fix(run-pipeline-emscripten): fix reading composite transforms

The first item in a composite transform list does not have input arrays.

Author: thewtex

packages/core/typescript/itk-wasm/src/pipeline/internal/run-pipeline-emscripten.ts

@@ -22,7 +22,7 @@ const haveSharedArrayBuffer = typeof globalThis.SharedArrayBuffer === 'function'
 const encoder = new TextEncoder()
 const decoder = new TextDecoder('utf-8')
 
-function readFileSharedArray(
+function readFileSharedArray (
   emscriptenModule: PipelineEmscriptenModule,
   path: string
 ): Uint8Array {
@@ -42,7 +42,7 @@ function readFileSharedArray(
   return array
 }
 
-function memoryUint8SharedArray(
+function memoryUint8SharedArray (
   emscriptenModule: PipelineEmscriptenModule,
   byteOffset: number,
   length: number
@@ -63,7 +63,7 @@ function memoryUint8SharedArray(
   return array
 }
 
-function setPipelineModuleInputArray(
+function setPipelineModuleInputArray (
   emscriptenModule: PipelineEmscriptenModule,
   dataArray: TypedArray | null,
   inputIndex: number,
@@ -82,7 +82,7 @@ function setPipelineModuleInputArray(
   return dataPtr
 }
 
-function setPipelineModuleInputJSON(
+function setPipelineModuleInputJSON (
   emscriptenModule: PipelineEmscriptenModule,
   dataObject: object,
   inputIndex: number
@@ -98,13 +98,13 @@ function setPipelineModuleInputJSON(
   emscriptenModule.stringToUTF8(dataJSON, jsonPtr, length)
 }
 
-function getPipelineModuleOutputArray(
+function getPipelineModuleOutputArray (
   emscriptenModule: PipelineEmscriptenModule,
   outputIndex: number,
   subIndex: number,
   componentType:
-    | (typeof IntTypes)[keyof typeof IntTypes]
-    | (typeof FloatTypes)[keyof typeof FloatTypes]
+  | (typeof IntTypes)[keyof typeof IntTypes]
+  | (typeof FloatTypes)[keyof typeof FloatTypes]
 ): TypedArray | Float32Array | Uint32Array | null {
   const dataPtr = emscriptenModule.ccall(
     'itk_wasm_output_array_address',
@@ -123,7 +123,7 @@ function getPipelineModuleOutputArray(
   return data
 }
 
-function getPipelineModuleOutputJSON(
+function getPipelineModuleOutputJSON (
   emscriptenModule: PipelineEmscriptenModule,
   outputIndex: number
 ): object {
@@ -138,7 +138,7 @@ function getPipelineModuleOutputJSON(
   return dataObject
 }
 
-function runPipelineEmscripten(
+function runPipelineEmscripten (
   pipelineModule: PipelineEmscriptenModule,
   args: string[],
   outputs: PipelineOutput[] | null,
@@ -313,21 +313,34 @@ function runPipelineEmscripten(
         case InterfaceTypes.TransformList: {
           const transformList = input.data as TransformList
           const transformListJSON: any = []
-          transformList.forEach((transform, transformIndex) => {
-            const fixedParameterPtr = setPipelineModuleInputArray(
-              pipelineModule,
-              transform.fixedParameters,
-              index,
-              transformIndex * 2
-            )
-            const fixedParameters = `data:application/vnd.itk.address,0:${fixedParameterPtr}`
-            const parameterPtr = setPipelineModuleInputArray(
-              pipelineModule,
-              transform.parameters,
-              index,
-              transformIndex * 2 + 1
-            )
-            const parameters = `data:application/vnd.itk.address,0:${parameterPtr}`
+          let inputArrayIndex = 0
+          transformList.forEach((transform) => {
+            let fixedParameters = ''
+            let parameters = ''
+
+            // Skip setting input arrays for Composite transforms as they don't have array data
+            if (
+              transform.transformType.transformParameterization !== 'Composite'
+            ) {
+              const fixedParameterPtr = setPipelineModuleInputArray(
+                pipelineModule,
+                transform.fixedParameters,
+                index,
+                inputArrayIndex
+              )
+              fixedParameters = `data:application/vnd.itk.address,0:${fixedParameterPtr}`
+              inputArrayIndex += 1
+
+              const parameterPtr = setPipelineModuleInputArray(
+                pipelineModule,
+                transform.parameters,
+                index,
+                inputArrayIndex
+              )
+              parameters = `data:application/vnd.itk.address,0:${parameterPtr}`
+              inputArrayIndex += 1
+            }
+
             const transformJSON = {
               transformType: transform.transformType,
               numberOfFixedParameters: transform.numberOfFixedParameters,

packages/core/typescript/itk-wasm/test/node/pipeline/run-pipeline-node-test.js

@@ -145,6 +145,10 @@ function readCompositeTransform() {
 
     // Skip the composite transform (index 0) as it doesn't have separate data files
     if (transform.transformType.transformParameterization === 'Composite') {
+      // transform.fixedParameters = new Float64Array(0)
+      // transform.parameters = new Float32Array(0)
+      transform.fixedParameters = null
+      transform.parameters = null
       continue
     }
 
