feat(transform-io); dispatch read and write functions

packages/image-io/pixi.toml

@@ -85,6 +85,7 @@ pyodide-py = ">=0.26.3, <0.27"
 pytest-pyodide = ">=0.58.3, <0.59"
 itk-webassemblyinterface = ">=1.0b175, <2"
 itkwasm = ">=1.0b179, <2"
+itkwasm-image-io-wasi = { path = "python/itkwasm-image-io-wasi", editable = true }
 
 [feature.python.tasks.test-wasi]
 cmd = "pytest"

packages/mesh-io/pixi.toml

@@ -85,6 +85,7 @@ pyodide-py = ">=0.26.3, <0.27"
 pytest-pyodide = ">=0.58.3, <0.59"
 itk-webassemblyinterface = ">=1.0b175, <2"
 itkwasm = ">=1.0b179, <2"
+itkwasm-mesh-io-wasi = { path = "python/itkwasm-mesh-io-wasi", editable = true }
 
 [feature.python.tasks.test-wasi]
 cmd = "pytest"

packages/transform-io/pixi.toml

@@ -85,6 +85,7 @@ pyodide-py = ">=0.26.4, <0.27"
 pytest-pyodide = ">=0.58.3, <0.59"
 itk-webassemblyinterface = ">=1.0b175, <2"
 itkwasm = ">=1.0b185, <2"
+itkwasm-transform-io-wasi = { path = "python/itkwasm-transform-io-wasi", editable = true }
 
 [feature.python.tasks.test-wasi]
 cmd = "pytest"

packages/transform-io/python/itkwasm-transform-io-wasi/tests/common.py

@@ -5,7 +5,7 @@
 
 test_input_path = Path(__file__).parent / ".." / ".." / ".." / "test" / "data" / "input"
 test_baseline_path = Path(__file__).parent / ".." / ".." / ".." / "test" / "data" / "baseline"
-test_output_path = Path(__file__).parent / ".." / ".." / ".." / "test" / "data" / "output" / "python"
+test_output_path = Path(__file__).parent / ".." / ".." / ".." / "test" / "data" / "output" / "python-wasi"
 test_output_path.mkdir(parents=True, exist_ok=True)
 
 def verify_test_linear_transform(transform_list: TransformList):
@@ -20,4 +20,4 @@ def verify_test_linear_transform(transform_list: TransformList):
       0.65631490118447, 0.5806583745824385, -0.4817536741017158,
       -0.7407986817430222, 0.37486398378429736, -0.5573995934598175,
       -0.14306664045479867, 0.7227121458012518, 0.676179776908723,
-      -65.99999999999997, 69.00000000000004, 32.000000000000036]))
+      -65.99999999999997, 69.00000000000004, 32.000000000000036]))

packages/transform-io/python/itkwasm-transform-io/itkwasm_transform_io/__init__.py

@@ -1,7 +1,10 @@
-# Generated file. To retain edits, remove this comment.
-
 """itkwasm-transform-io: Input and output for scientific and medical coordinate transform file formats."""
 
+from .read_transform_async import read_transform_async, transformread_async
+from .read_transform import read_transform, transformread
+from .write_transform_async import write_transform_async, transformwrite_async
+from .write_transform import write_transform, transformwrite
+
 from .hdf5_read_transform_async import hdf5_read_transform_async
 from .hdf5_read_transform import hdf5_read_transform
 from .hdf5_write_transform_async import hdf5_write_transform_async

packages/transform-io/python/itkwasm-transform-io/itkwasm_transform_io/read_transform.py

@@ -0,0 +1,36 @@
+import os
+from typing import Optional, Union
+
+from itkwasm import (
+    environment_dispatch,
+    TransformList,
+)
+
+def read_transform(
+    serialized_transform: os.PathLike,
+    float_parameters: bool = False,
+) -> TransformList:
+    """Read a transform file format and convert it to the ITK-Wasm file format
+
+    :param serialized_transform: Input transform serialized in the file format
+    :type  serialized_transform: os.PathLike
+
+    :param float_parameters: Use float for the parameter value type. The default is double.
+    :type  float_parameters: bool
+
+    :return: Output transform
+    :rtype:  TransformList
+    """
+    func = environment_dispatch("itkwasm_transform_io", "read_transform")
+    output = func(serialized_transform, float_parameters=float_parameters)
+    return output
+
+def transformread(
+    serialized_transform: os.PathLike,
+    float_parameters: bool = False,
+) -> TransformList:
+    return read_transform(serialized_transform, float_parameters=float_parameters)
+
+transformread.__doc__ = f"""{read_transform.__doc__}
+    Alias for read_transform.
+    """

packages/transform-io/python/itkwasm-transform-io/itkwasm_transform_io/read_transform_async.py

