feat(mesh-io): add read_mesh, read_mesh_async, write_mesh, write_mesh…

…_async

.gitignore

@@ -84,6 +84,7 @@ packages/image-io/typescript/demo-app-rollup/
 packages/image-io/python/itkwasm-image-io-wasi/itkwasm_image_io_wasi/wasm_modules/
 
 packages/mesh-io/test/
+packages/mesh-io/python/itkwasm-mesh-io-wasi/itkwasm_mesh_io_wasi/wasm_modules/
 
 cypress/screenshots/
 cypress/videos/

package.json

@@ -52,16 +52,16 @@
     "build:bindgen:typescript:image-io": "./src/itk-wasm-cli.js -s packages/image-io -b emscripten-build bindgen --package-version 0.5.0 --package-name @itk-wasm/image-io --package-description \"Input and output for scientific and medical image file formats.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
     "build:bindgen:python:image-io": "./src/itk-wasm-cli.js -s packages/image-io -b wasi-build bindgen --interface python --package-name itkwasm-image-io --package-description \"Input and output for scientific and medical image file formats.\" --package-version 0.5.0 --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
     "build:emscripten:mesh-io": "node ./src/itk-wasm-cli.js -s packages/mesh-io -b emscripten-build build",
-    "build:bindgen:typescript:mesh-io": "./src/itk-wasm-cli.js -s packages/mesh-io -b emscripten-build bindgen --package-version 0.1.0 --package-name @itk-wasm/mesh-io --package-description \"Input and output for scientific and medical image file formats.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
-    "build:bindgen:python:mesh-io": "./src/itk-wasm-cli.js -s packages/mesh-io -b wasi-build bindgen --interface python --package-name itkwasm-mesh-io --package-description \"Input and output for scientific and medical image file formats.\" --package-version 0.1.0 --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
+    "build:bindgen:typescript:mesh-io": "./src/itk-wasm-cli.js -s packages/mesh-io -b emscripten-build bindgen --package-version 0.2.0 --package-name @itk-wasm/mesh-io --package-description \"Input and output for scientific and medical image file formats.\" --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
+    "build:bindgen:python:mesh-io": "./src/itk-wasm-cli.js -s packages/mesh-io -b wasi-build bindgen --interface python --package-name itkwasm-mesh-io --package-description \"Input and output for scientific and medical image file formats.\" --package-version 0.2.0 --repository 'https://github.com/InsightSoftwareConsortium/itk-wasm'",
     "build:emscripten:packages": "npm run build:emscripten:compress-stringify && npm run build:bindgen:typescript:compress-stringify && npm run build:emscripten:dicom && npm run build:bindgen:typescript:dicom && npm run build:emscripten:compare-images && npm run build:bindgen:typescript:compare-images && npm run build:emscripten:image-io && npm run build:bindgen:typescript:image-io && npm run build:emscripten:mesh-io && npm run build:bindgen:typescript:mesh-io",
     "build:wasi": "node ./src/build-wasi.js && npm run build:wasi:packages",
     "build:wasi:compress-stringify": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/compress-stringify -b wasi-build build",
     "build:wasi:dicom": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/dicom -b wasi-build build",
     "build:wasi:compare-images": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/compare-images -b wasi-build build",
     "build:wasi:image-io": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/image-io -b wasi-build build",
     "build:wasi:mesh-io": "node ./src/itk-wasm-cli.js -i itkwasm/wasi:latest -s packages/mesh-io -b wasi-build build",
-    "build:wasi:packages": "npm run build:wasi:compress-stringify && npm run build:bindgen:python:compress-stringify && npm run build:wasi:compare-images && npm run build:bindgen:python:compare-images && npm run build:wasi:dicom && npm run build:bindgen:python:dicom && npm run build:wasi:image-io && npm run build:bindgen:python:image-io",
+    "build:wasi:packages": "npm run build:wasi:compress-stringify && npm run build:bindgen:python:compress-stringify && npm run build:wasi:compare-images && npm run build:bindgen:python:compare-images && npm run build:wasi:dicom && npm run build:bindgen:python:dicom && npm run build:wasi:image-io && npm run build:bindgen:python:image-io && npm run build:wasi:mesh-io && npm run build:bindgen:python:mesh-io",
     "cypress:open": "npx cypress open",
     "cypress:run": "npx cypress run --config defaultCommandTimeout=8000",
     "cypress:install": "npx cypress install",

packages/image-io/python/itkwasm-image-io/pyproject.toml

@@ -23,6 +23,7 @@ classifiers = [
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
 ]
 keywords = [
   "itkwasm",

