generate_pixel_cluster_mask is really slow

[ngreenwald]

Is your feature request related to a problem? Please describe.
This function is extremely slow.

Describe the solution you'd like
We should look and see if using alternative indexing, similar to what regionprops does, can lead to a performance speedup

[alex-l-kong]

Currently, I'm trying to work a solution that uses 1D indexing; 2D arrays are notorious for cache misses. I've timed it and we get a significant speed up (around 3-3.5x per FOV), just need to ensure correctness.

[ngreenwald]

Got it. I remember when we switched to tuple-based indexing in segmentation it also provided a massive speedup. Not sure if this works for reassignment as well or just for getting values out of the array, can you take a look and see how this compares in terms of performance?

ark-analysis/ark/segmentation/signal_extraction.py

Line 21 in a84cf4d

channel_values = image_data.values[tuple(cell_coords.T)]

[alex-l-kong]

@ngreenwald sure, I'll do some timing analysis on my end and see which one ends up working faster.