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Fixes #298: Repeatedly appending parent path to flatFiles #305

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Fixes #298: Repeatedly appending parent path to flatFiles #305

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bbbfa24
`spio.cosmx` appends path two times to the file name
mayank-singh-sikarwar Apr 29, 2025
cb147e2
`spio.cosmx` appends path two times to the file name Fixes #298
mayank-singh-sikarwar Apr 29, 2025
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9 changes: 6 additions & 3 deletions src/spatialdata_io/readers/cosmx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@ def cosmx(
-------
:class:`spatialdata.SpatialData`
"""
print("This is the local version")
path = Path(path)

# tries to infer dataset_id from the name of the counts file
Expand Down Expand Up @@ -102,10 +103,12 @@ def cosmx(
if not labels_dir.exists():
raise FileNotFoundError(f"Labels directory not found: {labels_dir}.")

counts = pd.read_csv(path / counts_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)
counts = pd.read_csv(counts_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)
print(counts.head())
counts.index = counts.index.astype(str).str.cat(counts.pop(CosmxKeys.FOV).astype(str).values, sep="_")

obs = pd.read_csv(path / meta_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)
obs = pd.read_csv(meta_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)
print(obs.head())
obs[CosmxKeys.FOV] = pd.Categorical(obs[CosmxKeys.FOV].astype(str))
obs[CosmxKeys.REGION_KEY] = pd.Categorical(obs[CosmxKeys.FOV].astype(str).apply(lambda s: s + "_labels"))
obs[CosmxKeys.INSTANCE_KEY] = obs.index.astype(np.int64)
Expand Down Expand Up @@ -253,7 +256,7 @@ def cosmx(
with tempfile.TemporaryDirectory() as tmpdir:
print("converting .csv to .parquet to improve the speed of the slicing operations... ", end="")
assert transcripts_file is not None
transcripts_data = pd.read_csv(path / transcripts_file, header=0)
transcripts_data = pd.read_csv(transcripts_file, header=0)
transcripts_data.to_parquet(Path(tmpdir) / "transcripts.parquet")
print("done")

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