feat(mesh-io): add wasi read_mesh, write_mesh

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

@@ -1,7 +1,8 @@
-# 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 .read_mesh import read_mesh, meshread
+from .write_mesh import write_mesh, meshwrite
+
 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

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

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

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

@@ -0,0 +1,61 @@
+import os
+import importlib
+from pathlib import Path
+
+from itkwasm import Mesh
+
+from .extension_to_mesh_io import extension_to_mesh_io
+from .mesh_io_index import mesh_io_index
+
+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
+    """
+    extension = ''.join(Path(serialized_mesh).suffixes)
+
+    io = None
+    if extension in extension_to_mesh_io:
+        func = f"{extension_to_mesh_io[extension]}_read_mesh"
+        mod_name = f"itkwasm_mesh_io_wasi.{func}"
+        mod = importlib.import_module(mod_name)
+        io = getattr(mod, func)
+    else:
+        for ioname in mesh_io_index:
+            func = f"{ioname}_read_mesh"
+            mod_name = f"itkwasm_mesh_io_wasi.{func}"
+            mod = importlib.import_module(mod_name)
+            io = getattr(mod, func)
+            could_read, mesh = io(serialized_mesh, information_only=information_only)
+            if could_read:
+                return mesh
+
+    if io is None:
+        raise RuntimeError(f"Could not find an mesh reader for {extension}")
+
+    could_read, mesh = io(serialized_mesh, information_only=information_only)
+    if not could_read:
+        raise RuntimeError(f"Could not read {serialized_mesh}")
+
+    return mesh
+
+
+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-wasi/itkwasm_mesh_io_wasi/write_mesh.py

@@ -0,0 +1,68 @@
+import os
+import importlib
+from pathlib import Path
+
+from itkwasm import Mesh, PixelTypes, IntTypes, FloatTypes
+
+from .extension_to_mesh_io import extension_to_mesh_io
+from .mesh_io_index import mesh_io_index
+
+def write_mesh(
+    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
+    """
+    extension = ''.join(Path(serialized_mesh).suffixes)
+
+    io = None
+    if extension in extension_to_mesh_io:
+        func = f"{extension_to_mesh_io[extension]}_write_mesh"
+        mod_name = f"itkwasm_mesh_io_wasi.{func}"
+        mod = importlib.import_module(mod_name)
+        io = getattr(mod, func)
+    else:
+        for ioname in mesh_io_index:
+            func = f"{ioname}_write_mesh"
+            mod_name = f"itkwasm_mesh_io_wasi.{func}"
+            mod = importlib.import_module(mod_name)
+            io = getattr(mod, func)
+            could_write = io(mesh, serialized_mesh, information_only=information_only, use_compression=use_compression)
+            if could_write:
+                return
+
+    if io is None:
+        raise RuntimeError(f"Could not find an mesh writer for {extension}")
+
+    could_write = io(mesh, serialized_mesh, information_only=information_only, use_compression=use_compression)
+    if not could_write:
+        raise RuntimeError(f"Could not write {serialized_mesh}")
+
+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-wasi/tests/test_read_write_mesh.py

@@ -0,0 +1,48 @@
+from itkwasm import IntTypes, FloatTypes
+import numpy as np
+
+from itkwasm_mesh_io_wasi 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)