feat(Python): Add Pyodide Image support

packages/core/python/itkwasm/README.md

@@ -1,3 +1,19 @@
 # itkwasm
 
 Python interface to [itk-wasm](https://wasm.itk.org) WebAssembly modules.
+
+## Development
+
+Thank you for contributing a pull request!
+
+**Welcome to the ITK community!**
+
+We are glad you are here and appreciate your contribution. Please keep in mind our [community participation guidelines](https://github.com/InsightSoftwareConsortium/ITK/blob/main/CODE_OF_CONDUCT.md).
+
+```
+git clone https://github.com/InsightSoftwareConsortium/itk-wasm
+cd itk-wasm/packages/core/python/itkwasm
+pip install hatch
+hatch run download-pyodide
+hatch run test
+```

packages/core/python/itkwasm/itkwasm/__init__.py

@@ -18,7 +18,6 @@
 from .int_types import IntTypes
 from .pixel_types import PixelTypes
 from .environment_dispatch import environment_dispatch, function_factory
-from .js_package_config import JsPackageConfig
 
 __all__ = [
   "InterfaceTypes",
@@ -42,5 +41,4 @@
   "PixelTypes",
   "environment_dispatch",
   "function_factory",
-  "JsPackageConfig",
-]
+  ]

packages/core/python/itkwasm/itkwasm/_to_numpy_array.py

@@ -0,0 +1,28 @@
+import numpy as np
+
+from .int_types import IntTypes
+from .float_types import FloatTypes
+
+def _to_numpy_array(component_type, buf):
+    if component_type == IntTypes.UInt8:
+        return np.frombuffer(buf, dtype=np.uint8)
+    elif component_type == IntTypes.Int8:
+        return np.frombuffer(buf, dtype=np.int8)
+    elif component_type == IntTypes.UInt16:
+        return np.frombuffer(buf, dtype=np.uint16)
+    elif component_type == IntTypes.Int16:
+        return np.frombuffer(buf, dtype=np.int16)
+    elif component_type == IntTypes.UInt32:
+        return np.frombuffer(buf, dtype=np.uint32)
+    elif component_type == IntTypes.Int32:
+        return np.frombuffer(buf, dtype=np.int32)
+    elif component_type == IntTypes.UInt64:
+        return np.frombuffer(buf, dtype=np.uint64)
+    elif component_type == IntTypes.Int64:
+        return np.frombuffer(buf, dtype=np.int64)
+    elif component_type == FloatTypes.Float32:
+        return np.frombuffer(buf, dtype=np.float32)
+    elif component_type == FloatTypes.Float64:
+        return np.frombuffer(buf, dtype=np.float64)
+    else:
+        raise ValueError('Unsupported component type')

packages/core/python/itkwasm/itkwasm/image.py

@@ -20,7 +20,7 @@ class ImageType:
     components: int = 1
 
 def _default_direction() -> ArrayLike:
-    return np.empty((0,), np.float32)
+    return np.empty((0,), np.float64)
 
 @dataclass
 class Image:
@@ -45,7 +45,7 @@ def __post_init__(self):
             self.spacing += [1.0,] * dimension
 
         if len(self.direction) == 0:
-            self.direction = np.eye(dimension).astype(np.float32).ravel()
+            self.direction = np.eye(dimension).astype(np.float64)
 
         if len(self.size) == 0:
             self.size += [1,] * dimension

packages/core/python/itkwasm/itkwasm/pipeline.py

@@ -19,35 +19,11 @@
 from .polydata import PolyData
 from .int_types import IntTypes
 from .float_types import FloatTypes
+from ._to_numpy_array import _to_numpy_array
 
 if sys.platform != "emscripten":
     from wasmtime import Config, Store, Engine, Module, WasiConfig, Linker
 
