Merge pull request #1191 from thewtex/transform-io

transform io
InsightSoftwareConsortium · Aug 11, 2024 · 332bec1 · 332bec1
2 parents 598bf1c + e5d17e2
commit 332bec1
Show file tree

Hide file tree

Showing 149 changed files with 5,713 additions and 192 deletions.
diff --git a/ITKKWStyleOverwrite.txt b/ITKKWStyleOverwrite.txt
@@ -6,3 +6,4 @@ itkSupportInputMeshTypesTest\.cxx Namespace Disable
 itkSupportInputMeshTypesMemoryIOTest\.cxx Namespace Disable
 itkSupportInputPolyDataTypesTest\.cxx Namespace Disable
 itkFloatTypesJSON\.h Namespace Disable
+itkOutputTransformIO\.h Namespace Disable
diff --git a/docs/cxx/interface_types.md b/docs/cxx/interface_types.md
@@ -9,6 +9,7 @@ itk-wasm execution pipelines support the following [interface types](https://git
 - [Image](../typescript/interface_types/Image)
 - [Mesh](../typescript/interface_types/Mesh)
 - [PolyData](../typescript/interface_types/PolyData)
+- [Transform](../typescript/interface_types/Transform)
 - [JsonCompatible](../typescript/interface_types/JsonCompatible)
 
 These interfaces types are supported in the [Emscripten interface](../typescript/browser_pipelines), [WASI](https://wasi.dev/) embedding interfaces, and native or virtual [filesystem IO](../introduction/file_formats/index). They are intended to be forward-compatible with the [WebAssembly Component Model](https://github.com/WebAssembly/component-model).

diff --git a/include/itkTransformJSON.h b/include/itkTransformJSON.h
@@ -23,6 +23,7 @@
 #include <vector>
 
 #include "itkCompositeTransformIOHelper.h"
+#include "itkMetaDataDictionaryJSON.h"
 
 #include "glaze/glaze.hpp"
 
@@ -36,12 +37,13 @@ namespace itk
     Euler2D,
     Euler3D,
     Rigid2D,
+    Rigid3D,
     Rigid3DPerspective,
-    VersorRigid3D,
     Versor,
+    VersorRigid3D,
+    Scale,
     ScaleLogarithmic,
     ScaleSkewVersor3D,
-    Scale,
     Similarity2D,
     Similarity3D,
     QuaternionRigid,
@@ -52,11 +54,11 @@ namespace itk
     BSplineSmoothingOnUpdateDisplacementField,
     ConstantVelocityField,
     DisplacementField,
-    GaussianExponentialDiffeomorphic,
     GaussianSmoothingOnUpdateDisplacementField,
-    GaussianSmoothingOnUpdateTimeVaryingVelocityField,
-    TimeVaryingVelocityField,
+    GaussianExponentialDiffeomorphic,
     VelocityField,
+    TimeVaryingVelocityField,
+    GaussianSmoothingOnUpdateTimeVaryingVelocityField,
   };
 
   /** \class TransformTypeJSON
@@ -85,13 +87,15 @@ namespace itk
     uint64_t numberOfFixedParameters{ 0 };
     uint64_t numberOfParameters{ 0 };
 
-    std::string name { "transform" };
+    std::string name { "Transform" };
 
     std::string inputSpaceName;
     std::string outputSpaceName;
 
     std::string fixedParameters;
     std::string parameters;
+
+    MetadataJSON metadata;
   };
 
