feat(mesh-io): python wasi mz3 support

Author: thewtex

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

@@ -12,6 +12,8 @@
 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 .mz3_read_mesh import mz3_read_mesh
+from .mz3_write_mesh import mz3_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
@@ -27,6 +29,8 @@
 from .wasm_zstd_read_mesh import wasm_zstd_read_mesh
 from .wasm_zstd_write_mesh import wasm_zstd_write_mesh
 
+from .mz3_read_point_set import mz3_read_point_set
+from .mz3_write_point_set import mz3_write_point_set
 from .obj_read_point_set import obj_read_point_set
 from .obj_write_point_set import obj_write_point_set
 from .off_read_point_set import off_read_point_set

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

@@ -5,6 +5,7 @@
     ('.byu', 'byu'),
     ('.fsa', 'free_surfer_ascii'),
     ('.fsb', 'free_surfer_binary'),
+    ('.mz3', 'mz3'),
     ('.obj', 'obj'),
     ('.off', 'off'),
     ('.stl', 'stl'),

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

@@ -1,6 +1,7 @@
 from collections import OrderedDict
 
 extension_to_point_set_io = OrderedDict([
+    ('.mz3', 'mz3'),
     ('.vtk', 'vtk_poly_data'),
     ('.obj', 'obj'),
     ('.off', 'off'),

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

@@ -3,6 +3,8 @@
   'byu',
   'free_surfer_ascii',
   'free_surfer_binary',
+  'mz3',
+  'obj',
   'obj',
   'off',
   'stl',

packages/mesh-io/python/itkwasm-mesh-io-wasi/itkwasm_mesh_io_wasi/mz3_read_mesh.py

@@ -0,0 +1,76 @@
+# 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 mz3_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 mesh 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('mz3-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/mz3_read_point_set.py

@@ -0,0 +1,76 @@
+# 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,
+    PointSet,
+)
+
+def mz3_read_point_set(
+    serialized_point_set: os.PathLike,
+    information_only: bool = False,
+) -> Tuple[Any, PointSet]:
+    """Read a point set file format and convert it to the itk-wasm file format
+
+    :param serialized_point_set: Input point set serialized in the file format
+    :type  serialized_point_set: os.PathLike
+
+    :param information_only: Only read point set metadata -- do not read pixel data.
+    :type  information_only: bool
+
+    :return: Whether the input could be read. If false, the output point set is not valid.
+    :rtype:  Any
+
+    :return: Output point set
+    :rtype:  PointSet
+    """
+    global _pipeline
+    if _pipeline is None:
+        _pipeline = Pipeline(file_resources('itkwasm_mesh_io_wasi').joinpath(Path('wasm_modules') / Path('mz3-read-point-set.wasi.wasm')))
+
+    pipeline_outputs: List[PipelineOutput] = [
+        PipelineOutput(InterfaceTypes.JsonCompatible),
+        PipelineOutput(InterfaceTypes.PointSet),
+    ]
+
+    pipeline_inputs: List[PipelineInput] = [
+        PipelineInput(InterfaceTypes.BinaryFile, BinaryFile(PurePosixPath(serialized_point_set))),
+    ]
+
+    args: List[str] = ['--memory-io',]
+    # Inputs
+    if not Path(serialized_point_set).exists():
+        raise FileNotFoundError("serialized_point_set does not exist")
+    args.append(str(PurePosixPath(serialized_point_set)))
+    # Outputs
+    could_read_name = '0'
+    args.append(could_read_name)
+
+    point_set_name = '1'
+    args.append(point_set_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/mz3_write_mesh.py

@@ -0,0 +1,86 @@
+# 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 mz3_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 mesh 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('mz3-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/mz3_write_point_set.py

@@ -0,0 +1,86 @@
+# 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,
+    PointSet,
+    BinaryFile,
+)
+
+def mz3_write_point_set(
+    point_set: PointSet,
+    serialized_point_set: str,
+    information_only: bool = False,
+    use_compression: bool = False,
+    binary_file_type: bool = False,
+) -> Tuple[Any]:
+    """Write an ITK-Wasm file format converted to a point set file format
+
+    :param point_set: Input point set
+    :type  point_set: PointSet
+
+    :param serialized_point_set: Output point set
+    :type  serialized_point_set: str
+
+    :param information_only: Only write point set 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('mz3-write-point-set.wasi.wasm')))
+
+    pipeline_outputs: List[PipelineOutput] = [
+        PipelineOutput(InterfaceTypes.JsonCompatible),
+        PipelineOutput(InterfaceTypes.BinaryFile, BinaryFile(PurePosixPath(serialized_point_set))),
+    ]
+
+    pipeline_inputs: List[PipelineInput] = [
+        PipelineInput(InterfaceTypes.PointSet, point_set),
+    ]
+
+    args: List[str] = ['--memory-io',]
+    # Inputs
+    args.append('0')
+    # Outputs
+    could_write_name = '0'
+    args.append(could_write_name)
+
+    serialized_point_set_name = str(PurePosixPath(serialized_point_set))
+    args.append(serialized_point_set_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/point_set_io_index.py

@@ -1,5 +1,6 @@
 point_set_io_index = [
   'vtk_poly_data',
+  'mz3',
   'obj',
   'off',
   'wasm',