ENH: RFC 4 implementation

Author: thewtex

docs/rfc4.md

@@ -0,0 +1,230 @@
+# RFC 4: Anatomical Orientation Support
+
+RFC 4 adds support for anatomical orientation metadata to OME-NGFF axes,
+enabling precise description of spatial axis directions in biological and
+medical imaging data.
+
+## Overview
+
+Anatomical orientation refers to the specific arrangement and directional
+alignment of anatomical structures within an imaging dataset. This is crucial
+for ensuring accurate alignment and comparison of images to anatomical atlases,
+facilitating consistent analysis and interpretation of biological data.
+
+## Usage
+
+### Programmatic Usage
+
+#### Enabling RFC 4
+
+To enable RFC 4 support when writing OME-NGFF Zarr data, include `4` in the
+`enabled_rfcs` parameter:
+
+```python
+import ngff_zarr
+
+# Enable RFC 4 when converting to NGFF Zarr
+ngff_zarr.to_ngff_zarr(
+    store="output.ome.zarr",
+    multiscales=multiscales,
+    enabled_rfcs=[4]  # Enable RFC 4
+)
+```
+
+### CLI Usage
+
+RFC 4 can be enabled via the command line using the `--enable-rfc` flag:
+
+```bash
+# Convert a medical image with RFC 4 anatomical orientation enabled
+ngff-zarr -i image.nii.gz -o output.ome.zarr --enable-rfc 4
+
+# Enable multiple RFCs (when available)
+ngff-zarr -i image.nii.gz -o output.ome.zarr --enable-rfc 4 --enable-rfc 5
+
+# Without RFC 4 (default behavior - orientation metadata filtered out)
+ngff-zarr -i image.nii.gz -o output.ome.zarr
+```
+
+### ITK Integration
+
+When converting ITK images (including from NRRD, NIfTI, or DICOM formats),
+anatomical orientation is automatically added based on ITK's LPS coordinate
+system:
+
+```python
+import ngff_zarr
+from itk import imread
+
+# Read a medical image (NRRD, NIfTI, DICOM, etc.)
+image = imread("image.nrrd")
+
+# Convert to NGFF image with anatomical orientation
+ngff_image = ngff_zarr.itk_image_to_ngff_image(
+    image,
+    add_anatomical_orientation=True
+)
+
+# Convert to multiscales and write to Zarr with RFC 4 enabled
+multiscales = ngff_zarr.to_multiscales(ngff_image)
+ngff_zarr.to_ngff_zarr(
+    store="output.ome.zarr",
+    multiscales=multiscales,
+    enabled_rfcs=[4]
+)
+```
+
+### ITK-Wasm Integration
+
+Similar support is available for ITK-Wasm:
+
+```python
+import ngff_zarr
+from itkwasm_image_io import imread
+
+# Read with ITK-Wasm
+image = imread("image.nii.gz")
+
+# Convert with anatomical orientation
+ngff_image = ngff_zarr.itk_image_to_ngff_image(
+    image,
+    add_anatomical_orientation=True
+)
+```
+
+## Anatomical Orientation Values
+
+RFC 4 supports the following anatomical orientation values:
+
+- `left-to-right`: From left side to right lateral side
+- `right-to-left`: From right side to left lateral side
+- `anterior-to-posterior`: From front (anterior) to back (posterior)
+- `posterior-to-anterior`: From back (posterior) to front (anterior)
+- `inferior-to-superior`: From below (inferior) to above (superior)
+- `superior-to-inferior`: From above (superior) to below (inferior)
+- `dorsal-to-ventral`: From top/upper (dorsal) to belly/lower (ventral)
+- `ventral-to-dorsal`: From belly/lower (ventral) to top/upper (dorsal)
+- `dorsal-to-palmar`: From top/upper (dorsal) to palm of hand (palmar)
+- `palmar-to-dorsal`: From palm of hand (palmar) to top/upper (dorsal)
+- `dorsal-to-plantar`: From top/upper (dorsal) to sole of foot (plantar)
+- `plantar-to-dorsal`: From sole of foot (plantar) to top/upper (dorsal)
+
+## ITK LPS Coordinate System
+
+ITK uses the LPS (Left-to-right, Posterior-to-anterior, Superior-to-inferior)
+coordinate system by default. When converting ITK images, the following mappings
+are applied:
+
+- **X axis**: `left-to-right`
+- **Y axis**: `posterior-to-anterior`
+- **Z axis**: `inferior-to-superior`
+
+## Manual Orientation Specification
+
+You can also manually specify orientations:
+
+```python
+from ngff_zarr import (
+    AnatomicalOrientation,
+    AnatomicalOrientationValues,
+    NgffImage
+)
+import dask.array as da
+
+# Create orientation objects
+x_orientation = AnatomicalOrientation(
+    value=AnatomicalOrientationValues.left_to_right
+)
+y_orientation = AnatomicalOrientation(
+    value=AnatomicalOrientationValues.anterior_to_posterior
+)
+z_orientation = AnatomicalOrientation(
+    value=AnatomicalOrientationValues.inferior_to_superior
+)
+
+# Create NGFF image with orientations
+data = da.zeros((100, 100, 100))
+ngff_image = NgffImage(
+    data=data,
+    dims=("z", "y", "x"),
+    scale={"x": 1.0, "y": 1.0, "z": 1.0},
+    translation={"x": 0.0, "y": 0.0, "z": 0.0},
+    axes_orientations={
+        "x": x_orientation,
+        "y": y_orientation,
+        "z": z_orientation
+    }
+)
+```
+
+## Metadata Format
+
+When RFC 4 is enabled, spatial axes in the OME-NGFF metadata include an
+`orientation` field:
+
+```json
+{
+  "axes": [
+    {
+      "name": "z",
+      "type": "space",
+      "unit": "micrometer",
+      "orientation": {
+        "type": "anatomical",
+        "value": "inferior-to-superior"
+      }
+    },
+    {
+      "name": "y",
+      "type": "space",
+      "unit": "micrometer",
+      "orientation": {
+        "type": "anatomical",
+        "value": "posterior-to-anterior"
+      }
+    },
+    {
+      "name": "x",
+      "type": "space",
+      "unit": "micrometer",
+      "orientation": {
+        "type": "anatomical",
+        "value": "left-to-right"
+      }
+    }
+  ]
+}
+```
+
+## RFC 4 Functions
+
+### Core Functions
+
+- `itk_lps_to_anatomical_orientation(axis_name)`: Map ITK LPS axes to
+  orientations
+- `add_anatomical_orientation_to_axis(axis_dict, orientation)`: Add orientation
+  to axis
+- `remove_anatomical_orientation_from_axis(axis_dict)`: Remove orientation from
+  axis
+
+### Data Classes
+
+- `AnatomicalOrientation`: Orientation specification with type and value
+- `AnatomicalOrientationValues`: Enum of supported orientation values
+
+## Compatibility
+
+When RFC 4 is not enabled (the default), orientation metadata is automatically
+filtered out during Zarr writing to maintain compatibility with standard
+OME-NGFF consumers.
+
+## Best Practices
+
+1. **Enable RFC 4** when working with medical/biological images where
+   orientation matters
+2. **Use ITK integration** for automatic LPS-based orientation when converting
+   from medical image formats
+3. **Document orientation assumptions** in your analysis pipelines when working
+   with oriented data
+4. **Validate orientations** match your expectations, especially when combining
+   data from different sources

