Merge pull request #67 from thewtex/cli-io-wasm

Cli io wasm
thewtex · Jan 26, 2024 · b114c34 · b114c34
2 parents f16f650 + f2a57ca
commit b114c34
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Showing 4 changed files with 60 additions and 6 deletions.
diff --git a/ngff_zarr/cli_input_to_ngff_image.py b/ngff_zarr/cli_input_to_ngff_image.py
@@ -21,6 +21,14 @@ def cli_input_to_ngff_image(
     if backend is ConversionBackend.ZARR_ARRAY:
         arr = zarr.open_array(input[0], mode="r")
         return to_ngff_image(arr)
+    if backend is ConversionBackend.ITKWASM:
+        try:
+            import itkwasm_image_io
+        except ImportError:
+            print("[red]Please install the [i]itkwasm-image-io[/i] package.")
+            sys.exit(1)
+        image = itkwasm_image_io.imread(input[0])
+        return itk_image_to_ngff_image(image)
     if backend is ConversionBackend.ITK:
         try:
             import itk

diff --git a/ngff_zarr/detect_cli_io_backend.py b/ngff_zarr/detect_cli_io_backend.py
@@ -6,6 +6,7 @@
 conversion_backends = [
     ("NGFF_ZARR", "ngff_zarr"),
     ("ZARR_ARRAY", "zarr"),
+    ("ITKWASM", "itkwasm_image_io"),
     ("ITK", "itk"),
     ("TIFFFILE", "tifffile"),
     ("IMAGEIO", "imageio"),
@@ -24,15 +25,58 @@ def detect_cli_io_backend(input: List[str]) -> ConversionBackend:
     if extension in ngff_zarr_supported_extensions:
         return ConversionBackend.NGFF_ZARR
 
+    itkwasm_supported_extensions = (
+        ".bmp",
+        ".dcm",
+        ".gipl",
+        ".gipl.gz",
+        ".hdf5",
+        ".jpg",
+        ".jpeg",
+        ".iwi",
+        ".iwi.cbor",
+        ".iwi.cbor.zst",
+        ".lsm",
+        ".mnc",
+        ".mnc.gz",
+        ".mnc2",
+        ".mgh",
+        ".mhz",
+        ".mha",
+        ".mhd",
+        ".mrc",
+        ".nia",
+        ".nii",
+        ".nii.gz",
+        ".hdr",
+        ".nrrd",
+        ".nhdr",
+        ".png",
+        ".pic",
+        ".vtk",
+        ".aim",
+        ".isq",
+        ".fdf",
+    )
+    if (
+        extension in itkwasm_supported_extensions
+        and len(input) == 1
+        and Path(input[0]).is_file()
+        and Path(input[0]).stat().st_size < 2e9
+    ):
+        return ConversionBackend.ITKWASM
+
     itk_supported_extensions = (
         ".bmp",
         ".dcm",
         ".gipl",
+        ".gipl.gz",
         ".hdf5",
         ".jpg",
         ".jpeg",
         ".iwi",
         ".iwi.cbor",
+        ".iwi.cbor.zst",
         ".lsm",
         ".mnc",
         ".mnc.gz",
@@ -52,6 +96,7 @@ def detect_cli_io_backend(input: List[str]) -> ConversionBackend:
         ".pic",
         ".vtk",
         ".isq",  # Requires pip install itk-ioscanco,
+        ".aim",  # Requires pip install itk-ioscanco,
         ".fdf",  # Requires pip install itk-iofdf
     )
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -66,6 +66,7 @@ cli = [
     "dask[distributed]",
     "itk-filtering>=5.3.0",
     "itk-io>=5.3.0",
+    "itkwasm-image-io",
     "imageio",
     "tifffile",
     "imagecodecs",
@@ -76,6 +77,7 @@ test = [
     "pooch",
     "itkwasm",
     "itk-io>=5.3.0",
+    "itkwasm-image-io",
     "itk-filtering>=5.3.0",
     "tifffile",
     "jsonschema",

diff --git a/test/_data.py b/test/_data.py
@@ -1,9 +1,9 @@
 import sys
 from pathlib import Path
 
-import itk
 import pooch
 import pytest
+from itkwasm_image_io import imread
 from ngff_zarr import itk_image_to_ngff_image, to_ngff_zarr
 from zarr.storage import DirectoryStore, MemoryStore
 
@@ -27,24 +27,23 @@ def input_images():
     )
     result = {}
 
-    image = itk.imread(test_data_dir / "input" / "cthead1.png")
+    image = imread(test_data_dir / "input" / "cthead1.png")
     image_ngff = itk_image_to_ngff_image(image)
     result["cthead1"] = image_ngff
 
     result["lung_series"] = test_data_dir / "input" / "lung_series" / "*"
 
-    image = itk.imread(
+    image = imread(
         test_data_dir / "input" / "brain_two_components.nrrd",
-        itk.VariableLengthVector[itk.SS],
     )
     image_ngff = itk_image_to_ngff_image(image)
     result["brain_two_components"] = image_ngff
 
-    image = itk.imread(test_data_dir / "input" / "2th_cthead1.png")
+    image = imread(test_data_dir / "input" / "2th_cthead1.png")
     image_ngff = itk_image_to_ngff_image(image)
     result["2th_cthead1"] = image_ngff
 
-    image = itk.imread(test_data_dir / "input" / "MR-head.nrrd")
+    image = imread(test_data_dir / "input" / "MR-head.nrrd")
     image_ngff = itk_image_to_ngff_image(image)
     result["MR-head"] = image_ngff