feat(itkwasm-image-io-wasi): add read_image, imread

packages/core/python/itkwasm/itkwasm/cast_image.py

@@ -12,7 +12,21 @@
 def cast_image(input_image: Image,
                pixel_type: Optional[PixelTypes]=None,
                component_type: Optional[Union[IntTypes, FloatTypes]]=None) -> Image:
-    """Cast an image to another pixel type and / or component type."""
+    """Cast an image to another pixel type and / or component type.
+
+    :param input_image: Image to be cast.
+    :type  input_image: Image
+
+    :param pixel_type: Pixel type to cast to.
+    :type  pixel_Type: Optional[PixelTypes]
+
+    :param component_type: Component type to cast to.
+    :type  component_type: Optional[Union[IntTypes, FloatTypes]]
+
+    :return: Cast image. Event if pixel_type or component_type are not specified, a copy is made.
+    :rtype:  Image
+
+    """
     output_image_type = ImageType(**asdict(input_image.imageType))
 
     if pixel_type is not None:

packages/image-io/python/itkwasm-image-io-wasi/itkwasm_image_io_wasi/__init__.py

@@ -1,7 +1,7 @@
-# Generated file. To retain edits, remove this comment.
-
 """itkwasm-image-io-wasi: Input and output for scientific and medical image file formats. WASI implementation."""
 
+from .read_image import read_image, imread
+
 from .bio_rad_read_image import bio_rad_read_image
 from .bio_rad_write_image import bio_rad_write_image
 from .bmp_read_image import bmp_read_image

packages/image-io/python/itkwasm-image-io-wasi/itkwasm_image_io_wasi/extension_to_image_io.py

@@ -0,0 +1,56 @@
+from collections import OrderedDict
+
+extension_to_image_io = OrderedDict([
+  ('.bmp', 'bmp'),
+
+  ('.dcm', 'gdcm'),
+
+  ('.gipl', 'gipl'),
+  ('.gipl.gz', 'gipl'),
+
+  ('.hdf5', 'hdf5'),
+
+  ('.jpg', 'jpeg'),
+  ('.jpeg', 'jpeg'),
+
+  ('.iwi', 'wasm'),
+  ('.iwi.cbor', 'wasm'),
+  ('.iwi.cbor.zst', 'wasm_zstd'),
+
+  ('.lsm', 'lsm'),
+
+  ('.mnc', 'mnc'),
+  ('.mnc.gz', 'mnc'),
+  ('.mnc2', 'mnc'),
+
+  ('.mgh', 'mgh'),
+  ('.mgz', 'mgh'),
+  ('.mgh.gz', 'mgh'),
+
+  ('.mha', 'meta'),
+  ('.mhd', 'meta'),
+
+  ('.mrc', 'mrc'),
+
+  ('.nia', 'nifti'),
+  ('.nii', 'nifti'),
+  ('.nii.gz', 'nifti'),
+  ('.hdr', 'nifti'),
+
+  ('.nrrd', 'nrrd'),
+  ('.nhdr', 'nrrd'),
+
+  ('.png', 'png'),
+
+  ('.pic', 'bio_rad'),
+
+  ('.tif', 'tiff'),
+  ('.tiff', 'tiff'),
+
+  ('.vtk', 'vtk'),
+
+  ('.isq', 'scanco'),
+  ('.aim', 'scanco'),
+
+  ('.fdf', 'fdf'),
+])

packages/image-io/python/itkwasm-image-io-wasi/itkwasm_image_io_wasi/image_io_index.py

@@ -0,0 +1,25 @@
+image_io_index = [
+  'png',
+  'meta',
+  'tiff',
+  'nifti',
+  'jpeg',
+  'nrrd',
+  'vtk',
+  'bmp',
+  'hdf5',
+  'minc',
+  'mrc',
+  'lsm',
+  'mgh',
+  'bio_rad',
+  'gipl',
+  'ge_adw',
+  'ge4',
+  'ge5',
+  'gdcm',
+  'scanco',
+  'wasm',
+  'wasm_zstd',
+]
+

packages/image-io/python/itkwasm-image-io-wasi/itkwasm_image_io_wasi/read_image.py

