feat(mesh-io-emscripten): add read_image_async, write_image_async

Author: thewtex

packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/__init__.py

@@ -2,6 +2,9 @@
 
 """itkwasm-mesh-io-emscripten: Input and output for scientific and medical image file formats. Emscripten implementation."""
 
+from .read_mesh_async import read_mesh_async
+from .write_mesh_async import write_mesh_async
+
 from .byu_read_mesh_async import byu_read_mesh_async
 from .byu_write_mesh_async import byu_write_mesh_async
 from .free_surfer_ascii_read_mesh_async import free_surfer_ascii_read_mesh_async

packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/extension_to_mesh_io.py

@@ -0,0 +1,16 @@
+from collections import OrderedDict
+
+extension_to_mesh_io = OrderedDict([
+    ('.vtk', 'vtkPolyData'),
+    ('.byu', 'byu'),
+    ('.fsa', 'freeSurferAscii'),
+    ('.fsb', 'freeSurferBinary'),
+    ('.obj', 'obj'),
+    ('.off', 'off'),
+    ('.stl', 'stl'),
+    ('.swc', 'swc'),
+    ('.iwm', 'wasm'),
+    ('.iwm.cbor', 'wasm'),
+    ('.iwm.cbor.zst', 'wasmZstd'),
+    ('.bmp', 'bmp'),
+])

packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/mesh_io_index.py

@@ -0,0 +1,13 @@
+mesh_io_index = [
+    'vtk_poly_data',
+    'byu',
+    'free_surfer_ascii',
+    'free_surfer_binary',
+    'obj',
+    'off',
+    'stl',
+    'swc',
+    'wasm',
+    'wasm_zstd',
+]
+

packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/read_mesh_async.py

@@ -0,0 +1,88 @@
+import os
+from typing import Optional, Union
+from pathlib import Path
+
+from itkwasm import (
+    Mesh,
+    BinaryFile,
+)
+
+from .js_package import js_package
+
+from itkwasm.pyodide import (
+    to_js,
+    to_py,
+    js_resources
+)
+
+from .extension_to_mesh_io import extension_to_mesh_io
+from .mesh_io_index import mesh_io_index
+
+async def read_mesh_async(
+    serialized_mesh: os.PathLike,
+    information_only: bool = False,
+) -> Mesh:
+    """Read an mesh file format and convert it to the itk-wasm file format
+
+    :param serialized_mesh: Input mesh serialized in the file format
+    :type  serialized_mesh: os.PathLike
+
+    :param information_only: Only read mesh metadata -- do not read pixel data.
+    :type  information_only: bool
+
+    :return: Output mesh
+    :rtype:  Mesh
+    """
+    js_module = await js_package.js_module
+    web_worker = js_resources.web_worker
+
+    kwargs = {}
+    if information_only:
+        kwargs["informationOnly"] = to_js(information_only)
+
+    extension = ''.join(Path(serialized_mesh).suffixes)
+
+    io = None
+    if extension in extension_to_mesh_io:
+        func = f"{extension_to_mesh_io[extension]}ReadMesh"
+        io = getattr(js_module, func)
+    else:
+        for ioname in mesh_io_index:
+            func = f"{ioname}ReadMesh"
+            io = getattr(js_module, func)
+            outputs = await io(web_worker, to_js(BinaryFile(serialized_mesh)), **kwargs)
+            outputs_object_map = outputs.as_object_map()
+            web_worker = outputs_object_map['webWorker']
+            js_resources.web_worker = web_worker
+            could_read = to_py(outputs_object_map['couldRead'])
+            if could_read:
+                mesh = to_py(outputs_object_map['mesh'])
+                return mesh
+
+    if io is None:
+        raise RuntimeError(f"Could not find an mesh reader for {extension}")
+
+    outputs = await js_module.readMesh(web_worker, to_js(BinaryFile(serialized_mesh)), **kwargs)
+    outputs = await io(web_worker, to_js(BinaryFile(serialized_mesh)), **kwargs)
+    outputs_object_map = outputs.as_object_map()
+    web_worker = outputs_object_map['webWorker']
+    could_read = to_py(outputs_object_map['couldRead'])
+
+    if not could_read:
+        raise RuntimeError(f"Could not read {serialized_mesh}")
+
+    js_resources.web_worker = web_worker
+
+    mesh = to_py(outputs_object_map['mesh'])
+
+    return mesh
+
+async def meshread_async(
+    serialized_mesh: os.PathLike,
+    information_only: bool = False,
+) -> Mesh:
+    return await read_mesh_async(serialized_mesh, information_only=information_only)
+
+meshread_async.__doc__ = f"""{read_mesh_async.__doc__}
+    Alias for read_mesh_async.
+    """

packages/mesh-io/python/itkwasm-mesh-io-emscripten/itkwasm_mesh_io_emscripten/write_mesh_async.py

