Merge pull request InsightSoftwareConsortium#1134 from thewtex/python…

…-cache-dir

feat(python): support ITKWASM_CACHE_DIR for cache directory

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

@@ -1,9 +1,9 @@
 """itkwasm: Python interface to itk-wasm WebAssembly modules."""
 
-__version__ = "1.0b171"
+__version__ = "1.0b175"
 
 from .interface_types import InterfaceTypes
-from .image import Image, ImageType
+from .image import Image, ImageType, ImageRegion
 from .pointset import PointSet, PointSetType
 from .mesh import Mesh, MeshType
 from .polydata import PolyData, PolyDataType
@@ -21,36 +21,41 @@
 from .environment_dispatch import environment_dispatch, function_factory
 from .cast_image import cast_image
 from .image_from_array import image_from_array
-from .to_numpy_array import array_like_to_numpy_array, array_like_to_bytes, buffer_to_numpy_array
+from .to_numpy_array import (
+    array_like_to_numpy_array,
+    array_like_to_bytes,
+    buffer_to_numpy_array,
+)
 from .to_cupy_array import array_like_to_cupy_array
 
 __all__ = [
-  "InterfaceTypes",
-  "Pipeline",
-  "PipelineInput",
-  "PipelineOutput",
-  "Image",
-  "ImageType",
-  "PointSet",
-  "PointSetType",
-  "Mesh",
-  "MeshType",
-  "PolyData",
-  "PolyDataType",
-  "BinaryFile",
-  "BinaryStream",
-  "TextFile",
-  "TextStream",
-  "JsonCompatible",
-  "FloatTypes",
-  "IntTypes",
-  "PixelTypes",
-  "environment_dispatch",
-  "function_factory",
-  "cast_image",
-  "image_from_array",
-  "array_like_to_numpy_array",
-  "array_like_to_bytes",
-  "array_like_to_cupy_array",
-  "buffer_to_numpy_array",
-  ]
+    "InterfaceTypes",
+    "Pipeline",
+    "PipelineInput",
+    "PipelineOutput",
+    "Image",
+    "ImageType",
+    "ImageRegion",
+    "PointSet",
+    "PointSetType",
+    "Mesh",
+    "MeshType",
+    "PolyData",
+    "PolyDataType",
+    "BinaryFile",
+    "BinaryStream",
+    "TextFile",
+    "TextStream",
+    "JsonCompatible",
+    "FloatTypes",
+    "IntTypes",
+    "PixelTypes",
+    "environment_dispatch",
+    "function_factory",
+    "cast_image",
+    "image_from_array",
+    "array_like_to_numpy_array",
+    "array_like_to_bytes",
+    "array_like_to_cupy_array",
+    "buffer_to_numpy_array",
+]

packages/core/python/itkwasm/itkwasm/binary_file.py

@@ -1,6 +1,7 @@
 from dataclasses import dataclass
 from pathlib import PurePosixPath
 
+
 @dataclass
 class BinaryFile:
-    path: PurePosixPath
+    path: PurePosixPath

packages/core/python/itkwasm/itkwasm/binary_stream.py

@@ -1,5 +1,6 @@
 from dataclasses import dataclass
 
+
 @dataclass
 class BinaryStream:
-    data: bytes
+    data: bytes

packages/core/python/itkwasm/itkwasm/cast_image.py

@@ -9,9 +9,12 @@
 from .int_types import IntTypes
 from .float_types import FloatTypes
 
-def cast_image(input_image: Image,
-               pixel_type: Optional[PixelTypes]=None,
-               component_type: Optional[Union[IntTypes, FloatTypes]]=None) -> Image:
+
+def cast_image(
+    input_image: Image,
+    pixel_type: Optional[PixelTypes] = None,
+    component_type: Optional[Union[IntTypes, FloatTypes]] = None,
+) -> Image:
     """Cast an image to another pixel type and / or component type.
 
     :param input_image: Image to be cast.
@@ -72,6 +75,6 @@ def cast_image(input_image: Image,
             elif component_type == FloatTypes.Float64:
                 output_image.data = input_image.data.astype(np.float64)
             else:
-                raise ValueError('Unsupported component type')
+                raise ValueError("Unsupported component type")
 
     return output_image

packages/core/python/itkwasm/itkwasm/environment_dispatch.py

@@ -2,18 +2,20 @@
 import sys
 import importlib
 import sys
+
 if sys.version_info < (3, 10):
     from importlib_metadata import entry_points
 else:
     from importlib.metadata import entry_points
 
