feat(mesh-io): bindgen wasi output

packages/mesh-io/python/itkwasm-mesh-io-wasi/README.md

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+# itkwasm-mesh-io-wasi
+
+[![PyPI version](https://badge.fury.io/py/itkwasm-mesh-io-wasi.svg)](https://badge.fury.io/py/itkwasm-mesh-io-wasi)
+
+Input and output for scientific and medical image file formats. WASI implementation.
+
+This package provides the WASI WebAssembly implementation. It is usually not called directly. Please use [`itkwasm-mesh-io`](https://pypi.org/project/itkwasm-mesh-io/) instead.
+
+
+## Installation
+
+```sh
+pip install itkwasm-mesh-io-wasi
+```
+
+## Development
+
+```sh
+pip install pytest
+pip install -e .
+pytest
+
+# or
+pip install hatch
+hatch run test
+```

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

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+# Generated file. To retain edits, remove this comment.
+
+"""itkwasm-mesh-io-wasi: Input and output for scientific and medical image file formats. WASI implementation."""
+
+from .byu_read_mesh import byu_read_mesh
+from .byu_write_mesh import byu_write_mesh
+from .free_surfer_ascii_read_mesh import free_surfer_ascii_read_mesh
+from .free_surfer_ascii_write_mesh import free_surfer_ascii_write_mesh
+from .free_surfer_binary_read_mesh import free_surfer_binary_read_mesh
+from .free_surfer_binary_write_mesh import free_surfer_binary_write_mesh
+from .obj_read_mesh import obj_read_mesh
+from .obj_write_mesh import obj_write_mesh
+from .off_read_mesh import off_read_mesh
+from .off_write_mesh import off_write_mesh
+from .stl_read_mesh import stl_read_mesh
+from .stl_write_mesh import stl_write_mesh
+from .swc_read_mesh import swc_read_mesh
+from .swc_write_mesh import swc_write_mesh
+from .vtk_poly_data_read_mesh import vtk_poly_data_read_mesh
+from .vtk_poly_data_write_mesh import vtk_poly_data_write_mesh
+from .wasm_read_mesh import wasm_read_mesh
+from .wasm_write_mesh import wasm_write_mesh
+from .wasm_zstd_read_mesh import wasm_zstd_read_mesh
+from .wasm_zstd_write_mesh import wasm_zstd_write_mesh
+
+from ._version import __version__

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

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+__version__ = "0.1.0"

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

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+# Generated file. To retain edits, remove this comment.
+
+from pathlib import Path, PurePosixPath
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from importlib_resources import files as file_resources
+
+_pipeline = None
+
+from itkwasm import (
+    InterfaceTypes,
+    PipelineOutput,
+    PipelineInput,
+    Pipeline,
+    BinaryFile,
+    Mesh,
+)
+
+def byu_read_mesh(
+    serialized_mesh: os.PathLike,
+    information_only: bool = False,
+) -> Tuple[Any, Mesh]:
+    """Read a 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 image metadata -- do not read pixel data.
+    :type  information_only: bool
+
+    :return: Whether the input could be read. If false, the output mesh is not valid.
+    :rtype:  Any
+
+    :return: Output mesh
+    :rtype:  Mesh
+    """
+    global _pipeline
+    if _pipeline is None:
+        _pipeline = Pipeline(file_resources('itkwasm_mesh_io_wasi').joinpath(Path('wasm_modules') / Path('byu-read-mesh.wasi.wasm')))
+
+    pipeline_outputs: List[PipelineOutput] = [
+        PipelineOutput(InterfaceTypes.JsonCompatible),
+        PipelineOutput(InterfaceTypes.Mesh),
+    ]
+
+    pipeline_inputs: List[PipelineInput] = [
+        PipelineInput(InterfaceTypes.BinaryFile, BinaryFile(PurePosixPath(serialized_mesh))),
+    ]
+
+    args: List[str] = ['--memory-io',]
+    # Inputs
+    if not Path(serialized_mesh).exists():
+        raise FileNotFoundError("serialized_mesh does not exist")
+    args.append(str(PurePosixPath(serialized_mesh)))
+    # Outputs
+    could_read_name = '0'
+    args.append(could_read_name)
+
+    mesh_name = '1'
+    args.append(mesh_name)
+
+    # Options
+    input_count = len(pipeline_inputs)
+    if information_only:
+        args.append('--information-only')
+
+
+    outputs = _pipeline.run(args, pipeline_outputs, pipeline_inputs)
+
+    result = (
+        outputs[0].data,
+        outputs[1].data,
+    )
+    return result
+