   /** \class TransformListJSON
@@ -166,6 +170,10 @@ auto transformListToTransformListJSON(std::list<typename TTransformBase::ConstPo
     {
       transformJSON.transformType.transformParameterization = JSONTransformParameterizationEnum::Rigid2D;
     }
+    else if (pString == "Rigid3DTransform")
+    {
+      transformJSON.transformType.transformParameterization = JSONTransformParameterizationEnum::Rigid3D;
+    }
     else if (pString == "Rigid3DPerspectiveTransform")
     {
       transformJSON.transformType.transformParameterization = JSONTransformParameterizationEnum::Rigid3DPerspective;
@@ -178,6 +186,10 @@ auto transformListToTransformListJSON(std::list<typename TTransformBase::ConstPo
     {
       transformJSON.transformType.transformParameterization = JSONTransformParameterizationEnum::Versor;
     }
+    else if (pString == "ScaleTransform")
+    {
+      transformJSON.transformType.transformParameterization = JSONTransformParameterizationEnum::Scale;
+    }
     else if (pString == "ScaleLogarithmicTransform")
     {
       transformJSON.transformType.transformParameterization = JSONTransformParameterizationEnum::ScaleLogarithmic;
@@ -186,10 +198,6 @@ auto transformListToTransformListJSON(std::list<typename TTransformBase::ConstPo
     {
       transformJSON.transformType.transformParameterization = JSONTransformParameterizationEnum::ScaleSkewVersor3D;
     }
-    else if (pString == "ScaleTransform")
-    {
-      transformJSON.transformType.transformParameterization = JSONTransformParameterizationEnum::Scale;
-    }
     else if (pString == "Similarity2DTransform")
     {
       transformJSON.transformType.transformParameterization = JSONTransformParameterizationEnum::Similarity2D;
@@ -315,6 +323,9 @@ auto transformListToTransformListJSON(std::list<typename TTransformBase::ConstPo
       transformJSON.parameters = "data:application/vnd.itk.path,data/" + std::to_string(count) + "/parameters.raw";
     }
 
+    auto dictionary = currentTransform->GetMetaDataDictionary();
+    metaDataDictionaryToJSON(dictionary, transformJSON.metadata);
+
     transformListJSON.push_back(transformJSON);
     ++count;
   }
@@ -327,33 +338,35 @@ auto transformListToTransformListJSON(std::list<typename TTransformBase::ConstPo
 template <>
 struct glz::meta<itk::JSONTransformParameterizationEnum> {
   using enum itk::JSONTransformParameterizationEnum;
-  static constexpr auto value = glz::enumerate(Identity,
-  Composite,
-  Translation,
-  Euler2D,
-  Euler3D,
-  Rigid2D,
-  Rigid3DPerspective,
-  VersorRigid3D,
-  Versor,
-  ScaleLogarithmic,
-  ScaleSkewVersor3D,
-  Scale,
-  Similarity2D,
-  Similarity3D,
-  QuaternionRigid,
-  Affine,
-  ScalableAffine,
-  AzimuthElevationToCartesian,
-  BSpline,
-  BSplineSmoothingOnUpdateDisplacementField,
-  ConstantVelocityField,
-  DisplacementField,
-  GaussianExponentialDiffeomorphic,
-  GaussianSmoothingOnUpdateDisplacementField,
-  GaussianSmoothingOnUpdateTimeVaryingVelocityField,
-  TimeVaryingVelocityField,
-  VelocityField
+  static constexpr auto value = glz::enumerate(
+    Composite,
+    Identity,
+    Translation,
+    Euler2D,
+    Euler3D,
+    Rigid2D,
+    Rigid3D,
+    Rigid3DPerspective,
+    Versor,
+    VersorRigid3D,
+    ScaleLogarithmic,
+    ScaleSkewVersor3D,
+    Scale,
+    Similarity2D,
+    Similarity3D,
+    QuaternionRigid,
+    Affine,
+    ScalableAffine,
+    AzimuthElevationToCartesian,
+    BSpline,
+    BSplineSmoothingOnUpdateDisplacementField,
+    ConstantVelocityField,
+    DisplacementField,
+    GaussianSmoothingOnUpdateDisplacementField,
+    GaussianExponentialDiffeomorphic,
+    VelocityField,
+    TimeVaryingVelocityField,
+    GaussianSmoothingOnUpdateTimeVaryingVelocityField
   );
 };
 