-def _to_numpy_array(component_type, buf):
-    if component_type == IntTypes.UInt8:
-        return np.frombuffer(buf, dtype=np.uint8)
-    elif component_type == IntTypes.Int8:
-        return np.frombuffer(buf, dtype=np.int8)
-    elif component_type == IntTypes.UInt16:
-        return np.frombuffer(buf, dtype=np.uint16)
-    elif component_type == IntTypes.Int16:
-        return np.frombuffer(buf, dtype=np.int16)
-    elif component_type == IntTypes.UInt32:
-        return np.frombuffer(buf, dtype=np.uint32)
-    elif component_type == IntTypes.Int32:
-        return np.frombuffer(buf, dtype=np.int32)
-    elif component_type == IntTypes.UInt64:
-        return np.frombuffer(buf, dtype=np.uint64)
-    elif component_type == IntTypes.Int64:
-        return np.frombuffer(buf, dtype=np.int64)
-    elif component_type == FloatTypes.Float32:
-        return np.frombuffer(buf, dtype=np.float32)
-    elif component_type == FloatTypes.Float64:
-        return np.frombuffer(buf, dtype=np.float64)
-    else:
-        raise ValueError('Unsupported component type')
-
-
 class Pipeline:
     """Run an itk-wasm WASI pipeline."""
 

packages/core/python/itkwasm/itkwasm/pyodide.py

@@ -0,0 +1,83 @@
+from dataclasses import dataclass, asdict
+from typing import Optional
+
+from .image import Image, ImageType
+from .pointset import PointSet, PointSetType
+from .mesh import Mesh, MeshType
+from .polydata import PolyData, PolyDataType
+from .binary_file import BinaryFile
+from .binary_stream import BinaryStream
+from .text_file import TextFile
+from .text_stream import TextStream
+from .float_types import FloatTypes
+from .int_types import IntTypes
+from .pixel_types import PixelTypes
+from ._to_numpy_array import _to_numpy_array
+
+@dataclass
+class JsPackageConfig:
+    module_url: str
+    pipelines_base_url: Optional[str] = None
+    pipeline_worker_url: Optional[str] = None
+
+class JsPackage:
+    def __init__(self, config: JsPackageConfig):
+        self._config = config
+        self._js_module = None
+
+    @property
+    def config(self):
+        return self._config
+
+    @config.setter
+    def config(self, value):
+        self._config = value
+
+    @property
+    async def js_module(self):
+        if self._js_module is not None:
+            return self._js_module
+        from pyodide.code import run_js
+        js_module = await run_js(f"import('{self._config.module_url}')")
+        if self._config.pipelines_base_url is not None:
+            js_module.setPipelinesBaseUrl(self._config.pipelines_base_url)
+        if self._config.pipeline_worker_url is not None:
+            js_module.setPipelineWorkerUrl(self._config.pipeline_worker_url)
+        self._js_module = js_module
+        return js_module
+
+class JsResources:
+    def __init__(self):
+        self._web_worker = None
+
+    @property
+    def web_worker(self):
+        return self._web_worker
+
+    @web_worker.setter
+    def web_worker(self, value):
+        self._web_worker = value
+
+js_resources = JsResources()
+
+def to_py(js_proxy):
+    import pyodide
+    if hasattr(js_proxy, "imageType"):
+        image_dict = js_proxy.to_py()
+        image_type = image_dict['imageType']
+        dimension = image_type['dimension']
+        component_type = image_type['componentType']
+        image_dict['direction'] = _to_numpy_array(str(FloatTypes.Float64), image_dict['direction']).reshape((dimension, dimension))
+        image_dict['data'] = _to_numpy_array(component_type, image_dict['data']).reshape((dimension, dimension))
+        return Image(**image_dict)
+    return js_proxy.to_py()
+
+def to_js(py):
+    import pyodide
+    import js
+    if isinstance(py, Image):
+        image_dict = asdict(py)
+        image_dict['direction'] = image_dict['direction'].ravel()
+        image_dict['data'] = image_dict['data'].ravel()
+        return pyodide.ffi.to_js(image_dict, dict_converter=js.Object.fromEntries)
+    return py

packages/core/python/itkwasm/pyproject.toml

@@ -41,16 +41,29 @@ Home = "https://wasm.itk.org/"
 Source = "https://github.com/InsightSoftwareConsortium/itk-wasm"
 Issues = "https://github.com/InsightSoftwareConsortium/itk-wasm/issues"
 