+
 class FunctionFactory:
     def __init__(self):
         self._registered: Dict[Tuple[str, str], Set[Callable]] = {}
         self._priorities: Dict[Callable, int] = {}
         self._has_entry_point_lookup: Set[Tuple[str, str]] = set()
 
-    def register(self, interface_package: str, func_name: str, func: Callable, priority: int=1)-> None:
+    def register(self, interface_package: str, func_name: str, func: Callable, priority: int = 1) -> None:
         key = (interface_package, func_name)
         registered = self._registered.get(key, set())
         registered.add(func)
@@ -23,9 +25,9 @@ def register(self, interface_package: str, func_name: str, func: Callable, prior
     def lookup(self, interface_package: str, func_name: str) -> Optional[Set[Callable]]:
         key = (interface_package, func_name)
         if not key in self._has_entry_point_lookup:
-            discovered_funcs = entry_points(group=f'{interface_package}.{func_name}')
+            discovered_funcs = entry_points(group=f"{interface_package}.{func_name}")
             for ep in discovered_funcs:
-                priority = ep.name.partition('.priority.')[2]
+                priority = ep.name.partition(".priority.")[2]
                 if priority:
                     priority = int(priority)
                 else:
@@ -40,17 +42,20 @@ def highest_priority(self, interface_package: str, func_name: str) -> Optional[C
         registered = self.lookup(interface_package, func_name)
         if registered is None:
             return None
-        highest = max(self._registered[(interface_package, func_name)], key=lambda x: self._priorities[x])
+        highest = max(
+            self._registered[(interface_package, func_name)],
+            key=lambda x: self._priorities[x],
+        )
         if self._priorities[highest] < 1:
             return None
         return highest
 
-    def set_priority(self, func: Callable, priority: int)-> None:
+    def set_priority(self, func: Callable, priority: int) -> None:
         if func not in self._priorities:
             raise ValueError(f"Function {func} has not been registered")
         self._priorities[func] = priority
 
-    def get_priority(self, func: Callable)-> int:
+    def get_priority(self, func: Callable) -> int:
         if func not in self._priorities:
             raise ValueError(f"Function {func} has not been registered")
         return self._priorities[func]
@@ -61,22 +66,24 @@ def disable(self, interface_package: str, func_name: str):
         for func in registered:
             self._priorities[func] = -1
 
+
 function_factory = FunctionFactory()
 
+
 def environment_dispatch(interface_package: str, func_name: str) -> Callable:
     factory_func = function_factory.highest_priority(interface_package, func_name)
     if factory_func is not None:
         return factory_func
 
     if sys.platform != "emscripten":
-        if func_name.endswith('_async'):
-            raise ValueError('async function are only implemented for emscripten')
+        if func_name.endswith("_async"):
+            raise ValueError("async function are only implemented for emscripten")
         package = f"{interface_package}_wasi"
     else:
-        if not func_name.endswith('_async'):
-            raise ValueError('emscripten only implements the _async version of this function')
+        if not func_name.endswith("_async"):
+            raise ValueError("emscripten only implements the _async version of this function")
         package = f"{interface_package}_emscripten"
     mod = importlib.import_module(package)
     func = getattr(mod, func_name)
 
-    return func
+    return func

packages/core/python/itkwasm/itkwasm/float_types.py

@@ -1,12 +1,13 @@
 from enum import Enum
 
+
 class FloatTypes(str, Enum):
-    Float32 = 'float32'
-    Float64 = 'float64'
-    SpacePrecisionType = 'float64'
+    Float32 = "float32"
+    Float64 = "float64"
+    SpacePrecisionType = "float64"
 
     def __str__(self):
         return str(self.value)
 
     def __repr__(self):
-        return f'"{str(self.value)}"'
+        return f'"{str(self.value)}"'

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

@@ -12,40 +12,65 @@
 from .float_types import FloatTypes
 from .pixel_types import PixelTypes
 
+
 @dataclass
 class ImageType:
     dimension: int = 2
     componentType: Union[IntTypes, FloatTypes] = IntTypes.UInt8
     pixelType: PixelTypes = PixelTypes.Scalar
     components: int = 1
 
+
 def _default_direction() -> ArrayLike:
     return np.empty((0,), np.float64)
 