diff --git a/include/itkWasmImageToImageFilter.hxx b/include/itkWasmImageToImageFilter.hxx
@@ -206,14 +206,21 @@ WasmImageToImageFilter<TImage>
   RegionType bufferedRegion;
   RegionType largestRegion;
   using SizeType = typename ImageType::SizeType;
-  SizeType largestSize;
   SizeValueType totalSize = 1;
   for (unsigned int i = 0; i < Dimension; ++i)
   {
-    bufferedRegion.SetIndex(i, imageJSON.bufferedRegion.index[i]);
-    bufferedRegion.SetSize(i, imageJSON.bufferedRegion.size[i]);
+    if (imageJSON.bufferedRegion.size.size())
+    {
+      bufferedRegion.SetIndex(i, imageJSON.bufferedRegion.index[i]);
+      bufferedRegion.SetSize(i, imageJSON.bufferedRegion.size[i]);
+    }
+    else
+    {
+      bufferedRegion.SetIndex(i, 0);
+      bufferedRegion.SetSize(i, imageJSON.size[i]);
+    }
+    totalSize *= imageJSON.bufferedRegion.size[i];
     largestRegion.SetSize(i, imageJSON.size[i]);
-    totalSize *= largestSize[i];
   }
   filter->SetBufferedRegion(bufferedRegion);
   filter->SetLargestPossibleRegion(largestRegion);

diff --git a/include/itkWasmMeshIO.h b/include/itkWasmMeshIO.h
@@ -32,11 +32,11 @@ namespace itk
  * \brief Read and write the an itk::Mesh in a format for interfacing in WebAssembly (Wasm).
  *
  * This format is intended to facilitate data exchange in itk-wasm.
- * It reads and writes an itk-wasm Mesh object where TypedArrays are
+ * It reads and writes an ITK-Wasm Mesh object where TypedArrays are
  * replaced by binary files on the filesystem or in a CBOR file.
  *
  * The file extensions used are .iwm and .iwm.cbor.
- * 
+ *
  * \ingroup IOFilters
  * \ingroup WebAssemblyInterface
  */

diff --git a/include/itkWasmTransformIO.h b/include/itkWasmTransformIO.h
@@ -86,7 +86,7 @@ class ITK_TEMPLATE_EXPORT WasmTransformIOTemplate : public TransformIOBaseTempla
 #if !defined(ITK_WRAPPING_PARSER)
   /** Get the JSON representation of the mesh information. */
   auto
-  GetJSON() -> TransformListJSON;
+  GetJSON(bool inMemory=false) -> TransformListJSON;
 #endif
 
 protected:
@@ -95,7 +95,7 @@ class ITK_TEMPLATE_EXPORT WasmTransformIOTemplate : public TransformIOBaseTempla
   void
   PrintSelf(std::ostream & os, Indent indent) const override;
 
-  auto
+  virtual auto
   ReadTransformInformation() -> const TransformListJSON;
   void
   ReadFixedParameters(const TransformListJSON & json);
@@ -109,12 +109,8 @@ class ITK_TEMPLATE_EXPORT WasmTransformIOTemplate : public TransformIOBaseTempla
   void
   WriteParameters();
 
-  /** Reads in the transform information and populates the related buffers. */
-  void
-  ReadCBOR();
-  /** Writes the buffers into the CBOR item and the buffer out to disk. */
-  void
-  WriteCBOR();
+  void ReadCBOR(void * buffer = nullptr, unsigned char * cborBuffer = nullptr, size_t cborBufferLength = 0);
+  size_t WriteCBOR(const void * buffer = nullptr, unsigned char ** cborBuffer = nullptr, bool allocateCBORBuffer = false);
 
   cbor_item_t * m_CBORRoot{ nullptr };
 

diff --git a/include/itkWasmTransformToTransformFilter.hxx b/include/itkWasmTransformToTransformFilter.hxx
@@ -251,6 +251,9 @@ WasmTransformToTransformFilter<TTransform>
       transform->CopyInFixedParameters(fixedPtr, fixedPtr + transformJSON.numberOfFixedParameters);
       ParametersValueType * paramsPtr = reinterpret_cast< ParametersValueType * >( std::strtoull(transformJSON.parameters.substr(35).c_str(), nullptr, 10) );
       transform->CopyInParameters(paramsPtr, paramsPtr + transformJSON.numberOfParameters);
+
+      auto dictionary = transform->GetMetaDataDictionary();
+      jsonToMetaDataDictionary(transformJSON.metadata, dictionary);
     }
 
