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MACSIMA parse subfolders only when explicitly requested #379

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MACSIMA parse subfolders only when explicitly requested #379

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92fcf8a
Change parsing defaults!
MSHelm Feb 27, 2026
861155a
Skip empty folders when parsing multiple folders
MSHelm Feb 27, 2026
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20 changes: 5 additions & 15 deletions src/spatialdata_io/readers/macsima.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,6 @@ class MACSimaParsingStyle(ModeEnum):
PROCESSED_SINGLE_FOLDER = "processed_single_folder"
PROCESSED_MULTIPLE_FOLDERS = "processed_multiple_folders"
RAW = "raw"
AUTO = "auto"


@dataclass
Expand Down Expand Up @@ -223,7 +222,7 @@ def get_stack(self) -> da.Array:

def macsima(
path: str | Path,
parsing_style: MACSimaParsingStyle | str = MACSimaParsingStyle.AUTO,
parsing_style: MACSimaParsingStyle | str = MACSimaParsingStyle.PROCESSED_SINGLE_FOLDER,
filter_folder_names: list[str] | None = None,
imread_kwargs: Mapping[str, Any] = MappingProxyType({}),
subset: int | None = None,
Expand Down Expand Up @@ -294,18 +293,6 @@ def macsima(
if not isinstance(parsing_style, MACSimaParsingStyle):
parsing_style = MACSimaParsingStyle(parsing_style)

if parsing_style == MACSimaParsingStyle.AUTO:
assert path.is_dir(), f"Path {path} is not a directory."

if any(p.suffix in [".tif", ".tiff"] for p in path.iterdir()):
# if path contains tifs, do parse_processed_folder on path
parsing_style = MACSimaParsingStyle.PROCESSED_SINGLE_FOLDER
elif all(p.is_dir() for p in path.iterdir() if not p.name.startswith(".")):
# if path contains only folders or hidden files, do parse_processed_folder on each folder
parsing_style = MACSimaParsingStyle.PROCESSED_MULTIPLE_FOLDERS
else:
raise ValueError(f"Cannot determine parsing style for path {path}. Please specify the parsing style.")

if parsing_style == MACSimaParsingStyle.PROCESSED_SINGLE_FOLDER:
return parse_processed_folder(
path=path,
Expand All @@ -331,6 +318,9 @@ def macsima(
for p in path.iterdir()
if p.is_dir() and (not filter_folder_names or not any(f in p.name for f in filter_folder_names))
]:
if not len(list(p.glob("*.tif*"))):
warnings.warn(f"No tif files found in {p}, skipping it!", UserWarning, stacklevel=2)
continue
sdatas[p.stem] = parse_processed_folder(
path=p,
imread_kwargs=imread_kwargs,
Expand Down Expand Up @@ -624,7 +614,7 @@ def parse_processed_folder(
nuclei_channel_name: str = "DAPI",
split_threshold_nuclei_channel: int | None = 2,
skip_rounds: list[int] | None = None,
file_pattern: str = "*.tif*",
file_pattern: str = "**/*.tif*",
include_cycle_in_channel_name: bool = False,
) -> SpatialData:
"""Parse a single folder containing images from a cyclical imaging platform."""
Expand Down
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