Merge pull request #1428 from thewtex/image-from-array-buffered-default

image from array buffered default

Author: thewtex

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

@@ -1,6 +1,6 @@
 """itkwasm: Python interface to itk-wasm WebAssembly modules."""
 
-__version__ = "1.0b191"
+__version__ = "1.0b193"
 
 from .interface_types import InterfaceTypes
 from .image import Image, ImageType, ImageRegion

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

@@ -34,11 +34,15 @@ class ImageRegion:
 @dataclass
 class Image:
     imageType: Union[ImageType, Dict] = field(default_factory=ImageType)
+
     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
@@ -67,10 +71,18 @@ def __post_init__(self):
             ] * dimension
 
         if self.bufferedRegion is None:
-            self.bufferedRegion = ImageRegion(
-                index=[
-                    0,
-                ]
-                * dimension,
-                size=self.size,
-            )
+            if self.data is not None:
+                self.bufferedRegion = ImageRegion(
+                    index=(0,) * dimension,
+                    size=self.data.shape[:dimension][::-1],
+                )
+            else:
+                self.bufferedRegion = ImageRegion(
+                    index=[
+                        0,
+                    ]
+                    * dimension,
+                    size=self.size,
+                )
+        elif isinstance(self.bufferedRegion, dict):
+            self.bufferedRegion = ImageRegion(**self.bufferedRegion)

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

@@ -5,7 +5,7 @@
 except ImportError:
     from numpy import ndarray as ArrayLike
 
-from .image import Image, ImageType
+from .image import Image, ImageType, ImageRegion
 from .to_numpy_array import _dtype_to_component_type
 
 from .pixel_types import PixelTypes
@@ -42,5 +42,9 @@ def image_from_array(arr, is_vector: bool = False, image_type: Optional[ImageTyp
     image = Image(imageType=image_type)
     image.size = arr.shape[:dimension][::-1]
     image.data = arr
+    image.bufferedRegion = ImageRegion(
+        index=(0,) * dimension,
+        size=image.size,
+    )
 
     return image

packages/core/python/itkwasm/pixi.lock

@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "itkwasm"
 description = "Python interface to itk-wasm WebAssembly (Wasm) modules."
-authors = [{name = "Matt McCormick", email = "matt@mmmccormick.com"}]
+authors = [{name = "Matt McCormick", email = "matt@fideus.io"}]
 readme = "README.md"
 license = {file = "LICENSE"}
 classifiers = [

packages/core/python/itkwasm/pyproject.toml

@@ -2,7 +2,7 @@
 
 import itk
 
-from itkwasm import Image
+from itkwasm import Image, ImageType
 from dataclasses import asdict
 import numpy as np
 
@@ -12,6 +12,10 @@ def test_image():
     itk_image = itk.imread(data, itk.UC)
     itk_image_dict = itk.dict_from_image(itk_image)
     itkwasm_image = Image(**itk_image_dict)
+    assert itkwasm_image.bufferedRegion.index[0] == 0
+    assert itkwasm_image.bufferedRegion.index[1] == 0
+    assert itkwasm_image.bufferedRegion.size[0] == 256
+    assert itkwasm_image.bufferedRegion.size[1] == 256
     itkwasm_image_dict = asdict(itkwasm_image)
     itk_image_roundtrip = itk.image_from_dict(itkwasm_image_dict)
     difference = np.sum(itk.comparison_image_filter(itk_image, itk_image_roundtrip))
@@ -38,3 +42,40 @@ def test_image_defaults():
 
     assert isinstance(image.metadata, dict)
     assert image.data == None
+
+def test_image_with_data():
+    """Test creating an Image with data."""
+    image_type = ImageType(
+        dimension=2,
+        componentType="uint8",
+        pixelType="Scalar",
+        components=1,
+    )
+    data = np.zeros((5, 6), dtype=np.uint8)
+
+    image = Image(
+        imageType=image_type,
+        data=data,
+    )
+
+    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
+
+    assert isinstance(image.metadata, dict)
+    assert np.array_equal(image.data, data)
+    assert image.bufferedRegion.index[0] == 0
+    assert image.bufferedRegion.index[1] == 0
+    assert image.bufferedRegion.size[0] == 6
+    assert image.bufferedRegion.size[1] == 5

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

@@ -50,3 +50,16 @@ def test_image_from_array_explicit():
     assert image.imageType.componentType == FloatTypes.Float32
     assert image.imageType.pixelType == PixelTypes.VariableLengthVector
     assert image.imageType.components == 3
+
+def test_image_from_array_buffered_region():
+    arr = np.random.rand(9, 9, 3)
+    image = image_from_array(arr, is_vector=True)
+    assert np.array_equal(arr, image.data)
+    assert image.imageType.dimension == 2
+    assert image.imageType.componentType == FloatTypes.Float64
+    assert image.imageType.pixelType == PixelTypes.VariableLengthVector
+    assert image.imageType.components == 3
+    assert image.bufferedRegion.index[0] == 0
+    assert image.bufferedRegion.index[1] == 0
+    assert image.bufferedRegion.size[0] == 9
+    assert image.bufferedRegion.size[1] == 9

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

@@ -1,6 +1,7 @@
 from dataclasses import asdict
 
 from itkwasm import PolyData
+import itkwasm
 
 
 def test_polydata():