@@ -0,0 +1,36 @@
+import os
+from typing import Optional, Union
+
+from itkwasm import (
+    environment_dispatch,
+    TransformList,
+)
+
+async def read_transform_async(
+    serialized_transform: os.PathLike,
+    float_parameters: bool = False,
+) -> TransformList:
+    """Read an transform file format and convert it to the ITK-Wasm file format.
+
+    :param serialized_transform: Input transform serialized in the file format
+    :type  serialized_transform: os.PathLike
+
+    :param float_parameters: Use float for the parameter value type. The default is double.
+    :type  float_parameters: bool
+
+    :return: Output transform
+    :rtype:  TransformList
+    """
+    func = environment_dispatch("itkwasm_transform_io", "read_transform_async")
+    output = await func(serialized_transform, float_parameters=float_parameters)
+    return output
+
+async def transformread_async(
+    serialized_transform: os.PathLike,
+    float_parameters: bool = False,
+) -> TransformList:
+    return await read_transform_async(serialized_transform, float_parameters=float_parameters)
+
+transformread_async.__doc__ = f"""{read_transform_async.__doc__}
+    Alias for read_transform.
+    """

packages/transform-io/python/itkwasm-transform-io/itkwasm_transform_io/write_transform.py

@@ -0,0 +1,43 @@
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from itkwasm import (
+    environment_dispatch,
+    TransformList,
+)
+
+def write_transform(
+    transform: TransformList,
+    serialized_transform: str,
+    float_parameters: bool = False,
+    use_compression: bool = False,
+) -> None:
+    """Write an ITK-Wasm file format converted to a transform file format
+
+    :param transform: Input transform
+    :type  transform: TransformList
+
+    :param serialized_transform: Output transform serialized in the file format.
+    :type  serialized_transform: str
+
+    :param float_parameters: Use float for the parameter value type. The default is double.
+    :type  float_parameters: bool
+
+    :param use_compression: Use compression in the written file
+    :type  use_compression: bool
+    """
+    func = environment_dispatch("itkwasm_transform_io", "write_transform")
+    func(transform, serialized_transform, float_parameters=float_parameters, use_compression=use_compression)
+    return
+
+def transformwrite(
+    transform: TransformList,
+    serialized_transform: os.PathLike,
+    float_parameters: bool = False,
+    use_compression: bool = False,
+) -> None:
+    return write_transform(transform, serialized_transform, float_parameters=float_parameters, use_compression=use_compression)
+
+transformwrite.__doc__ = f"""{write_transform.__doc__}
+    Alias for write_transform.
+    """

packages/transform-io/python/itkwasm-transform-io/itkwasm_transform_io/write_transform_async.py

@@ -0,0 +1,43 @@
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from itkwasm import (
+    environment_dispatch,
+    TransformList,
+)
+
+async def write_transform_async(
+    transform: TransformList,
+    serialized_transform: str,
+    float_parameters: bool = False,
+    use_compression: bool = False,
+) -> None:
+    """Write an ITK-Wasm file format converted to a transform file format.
+
+    :param transform: Input transform
+    :type  transform: TransformList
+
+    :param serialized_transform: Output transform serialized in the file format.
+    :type  serialized_transform: str
+
+    :param float_parameters: Only write transform metadata -- do not write pixel data.
+    :type  float_parameters: bool
+
+    :param use_compression: Use compression in the written file
+    :type  use_compression: bool
+    """
+    func = environment_dispatch("itkwasm_transform_io", "write_transform_async")
+    await func(transform, serialized_transform, float_parameters=float_parameters, use_compression=use_compression)
+    return
+
+async def transformwrite_async(
+    transform: TransformList,
+    serialized_transform: os.PathLike,
+    float_parameters: bool = False,
+    use_compression: bool = False,
+) -> None:
+    return await write_transform_async(transform, serialized_transform, float_parameters=float_parameters, use_compression=use_compression)
+
+transformwrite_async.__doc__ = f"""{write_transform_async.__doc__}
+    Alias for write_transform.
+    """