     ++count;

diff --git a/model/itk-wasm.yml b/model/itk-wasm.yml
@@ -644,12 +644,13 @@ enums:
       Euler2D:
       Euler3D:
       Rigid2D:
+      Rigid3D:
       Rigid3DPerspective:
-      VersorRigid3D:
       Versor:
+      VersorRigid3D:
+      Scale:
       ScaleLogarithmic:
       ScaleSkewVersor3D:
-      Scale:
       Similarity2D:
       Similarity3D:
       QuaternionRigid:
@@ -660,8 +661,8 @@ enums:
       BSplineSmoothingOnUpdateDisplacementField:
       ConstantVelocityField:
       DisplacementField:
-      GaussianExponentialDiffeomorphic:
       GaussianSmoothingOnUpdateDisplacementField:
-      GaussianSmoothingOnUpdateTimeVaryingVelocityField:
-      TimeVaryingVelocityField:
+      GaussianExponentialDiffeomorphic:
       VelocityField:
+      TimeVaryingVelocityField:
+      GaussianSmoothingOnUpdateTimeVaryingVelocityField:
diff --git a/packages/core/python/itkwasm/itkwasm/__init__.py b/packages/core/python/itkwasm/itkwasm/__init__.py
@@ -1,11 +1,12 @@
 """itkwasm: Python interface to itk-wasm WebAssembly modules."""
 
-__version__ = "1.0b175"
+__version__ = "1.0b178"
 
 from .interface_types import InterfaceTypes
 from .image import Image, ImageType, ImageRegion
 from .pointset import PointSet, PointSetType
 from .mesh import Mesh, MeshType
+from .transform import Transform, TransformType, TransformParameterizations
 from .polydata import PolyData, PolyDataType
 from .binary_file import BinaryFile
 from .binary_stream import BinaryStream
@@ -42,6 +43,9 @@
     "MeshType",
     "PolyData",
     "PolyDataType",
+    "Transform",
+    "TransformType",
+    "TransformParameterizations",
     "BinaryFile",
     "BinaryStream",
     "TextFile",

diff --git a/packages/core/python/itkwasm/itkwasm/interface_types.py b/packages/core/python/itkwasm/itkwasm/interface_types.py
@@ -1,12 +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"
+class InterfaceTypes(str, Enum):
+    TextFile = "TextFile"
+    BinaryFile = "BinaryFile"
+    TextStream = "TextStream"
+    BinaryStream = "BinaryStream"
+    Image = "Image"
+    Mesh = "Mesh"
+    PolyData = "PolyData"
+    Transform = "Transform"
+    JsonCompatible = "JsonCompatible"
diff --git a/packages/core/python/itkwasm/itkwasm/mesh.py b/packages/core/python/itkwasm/itkwasm/mesh.py
@@ -46,6 +46,8 @@ class Mesh:
     numberOfCellPixels: int = 0
     cellData: Optional[ArrayLike] = None
 
+    metadata: Dict = field(default_factory=dict)
+
     def __post_init__(self):
         if isinstance(self.meshType, dict):
             self.meshType = MeshType(**self.meshType)
diff --git a/packages/core/python/itkwasm/itkwasm/pointset.py b/packages/core/python/itkwasm/itkwasm/pointset.py
@@ -34,6 +34,8 @@ class PointSet:
     numberOfPointPixels: int = 0
     pointData: Optional[ArrayLike] = None
 
+    metadata: Dict = field(default_factory=dict)
+
     def __post_init__(self):
         if isinstance(self.pointSetType, dict):
             self.pointSetType = PointSetType(**self.pointSetType)