MACSIMA parse subfolders only when explicitly requested

src/spatialdata_io/__main__.py

@@ -794,9 +794,9 @@ def xenium_wrapper(
 @_input_output_click_options
 @click.option(
     "--parsing-style",
-    type=click.Choice(["auto", "processed_single_folder", "processed_multiple_folders", "raw"]),
-    default="auto",
-    help="Parsing style for MACSima data. [default: auto]",
+    type=click.Choice(["processed_single_folder", "processed_multiple_folders", "raw"]),
+    default="processed_single_folder",
+    help="Parsing style for MACSima data. [default: processed_single_folder]",
 )
 @click.option(
     "--filter-folder-names",
@@ -870,7 +870,7 @@ def macsima_wrapper(
     input: str,
     output: str,
     *,
-    parsing_style: str = "auto",
+    parsing_style: str = "processed_single_folder",
     filter_folder_names: list[str] | None = None,
     subset: int | None = None,
     c_subset: int | None = None,

src/spatialdata_io/readers/macsima.py

@@ -48,7 +48,6 @@ class MACSimaParsingStyle(ModeEnum):
     PROCESSED_SINGLE_FOLDER = "processed_single_folder"
     PROCESSED_MULTIPLE_FOLDERS = "processed_multiple_folders"
     RAW = "raw"
-    AUTO = "auto"
 
 
 @dataclass
@@ -224,7 +223,7 @@ 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,
@@ -255,7 +254,8 @@ def macsima(
     path
         Path to the directory containing the data.
     parsing_style
-        Parsing style to use. If ``auto``, the parsing style is determined based on the contents of the path.
+        Parsing style to use. If ``processed_single_folder``, all subfolders of ``path`` are combined into a stack.
+        If ``processed_multiple_folders``, a stack is created for each folder directly beneath ``path``.
     filter_folder_names
         List of folder names to filter out when parsing multiple folders.
     imread_kwargs
@@ -295,19 +295,13 @@ 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:
+        if filter_folder_names:
+            warnings.warn(
+                "single_processed_folder was requested but filter_folder_names was specified. Note that it is ignored here, filtering only happens for processed_multi_folders!",
+                UserWarning,
+                stacklevel=2,
+            )
         return parse_processed_folder(
             path=path,
             imread_kwargs=imread_kwargs,
@@ -332,6 +326,9 @@ 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,
@@ -625,7 +622,7 @@ 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."""

tests/test_macsima.py

@@ -35,7 +35,6 @@
     _parse_v1_ome_metadata,
     macsima,
 )
-from tests._utils import skip_if_below_python_version
 
 RNG = da.random.default_rng(seed=0)
 
@@ -101,7 +100,6 @@ def test_exception_on_no_valid_files(tmp_path: Path) -> None:
         macsima(tmp_path)
 
 
-@skip_if_below_python_version()
 @pytest.mark.parametrize(
     "dataset,expected",
     [
@@ -123,7 +121,6 @@ def test_image_size(dataset: str, expected: dict[str, Any]) -> None:
     assert extent == expected
 
 
-@skip_if_below_python_version()
 @pytest.mark.parametrize(
     "dataset,expected",
     [("OMAP10_small", 4), ("OMAP23_small", 5)],
@@ -139,7 +136,6 @@ def test_total_channels(dataset: str, expected: int) -> None:
     assert channels == expected
 
 
-@skip_if_below_python_version()
 @pytest.mark.parametrize(
     "dataset,expected",
     [
@@ -161,7 +157,6 @@ def test_channel_names_with_cycle_in_name(dataset: str, expected: list[str]) ->
     assert list(channels) == expected
 
 
-@skip_if_below_python_version()
 @pytest.mark.parametrize(
     "dataset,expected",
     [
@@ -178,7 +173,6 @@ def test_total_rounds(dataset: str, expected: list[int]) -> None:
     assert max_cycle == expected
 
 
-@skip_if_below_python_version()
 @pytest.mark.parametrize(
     "dataset,skip_rounds,expected",
     [
@@ -201,6 +195,57 @@ def test_skip_rounds(dataset: str, skip_rounds: list[int], expected: list[str])
     assert list(channels) == expected, f"Expected {expected}, got {list(channels)}"
 
