BUG: Fixed Performance Issue In semantic_segmentor.py

[vqdang]

Carry on from #285 with a dedicated branch for this fix.
Linked to #287

Check list:

• Check feature extractor integrity
• Performance gain measurement: 21.67s (new) vs 45.564 (old) using a 4k x 4k WSI

@ByteHexler To add clarification on the origin of this performance issue.

tiatoolbox/tiatoolbox/models/engine/semantic_segmentor.py

Lines 670 to 673 in ca0ece6

	cum_output.extend(sample_outputs)
	# TODO: detach or hook this into a parallel process
	self._process_predictions(
	cum_output, wsi_reader, ioconfig, save_path, cache_dir

self._process_predictions is called every time cum_output is updated. We will process n**2 time compared to the normal n times. As such, depending on the size of the WSI, this can lead to a significant slowdown, and potentially crash the system because many machines won't be able to hold an entire WSI in the memory. In the initial design, we assumed that

tiatoolbox/tiatoolbox/models/engine/semantic_segmentor.py

Line 681 in ca0ece6

def _process_predictions(

which calls

tiatoolbox/tiatoolbox/models/engine/semantic_segmentor.py

Line 736 in ca0ece6

def merge_prediction(

with free_prediction=True will free up the prediction in place, however, this did not work as expected.

[codecov]

Codecov Report

Merging #313 (e7d7048) into develop (fbce1b7) will increase coverage by 0.02%.
The diff coverage is 100.00%.

❗ Current head e7d7048 differs from pull request most recent head b050fa4. Consider uploading reports for the commit b050fa4 to get more accurate results

@@             Coverage Diff             @@
##           develop     #313      +/-   ##
===========================================
+ Coverage    99.82%   99.84%   +0.02%     
===========================================
  Files           53       55       +2     
  Lines         5004     5173     +169     
  Branches       823      878      +55     
===========================================
+ Hits          4995     5165     +170     
  Misses           2        2              
+ Partials         7        6       -1     

Impacted Files	Coverage Δ
...oolbox/models/engine/nucleus_instance_segmentor.py	98.50% <ø> (ø)
tiatoolbox/models/engine/semantic_segmentor.py	100.00% <100.00%> (ø)
tiatoolbox/cli/__init__.py	100.00% <0.00%> (ø)
tiatoolbox/cli/save_tiles.py	100.00% <0.00%> (ø)
tiatoolbox/cli/slide_info.py	100.00% <0.00%> (ø)
tiatoolbox/cli/stain_norm.py	100.00% <0.00%> (ø)
tiatoolbox/cli/read_bounds.py	100.00% <0.00%> (ø)
tiatoolbox/cli/tissue_mask.py	100.00% <0.00%> (ø)
tiatoolbox/tools/stainnorm.py	100.00% <0.00%> (ø)
tiatoolbox/cli/patch_predictor.py	100.00% <0.00%> (ø)
... and 10 more

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[shaneahmed]

Thanks @vqdang
I will merge once @simongraham has approved it.

[simongraham]

Looks fine.

[simongraham]

Looks fine.

[ByteHexler]

@vqdang thank you a lot for implementing the fix. Great work.