Error when running seg2explorer

[HarryZhang1224]

I installed the latest version of segger and ran into some issues with seg2explorer.

get_flatten_version(polygon_vertices, max_value)
     29         flattened.append(vertices[:max_value])
     30     else:
---> 31         flattened.append(vertices + [(0.0, 0.0)] * (max_value - len(vertices)))
     32 return np.array(flattened, dtype=np.float32)

ValueError: operands could not be broadcast together with shapes (7,2) (121,2) 

This error seemed to be from concatenating a numpy array with a list, which was interpreted by numpy as the add operation. I added this line to resolve the error.

if isinstance(vertices, np.ndarray):
            vertices = vertices.tolist()

The other error is from opening the source cells.zarr.zip file (zarr was also not imported), which I got and resolved with:

No group found in store StorePath(LocalStore, 'file://cells.zarr.zip') at path ''

from zarr.storage import ZipStore
import zarr
source_zarr_store = ZipStore(source_path / "cells.zarr.zip", mode="r") # added this line
existing_store = zarr.open(source_zarr_store, mode="r")

I also found that using that with the output of the new version of seg2explorer, xeniumranger hangs on importing nuclear and cell segmentation. The inputs to Xenium ranger were computed by using the function provided in #83.

[EliHei2]

please refer to #121

[EliHei2]

@HarryZhang1224 Thanks the suggestions were very helpful and fixed the problem!

[EliHei2]

@HarryZhang1224 the most recent commit should fix all bugs with Xenium explorer, could you please check?

[HarryZhang1224]

@HarryZhang1224 the most recent commit should fix all bugs with Xenium explorer, could you please check?

@EliHei2 Thanks! The seg2explorer function is working now. It isn't clear to me how to directly import the output to Xenium explorer for visualization though. I have been using the function provided by @MiracleEaTu in #83 to run xeniumrange import-segmentation. Is there a more efficient way?