Change CmakeLists to build image-sets-normalization for WASI.

Fix wasi/__init__ to expose image_sets_normalization.

Author: PaulHax

packages/dicom/CMakeLists.txt

@@ -5,3 +5,14 @@ set(CMAKE_CXX_STANDARD 17)
 
 add_subdirectory(gdcm)
 add_subdirectory(dcmtk)
+
+enable_testing()
+
+add_test(NAME image-sets-normalization-help COMMAND image-sets-normalization --help)
+
+add_test(NAME image-sets-normalization-smoke
+  COMMAND image-sets-normalization image-sets.json --files
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/DicomImageOrientationTest/ImageOrientation.1.dcm
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/DicomImageOrientationTest/ImageOrientation.2.dcm
+    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/DicomImageOrientationTest/ImageOrientation.3.dcm
+)

packages/dicom/gdcm/CMakeLists.txt

@@ -10,6 +10,9 @@ include(${ITK_USE_FILE})
 add_executable(read-image-dicom-file-series read-image-dicom-file-series.cxx)
 target_link_libraries(read-image-dicom-file-series PUBLIC ${ITK_LIBRARIES})
 
+add_executable(image-sets-normalization image-sets-normalization.cxx)
+target_link_libraries(image-sets-normalization PUBLIC ${ITK_LIBRARIES})
+
 if (WASI)
   return()
 endif()
@@ -63,22 +66,6 @@ add_dependencies(${Iconv} ${Iconv_LIBRARY})
 add_executable(read-dicom-tags read-dicom-tags.cxx)
 target_link_libraries(read-dicom-tags PUBLIC ${ITK_LIBRARIES} ${Iconv_LIBRARIES} ${Iconv})
 
-
-add_executable(image-sets-normalization image-sets-normalization.cxx)
-target_link_libraries(image-sets-normalization PUBLIC ${ITK_LIBRARIES})
-
-enable_testing()
-
-add_test(NAME image-sets-normalization-help COMMAND image-sets-normalization --help)
-
-add_test(NAME image-sets-normalization-smoke
-  COMMAND image-sets-normalization image-sets.json --files
-    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/DicomImageOrientationTest/ImageOrientation.1.dcm
-    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/DicomImageOrientationTest/ImageOrientation.2.dcm
-    ${CMAKE_CURRENT_SOURCE_DIR}/test/data/input/DicomImageOrientationTest/ImageOrientation.3.dcm
-)
-
-
 if (EMSCRIPTEN)
   foreach(dicom_io_module
       read-image-dicom-file-series

packages/dicom/python/itkwasm-dicom-emscripten/itkwasm_dicom_emscripten/image_sets_normalization_async.py

@@ -0,0 +1,52 @@
+# Generated file. To retain edits, remove this comment.
+
+from pathlib import Path
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from .js_package import js_package
+
+from itkwasm.pyodide import (
+    to_js,
+    to_py,
+    js_resources
+)
+from itkwasm import (
+    InterfaceTypes,
+    BinaryFile,
+)
+
+async def image_sets_normalization_async(
+    files: List[os.PathLike] = [],
+) -> Any:
+    """Group DICOM files into image sets
+
+    :param files: DICOM files
+    :type  files: os.PathLike
+
+    :return: Image sets JSON
+    :rtype:  Any
+    """
+    js_module = await js_package.js_module
+    web_worker = js_resources.web_worker
+
+    kwargs = {}
+    if files is not None:
+        kwargs["files"] = to_js(BinaryFile(files))
+
+    outputs = await js_module.imageSetsNormalization(webWorker=web_worker, noCopy=True, **kwargs)
+
+    output_web_worker = None
+    output_list = []
+    outputs_object_map = outputs.as_object_map()
+    for output_name in outputs.object_keys():
+        if output_name == 'webWorker':
+            output_web_worker = outputs_object_map[output_name]
+        else:
+            output_list.append(to_py(outputs_object_map[output_name]))
+
+    js_resources.web_worker = output_web_worker
+
+    if len(output_list) == 1:
+        return output_list[0]
+    return tuple(output_list)

packages/dicom/python/itkwasm-dicom-emscripten/itkwasm_dicom_emscripten/js_package.py

