Merge pull request #1277 from thewtex/transform-io-python

transform io python

.github/workflows/python-wasm.yml

@@ -25,7 +25,7 @@ jobs:
       matrix:
         os: [ubuntu-22.04, windows-2022, macos-14]
         python-minor-version: [11, 12]
-        package: [compress-stringify, compare-images, dicom, mesh-io, image-io, downsample]
+        package: [compress-stringify, compare-images, dicom, mesh-io, image-io, transform-io, downsample]
 
     steps:
       - name: Checkout

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

@@ -1,6 +1,6 @@
 """itkwasm: Python interface to itk-wasm WebAssembly modules."""
 
-__version__ = "1.0b180"
+__version__ = "1.0b185"
 
 from .interface_types import InterfaceTypes
 from .image import Image, ImageType, ImageRegion

packages/core/python/itkwasm/itkwasm/interface_types.py

@@ -9,5 +9,5 @@ class InterfaceTypes(str, Enum):
     Mesh = "Mesh"
     PointSet = "PointSet"
     PolyData = "PolyData"
-    Transform = "Transform"
+    TransformList = "TransformList"
     JsonCompatible = "JsonCompatible"

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

@@ -22,6 +22,7 @@
 from .binary_file import BinaryFile
 from .image import Image
 from .mesh import Mesh
+from .transform import Transform
 from .point_set import PointSet
 from .polydata import PolyData
 from .json_compatible import JsonCompatible
@@ -45,6 +46,8 @@
         WasiConfig,
         Linker,
         WasmtimeError,
+        DirPerms,
+        FilePerms
     )
 
     # Get the value of the ITKWASM_CACHE_DIR environment variable
@@ -83,7 +86,7 @@ def __init__(
         wasi_config.argv = args
 
         for preopen in preopen_directories:
-            wasi_config.preopen_dir(preopen, preopen)
+            wasi_config.preopen_dir(preopen, preopen, DirPerms.READ_WRITE, FilePerms.READ_WRITE)
 
         store.set_wasi(wasi_config)
 
@@ -299,6 +302,34 @@ def run(
                     "pointData": f"data:application/vnd.itk.address,0:{point_data_ptr}",
                 }
                 ri.set_input_json(point_set_json, index)
+            elif input_.type == InterfaceTypes.TransformList:
+                transform_list = input_.data
+                transform_list_json = []
+                for idx, transform in enumerate(transform_list):
+                    if transform.numberOfFixedParameters:
+                        fpv = array_like_to_bytes(transform.fixedParameters)
+                    else:
+                        fpv = bytes([])
+                    fixed_parameters_ptr = ri.set_input_array(fpv, index, idx * 2)
+                    fixed_parameters  = f"data:application/vnd.itk.address,0:{fixed_parameters_ptr}"
+                    if transform.numberOfParameters:
+                        pv = array_like_to_bytes(transform.parameters)
+                    else:
+                        pv = bytes([])
+                    parameters_ptr = ri.set_input_array(pv, index, idx * 2 + 1)
+                    parameters = f"data:application/vnd.itk.address,0:{parameters_ptr}"
+                    transform_json = {
+                        "transformType": asdict(transform.transformType),
+                        "numberOfFixedParameters": transform.numberOfFixedParameters,
+                        "numberOfParameters": transform.numberOfParameters,
+                        "name": transform.name,
+                        "inputSpaceName": transform.inputSpaceName,
+                        "outputSpaceName": transform.outputSpaceName,
+                        "fixedParameters": fixed_parameters,
+                        "parameters": parameters,
+                    }
+                    transform_list_json.append(transform_json)
+                ri.set_input_json(transform_list_json, index)
             elif input_.type == InterfaceTypes.PolyData:
                 polydata = input_.data
                 if polydata.numberOfPoints:
@@ -489,6 +520,27 @@ def run(
                         point_set.pointData = buffer_to_numpy_array(point_set.pointSetType.pointPixelComponentType, bytes([]))
 
