mlarray 0.0.23__py3-none-any.whl

mlarray/__init__.py

@@ -0,0 +1,54 @@
+"""A standardized blosc2 image reader and writer for medical images.."""
+
+from importlib import metadata as _metadata
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from mlarray.mlarray import MLArray, MLARRAY_DEFAULT_PATCH_SIZE
+    from mlarray.meta import Meta, MetaBlosc2, MetaSpatial
+    from mlarray.utils import is_serializable
+    from mlarray.cli import cli_print_header, cli_convert_to_mlarray
+
+__all__ = [
+    "__version__",
+    "MLArray",
+    "MLARRAY_DEFAULT_PATCH_SIZE",
+    "Meta",
+    "MetaBlosc2",
+    "MetaSpatial",
+    "is_serializable",
+    "cli_print_header",
+    "cli_convert_to_mlarray",
+]
+
+try:
+    __version__ = _metadata.version(__name__)
+except _metadata.PackageNotFoundError:  # pragma: no cover - during editable installs pre-build
+    __version__ = "0.0.0"
+
+
+def __getattr__(name: str):
+    if name in {"MLArray", "MLARRAY_DEFAULT_PATCH_SIZE"}:
+        from mlarray.mlarray import MLArray, MLARRAY_DEFAULT_PATCH_SIZE
+
+        return MLArray if name == "MLArray" else MLARRAY_DEFAULT_PATCH_SIZE
+    if name in {"Meta", "MetaBlosc2", "MetaSpatial"}:
+        from mlarray.meta import Meta, MetaBlosc2, MetaSpatial
+
+        return {"Meta": Meta, "MetaBlosc2": MetaBlosc2, "MetaSpatial": MetaSpatial}[name]
+    if name == "is_serializable":
+        from mlarray.utils import is_serializable
+
+        return is_serializable
+    if name in {"cli_print_header", "cli_convert_to_mlarray"}:
+        from mlarray.cli import cli_print_header, cli_convert_to_mlarray
+
+        return {
+            "cli_print_header": cli_print_header,
+            "cli_convert_to_mlarray": cli_convert_to_mlarray,
+        }[name]
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+
+def __dir__():
+    return sorted(__all__)

mlarray/cli.py

@@ -0,0 +1,58 @@
+import argparse
+import json
+from typing import Union
+from pathlib import Path
+from mlarray import MLArray
+
+try:
+    from medvol import MedVol
+except ImportError:
+    MedVol = None
+
+
+def print_header(filepath: Union[str, Path]) -> None:
+    """Print the MLArray metadata header for a file.
+
+    Args:
+        filepath: Path to a ".mla" or ".b2nd" file.
+    """
+    meta = MLArray(filepath).meta
+    if meta is None:
+        print("null")
+        return
+    print(json.dumps(meta.to_dict(include_none=True), indent=2, sort_keys=True))
+
+
+def convert_to_mlarray(load_filepath: Union[str, Path], save_filepath: Union[str, Path]):
+    if MedVol is None:
+        raise RuntimeError("medvol is required for mlarray_convert; install with 'pip install mlarray[all]'.")
+    image_meta_format = None
+    if str(load_filepath).endswith(f".nii.gz") or str(load_filepath).endswith(f".nii"):
+        image_meta_format = "nifti"
+    elif str(load_filepath).endswith(f".nrrd"):
+        image_meta_format = "nrrd"
+    image_medvol = MedVol(load_filepath)
+    image_mlarray = MLArray(image_medvol.array, spacing=image_medvol.spacing, origin=image_medvol.origin, direction=image_medvol.direction, meta=image_medvol.header)
+    image_mlarray.meta._image_meta_format = image_meta_format
+    image_mlarray.save(save_filepath)
+
+
+def cli_print_header() -> None:
+    parser = argparse.ArgumentParser(
+        prog="mlarray_header",
+        description="Print the MLArray metadata header for a file.",
+    )
+    parser.add_argument("filepath", help="Path to a .mla or .b2nd file.")
+    args = parser.parse_args()
+    print_header(args.filepath)
+
+
+def cli_convert_to_mlarray() -> None:
+    parser = argparse.ArgumentParser(
+        prog="mlarray_convert",
+        description="Convert a NiFTi or NRRD file to MLArray and copy all metadata.",
+    )
+    parser.add_argument("load_filepath", help="Path to the NiFTi (.nii.gz, .nii) or NRRD (.nrrd) file to load.")
+    parser.add_argument("save_filepath", help="Path to the MLArray (.mla) file to save.")
+    args = parser.parse_args()
+    convert_to_mlarray(args.load_filepath, args.save_filepath)