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add v2-3 conv #134

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Merged
dariarom94 merged 1 commit into from
Jun 17, 2026
Merged

add v2-3 conv #134

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18 changes: 17 additions & 1 deletion src/data_processors/process_dataset/script.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@
import spatialdata as sd
import os
import shutil
import tempfile
from pathlib import Path

### VIASH START
par = {
Expand Down Expand Up @@ -172,8 +174,22 @@ def subsample_adata_group_balanced(adata, group_key, n_samples, seed=0):
# Load the single-cell data
adata = ad.read_h5ad(par["input_sc"])

# Migrate zarr v2 stores to v3 before reading (zarr v2 uses .zattrs; zarr v3 uses zarr.json)
input_sp = par["input_sp"]
_tmp_dir = None
if Path(input_sp, ".zattrs").exists():
print(f"Detected zarr v2 store at {input_sp}, migrating to zarr v3...")
_tmp_dir = tempfile.mkdtemp()
_tmp_path = os.path.join(_tmp_dir, "dataset.zarr")
_sdata_v2 = sd.read_zarr(input_sp)
_sdata_v2.write(_tmp_path)
del _sdata_v2
input_sp = _tmp_path

# Load the spatial data
sdata = sd.read_zarr(par["input_sp"])
sdata = sd.read_zarr(input_sp)
if _tmp_dir is not None:
shutil.rmtree(_tmp_dir)

# Subset single-cell data if it is too large
N_MAX_SC = 120000
Expand Down
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