WIP: ENH: Add cuCIM file reading support

ngff_zarr/cli_input_to_ngff_image.py

@@ -1,12 +1,14 @@
 import sys
 
+import numpy as np
 import zarr
 from dask.array.image import imread as daimread
 from rich import print
 
 from .detect_cli_io_backend import ConversionBackend
 from .from_ngff_zarr import from_ngff_zarr
 from .itk_image_to_ngff_image import itk_image_to_ngff_image
+from .methods._support import _spatial_dims
 from .ngff_image import NgffImage
 from .to_ngff_image import to_ngff_image
 
@@ -48,6 +50,28 @@ def imread(filename):
             return itk_image_to_ngff_image(image)
         image = itk.imread(input)
         return itk_image_to_ngff_image(image)
+    if backend is ConversionBackend.CUCIM:
+        try:
+            import cucim
+
+            cuimage = cucim.CuImage(str(input[0]))
+            data = np.array(cuimage)
+            dims = tuple(d for d in cuimage.dims.lower())
+            spatial_dims = set(dims).intersection(_spatial_dims)
+            spatial_dims = [d for d in dims if d in spatial_dims]
+            spatial_dims_str = "".join(spatial_dims).upper()
+            translation = {d: 0.0 for d in spatial_dims}
+            for idx, dim in enumerate(spatial_dims):
+                # cucim: Should origin have a dim_order argument like spacing?
+                translation[dim] = cuimage.origin[idx]
+            spacing = cuimage.spacing(spatial_dims_str)
+            scale = {d: 1.0 for d in spatial_dims}
+            for idx, dim in enumerate(spatial_dims):
+                scale[dim] = spacing[idx]
+            return to_ngff_image(data, dims=dims, translation=translation, scale=scale)
+        except ImportError:
+            print("[red]Please install the [i]cucim[/i] package.")
+            sys.exit(1)
     if backend is ConversionBackend.TIFFFILE:
         try:
             import tifffile

ngff_zarr/detect_cli_io_backend.py

@@ -1,3 +1,4 @@
+import importlib.util
 import sys
 from enum import Enum
 from pathlib import Path
@@ -8,6 +9,7 @@
     ("ZARR_ARRAY", "zarr"),
     ("ITKWASM", "itkwasm_image_io"),
     ("ITK", "itk"),
+    ("CUCIM", "cucim"),
     ("TIFFFILE", "tifffile"),
     ("IMAGEIO", "imageio"),
 ]
@@ -103,6 +105,12 @@ def detect_cli_io_backend(input: List[str]) -> ConversionBackend:
     if extension in itk_supported_extensions:
         return ConversionBackend.ITK
 
+    if importlib.util.find_spec("cucim") is not None:
+        cucim_supported_extensions = (".svs", ".tif", ".tiff")
+
+        if extension in cucim_supported_extensions:
+            return ConversionBackend.CUCIM
+
     try:
         import tifffile
 

test/test_cli_input_to_ngff_image.py

@@ -1,3 +1,4 @@
+import pytest
 from ngff_zarr import ConversionBackend, cli_input_to_ngff_image
 
 from ._data import test_data_dir
@@ -37,6 +38,21 @@ def test_cli_input_to_ngff_image_tifffile(input_images):  # noqa: ARG001
     assert image.dims == ("z", "y", "x")
 
 
+def test_cli_input_to_ngff_image_cucim(input_images):  # noqa: ARG001
+    pytest.importorskip("cucim")
+    input = [
+        test_data_dir
+        / "input"
+        / "TCGA-C8-A26W-01A-01-TSA.5870b3d4-a81e-423e-bb93-5897ebc922a3.svs"
+    ]
+    image = cli_input_to_ngff_image(ConversionBackend.CUCIM, input)
+    assert image.dims == ("y", "x", "c")
+    assert image.translation["x"] == 0.0
+    assert image.translation["y"] == 0.0
+    assert image.scale["x"] == 1.0
+    assert image.scale["y"] == 1.0
+
+
 def test_cli_input_to_ngff_image_imageio(input_images):  # noqa: ARG001
     input = [
         test_data_dir / "input" / "cthead1.png",

test/test_detect_cli_input_backend.py

@@ -1,3 +1,5 @@
+import importlib.util
+
 from ngff_zarr import ConversionBackend, detect_cli_io_backend
 
 
@@ -18,7 +20,10 @@ def test_detect_tifffile_input_backend():
             f"file{extension}",
         ]
     )
-    assert backend == ConversionBackend.TIFFFILE
+    if importlib.util.find_spec("cucim") is not None:
+        assert backend == ConversionBackend.CUCIM
+    else:
+        assert backend == ConversionBackend.TIFFFILE
 
 
 def test_detect_imageio_input_backend():