                     output_data = PipelineOutput(InterfaceTypes.PointSet, point_set)
+                elif output.type == InterfaceTypes.TransformList:
+                    transform_list_json = ri.get_output_json(index)
+                    transform_list = []
+                    for idx, transform_json in enumerate(transform_list_json):
+                        transform = Transform(**transform_json)
+                        if transform.numberOfFixedParameters > 0:
+                            data_ptr = ri.get_output_array_address(0, index, idx * 2)
+                            data_size = ri.get_output_array_size(0, index, idx * 2)
+                            transform.fixedParameters = buffer_to_numpy_array(
+                                transform.transformType.parametersValueType,
+                                ri.wasmtime_lift(data_ptr, data_size),
+                            )
+                        if transform.numberOfParameters > 0:
+                            data_ptr = ri.get_output_array_address(0, index, idx * 2 + 1)
+                            data_size = ri.get_output_array_size(0, index, idx * 2 + 1)
+                            transform.parameters = buffer_to_numpy_array(
+                                transform.transformType.parametersValueType,
+                                ri.wasmtime_lift(data_ptr, data_size),
+                            )
+                        transform_list.append(transform)
+                    output_data = PipelineOutput(InterfaceTypes.TransformList, transform_list)
                 elif output.type == InterfaceTypes.PolyData:
                     polydata_json = ri.get_output_json(index)
                     polydata = PolyData(**polydata_json)

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

@@ -5,6 +5,7 @@
 from .point_set import PointSet, PointSetType
 from .mesh import Mesh, MeshType
 from .polydata import PolyData, PolyDataType
+from .transform import Transform, TransformType
 from .binary_file import BinaryFile
 from .binary_stream import BinaryStream
 from .text_file import TextFile
@@ -147,6 +148,20 @@ def to_py(js_proxy):
         if polydata_dict["cellData"] is not None:
             polydata_dict["cellData"] = buffer_to_numpy_array(cell_pixel_component_type, polydata_dict["cellData"])
         return PolyData(**polydata_dict)
+    elif hasattr(js_proxy, "transformType"):
+        transform_dict = js_proxy.to_py()
+        transform_type = TransformType(**transform_dict["transformType"])
+        transform_dict["transformType"] = transform_type
+        parameters_value_type = transform_type.parametersValueType
+        if transform_dict["fixedParameters"] is not None:
+            transform_dict["fixedParameters"] = buffer_to_numpy_array(
+                parameters_value_type, transform_dict["fixedParameters"]
+            )
+        if transform_dict["parameters"] is not None:
+            transform_dict["parameters"] = buffer_to_numpy_array(
+                parameters_value_type, transform_dict["parameters"]
+            )
+        return Transform(**transform_dict)
     elif hasattr(js_proxy, "path") and hasattr(js_proxy, "data") and isinstance(js_proxy.data, str):
         with open(js_proxy.path, "w") as fp:
             fp.write(js_proxy.data)
@@ -222,6 +237,13 @@ def to_js(py, **kwargs):
         if polydata_dict["cellData"] is not None:
             polydata_dict["cellData"] = polydata_dict["cellData"].ravel()
         return pyodide.ffi.to_js(polydata_dict, dict_converter=js.Object.fromEntries)
+    elif isinstance(py, Transform):
+        transform_dict = asdict(py)
+        if transform_dict["fixedParameters"] is not None:
+            transform_dict["fixedParameters"] = transform_dict["fixedParameters"].ravel()
+        if transform_dict["parameters"] is not None:
+            transform_dict["parameters"] = transform_dict["parameters"].ravel()
+        return pyodide.ffi.to_js(transform_dict, dict_converter=js.Object.fromEntries)
     elif isinstance(py, TextStream):
         text_stream_dict = asdict(py)
         return pyodide.ffi.to_js(text_stream_dict, dict_converter=js.Object.fromEntries)

packages/core/python/itkwasm/itkwasm/transform.py

@@ -8,6 +8,8 @@
     from numpy import ndarray as ArrayLike
 import numpy as np
 
+from .float_types import FloatTypes
+
 class TransformParameterizations(str, Enum):
     Composite = "Composite"
     Identity = "Identity"
@@ -40,9 +42,10 @@ class TransformParameterizations(str, Enum):
 
 @dataclass
 class TransformType:
+    transformParameterization: TransformParameterizations = TransformParameterizations.Identity
+    parametersValueType: FloatTypes = FloatTypes.Float64
     inputDimension: int = 3
     outputDimension: int = 3
-    transformParameterization: TransformParameterizations = TransformParameterizations.Identity
 
 @dataclass
 class Transform: