WIP: ENH: WASM binding output paths are passed as input function argu…

…ments

package.json

@@ -11,7 +11,7 @@
     "build:wasi:debug": "itk-wasm -i itkwasm/wasi:20230917-38fb6f92-debug build -- -DCMAKE_BUILD_TYPE:STRING=Debug",
     "build:testData": "dam download wasm/test/data wasm/test/data.tar.gz bafybeiblzvqdyzykgfy47qfuec3mysd7s4not6t7hgrwkxyuhjmwesqdgi https://data.kitware.com/api/v1/file/64ebf79837a2250d4df1463e/download https://w3s.link/ipfs/bafybeibfwkkoiugogidxetnqor76dzppfrbaspimjuyz2vdqdtqe4s7are",
     "bindgen:typescript": "/home/matt/src/itk-wasm/src/itk-wasm-cli.js -b emscripten-build bindgen --output-dir wasm/typescript --package-name @itk-wasm/elastix --package-version 0.1.0 --package-description \"A toolbox for rigid and nonrigid registration of images.\" --repository 'https://github.com/InsightSoftwareConsortium/ITKElastix'",
-    "bindgen:python": "itk-wasm -b wasi-build bindgen --interface python --output-dir wasm/python --package-name itkwasm-elastix --package-version 0.1.0 --package-description \"A toolbox for rigid and nonrigid registration of images.\" --repository 'https://github.com/InsightSoftwareConsortium/ITKElastix'",
+    "bindgen:python": "/home/matt/src/itk-wasm/src/itk-wasm-cli.js -b wasi-build bindgen --interface python --output-dir wasm/python --package-name itkwasm-elastix --package-version 0.1.0 --package-description \"A toolbox for rigid and nonrigid registration of images.\" --repository 'https://github.com/InsightSoftwareConsortium/ITKElastix'",
     "test": "npm run test:wasi",
     "test:wasi": "itk-wasm test --test-dir wasm -- -V",
     "clean": "git clean -fdx -e node_modules"

wasm/elastix-wasm.cxx

@@ -73,7 +73,7 @@ class PipelineFunctor
     pipeline.add_option("result", resultImage, "Resampled moving image")->required()->type_name("OUTPUT_IMAGE");
 
     std::string outputTransform;
-    pipeline.add_option("transform", outputTransform, "Fixed-to-moving transform")
+    pipeline.add_option("transform", outputTransform, "Fixed-to-moving transform file")
       ->required()
       ->type_name("OUTPUT_BINARY_FILE");
 

wasm/python/itkwasm-elastix-emscripten/itkwasm_elastix_emscripten/elastix_async.py

@@ -21,16 +21,20 @@
 
 async def elastix_async(
     parameter_object: Any,
+    transform: str,
     fixed: Optional[Image] = None,
     moving: Optional[Image] = None,
     initial_transform: Optional[os.PathLike] = None,
     initial_transform_parameter_object: Optional[Any] = None,
-) -> Tuple[Image, os.PathLike, Any]:
+) -> Tuple[Image, Any]:
     """Rigid and non-rigid registration of images.
 
     :param parameter_object: Elastix parameter object representation
     :type  parameter_object: Any
 
+    :param transform: Fixed-to-moving transform file
+    :type  transform: str
+
     :param fixed: Fixed image
     :type  fixed: Image
 
@@ -46,9 +50,6 @@ async def elastix_async(
     :return: Resampled moving image
     :rtype:  Image
 
-    :return: Fixed-to-moving transform
-    :rtype:  os.PathLike
-
     :return: Elastix optimized transform parameter object representation
     :rtype:  Any
     """

wasm/python/itkwasm-elastix-emscripten/itkwasm_elastix_emscripten/write_parameter_files_async.py

@@ -20,14 +20,15 @@
 
 async def write_parameter_files_async(
     parameter_object: Any,
+    parameter_files: List[str],
 ) -> os.PathLike:
     """Write an elastix parameter text file from a parameter object.
 
-    :param parameter_object: Elastix parameter object representation
+    :param parameter_object: Elastix parameter object representation.
     :type  parameter_object: Any
 
-    :return: Elastix parameter files
-    :rtype:  os.PathLike
+    :param parameter_files: Elastix parameter files, must have the same length as the number of parameter maps in the parameter object.
+    :type  parameter_files: List[str]
     """
     js_module = await js_package.js_module
     web_worker = js_resources.web_worker

wasm/python/itkwasm-elastix-wasi/itkwasm_elastix_wasi/default_parameter_map.py

@@ -1,7 +1,5 @@
 # Generated file. To retain edits, remove this comment.
 
-# Generated file. Do not edit.
-
 from pathlib import Path, PurePosixPath
 import os
 from typing import Dict, Tuple, Optional, List, Any
@@ -51,8 +49,11 @@ def default_parameter_map(
     # Inputs
     args.append(str(transform_name))
     # Outputs
-    args.append('0')
+    parameter_map_name = '0'
+    args.append(parameter_map_name)
+
     # Options
+    input_count = len(pipeline_inputs)
     if number_of_resolutions:
         args.append('--number-of-resolutions')
         args.append(str(number_of_resolutions))

wasm/python/itkwasm-elastix-wasi/itkwasm_elastix_wasi/elastix.py

@@ -1,7 +1,5 @@
 # Generated file. To retain edits, remove this comment.
 
-# Generated file. Do not edit.
-
 from pathlib import Path, PurePosixPath
 import os
 from typing import Dict, Tuple, Optional, List, Any
@@ -21,16 +19,20 @@
 
 def elastix(
     parameter_object: Any,
+    transform: str,
     fixed: Optional[Image] = None,
     moving: Optional[Image] = None,
     initial_transform: Optional[os.PathLike] = None,
     initial_transform_parameter_object: Optional[Any] = None,
-) -> Tuple[Image, os.PathLike, Any]:
+) -> Tuple[Image, Any]:
     """Rigid and non-rigid registration of images.
 