 
+def test_unsupported_parsing_styles() -> None:
+    with pytest.raises(ValueError, match="Invalid option `not_a_parsing_style` for `MACSimaParsingStyle`."):
+        macsima(Path(), parsing_style="not_a_parsing_style")
+
+
+def test_processed_single_folder_parsing_returns_a_single_image_stack(tmp_path: Path) -> None:
+    omap10_path = Path("./data/OMAP10_small")
+    shutil.copytree(omap10_path, tmp_path / "OMAP10_small_1")
+    shutil.copytree(omap10_path, tmp_path / "OMAP10_small_2")
+
+    sdata = macsima(tmp_path, parsing_style="processed_single_folder")
+
+    assert len(sdata.images) == 1
+    # omap10_small has 4 channels, so we expect 8 here
+    el = sdata[list(sdata.images.keys())[0]]
+    assert len(get_channel_names(el)) == 8
+    assert len(sdata.tables) == 1
+
+
+def test_processed_single_folder_parsing_warns_when_specifying_filtered_folders(tmp_path: Path) -> None:
+    omap10_path = Path("./data/OMAP10_small")
+    shutil.copytree(omap10_path, tmp_path / "OMAP10_small_1")
+    shutil.copytree(omap10_path, tmp_path / "OMAP10_small_2")
+    with pytest.warns(UserWarning, match="filtering only happens for processed_multi_folders"):
+        macsima(tmp_path, parsing_style="processed_single_folder", filter_folder_names=["OMAP10_small_2"])
+
+
+def test_processed_multiple_folders_returns_an_image_stack_per_subfolder(tmp_path: Path) -> None:
+    omap10_path = Path("./data/OMAP10_small")
+    shutil.copytree(omap10_path, tmp_path / "OMAP10_small_1")
+    shutil.copytree(omap10_path, tmp_path / "OMAP10_small_2")
+
+    sdata = macsima(tmp_path, parsing_style="processed_multiple_folders")
+
+    assert len(sdata.images) == 2
+    for el in sdata.images.keys():
+        assert len(get_channel_names(sdata[el])) == 4
+    assert len(sdata.tables) == 2
+
+
+def test_processed_multiple_folders_skips_filtered_folder_names(tmp_path: Path) -> None:
+    shutil.copytree(Path("./data/OMAP10_small"), tmp_path / "OMAP10_small")
+    shutil.copytree(Path("./data/OMAP23_small"), tmp_path / "OMAP23_small")
+
+    sdata = macsima(tmp_path, parsing_style="processed_multiple_folders", filter_folder_names=["OMAP10_small"])
+    assert len(sdata.images) == 1
+    assert list(sdata.images.keys()) == ["OMAP23_small_image"]
+    assert len(sdata.tables) == 1
+    assert list(sdata.tables.keys()) == ["OMAP23_small_table"]
+
+
 METADATA_COLUMN_ORDER = [
     "cycle",
     "imagetype",
@@ -242,7 +287,6 @@ def test_skip_rounds(dataset: str, skip_rounds: list[int], expected: list[str])
 )
 
 
-@skip_if_below_python_version()
 @pytest.mark.parametrize(
     "dataset,expected_df",
     [
@@ -262,11 +306,6 @@ def test_metadata_table(dataset: str, expected_df: pd.DataFrame) -> None:
     pd.testing.assert_frame_equal(actual, expected_df)
 
 
-def test_parsing_style() -> None:
-    with pytest.raises(ValueError):
-        macsima(Path(), parsing_style="not_a_parsing_style")
-
-
 def test_mci_sort_by_channel() -> None:
     sizes = [100, 200, 300]
     c_names = ["test11", "test3", "test2"]
@@ -315,7 +354,6 @@ def test_mci_array_reference() -> None:
     assert da.all(mci.data[0] == orig_arr1)
 
 
-@skip_if_below_python_version()
 @pytest.mark.parametrize("dataset", ["OMAP10_small", "OMAP23_small"])
 def test_cli_macsima(runner: CliRunner, dataset: str) -> None:
     f = Path("./data") / dataset