+
+@dataclass
+class ImageRegion:
+    index: Sequence[int] = field(default_factory=list)
+    size: Sequence[int] = field(default_factory=list)
+
+
 @dataclass
 class Image:
     imageType: Union[ImageType, Dict] = field(default_factory=ImageType)
-    name: str = 'Image'
+    name: str = "Image"
     origin: Sequence[float] = field(default_factory=list)
     spacing: Sequence[float] = field(default_factory=list)
     direction: ArrayLike = field(default_factory=_default_direction)
     size: Sequence[int] = field(default_factory=list)
     metadata: Dict = field(default_factory=dict)
     data: Optional[ArrayLike] = None
+    bufferedRegion: Optional[ImageRegion] = None
 
     def __post_init__(self):
         if isinstance(self.imageType, dict):
             self.imageType = ImageType(**self.imageType)
 
         dimension = self.imageType.dimension
         if len(self.origin) == 0:
-            self.origin += [0.0,] * dimension
+            self.origin += [
+                0.0,
+            ] * dimension
 
         if len(self.spacing) == 0:
-            self.spacing += [1.0,] * dimension
+            self.spacing += [
+                1.0,
+            ] * dimension
 
         if len(self.direction) == 0:
             self.direction = np.eye(dimension).astype(np.float64)
 
         if len(self.size) == 0:
-            self.size += [1,] * dimension
+            self.size += [
+                1,
+            ] * dimension
+
+        if self.bufferedRegion is None:
+            self.bufferedRegion = ImageRegion(
+                index=[
+                    0,
+                ]
+                * dimension,
+                size=self.size,
+            )

packages/core/python/itkwasm/itkwasm/image_from_array.py

@@ -1,4 +1,5 @@
 from typing import Optional
+
 try:
     from numpy.typing import ArrayLike
 except ImportError:
@@ -9,6 +10,7 @@
 
 from .pixel_types import PixelTypes
 
+
 def image_from_array(arr, is_vector: bool = False, image_type: Optional[ImageType] = None) -> Image:
     """Convert a numpy array-like to an itkwasm Image.
 
@@ -33,7 +35,7 @@ def image_from_array(arr, is_vector: bool = False, image_type: Optional[ImageTyp
         image_type = ImageType(
             dimension=dimension,
             componentType=_dtype_to_component_type(arr.dtype),
-            pixelType=PixelTypes.Scalar if not is_vector else PixelTypes.VariableLengthVector,
+            pixelType=(PixelTypes.Scalar if not is_vector else PixelTypes.VariableLengthVector),
             components=arr.shape[-1] if is_vector else 1,
         )
 

packages/core/python/itkwasm/itkwasm/int_types.py

@@ -1,19 +1,20 @@
 from enum import Enum
 
+
 class IntTypes(str, Enum):
-    Int8 = 'int8'
-    UInt8 = 'uint8'
-    Int16 = 'int16'
-    UInt16 = 'uint16'
-    Int32 = 'int32'
-    UInt32 = 'uint32'
-    Int64 = 'int64'
-    UInt64 = 'uint64'
+    Int8 = "int8"
+    UInt8 = "uint8"
+    Int16 = "int16"
+    UInt16 = "uint16"
+    Int32 = "int32"
+    UInt32 = "uint32"
+    Int64 = "int64"
+    UInt64 = "uint64"
 
-    SizeValueType = 'uint64'
-    IdentifierType = 'uint64'
-    IndexValueType = 'int64'
-    OffsetValueType = 'int64'
+    SizeValueType = "uint64"
+    IdentifierType = "uint64"
+    IndexValueType = "int64"
+    OffsetValueType = "int64"
 
     def __str__(self):
         return str(self.value)

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

@@ -1,11 +1,12 @@
 from enum import Enum
 
+
 class InterfaceTypes(Enum):
-    TextFile = 'InterfaceTextFile'
-    BinaryFile = 'InterfaceBinaryFile'
-    TextStream = 'InterfaceTextStream'
-    BinaryStream = 'InterfaceBinaryStream'
-    Image = 'InterfaceImage'
-    Mesh = 'InterfaceMesh'
-    PolyData = 'InterfacePolyData'
-    JsonCompatible = 'InterfaceJsonCompatible'
+    TextFile = "InterfaceTextFile"
+    BinaryFile = "InterfaceBinaryFile"
+    TextStream = "InterfaceTextStream"
+    BinaryStream = "InterfaceBinaryStream"
+    Image = "InterfaceImage"
+    Mesh = "InterfaceMesh"
+    PolyData = "InterfacePolyData"
+    JsonCompatible = "InterfaceJsonCompatible"

packages/core/python/itkwasm/itkwasm/json_compatible.py

@@ -1,4 +1,3 @@
 from typing import Dict, Union, List
 
-JsonCompatible = Union[Dict[str, "JsonCompatible"], None, bool, str, int,
-        float, List["JsonCompatible"]]
+JsonCompatible = Union[Dict[str, "JsonCompatible"], None, bool, str, int, float, List["JsonCompatible"]]