
+ Misses       284     283    -1     

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[IgorTatarnikov]

Looks great thank you! Unfortunately, removing the plane transformation breaks the sagittal orientation slicing in both the 2D and 3D heatmaps.

I believe this issue will have to be resolved in brainrender and will address #72 and #55 at the same time.

[IgorTatarnikov]

This line is required for sagittal slicing to work correctly. There are some underlying oddities in how brainrender handles the last spatial dimension (x in zyx representation). Without this line sagittal slices in 2D look like:

This was generated by running the heatmap_2d.py example specifying the sagittal orientation. It should look something like:

I believe this is tied together with #72 and #55. I think getting rid of this line will require changes in brainrender.