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

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+# Generated file. To retain edits, remove this comment.
+
+from pathlib import Path, PurePosixPath
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from importlib_resources import files as file_resources
+
+_pipeline = None
+
+from itkwasm import (
+    InterfaceTypes,
+    PipelineOutput,
+    PipelineInput,
+    Pipeline,
+    Mesh,
+    BinaryFile,
+)
+
+def byu_write_mesh(
+    mesh: Mesh,
+    serialized_mesh: str,
+    information_only: bool = False,
+    use_compression: bool = False,
+    binary_file_type: bool = False,
+) -> Tuple[Any]:
+    """Write an itk-wasm file format converted to an mesh file format
+
+    :param mesh: Input mesh
+    :type  mesh: Mesh
+
+    :param serialized_mesh: Output mesh
+    :type  serialized_mesh: str
+
+    :param information_only: Only write image metadata -- do not write pixel data.
+    :type  information_only: bool
+
+    :param use_compression: Use compression in the written file, if supported
+    :type  use_compression: bool
+
+    :param binary_file_type: Use a binary file type in the written file, if supported
+    :type  binary_file_type: bool
+
+    :return: Whether the input could be written. If false, the output mesh is not valid.
+    :rtype:  Any
+    """
+    global _pipeline
+    if _pipeline is None:
+        _pipeline = Pipeline(file_resources('itkwasm_mesh_io_wasi').joinpath(Path('wasm_modules') / Path('byu-write-mesh.wasi.wasm')))
+
+    pipeline_outputs: List[PipelineOutput] = [
+        PipelineOutput(InterfaceTypes.JsonCompatible),
+        PipelineOutput(InterfaceTypes.BinaryFile, BinaryFile(PurePosixPath(serialized_mesh))),
+    ]
+
+    pipeline_inputs: List[PipelineInput] = [
+        PipelineInput(InterfaceTypes.Mesh, mesh),
+    ]
+
+    args: List[str] = ['--memory-io',]
+    # Inputs
+    args.append('0')
+    # Outputs
+    could_write_name = '0'
+    args.append(could_write_name)
+
+    serialized_mesh_name = str(PurePosixPath(serialized_mesh))
+    args.append(serialized_mesh_name)
+
+    # Options
+    input_count = len(pipeline_inputs)
+    if information_only:
+        args.append('--information-only')
+
+    if use_compression:
+        args.append('--use-compression')
+
+    if binary_file_type:
+        args.append('--binary-file-type')
+
+
+    outputs = _pipeline.run(args, pipeline_outputs, pipeline_inputs)
+
+    result = outputs[0].data
+    return result
+