@@ -164,7 +168,7 @@ function readCompositeTransform() {
       ),
       null
     )
-    const fixedParameters = new Float32Array(
+    const fixedParameters = new Float64Array(
       fixedParametersBuffer.buffer.slice(
         fixedParametersBuffer.byteOffset,
         fixedParametersBuffer.byteOffset + fixedParametersBuffer.byteLength
@@ -606,16 +610,16 @@ test.only('runPipelineNode writes and reads a CompositeTransform itk.TransformLi
       'Rigid2D parameters should be Float32Array'
     )
     t.true(
-      rigid2DTransform.fixedParameters instanceof Float32Array,
-      'Rigid2D fixedParameters should be Float32Array'
+      rigid2DTransform.fixedParameters instanceof Float64Array,
+      'Rigid2D fixedParameters should be Float64Array'
     )
     t.true(
       affineTransform.parameters instanceof Float32Array,
       'Affine parameters should be Float32Array'
     )
     t.true(
-      affineTransform.fixedParameters instanceof Float32Array,
-      'Affine fixedParameters should be Float32Array'
+      affineTransform.fixedParameters instanceof Float64Array,
+      'Affine fixedParameters should be Float64Array'
     )
   }
 
@@ -625,7 +629,7 @@ test.only('runPipelineNode writes and reads a CompositeTransform itk.TransformLi
     'pipelines',
     'emscripten-build',
     'transform-read-write-pipeline',
-    'transform-read-write-test'
+    'transform-read-write-composite-test'
   )
   const args = ['0', '0', '--memory-io']
   const desiredOutputs = [{ type: InterfaceTypes.TransformList }]

packages/core/typescript/itk-wasm/test/pipelines/transform-read-write-pipeline/CMakeLists.txt

@@ -17,6 +17,9 @@ include(${ITK_USE_FILE})
 add_executable(transform-read-write-test transform-read-write-test.cxx)
 target_link_libraries(transform-read-write-test PUBLIC ${ITK_LIBRARIES})
 
+add_executable(transform-read-write-composite-test transform-read-write-composite-test.cxx)
+target_link_libraries(transform-read-write-composite-test PUBLIC ${ITK_LIBRARIES})
+
 enable_testing()
 add_test(NAME transform-read-write-test
   COMMAND transform-read-write-test ${CMAKE_CURRENT_SOURCE_DIR}/LinearTransform.h5

packages/core/typescript/itk-wasm/test/pipelines/transform-read-write-pipeline/transform-read-write-composite-test.cxx

@@ -0,0 +1,49 @@
+/*=========================================================================
+ *
+ *  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.
+ *
+ *=========================================================================*/
+#include "itkCompositeTransform.h"
+#include "itkInputTransform.h"
+#include "itkOutputTransform.h"
+#include "itkPipeline.h"
+
+int
+main(int argc, char * argv[])
+{
+  itk::wasm::Pipeline pipeline("transform-read-write-composite-test", "A test for reading and writing composite transforms", argc, argv);
+
+  using ParametersValueType = float;
+  constexpr unsigned int Dimension = 2;
+  using TransformType = itk::CompositeTransform<ParametersValueType, Dimension>;
+
+  using InputTransformType = itk::wasm::InputTransform<TransformType>;
+  InputTransformType inputTransform;
+  pipeline.add_option("input-transform", inputTransform, "The input transform")
+    ->required()
+    ->type_name("INPUT_TRANSFORM");
+
+  using OutputTransformType = itk::wasm::OutputTransform<TransformType>;
+  OutputTransformType outputTransform;
+  pipeline.add_option("output-transform", outputTransform, "The output transform")
+    ->required()
+    ->type_name("OUTPUT_TRANSFORM");
+
+  ITK_WASM_PARSE(pipeline);
+
+  outputTransform.Set(inputTransform.Get());
+
+  return EXIT_SUCCESS;
+}