-[project.optional-dependencies]
-test = [
+[tool.hatch.envs.default]
+dependencies = [
     "itk>=5.3.0",
     "pytest >=2.7.3",
+    "pytest-pyodide",
+]
+
+[tool.hatch.envs.default.scripts]
+test = [
+    "hatch build -t wheel",
+    "pytest --dist-dir=./dist --runtime=chrome -s",
+]
+download-pyodide = [
+  "wget -q https://github.com/pyodide/pyodide/releases/download/0.23.1/pyodide-0.23.1.tar.bz2 -O pyodide.tar.bz2",
+  "tar xjf pyodide.tar.bz2",
+  "rm -rf dist",
+  "mv pyodide dist",
 ]
 
 [tool.hatch.envs.docs]
 dependencies = [
-  "sphinx",
-  "pydata-sphinx-theme",
+    "sphinx",
+    "pydata-sphinx-theme",
 ]
 
 [tool.hatch.envs.docs.scripts]

packages/core/python/itkwasm/test/test_image.py

@@ -29,7 +29,7 @@ def test_image_defaults():
     assert image.origin[1] == 0.0
     assert image.spacing[0] == 1.0
     assert image.spacing[1] == 1.0
-    assert np.array_equal(image.direction, np.eye(2).astype(np.float32).ravel())
+    assert np.array_equal(image.direction, np.eye(2).astype(np.float32))
 
     assert image.size[0] == 1
     assert image.size[1] == 1

packages/core/python/itkwasm/test/test_js_package_config.py

@@ -1,6 +1,6 @@
 
 def test_itkwasm_js_package_config():
-  from itkwasm import JsPackageConfig
+  from itkwasm.pyodide import JsPackageConfig
   module_url = 'https://cdn.jsdelivr.net/npm/@itk-wasm/[email protected]/dist/bundles/compress-stringify.js'
   pipelines_base_url = 'https://cdn.jsdelivr.net/npm/@itk-wasm/[email protected]/dist/pipelines'
   pipeline_worker_url = 'https://cdn.jsdelivr.net/npm/@itk-wasm/[email protected]/dist/web-workers/pipeline.worker.js'

packages/core/python/itkwasm/test/test_pyodide.py

@@ -0,0 +1,59 @@
+from pytest_pyodide import run_in_pyodide
+import pytest
+
+from itkwasm import __version__ as test_package_version
+
+@pytest.fixture
+def package_wheel():
+    return f"itkwasm-{test_package_version}-py3-none-any.whl"
+
+@run_in_pyodide(packages=['micropip', 'numpy'])
+async def test_image_conversion(selenium, package_wheel):
+    import micropip
+    await micropip.install(package_wheel)
+
+    from itkwasm import Image
+    from itkwasm.pyodide import to_js, to_py
+    import numpy as np
+
+    image = Image()
+
+    assert image.imageType.dimension == 2
+    assert image.imageType.componentType == 'uint8'
+    assert image.imageType.pixelType == 'Scalar'
+    assert image.imageType.components == 1
+
+    assert image.name == "image"
+    assert image.origin[0] == 0.0
+    assert image.origin[1] == 0.0
+    assert image.spacing[0] == 1.0
+    assert image.spacing[1] == 1.0
+    assert np.array_equal(image.direction, np.eye(2).astype(np.float64))
+
+    assert image.size[0] == 1
+    assert image.size[1] == 1
+    image.size = [2, 2]
+
+    assert isinstance(image.metadata, dict)
+    assert image.data == None
+    image.data = np.arange(4, dtype=np.uint8).reshape((2,2))
+    image_js = to_js(image)
+
+    image_py = to_py(image_js)
+    assert image_py.imageType.dimension == 2
+    assert image_py.imageType.componentType == 'uint8'
+    assert image_py.imageType.pixelType == 'Scalar'
+    assert image_py.imageType.components == 1
+
+    assert image_py.name == "image"
+    assert image_py.origin[0] == 0.0
+    assert image_py.origin[1] == 0.0
+    assert image_py.spacing[0] == 1.0
+    assert image_py.spacing[1] == 1.0
+    assert np.array_equal(image_py.direction, np.eye(2).astype(np.float64))
+
+    assert image_py.size[0] == 2
+    assert image_py.size[1] == 2
+
+    assert isinstance(image_py.metadata, dict)
+    assert np.array_equal(image_py.data, np.arange(4, dtype=np.uint8).reshape((2,2)))