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

@@ -1,5 +1,3 @@
-# Generated file. To retain edits, remove this comment.
-
 """itkwasm-mesh-io-emscripten: Input and output for scientific and medical image file formats. Emscripten implementation."""
 
 from .read_mesh_async import read_mesh_async

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

@@ -1 +1 @@
-__version__ = "0.1.0"
+__version__ = "0.2.0"

packages/mesh-io/python/itkwasm-mesh-io-wasi/itkwasm_mesh_io_wasi/_version.py

@@ -1 +1 @@
-__version__ = "0.1.0"
+__version__ = "0.2.0"

packages/mesh-io/python/itkwasm-mesh-io/itkwasm_mesh_io/__init__.py

@@ -1,7 +1,10 @@
-# Generated file. To retain edits, remove this comment.
-
 """itkwasm-mesh-io: Input and output for scientific and medical image file formats."""
 
+from .read_mesh_async import read_mesh_async, meshread_async
+from .read_mesh import read_mesh, meshread
+from .write_mesh_async import write_mesh_async, meshwrite_async
+from .write_mesh import write_mesh, meshwrite
+
 from .byu_read_mesh_async import byu_read_mesh_async
 from .byu_read_mesh import byu_read_mesh
 from .byu_write_mesh_async import byu_write_mesh_async

packages/mesh-io/python/itkwasm-mesh-io/itkwasm_mesh_io/_version.py

@@ -1 +1 @@
-__version__ = "0.1.0"
+__version__ = "0.2.0"

packages/mesh-io/python/itkwasm-mesh-io/itkwasm_mesh_io/read_mesh.py

@@ -0,0 +1,36 @@
+import os
+from typing import Optional, Union
+
+from itkwasm import (
+    environment_dispatch,
+    Mesh,
+)
+
+def read_mesh(
+    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
+    """
+    func = environment_dispatch("itkwasm_mesh_io", "read_mesh")
+    output = func(serialized_mesh, information_only=information_only)
+    return output
+
+def meshread(
+    serialized_mesh: os.PathLike,
+    information_only: bool = False,
+) -> Mesh:
+    return read_mesh(serialized_mesh, information_only=information_only)
+
+meshread.__doc__ = f"""{read_mesh.__doc__}
+    Alias for read_mesh.
+    """

packages/mesh-io/python/itkwasm-mesh-io/itkwasm_mesh_io/read_mesh_async.py

@@ -0,0 +1,36 @@
+import os
+from typing import Optional, Union
+
+from itkwasm import (
+    environment_dispatch,
+    Mesh,
+)
+
+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
+    """
+    func = environment_dispatch("itkwasm_mesh_io", "read_mesh_async")
+    output = await func(serialized_mesh, information_only=information_only)
+    return output
+
+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.
+    """

packages/mesh-io/python/itkwasm-mesh-io/itkwasm_mesh_io/write_mesh.py

@@ -0,0 +1,43 @@
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from itkwasm import (
+    environment_dispatch,
+    Mesh,
+)
+
+def write_mesh(
+    mesh: Mesh,
+    serialized_mesh: str,
+    information_only: bool = False,
+    use_compression: bool = False,
+) -> None:
+    """Write an itk-wasm file format converted 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
+    """
+    func = environment_dispatch("itkwasm_mesh_io", "write_mesh")
+    func(mesh, serialized_mesh, information_only=information_only, use_compression=use_compression)
+    return
+
+def meshwrite(
+    mesh: Mesh,
+    serialized_mesh: os.PathLike,
+    information_only: bool = False,
+    use_compression: bool = False,
+) -> None:
+    return write_mesh(mesh, serialized_mesh, information_only=information_only, use_compression=use_compression)
+
+meshwrite.__doc__ = f"""{write_mesh.__doc__}
+    Alias for write_mesh.
+    """