@@ -0,0 +1,77 @@
+import os
+import importlib
+from pathlib import Path
+from typing import Optional, Union
+
+from itkwasm import Image, PixelTypes, IntTypes, FloatTypes, cast_image
+
+from .extension_to_image_io import extension_to_image_io
+from .image_io_index import image_io_index
+
+def read_image(
+    serialized_image: os.PathLike,
+    information_only: bool = False,
+    pixel_type: Optional[PixelTypes]=None,
+    component_type: Optional[Union[IntTypes, FloatTypes]]=None,
+) -> Image:
+    """Read an image file format and convert it to the itk-wasm file format.
+
+    :param serialized_image: Input image serialized in the file format
+    :type  serialized_image: os.PathLike
+
+    :param information_only: Only read image metadata -- do not read pixel data.
+    :type  information_only: bool
+
+    :param pixel_type: Pixel type to cast to.
+    :type  pixel_Type: Optional[PixelTypes]
+
+    :param component_type: Component type to cast to.
+    :type  component_type: Optional[Union[IntTypes, FloatTypes]]
+
+    :return: Output image
+    :rtype:  Image
+    """
+    file_name = Path(serialized_image).name
+    extension = ''.join(Path(serialized_image).suffixes)
+
+    io = None
+    if extension in extension_to_image_io:
+        func = f"{extension_to_image_io[extension]}_read_image"
+        mod_name = f"itkwasm_image_io_wasi.{func}"
+        mod = importlib.import_module(mod_name)
+        io = getattr(mod, func)
+    else:
+        for ioname in image_io_index:
+            func = f"{ioname}_read_image"
+            mod_name = f"itkwasm_image_io_wasi.{func}"
+            mod = importlib.import_module(mod_name)
+            io = getattr(mod, func)
+            could_read, image = io(serialized_image, information_only=information_only)
+            if could_read:
+                if pixel_type or component_type:
+                    image = cast_image(image, pixel_type=pixel_type, component_type=component_type)
+                return image
+
+    if io is None:
+        raise RuntimeError(f"Could not find an image reader for {extension}")
+
+    could_read, image = io(serialized_image, information_only=information_only)
+    if not could_read:
+        raise RuntimeError(f"Could not read {serialized_image}")
+
+    if pixel_type or component_type:
+        image = cast_image(image, pixel_type=pixel_type, component_type=component_type)
+    return image
+
+
+def imread(
+    serialized_image: os.PathLike,
+    information_only: bool = False,
+    pixel_type: Optional[PixelTypes]=None,
+    component_type: Optional[Union[IntTypes, FloatTypes]]=None,
+) -> Image:
+    return read_image(serialized_image, information_only=information_only, pixel_type=pixel_type, component_type=component_type)
+
+imread.__doc__ = f"""{read_image.__doc__}
+    Alias for read_image.
+    """

packages/image-io/python/itkwasm-image-io-wasi/tests/test_png.py

@@ -0,0 +1,43 @@
+from pathlib import Path
+
+from itkwasm_image_io_wasi import png_read_image, png_write_image
+
+from .common import test_input_path, test_output_path
+
+test_input_file_path = test_input_path / "cthead1.png"
+test_output_file_path = test_output_path / "png-test-cthead1.png"
+
+def verify_image(image):
+    assert image.imageType.dimension == 2
+    assert image.imageType.componentType == "uint8"
+    assert image.imageType.pixelType == "RGB"
+    assert image.imageType.components == 3
+    assert image.origin[0] == 0.0
+    assert image.origin[1] == 0.0
+    assert image.spacing[0] == 1.0
+    assert image.spacing[1] == 1.0
+    assert image.direction[0, 0] == 1.0
+    assert image.direction[0, 1] == 0.0
+    assert image.direction[1, 0] == 0.0
+    assert image.direction[1, 1] == 1.0
+    assert image.size[0] == 256
+    assert image.size[1] == 256
+    assert image.data.shape[1] == 256
+    assert image.data.shape[0] == 256
+
+def test_png_read_image():
+    could_read, image = png_read_image(test_input_file_path)
+    assert could_read
+    verify_image(image)
+
+def test_png_write_image():
+    could_read, image = png_read_image(test_input_file_path)
+    assert could_read
+
+    use_compression = False
+    could_write = png_write_image(image, test_output_file_path, use_compression)
+    assert could_write
+
+    could_read, image = png_read_image(test_output_file_path)
+    assert could_read
+    verify_image(image)

packages/image-io/python/itkwasm-image-io-wasi/tests/test_read_write_image.py

@@ -0,0 +1,58 @@
+from pathlib import Path
+
+from itkwasm import PixelTypes, IntTypes
+
+from itkwasm_image_io_wasi import read_image, imread
+
+from .common import test_input_path, test_output_path
+
+test_input_file_path = test_input_path / "cthead1.png"
+test_output_file_path = test_output_path / "read-write-cthead1.png"
+
+def verify_image(image):
+    assert image.imageType.dimension == 2
+    assert image.imageType.componentType == "uint8"
+    assert image.imageType.pixelType == "RGB"
+    assert image.imageType.components == 3
+    assert image.origin[0] == 0.0
+    assert image.origin[1] == 0.0
+    assert image.spacing[0] == 1.0
+    assert image.spacing[1] == 1.0
+    assert image.direction[0, 0] == 1.0
+    assert image.direction[0, 1] == 0.0
+    assert image.direction[1, 0] == 0.0
+    assert image.direction[1, 1] == 1.0
+    assert image.size[0] == 256
+    assert image.size[1] == 256
+    assert image.data.shape[1] == 256
+    assert image.data.shape[0] == 256
+
+def test_read_image():
+    image = read_image(test_input_file_path)
+    verify_image(image)
+
+def test_read_image_pixel_type():
+    image = read_image(test_input_file_path, pixel_type=PixelTypes.Vector)
+    assert image.imageType.pixelType == "Vector"
+
+def test_read_image_component_type():
+    image = read_image(test_input_file_path, component_type=IntTypes.UInt16)
+    assert image.imageType.componentType == "uint16"
+
+def test_imread():
+    image = imread(test_input_file_path)
+    verify_image(image)
+
+def test_write_image():
+    pass
+    return
+    could_read, image = png_read_image(test_input_file_path)
+    assert could_read
+
+    use_compression = False
+    could_write = png_write_image(image, test_output_file_path, use_compression)
+    assert could_write
+
+    could_read, image = png_read_image(test_output_file_path)
+    assert could_read
+    verify_image(image)

packages/image-io/typescript/src/extension-to-image-io.ts

@@ -48,6 +48,7 @@ const extensionToImageIo = new Map([
   ['vtk', 'vtk'],
 
   ['isq', 'scanco'],
+  ['aim', 'scanco'],
 
   ['fdf', 'fdf'],
 ])