Merge pull request #1111 from thewtex/transform-io

docs: add TransformList, Transform LinkML model

.github/workflows/cxx-python.yml

@@ -13,14 +13,17 @@ env:
 
 jobs:
   cxx-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/[email protected]
+    # itk-wasm branch
+    uses: thewtex/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@6868c9879405def5d7532e0437b57e78cbe0b6ea
     with:
       itk-module-deps: '[email protected]'
       ctest-options: '-E itkPipelineTest'
 
-  python-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/[email protected]
-    with:
-      itk-module-deps: 'InsightSoftwareConsortium/[email protected]'
-    secrets:
-      pypi_password: ${{ secrets.pypi_password }}
+  #python-build-workflow:
+    ## itk-wasm branch
+    #uses: thewtex/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@6868c9879405def5d7532e0437b57e78cbe0b6ea
+    #with:
+      #itk-module-deps: 'InsightSoftwareConsortium/[email protected]'
+      #manylinux-platforms: '["_2_28-x64","_2_28-aarch64"]'
+    #secrets:
+      #pypi_password: ${{ secrets.pypi_password }}

.gitignore

@@ -92,3 +92,5 @@ cypress/screenshots/
 cypress/videos/
 
 packages/core/typescript/itk-wasm/dist
+
+CMakePresets.json

CMakeLists.txt

@@ -9,27 +9,6 @@ endif()
 
 set(WebAssemblyInterface_LIBRARIES WebAssemblyInterface)
 
-option(BUILD_ITK_WASM_IO_MODULES "Build the itk-wasm ImageIO's and MeshIO's" OFF)
-if(BUILD_ITK_WASM_IO_MODULES)
-  set(WebAssemblyInterface_MeshIOModules
-    "ITKIOMeshBYU"
-    "ITKIOMeshFreeSurfer"
-    "ITKIOMeshOBJ"
-    "ITKIOMeshOFF"
-    "IOMeshSTL"
-    "IOMeshSWC"
-    "ITKIOMeshVTK"
-    CACHE STRING
-    "String delimited list of ITK mesh IO modules to support.")
-  set(meshios_ITKIOMeshBYU itkBYUMeshIO)
-  set(meshios_ITKIOMeshFreeSurfer itkFreeSurferAsciiMeshIO itkFreeSurferBinaryMeshIO)
-  set(meshios_ITKIOMeshVTK itkVTKPolyDataMeshIO)
-  set(meshios_ITKIOMeshOBJ itkOBJMeshIO)
-  set(meshios_ITKIOMeshOFF itkOFFMeshIO)
-  set(meshios_IOMeshSTL itkSTLMeshIO)
-  set(meshios_IOMeshSWC itkSWCMeshIO)
-endif()
-
 include(FetchContent)
 set(_itk_build_testing ${BUILD_TESTING})
 set(BUILD_TESTING OFF)
@@ -100,14 +79,23 @@ FetchContent_Declare(
 )
 
 set(glaze_GIT_REPOSITORY "https://github.com/stephenberry/glaze")
-# glaze v2.6.9
-set(glaze_GIT_TAG 6bcc20ce7eb59df60b94488a4f6be723731db00e)
+# glaze v2.9.3
+set(glaze_GIT_TAG fe49c8e1a057d11484e0bd88ffcbe60277e356fd)
 FetchContent_Declare(
   glaze
   GIT_REPOSITORY ${glaze_GIT_REPOSITORY}
   GIT_TAG        ${glaze_GIT_TAG}
   GIT_SHALLOW TRUE
 )
+if (MSVC)
+  string(REGEX MATCH "\/cl(.exe)?$" matched_cl ${CMAKE_CXX_COMPILER})
+  if (matched_cl)
+    # for a C++ standards compliant preprocessor, not needed for clang-cl
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Zc:preprocessor /permissive- /Zc:lambda")
+  endif()
+  # avoid warnings
+  set(CMAKE_CXX_STANDARD 23)
+endif()
 
 list(APPEND CMAKE_MODULE_PATH ${libcbor_SOURCE_DIR}/CMakeModules)
 FetchContent_MakeAvailable(rapidjson_lib cli11 rang libcbor cpp_base64 glaze)

