From 6e5f6c0489c87a8081a6ed2ac0daeeca299732de Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Mon, 4 Mar 2024 23:15:33 -0500
Subject: [PATCH] WIP: ENH: Use cuCIM in CLI conversion

---
 ngff_zarr/cli.py                   | 30 ++++++++++++++++++++++++++++++
 ngff_zarr/detect_cli_io_backend.py |  2 ++
 2 files changed, 32 insertions(+)

diff --git a/ngff_zarr/cli.py b/ngff_zarr/cli.py
index 259c45d..d0bf2c8 100755
--- a/ngff_zarr/cli.py
+++ b/ngff_zarr/cli.py
@@ -336,6 +336,36 @@ def shutdown_client(sig_id, frame):  # noqa: ARG001
             _multiscales_to_ngff_zarr(
                 live, args, output_store, rich_dask_progress, multiscales
             )
+        elif input_backend is ConversionBackend.CUCIM:
+            try:
+                # import cucim
+                # print('ARGS', args)
+
+                # cuimage = cucim.CuImage(str(args.input[0]))
+                if args.chunks is None:
+                    # Present the existing chunks and resolution levels
+                    # [...]
+                    # multiscales = cucim_image_to_multiscales(cuimage)
+                    pass
+
+                else:
+                    # ngff_image = cucim_image_to_ngff_image(cucimage)
+                    # multiscales = _ngff_image_to_multiscales(
+                    #     live,
+                    #     ngff_image,
+                    #     args,
+                    #     progress,
+                    #     rich_dask_progress,
+                    #     subtitle,
+                    #     method,
+                    # )
+                    pass
+                _multiscales_to_ngff_zarr(
+                    live, args, output_store, rich_dask_progress, multiscales
+                )
+            except ImportError:
+                sys.stdout.write("[red]Please install the [i]cucim[/i] package.\n")
+                sys.exit(1)
         elif input_backend is ConversionBackend.TIFFFILE:
             try:
                 import tifffile
diff --git a/ngff_zarr/detect_cli_io_backend.py b/ngff_zarr/detect_cli_io_backend.py
index ab293b7..5f821bd 100644
--- a/ngff_zarr/detect_cli_io_backend.py
+++ b/ngff_zarr/detect_cli_io_backend.py
@@ -105,6 +105,8 @@ def detect_cli_io_backend(input: List[str]) -> ConversionBackend:
     if extension in itk_supported_extensions:
         return ConversionBackend.ITK
 
+    extension = Path(input[0]).suffixes[-1].lower()
+
     if importlib.util.find_spec("cucim") is not None:
         cucim_supported_extensions = (".svs", ".tif", ".tiff")