ENH: Add Annotation Store Reader

[measty]

This PR adds an AnnotationStoreReader class that allows an annotation store to be read as if it were a WSI. That can be used wherever a WSIreader can be used.

For example, to extract overlay patches around a few random glands using PointsPatchExtractor:

SQ = SQLiteStore(path\to\store.db)
glands = SQ.query(where='props["type"] == "Gland"')
centroids = np.array([[gland.geometry.centroid.x, gland.geometry.centroid.y] for gland in glands.values()])
#get 6 random centroids
rand_centroids = centroids[np.random.randint(0, len(centroids), 6),:]
ann_reader = AnnotationStoreReader(db_path, base_wsi_reader=wsi)
extractor = PointsPatchExtractor(ann_reader, rand_centroids, patch_size=(1024, 1024))

#show the 6 patches in a 2x3 grid
patch_im = np.zeros((2048, 3072, 3), dtype=np.uint8)
for i, patch in enumerate(extractor):
    patch_im[1024*(i//3):1024*(i//3 + 1), (i%3)*1024:(i%3+1)*1024, :] = patch
plt.imshow(patch_im)
plt.show()

Can be used to draw annotations over its base wsi as an 'annotated slide' as above, or just as a standalone overlay mask as below right.

Also moves the annotation rendering code into the AnnotationRender class instead of in the AnnotationTileGenerator, so it can be reused as needed. It probably belongs more naturally there regardless.

Updates the rendering code a little as well with a few further options, for example options for a blur to give a more heatmap-like effect:

[codecov[bot]]

Codecov Report

Merging #476 (d8af126) into develop (1f0c8ea) will increase coverage by 0.03%. The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #476      +/-   ##
===========================================
+ Coverage    99.63%   99.67%   +0.03%     
===========================================
  Files           62       62              
  Lines         6378     6487     +109     
  Branches      1019     1074      +55     
===========================================
+ Hits          6355     6466     +111     
+ Misses          10        9       -1     
+ Partials        13       12       -1     

Impacted Files	Coverage Δ
tiatoolbox/wsicore/wsimeta.py	100.00% <ø> (ø)
tiatoolbox/annotation/storage.py	99.87% <100.00%> (ø)
tiatoolbox/tools/pyramid.py	100.00% <100.00%> (ø)
tiatoolbox/utils/visualization.py	100.00% <100.00%> (ø)
tiatoolbox/wsicore/wsireader.py	98.47% <100.00%> (+0.39%)	:arrow_up:
tiatoolbox/utils/image.py	100.00% <0.00%> (ø)

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[John-P]

Please see comments on other PR:

• https://github.com/TissueImageAnalytics/tiatoolbox/pull/445#issuecomment-1271385492
• https://github.com/TissueImageAnalytics/tiatoolbox/pull/445#issuecomment-1271392213