diff --git a/src/spatialdata_io/readers/cosmx.py b/src/spatialdata_io/readers/cosmx.py index 561fe914..09430f12 100644 --- a/src/spatialdata_io/readers/cosmx.py +++ b/src/spatialdata_io/readers/cosmx.py @@ -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 @@ -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) @@ -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")