packages/transform-io/python/itkwasm-transform-io/tests/common.py

@@ -0,0 +1,23 @@
+from pathlib import Path
+import numpy as np
+
+from itkwasm import TransformList, TransformParameterizations, FloatTypes
+
+test_input_path = Path(__file__).parent / ".." / ".." / ".." / "test" / "data" / "input"
+test_baseline_path = Path(__file__).parent / ".." / ".." / ".." / "test" / "data" / "baseline"
+test_output_path = Path(__file__).parent / ".." / ".." / ".." / "test" / "data" / "output" / "python-dispatch"
+test_output_path.mkdir(parents=True, exist_ok=True)
+
+def verify_test_linear_transform(transform_list: TransformList):
+    assert len(transform_list) == 1
+    transform = transform_list[0]
+    assert transform.transformType.transformParameterization == TransformParameterizations.Affine
+    assert transform.transformType.parametersValueType == FloatTypes.Float64
+    assert transform.numberOfParameters == 12
+    assert transform.numberOfFixedParameters == 3
+    np.testing.assert_allclose(transform.fixedParameters, np.array([0.0, 0.0, 0.0]))
+    np.testing.assert_allclose(transform.parameters, np.array([
+      0.65631490118447, 0.5806583745824385, -0.4817536741017158,
+      -0.7407986817430222, 0.37486398378429736, -0.5573995934598175,
+      -0.14306664045479867, 0.7227121458012518, 0.676179776908723,
+      -65.99999999999997, 69.00000000000004, 32.000000000000036]))

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

@@ -20,7 +20,7 @@ def emscripten_package_wheel():
 @pytest.fixture
 def input_data():
     from pathlib import Path
-    input_base_path = Path(__file__).parent.parent / 'test' / 'data'
+    input_base_path = Path(__file__).parent.parent.parent.parent / 'test' / 'data' / 'input'
     test_files = list(input_base_path.glob('*'))
     data = {}
     for test_file in test_files:

packages/transform-io/python/itkwasm-transform-io/tests/test_hdf5_read_transform.py

@@ -1,19 +1,12 @@
-import pytest
-import sys
+from pathlib import Path
 
-if sys.version_info < (3,10):
-    pytest.skip("Skipping pyodide tests on older Python", allow_module_level=True)
+from itkwasm_transform_io import hdf5_read_transform
 
-from pytest_pyodide import run_in_pyodide
+from .common import test_input_path, test_output_path, verify_test_linear_transform
 
-from .fixtures import emscripten_package_wheel, package_wheel, input_data
+test_input_file_path = test_input_path / "LinearTransform.h5"
 
-@run_in_pyodide(packages=['micropip'])
-async def test_hdf5_read_transform(selenium, package_wheel, emscripten_package_wheel):
-    import micropip
-    await micropip.install(emscripten_package_wheel)
-    await micropip.install(package_wheel)
-
-    from itkwasm_transform_io import hdf5_read_transform
-
-    # Write your test code here
+def test_hdf5_read_transform():
+    could_read, transform_list = hdf5_read_transform(test_input_file_path)
+    assert could_read
+    verify_test_linear_transform(transform_list)

packages/transform-io/python/itkwasm-transform-io/tests/test_hdf5_read_transform_async.py

@@ -0,0 +1,59 @@
+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 .fixtures import package_wheel, input_data, emscripten_package_wheel
+
+@run_in_pyodide(packages=['micropip'])
+async def test_hdf5_read_transform_async(selenium, package_wheel, emscripten_package_wheel, input_data):
+    import micropip
+    await micropip.install(emscripten_package_wheel)
+    await micropip.install(package_wheel)
+
+    from pathlib import Path
+
+    import numpy as np
+    from itkwasm import TransformParameterizations, FloatTypes
+
+    from itkwasm_transform_io import hdf5_read_transform_async, hdf5_write_transform_async
+
+    def write_input_data_to_fs(input_data, filename):
+        with open(filename, 'wb') as fp:
+            fp.write(input_data[filename])
+
+    def verify_test_linear_transform(transform_list):
+        assert len(transform_list) == 1
+        transform = transform_list[0]
+        assert transform.transformType.transformParameterization == TransformParameterizations.Affine
+        assert transform.transformType.parametersValueType == FloatTypes.Float64
+        assert transform.numberOfParameters == 12
+        assert transform.numberOfFixedParameters == 3
+        np.testing.assert_allclose(transform.fixedParameters, np.array([0.0, 0.0, 0.0]))
+        np.testing.assert_allclose(transform.parameters, np.array([
+        0.65631490118447, 0.5806583745824385, -0.4817536741017158,
+        -0.7407986817430222, 0.37486398378429736, -0.5573995934598175,
+        -0.14306664045479867, 0.7227121458012518, 0.676179776908723,
+        -65.99999999999997, 69.00000000000004, 32.000000000000036]))
+
+    test_file_path = 'LinearTransform.h5'
+    write_input_data_to_fs(input_data, test_file_path)
+
+    assert Path(test_file_path).exists()
+
+    could_read, transform = await hdf5_read_transform_async(test_file_path)
+    assert could_read
+    verify_test_linear_transform(transform)
+
+    test_output_file_path = 'out-LinearTransform.h5'
+
+    use_compression = False
+    could_write = await hdf5_write_transform_async(transform, test_output_file_path, use_compression)
+    assert could_write
+
+    could_read, transform = await hdf5_read_transform_async(test_output_file_path)
+    assert could_read
+    verify_test_linear_transform(transform)