@@ -0,0 +1,95 @@
+import os
+import importlib
+from pathlib import Path
+from typing import Optional, Union
+
+from itkwasm import Mesh, PixelTypes, IntTypes, FloatTypes, BinaryFile
+
+from itkwasm.pyodide import (
+    to_js,
+    to_py,
+    js_resources
+)
+
+from .js_package import js_package
+
+from .extension_to_mesh_io import extension_to_mesh_io
+from .mesh_io_index import mesh_io_index
+
+async def write_mesh_async(
+    mesh: Mesh,
+    serialized_mesh: os.PathLike,
+    information_only: bool = False,
+    use_compression: bool = False,
+) -> None:
+    """Write an itk-wasm Mesh to an mesh file format.
+
+    :param mesh: Input mesh
+    :type  mesh: Mesh
+
+    :param serialized_mesh: Output mesh serialized in the file format.
+    :type  serialized_mesh: str
+
+    :param information_only: Only write mesh metadata -- do not write pixel data.
+    :type  information_only: bool
+
+    :param use_compression: Use compression in the written file
+    :type  use_compression: bool
+
+    :param serialized_mesh: Input mesh serialized in the file format
+    :type  serialized_mesh: os.PathLike
+    """
+    js_module = await js_package.js_module
+    web_worker = js_resources.web_worker
+
+    kwargs = {}
+    if information_only:
+        kwargs["informationOnly"] = to_js(information_only)
+    if use_compression:
+        kwargs["useCompression"] = to_js(use_compression)
+
+    extension = ''.join(Path(serialized_mesh).suffixes)
+
+    io = None
+    if extension in extension_to_mesh_io:
+        func = f"{extension_to_mesh_io[extension]}WriteMesh"
+        io = getattr(js_module, func)
+    else:
+        for ioname in mesh_io_index:
+            func = f"{ioname}WriteMesh"
+            io = getattr(js_module, func)
+            outputs = await io(web_worker, to_js(mesh), to_js(serialized_mesh), **kwargs)
+            outputs_object_map = outputs.as_object_map()
+            web_worker = outputs_object_map['webWorker']
+            js_resources.web_worker = web_worker
+            could_write = to_py(outputs_object_map['couldWrite'])
+            if could_write:
+                to_py(outputs_object_map['serializedMesh'])
+                return
+
+    if io is None:
+        raise RuntimeError(f"Could not find an mesh writer for {extension}")
+
+    io = getattr(js_module, func)
+    outputs = await io(web_worker, to_js(mesh), to_js(serialized_mesh), **kwargs)
+    outputs_object_map = outputs.as_object_map()
+    web_worker = outputs_object_map['webWorker']
+    js_resources.web_worker = web_worker
+    could_write = to_py(outputs_object_map['couldWrite'])
+
+    if not could_write:
+        raise RuntimeError(f"Could not write {serialized_mesh}")
+
+    to_py(outputs_object_map['serializedMesh'])
+
+async def meshwrite_async(
+    mesh: Mesh,
+    serialized_mesh: os.PathLike,
+    information_only: bool = False,
+    use_compression: bool = False,
+) -> None:
+    return write_mesh_async(mesh, serialized_mesh, information_only=information_only, use_compression=use_compression)
+
+meshwrite_async.__doc__ = f"""{write_mesh_async.__doc__}
+    Alias for write_mesh.
+    """

packages/mesh-io/python/itkwasm-mesh-io-emscripten/test/test_read_write_mesh_async.py

@@ -0,0 +1,52 @@
+import sys
+
+if sys.version_info < (3,10):
+    pytest.skip("Skipping pyodide tests on older Python", allow_module_level=True)
+
+from pytest_pyodide import run_in_pyodide
+from .fixtures import package_wheel, input_data
+
+@run_in_pyodide(packages=['micropip', 'numpy'])
+async def test_read_write_mesh_async(selenium, package_wheel, input_data):
+    import micropip
+    await micropip.install(package_wheel)
+    def write_input_data_to_fs(input_data, filename):
+        with open(filename, 'wb') as fp:
+            fp.write(input_data[filename])
+
+    from pathlib import Path
+
+    from itkwasm import FloatTypes, IntTypes
+    import numpy as np
+
+    from itkwasm_mesh_io_emscripten import read_mesh_async, write_mesh_async
+
+
+    def verify_mesh(mesh):
+        assert mesh.meshType.dimension == 3
+        assert mesh.meshType.pointComponentType == FloatTypes.Float32
+        assert mesh.meshType.pointPixelComponentType == IntTypes.Int8
+        assert mesh.numberOfPoints == 2903
+        assert np.allclose(mesh.points.ravel()[0], 3.71636)
+        assert np.allclose(mesh.points.ravel()[1], 2.34339)
+        assert mesh.numberOfCells == 3263
+        assert mesh.cellBufferSize == 18856
+        assert mesh.cells[0] == 4
+        assert mesh.cells[1] == 4
+        assert mesh.cells[2] == 250
+
+    test_input_file_path = 'cow.vtk'
+    test_output_file_path = "read-write-cow.vtk"
+    write_input_data_to_fs(input_data, test_input_file_path)
+
+    assert Path(test_input_file_path).exists()
+
+
+    mesh = await read_mesh_async(test_input_file_path)
+    verify_mesh(mesh)
+
+    use_compression = False
+    await write_mesh_async(mesh, test_output_file_path, use_compression=use_compression)
+
+    mesh = await read_mesh_async(test_output_file_path)
+    verify_mesh(mesh)