get_centroids() slow on on labels elements
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
When trying to get centroids of labels, the function get_centroids is really taking forever, even on small data.
This makes it very difficult to run on real life data.
For example, it takes 3 minutes on a 848x2540 image. I tested with a tqdm in _get_centroids_for_axis to check what was taking time:
Computing centroids along the y axis: 100%|██████████| 848/848 [00:50<00:00, 16.78it/s]
Computing centroids along the x axis: 100%|██████████| 2540/2540 [02:04<00:00, 20.47it/s]
A minimal example to reproduce:
from spatialdata import get_centroids
from spatialdata.datasets import blobs
import time
sdata = blobs()
t = time.process_time()
get_centroids(sdata["blobs_labels"])
print (time.process_time() - t)
That shows around 10 seconds for a 512x512 image.
For comparion, the following code that also computes centroids, takes about 0.01 second:
from spatialdata import get_centroids
from spatialdata.datasets import blobs
import time
sdata = blobs()
import numpy as np
from skimage.measure import regionprops
import pandas as pd
t = time.process_time()
label_image = sdata["blobs_labels"].values.T
props = regionprops(label_image)
centroids = pd.DataFrame(
[p.centroid for p in props],
columns=["x", "y"],
index=[p.label for p in props]
)
print (time.process_time() - t)
As get_centroids() is used in to_legacy_anndata, it makes it also really slow on large datasets.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with get_centroids and _get_centroids_for_axis, then trace how to_legacy_anndata calls them. Run the minimal blobs example and compare its timing and centroid results with the regionprops approach; done means get_centroids preserves its results without the reported multi-minute slowdown.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, pandas, python
- Domain
- data, performance
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100