ENH(psoct.single_volume): more robust default key

linc_convert/modalities/psoct/single_volume.py

@@ -12,7 +12,7 @@
 from contextlib import contextmanager
 from functools import wraps
 from itertools import product
-from typing import Any, Callable, Optional
+from typing import Callable, Optional
 from warnings import warn
 
 import cyclopts
@@ -38,10 +38,10 @@
 
 
 def _automap(func: Callable) -> Callable:
-    """Decorator to automatically map the array in the mat file."""  # noqa: D401
+    """Automatically map the array in the mat file."""
 
     @wraps(func)
-    def wrapper(inp: str, out: str = None, **kwargs: dict) -> Any:  # noqa: ANN401
+    def wrapper(inp: str, out: str = None, **kwargs: dict) -> None:
         if out is None:
             out = os.path.splitext(inp[0])[0]
             out += ".nii.zarr" if kwargs.get("nii", False) else ".ome.zarr"
@@ -65,9 +65,12 @@ def _mapmat(fname: str, key: str = None) -> None:
     if key is None:
         if not len(f.keys()):
             raise Exception(f"{fname} is empty")
-        key = list(f.keys())[0]
+        for key in f.keys():
+            if key[:1] != '_':
+                break
         if len(f.keys()) > 1:
-            warn(f'More than one key in .mat file {fname}, arbitrarily loading "{key}"')
+            warn(f'More than one key in .mat file {fname}, '
+                 f'arbitrarily loading "{key}"')
 
     if key not in f.keys():
         raise Exception(f"Key {key} not found in file {fname}")
@@ -153,9 +156,9 @@ def convert(
     omz = zarr.group(store=omz, overwrite=True)
 
     if not hasattr(inp, "dtype"):
-        raise Exception("Input is not a numpy array. This is likely unexpected")
+        raise Exception("Input is not a numpy array. This is unexpected.")
     if len(inp.shape) < 3:
-        raise Exception("Input array is not 3d")
+        raise Exception("Input array is not 3d:", inp.shape)
     # Prepare chunking options
     opt = {
         "dimension_separator": r"/",
@@ -171,7 +174,9 @@ def convert(
     ni = ceildiv(inp.shape[2], inp_chunk[2])
 
     nblevels = min(
-        [int(math.ceil(math.log2(x))) for i, x in enumerate(inp.shape) if i != no_pool]
+        [int(math.ceil(math.log2(x)))
+         for i, x in enumerate(inp.shape)
+         if i != no_pool]
     )
     nblevels = min(nblevels, int(math.ceil(math.log2(max_load))))
     nblevels = min(nblevels, max_levels)
@@ -183,9 +188,9 @@ def convert(
     # iterate across input chunks
     for i, j, k in product(range(ni), range(nj), range(nk)):
         loaded_chunk = inp[
-            k * inp_chunk[0] : (k + 1) * inp_chunk[0],
-            j * inp_chunk[1] : (j + 1) * inp_chunk[1],
-            i * inp_chunk[2] : (i + 1) * inp_chunk[2],
+            k * inp_chunk[0]: (k + 1) * inp_chunk[0],
+            j * inp_chunk[1]: (j + 1) * inp_chunk[1],
+            i * inp_chunk[2]: (i + 1) * inp_chunk[2],
         ]
 
         print(
@@ -198,9 +203,9 @@ def convert(
 
         # save current chunk
         omz["0"][
-            k * inp_chunk[0] : k * inp_chunk[0] + loaded_chunk.shape[0],
-            j * inp_chunk[1] : j * inp_chunk[1] + loaded_chunk.shape[1],
-            i * inp_chunk[2] : i * inp_chunk[2] + loaded_chunk.shape[2],
+            k * inp_chunk[0]: k * inp_chunk[0] + loaded_chunk.shape[0],
+            j * inp_chunk[1]: j * inp_chunk[1] + loaded_chunk.shape[1],
+            i * inp_chunk[2]: i * inp_chunk[2] + loaded_chunk.shape[2],
         ] = loaded_chunk
 
     generate_pyramid(omz, nblevels - 1, mode="mean")
@@ -217,7 +222,9 @@ def convert(
         no_pool=no_pool,
         space_unit=ome_unit,
         space_scale=vx,
-        multiscales_type=("2x2x2" if no_pool is None else "2x2") + "mean window",
+        multiscales_type=(
+            ("2x2x2" if no_pool is None else "2x2") + "mean window"
+        ),
     )
 
     if not nii:
@@ -233,5 +240,6 @@ def convert(
     if center:
         affine = center_affine(affine, shape[:3])
     niftizarr_write_header(
-        omz, shape, affine, omz["0"].dtype, to_nifti_unit(unit), nifti_version=2
+        omz, shape, affine, omz["0"].dtype, to_nifti_unit(unit),
+        nifti_version=2
     )