     :param parameter_object: Elastix parameter object representation
     :type  parameter_object: Any
 
+    :param transform: Fixed-to-moving transform file
+    :type  transform: str
+
     :param fixed: Fixed image
     :type  fixed: Image
 
@@ -46,9 +48,6 @@ def elastix(
     :return: Resampled moving image
     :rtype:  Image
 
-    :return: Fixed-to-moving transform
-    :rtype:  os.PathLike
-
     :return: Elastix optimized transform parameter object representation
     :rtype:  Any
     """
@@ -70,21 +69,28 @@ def elastix(
     # Inputs
     args.append('0')
     # Outputs
-    args.append('0')
-    args.append(str(PurePosixPath(transform)))
-    args.append('2')
+    result_name = '0'
+    args.append(result_name)
+
+    transform_name = str(PurePosixPath(transform))
+    args.append(transform_name)
+
+    transform_parameter_object_name = '2'
+    args.append(transform_parameter_object_name)
+
     # Options
+    input_count = len(pipeline_inputs)
     if fixed is not None:
-        input_count_string = str(len(pipeline_inputs))
         pipeline_inputs.append(PipelineInput(InterfaceTypes.Image, fixed))
         args.append('--fixed')
-        args.append(input_count_string)
+        args.append(str(input_count))
+        input_count += 1
 
     if moving is not None:
-        input_count_string = str(len(pipeline_inputs))
         pipeline_inputs.append(PipelineInput(InterfaceTypes.Image, moving))
         args.append('--moving')
-        args.append(input_count_string)
+        args.append(str(input_count))
+        input_count += 1
 
     if initial_transform is not None:
         input_file = str(PurePosixPath(initial_transform))
@@ -93,17 +99,17 @@ def elastix(
         args.append(input_file)
 
     if initial_transform_parameter_object is not None:
-        input_count_string = str(len(pipeline_inputs))
         pipeline_inputs.append(PipelineInput(InterfaceTypes.JsonCompatible, initial_transform_parameter_object))
         args.append('--initial-transform-parameter-object')
-        args.append(input_count_string)
+        args.append(str(input_count))
+        input_count += 1
 
 
+    print(args, pipeline_outputs, pipeline_inputs)
     outputs = _pipeline.run(args, pipeline_outputs, pipeline_inputs)
 
     result = (
         outputs[0].data,
-        Path(outputs[1].data.path),
         outputs[2].data.data,
     )
     return result

wasm/python/itkwasm-elastix-wasi/itkwasm_elastix_wasi/read_parameter_files.py

@@ -1,7 +1,5 @@
 # Generated file. To retain edits, remove this comment.
 
-# Generated file. Do not edit.
-
 from pathlib import Path, PurePosixPath
 import os
 from typing import Dict, Tuple, Optional, List, Any
@@ -43,8 +41,11 @@ def read_parameter_files(
     args: List[str] = ['--memory-io',]
     # Inputs
     # Outputs
-    args.append('0')
+    parameter_object_name = '0'
+    args.append(parameter_object_name)
+
     # Options
+    input_count = len(pipeline_inputs)
     if len(parameter_files) < 1:
        raise ValueError('"parameter-files" kwarg must have a length > 1')
     if len(parameter_files) > 0:

wasm/python/itkwasm-elastix-wasi/itkwasm_elastix_wasi/write_parameter_files.py

@@ -1,7 +1,5 @@
 # Generated file. To retain edits, remove this comment.
 
-# Generated file. Do not edit.
-
 from pathlib import Path, PurePosixPath
 import os
 from typing import Dict, Tuple, Optional, List, Any
@@ -20,22 +18,28 @@
 
 def write_parameter_files(
     parameter_object: Any,
+    parameter_files: List[str],
 ) -> os.PathLike:
     """Write an elastix parameter text file from a parameter object.
 
-    :param parameter_object: Elastix parameter object representation
+    :param parameter_object: Elastix parameter object representation.
     :type  parameter_object: Any
 
-    :return: Elastix parameter files
-    :rtype:  os.PathLike
+    :param parameter_files: Elastix parameter files, must have the same length as the number of parameter maps in the parameter object.
+    :type  parameter_files: List[str]
     """
     global _pipeline
     if _pipeline is None:
         _pipeline = Pipeline(file_resources('itkwasm_elastix_wasi').joinpath(Path('wasm_modules') / Path('write-parameter-files.wasi.wasm')))
+    parameter_files_pipeline_outputs = [PipelineOutput(InterfaceTypes.TextFile, TextFile(PurePosixPath(p))) for p in parameter_files]
 
     pipeline_outputs: List[PipelineOutput] = [
-        PipelineOutput(InterfaceTypes.TextFile, TextFile(PurePosixPath(parameter_files))),
+        *parameter_files_pipeline_outputs,
     ]
+    output_index = 0
+    parameter_files_start = output_index
+    output_index += len(parameter_files)
+    parameter_files_end = output_index
 
     pipeline_inputs: List[PipelineInput] = [
         PipelineInput(InterfaceTypes.JsonCompatible, parameter_object),
@@ -45,11 +49,11 @@ def write_parameter_files(
     # Inputs
     args.append('0')
     # Outputs
-    args.append(str(PurePosixPath(parameter_files)))
+    args.extend([str(PurePosixPath(p)) for p in parameter_files])
+
     # Options
+    input_count = len(pipeline_inputs)
 
     outputs = _pipeline.run(args, pipeline_outputs, pipeline_inputs)
 
-    result = Path(outputs[0].data.path)
-    return result