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

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+# Generated file. To retain edits, remove this comment.
+
+from pathlib import Path, PurePosixPath
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from importlib_resources import files as file_resources
+
+_pipeline = None
+
+from itkwasm import (
+    InterfaceTypes,
+    PipelineOutput,
+    PipelineInput,
+    Pipeline,
+    BinaryFile,
+    Mesh,
+)
+
+def free_surfer_ascii_read_mesh(
+    serialized_mesh: os.PathLike,
+    information_only: bool = False,
+) -> Tuple[Any, Mesh]:
+    """Read a 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 image metadata -- do not read pixel data.
+    :type  information_only: bool
+
+    :return: Whether the input could be read. If false, the output mesh is not valid.
+    :rtype:  Any
+
+    :return: Output mesh
+    :rtype:  Mesh
+    """
+    global _pipeline
+    if _pipeline is None:
+        _pipeline = Pipeline(file_resources('itkwasm_mesh_io_wasi').joinpath(Path('wasm_modules') / Path('free-surfer-ascii-read-mesh.wasi.wasm')))
+
+    pipeline_outputs: List[PipelineOutput] = [
+        PipelineOutput(InterfaceTypes.JsonCompatible),
+        PipelineOutput(InterfaceTypes.Mesh),
+    ]
+
+    pipeline_inputs: List[PipelineInput] = [
+        PipelineInput(InterfaceTypes.BinaryFile, BinaryFile(PurePosixPath(serialized_mesh))),
+    ]
+
+    args: List[str] = ['--memory-io',]
+    # Inputs
+    if not Path(serialized_mesh).exists():
+        raise FileNotFoundError("serialized_mesh does not exist")
+    args.append(str(PurePosixPath(serialized_mesh)))
+    # Outputs
+    could_read_name = '0'
+    args.append(could_read_name)
+
+    mesh_name = '1'
+    args.append(mesh_name)
+
+    # Options
+    input_count = len(pipeline_inputs)
+    if information_only:
+        args.append('--information-only')
+
+
+    outputs = _pipeline.run(args, pipeline_outputs, pipeline_inputs)
+
+    result = (
+        outputs[0].data,
+        outputs[1].data,
+    )
+    return result
+

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

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+# Generated file. To retain edits, remove this comment.
+
+from pathlib import Path, PurePosixPath
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from importlib_resources import files as file_resources
+
+_pipeline = None
+
+from itkwasm import (
+    InterfaceTypes,
+    PipelineOutput,
+    PipelineInput,
+    Pipeline,
+    Mesh,
+    BinaryFile,
+)
+
+def free_surfer_ascii_write_mesh(
+    mesh: Mesh,
+    serialized_mesh: str,
+    information_only: bool = False,
+    use_compression: bool = False,
+    binary_file_type: bool = False,
+) -> Tuple[Any]:
+    """Write an itk-wasm file format converted to an mesh file format
+
+    :param mesh: Input mesh
+    :type  mesh: Mesh
+
+    :param serialized_mesh: Output mesh
+    :type  serialized_mesh: str
+
+    :param information_only: Only write image metadata -- do not write pixel data.
+    :type  information_only: bool
+
+    :param use_compression: Use compression in the written file, if supported
+    :type  use_compression: bool
+
+    :param binary_file_type: Use a binary file type in the written file, if supported
+    :type  binary_file_type: bool
+
+    :return: Whether the input could be written. If false, the output mesh is not valid.
+    :rtype:  Any
+    """
+    global _pipeline
+    if _pipeline is None:
+        _pipeline = Pipeline(file_resources('itkwasm_mesh_io_wasi').joinpath(Path('wasm_modules') / Path('free-surfer-ascii-write-mesh.wasi.wasm')))
+
+    pipeline_outputs: List[PipelineOutput] = [
+        PipelineOutput(InterfaceTypes.JsonCompatible),
+        PipelineOutput(InterfaceTypes.BinaryFile, BinaryFile(PurePosixPath(serialized_mesh))),
+    ]
+
+    pipeline_inputs: List[PipelineInput] = [
+        PipelineInput(InterfaceTypes.Mesh, mesh),
+    ]
+
+    args: List[str] = ['--memory-io',]
+    # Inputs
+    args.append('0')
+    # Outputs
+    could_write_name = '0'
+    args.append(could_write_name)
+
+    serialized_mesh_name = str(PurePosixPath(serialized_mesh))
+    args.append(serialized_mesh_name)
+
+    # Options
+    input_count = len(pipeline_inputs)
+    if information_only:
+        args.append('--information-only')
+
+    if use_compression:
+        args.append('--use-compression')
+
+    if binary_file_type:
+        args.append('--binary-file-type')
+
+
+    outputs = _pipeline.run(args, pipeline_outputs, pipeline_inputs)
+
+    result = outputs[0].data
+    return result
+