packages/mesh-io/python/itkwasm-mesh-io/itkwasm_mesh_io/write_mesh_async.py

@@ -0,0 +1,43 @@
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from itkwasm import (
+    environment_dispatch,
+    Mesh,
+)
+
+async def write_mesh_async(
+    mesh: Mesh,
+    serialized_mesh: str,
+    information_only: bool = False,
+    use_compression: bool = False,
+) -> None:
+    """Write an itk-wasm file format converted 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
+    """
+    func = environment_dispatch("itkwasm_mesh_io", "write_mesh_async")
+    await func(mesh, serialized_mesh, information_only=information_only, use_compression=use_compression)
+    return
+
+async def meshwrite_async(
+    mesh: Mesh,
+    serialized_mesh: os.PathLike,
+    information_only: bool = False,
+    use_compression: bool = False,
+) -> None:
+    return await 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/pyproject.toml

@@ -46,15 +46,29 @@ path = "itkwasm_mesh_io/_version.py"
 [tool.hatch.envs.default]
 dependencies = [
   "pytest",
+  "pytest-pyodide",
 ]
 
 [project.urls]
 Home = "https://github.com/InsightSoftwareConsortium/itk-wasm"
 Source = "https://github.com/InsightSoftwareConsortium/itk-wasm"
 
 [tool.hatch.envs.default.scripts]
-test = "pytest"
-
+test = [
+  "hatch build -t wheel",
+  "pytest --dist-dir=./dist --rt=chrome",
+]
+download-pyodide = [
+  "curl -L https://github.com/pyodide/pyodide/releases/download/0.24.1/pyodide-0.24.1.tar.bz2 -o pyodide.tar.bz2",
+  "tar xjf pyodide.tar.bz2",
+  "rm -rf dist pyodide.tar.bz2",
+  "mv pyodide dist",
+]
+serve = [
+  "hatch build -t wheel",
+  'echo "\nVisit http://localhost:8877/console.html\n"',
+  "python -m http.server --directory=./dist 8877",
+]
 
 [tool.hatch.build]
 exclude = [

packages/mesh-io/python/itkwasm-mesh-io/tests/fixtures.py

@@ -0,0 +1,26 @@
+import pytest
+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 itkwasm_mesh_io import __version__ as test_package_version
+
+@pytest.fixture
+def package_wheel():
+    return f"itkwasm_mesh_io-{test_package_version}-py3-none-any.whl"
+
+@pytest.fixture
+def input_data():
+    from pathlib import Path
+    input_base_path = Path('..', '..', 'test', 'data')
+    test_files = [
+        Path('input') / 'cow.vtk',
+    ]
+    data = {}
+    for f in test_files:
+        with open(input_base_path / f, 'rb') as fp:
+            data[str(f.name)] = fp.read()
+    return data

packages/mesh-io/python/itkwasm-mesh-io/tests/test_read_write_mesh.py

@@ -0,0 +1,48 @@
+from itkwasm import IntTypes, FloatTypes
+import numpy as np
+
+from itkwasm_mesh_io import read_mesh, meshread, write_mesh, meshwrite
+
+from .common import test_input_path, test_output_path
+
+test_input_file_path = test_input_path / "cow.vtk"
+test_output_file_path = test_output_path / "read-write-cow.vtk"
+
+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[0],3.71636)
+    assert np.allclose(mesh.points[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
+
+def test_read_mesh():
+    mesh = read_mesh(test_input_file_path)
+    verify_mesh(mesh)
+
+def test_meshread():
+    mesh = meshread(test_input_file_path)
+    verify_mesh(mesh)
+
+def test_write_mesh():
+    mesh = read_mesh(test_input_file_path)
+
+    use_compression = False
+    write_mesh(mesh, test_output_file_path, use_compression=use_compression)
+
+    mesh = read_mesh(test_output_file_path)
+    verify_mesh(mesh)
+
+def test_meshwrite():
+    mesh = meshread(test_input_file_path)
+
+    use_compression = False
+    meshwrite(mesh, test_output_file_path, use_compression=use_compression)
+
+    mesh = meshread(test_output_file_path)
+    verify_mesh(mesh)

packages/mesh-io/python/itkwasm-mesh-io/tests/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 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)