ITKKWStyleOverwrite.txt

@@ -5,3 +5,4 @@ itkSupportInputImageTypesMemoryIOTest\.cxx Namespace Disable
 itkSupportInputMeshTypesTest\.cxx Namespace Disable
 itkSupportInputMeshTypesMemoryIOTest\.cxx Namespace Disable
 itkSupportInputPolyDataTypesTest\.cxx Namespace Disable
+itkFloatTypesJSON\.h Namespace Disable

include/itkFloatTypesJSON.h

@@ -0,0 +1,42 @@
+/*=========================================================================
+ *
+ *  Copyright NumFOCUS
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         https://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+#ifndef itkFloatTypesJSON_h
+#define itkFloatTypesJSON_h
+
+#include <vector>
+
+#include "glaze/glaze.hpp"
+
+namespace itk
+{
+  enum class JSONFloatTypesEnum
+  {
+    float32,
+    float64,
+  };
+} // end namespace itk
+
+template <>
+struct glz::meta<itk::JSONFloatTypesEnum> {
+  using enum itk::JSONFloatTypesEnum;
+  static constexpr auto value = glz::enumerate(float32,
+  float64
+  );
+};
+
+#endif // itkFloatTypesJSON_h

include/itkInputMeshIO.h

@@ -21,6 +21,7 @@
 #include "itkPipeline.h"
 #include "itkWasmMeshIOBase.h"
 #include "itkWasmMeshIO.h"
+#include "itkWasmIOCommon.h"
 
 #ifndef ITK_WASM_NO_MEMORY_IO
 #include "itkWasmExports.h"
@@ -87,15 +88,15 @@ bool lexical_cast(const std::string &input, InputMeshIO &inputMeshIO)
     const std::string pointsString( pointsJson.GetString() );
     const char * pointsPtr = reinterpret_cast< char * >( std::strtoull(pointsString.substr(35).c_str(), nullptr, 10) );
     WasmMeshIOBase::DataContainerType * pointsContainer = wasmMeshIOBase->GetPointsContainer();
-    SizeValueType numberOfBytes = wasmMeshIO->GetNumberOfPoints() * wasmMeshIO->GetPointDimension() * WasmMeshIO::ITKComponentSize( wasmMeshIO->GetPointComponentType() );
+    SizeValueType numberOfBytes = wasmMeshIO->GetNumberOfPoints() * wasmMeshIO->GetPointDimension() * ITKComponentSize( wasmMeshIO->GetPointComponentType() );
     pointsContainer->resize(numberOfBytes);
     pointsContainer->assign(pointsPtr, pointsPtr + numberOfBytes);
 
     const rapidjson::Value & cellsJson = document["cells"];
     const std::string cellsString( cellsJson.GetString() );
     const char * cellsPtr = reinterpret_cast< char * >( std::strtoull(cellsString.substr(35).c_str(), nullptr, 10) );
     WasmMeshIOBase::DataContainerType * cellsContainer = wasmMeshIOBase->GetCellsContainer();
-    numberOfBytes = static_cast< SizeValueType >( wasmMeshIO->GetCellBufferSize() * WasmMeshIO::ITKComponentSize( wasmMeshIO->GetCellComponentType() ));
+    numberOfBytes = static_cast< SizeValueType >( wasmMeshIO->GetCellBufferSize() * ITKComponentSize( wasmMeshIO->GetCellComponentType() ));
     cellsContainer->resize(numberOfBytes);
     cellsContainer->assign(cellsPtr, cellsPtr + numberOfBytes);
 
@@ -105,7 +106,7 @@ bool lexical_cast(const std::string &input, InputMeshIO &inputMeshIO)
     WasmMeshIOBase::DataContainerType * pointDataContainer = wasmMeshIOBase->GetPointDataContainer();
     numberOfBytes =
       static_cast< SizeValueType >(
-          wasmMeshIO->GetNumberOfPointPixels() * wasmMeshIO->GetNumberOfPointPixelComponents() * WasmMeshIO::ITKComponentSize( wasmMeshIO->GetPointPixelComponentType() )
+          wasmMeshIO->GetNumberOfPointPixels() * wasmMeshIO->GetNumberOfPointPixelComponents() * ITKComponentSize( wasmMeshIO->GetPointPixelComponentType() )
           );
     pointDataContainer->resize(numberOfBytes);
     pointDataContainer->assign(pointDataPtr, pointDataPtr + numberOfBytes);
@@ -116,7 +117,7 @@ bool lexical_cast(const std::string &input, InputMeshIO &inputMeshIO)
     WasmMeshIOBase::DataContainerType * cellDataContainer = wasmMeshIOBase->GetCellDataContainer();
     numberOfBytes =
       static_cast< SizeValueType >(
-          wasmMeshIO->GetNumberOfPointPixels() * wasmMeshIO->GetNumberOfPointPixelComponents() * WasmMeshIO::ITKComponentSize( wasmMeshIO->GetPointPixelComponentType() )
+          wasmMeshIO->GetNumberOfPointPixels() * wasmMeshIO->GetNumberOfPointPixelComponents() * ITKComponentSize( wasmMeshIO->GetPointPixelComponentType() )
           );
     cellDataContainer->resize(numberOfBytes);
     cellDataContainer->assign(cellDataPtr, cellDataPtr + numberOfBytes);