Visualisation of the image & graph annotations

[KristinaUlicna]

When reviewing, please annotate an image in napari & then visualise it using the read_grace.ipynb notebook

Data processing:

• Comments out the inflammatory astype(int) from the image processing. Mentioned in Images converted into integers - why? #148
• When annotating in napari, marks the protruding nodes forming an TN edge as TN node. Discussed in Annotating true negative (TN) nodes in napari #143
• When annotating in napari, sets the contrast range of the image to min / max value. Resolves [BUG] Napari binarises synthetic images #108

Plotting / visualisation:

• Visualise the grace annotations overlaid on the image.
• Display a montage & average image per classifier training class.
• Plots simple graph & identifies isolated objects (i.e. connected components)

Graph analysis:

• Generates a ground truth (GT) graph to allow metric calculation
• Maintains all node & edge attributes in new GT graph: resolves Keep edge attributes by removing edges #158
• Shortlists visualisation options in read_grace.ipynb notebook: resolves Adding visualisation of graph to grace as an optional plot out  #136

[review-notebook-app]

Check out this pull request on 

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[KristinaUlicna]

Apologies for a seemingly massive PR, but all the changes are related to the visualisation / annotation update.
This PR needs to go in before metrics can be evaluated. Happy to discuss 🚀

[mooniean]

made some comments, but everything was running!

[KristinaUlicna]

made some comments, but everything was running!

@mooniean Could you comment on what you did / run to review? It's a significant PR with important data processing, I'd like to make sure it was checked correctly.

[mooniean]

made some comments, but everything was running!

@mooniean Could you comment on what you did / run to review? It's a significant PR with important data processing, I'd like to make sure it was checked correctly.

I've done the requested steps: opened image, annotated in napari, loaded it with read_grace.ipynb and ran the whole notebook. Everything was working, the correct things were being shown (apart from the graph being transposed without the image)