@@ -5,5 +5,6 @@
 from .structured_report_to_html import structured_report_to_html
 from .structured_report_to_text import structured_report_to_text
 from .read_image_dicom_file_series import read_image_dicom_file_series
+from .image_sets_normalization import image_sets_normalization
 
 from ._version import __version__

packages/dicom/python/itkwasm-dicom-wasi/itkwasm_dicom_wasi/__init__.py

@@ -0,0 +1,63 @@
+# Generated file. To retain edits, remove this comment.
+
+from pathlib import Path, PurePosixPath
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from importlib_resources import files as file_resources
+
+_pipeline = None
+
+from itkwasm import (
+    InterfaceTypes,
+    PipelineOutput,
+    PipelineInput,
+    Pipeline,
+    BinaryFile,
+)
+
+def image_sets_normalization(
+    files: List[os.PathLike] = [],
+) -> Any:
+    """Group DICOM files into image sets
+
+    :param files: DICOM files
+    :type  files: os.PathLike
+
+    :return: Image sets JSON
+    :rtype:  Any
+    """
+    global _pipeline
+    if _pipeline is None:
+        _pipeline = Pipeline(file_resources('itkwasm_dicom_wasi').joinpath(Path('wasm_modules') / Path('image-sets-normalization.wasi.wasm')))
+
+    pipeline_outputs: List[PipelineOutput] = [
+        PipelineOutput(InterfaceTypes.JsonCompatible),
+    ]
+
+    pipeline_inputs: List[PipelineInput] = [
+    ]
+
+    args: List[str] = ['--memory-io',]
+    # Inputs
+    # Outputs
+    image_sets_metadata_name = '0'
+    args.append(image_sets_metadata_name)
+
+    # Options
+    input_count = len(pipeline_inputs)
+    if len(files) < 1:
+       raise ValueError('"files" kwarg must have a length > 1')
+    if len(files) > 0:
+        args.append('--files')
+        for value in files:
+            input_file = str(PurePosixPath(value))
+            pipeline_inputs.append(PipelineInput(InterfaceTypes.BinaryFile, BinaryFile(value)))
+            args.append(input_file)
+
+
+    outputs = _pipeline.run(args, pipeline_outputs, pipeline_inputs)
+
+    result = outputs[0].data
+    return result
+

packages/dicom/python/itkwasm-dicom-wasi/itkwasm_dicom_wasi/image_sets_normalization.py

@@ -1,13 +1,16 @@
-# Generated file. To retain edits, remove this comment.
+from itkwasm_dicom_wasi import image_sets_normalization
 
 from .common import test_input_path, test_output_path
 
-def test_sort_dicom_series():
-    from itkwasm_dicom_wasi import image_sets_normalization
 
-    test_file_path = test_input_path / "DicomImageOrientationTest" / "ImageOrientation.1.dcm"
+def test_image_sets_normalization():
+    files = [
+        test_input_path / "DicomImageOrientationTest" / "ImageOrientation.1.dcm",
+        test_input_path / "DicomImageOrientationTest" / "ImageOrientation.2.dcm",
+        test_input_path / "DicomImageOrientationTest" / "ImageOrientation.3.dcm",
+    ]
 
-    assert test_file_path.exists()
+    assert files[0].exists()
 
-    output_text = image_sets_normalization([test_file_path])
+    output_text = image_sets_normalization(files)
     assert output_text

packages/dicom/python/itkwasm-dicom-wasi/itkwasm_dicom_wasi/wasm_modules/apply-presentation-state-to-image.wasi.wasm

@@ -0,0 +1,24 @@
+# Generated file. Do not edit.
+
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from itkwasm import (
+    environment_dispatch,
+    BinaryFile,
+)
+
+def image_sets_normalization(
+    files: List[os.PathLike] = [],
+) -> Any:
+    """Group DICOM files into image sets
+
+    :param files: DICOM files
+    :type  files: os.PathLike
+
+    :return: Image sets JSON
+    :rtype:  Any
+    """
+    func = environment_dispatch("itkwasm_dicom", "image_sets_normalization")
+    output = func(files=files)
+    return output

packages/dicom/python/itkwasm-dicom-wasi/itkwasm_dicom_wasi/wasm_modules/image-sets-normalization.wasi.wasm

@@ -0,0 +1,24 @@
+# Generated file. Do not edit.
+
+import os
+from typing import Dict, Tuple, Optional, List, Any
+
+from itkwasm import (
+    environment_dispatch,
+    BinaryFile,
+)
+
+async def image_sets_normalization_async(
+    files: List[os.PathLike] = [],
+) -> Any:
+    """Group DICOM files into image sets
+
+    :param files: DICOM files
+    :type  files: os.PathLike
+
+    :return: Image sets JSON
+    :rtype:  Any
+    """
+    func = environment_dispatch("itkwasm_dicom", "image_sets_normalization_async")
+    output = await func(files=files)
+    return output