py/ngff_zarr/__init__.py

@@ -36,14 +36,21 @@
     OmeroChannel,
     OmeroWindow,
 )
+from .rfc4 import (
+    AnatomicalOrientation,
+    AnatomicalOrientationValues,
+    itk_lps_to_anatomical_orientation,
+    is_rfc4_enabled,
+    add_anatomical_orientation_to_axis,
+    remove_anatomical_orientation_from_axis,
+)
 
 __all__ = [
     "__version__",
     "config",
     "NgffImage",
     "Multiscales",
     "to_ngff_image",
-    "from_ngff_image",
     "itk_image_to_ngff_image",
     "ngff_image_to_itk_image",
     "memory_usage",
@@ -73,4 +80,11 @@
     "Omero",
     "OmeroChannel",
     "OmeroWindow",
+    # RFC 4 - Anatomical Orientation
+    "AnatomicalOrientation",
+    "AnatomicalOrientationValues",
+    "itk_lps_to_anatomical_orientation",
+    "is_rfc4_enabled",
+    "add_anatomical_orientation_to_axis",
+    "remove_anatomical_orientation_from_axis",
 ]

py/ngff_zarr/cli.py

@@ -78,6 +78,7 @@ def _multiscales_to_ngff_zarr(
         progress=rich_dask_progress,
         use_tensorstore=args.use_tensorstore,
         version=args.ome_zarr_version,
+        enabled_rfcs=args.enable_rfc,
     )
 
 
@@ -214,6 +215,13 @@ def main():
         default="0.4",
         choices=["0.4", "0.5"],
     )
+    metadata_group.add_argument(
+        "--enable-rfc",
+        action="append",
+        type=int,
+        help="Enable specific RFC features. Can be used multiple times. Currently supported: 4 (anatomical orientation)",
+        metavar="RFC_NUMBER",
+    )
 
     processing_group = parser.add_argument_group("processing", "Processing options")
     processing_group.add_argument(

py/ngff_zarr/itk_image_to_ngff_image.py

@@ -3,10 +3,12 @@
 import dask.array
 
 from .ngff_image import NgffImage
+from .rfc4 import itk_lps_to_anatomical_orientation
 
 
 def itk_image_to_ngff_image(
     itk_image,
+    add_anatomical_orientation: bool = True,
     # anatomical_axes: bool = False,
     # axis_names: List[str] = None,
     # axis_units: List[str] = None,
@@ -72,4 +74,15 @@ def itk_image_to_ngff_image(
     origin = image_dict["origin"]
     translation = {dim: origin[::-1][idx] for idx, dim in enumerate(spatial_dims)}
 
-    return NgffImage(data, dims, scale, translation)
+    # Add anatomical orientation if requested
+    axes_orientations = None
+    if add_anatomical_orientation:
+        axes_orientations = {}
+        for dim in spatial_dims:
+            orientation = itk_lps_to_anatomical_orientation(dim)
+            if orientation is not None:
+                axes_orientations[dim] = orientation
+
+    return NgffImage(
+        data, dims, scale, translation, axes_orientations=axes_orientations
+    )

py/ngff_zarr/ngff_image.py

@@ -4,6 +4,7 @@
 from dask.array.core import Array as DaskArray
 
 from .v04.zarr_metadata import Units
+from .rfc4 import AnatomicalOrientation
 
 ComputedCallback = Callable[[], None]
 
@@ -16,4 +17,5 @@ class NgffImage:
     translation: Dict[str, float]
     name: str = "image"
     axes_units: Optional[Mapping[str, Units]] = None
+    axes_orientations: Optional[Mapping[str, AnatomicalOrientation]] = None
     computed_callbacks: List[ComputedCallback] = field(default_factory=list)