Rename sort-dicom-series to image-sets-normalization

Author: PaulHax

packages/dicom/CMakeLists.txt

@@ -5,4 +5,3 @@ set(CMAKE_CXX_STANDARD 17)
 
 add_subdirectory(gdcm)
 add_subdirectory(dcmtk)
-add_subdirectory(sort-dicom-series)

packages/dicom/gdcm/CMakeLists.txt

@@ -63,6 +63,22 @@ 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/sort-dicom-series/sort-dicom-series.cxx renamed to packages/dicom/gdcm/image-sets-normalization.cxx

@@ -25,28 +25,28 @@
 
 int main(int argc, char *argv[])
 {
-  itk::wasm::Pipeline pipeline("sort-dicom-series", "Group DICOM files into volumes", argc, argv);
+  itk::wasm::Pipeline pipeline("image-sets-normalization", "Group DICOM files into image sets", argc, argv);
 
   std::vector<std::string> files;
-  pipeline.add_option("--files", files, "DICOM files to group")->required()->check(CLI::ExistingFile)->type_size(1, -1)->type_name("INPUT_BINARY_FILE");
+  pipeline.add_option("--files", files, "DICOM files")->required()->check(CLI::ExistingFile)->type_size(1, -1)->type_name("INPUT_BINARY_FILE");
 
-  itk::wasm::OutputTextStream volumes;
-  pipeline.add_option("volumes", volumes, "Files grouped into volumes")->required()->type_name("OUTPUT_JSON");
+  itk::wasm::OutputTextStream imageSetsMetadata;
+  pipeline.add_option("image-sets-metadata", imageSetsMetadata, "Image sets JSON")->required()->type_name("OUTPUT_JSON");
 
   ITK_WASM_PARSE(pipeline);
 
-  rapidjson::Document volumesJson;
-  volumesJson.SetObject();
-  rapidjson::Document::AllocatorType &allocator = volumesJson.GetAllocator();
+  rapidjson::Document imageSetsJson;
+  imageSetsJson.SetObject();
+  rapidjson::Document::AllocatorType &allocator = imageSetsJson.GetAllocator();
 
   rapidjson::Value almostEqualValue;
   almostEqualValue.SetBool(false);
-  volumesJson.AddMember("almostEqual", almostEqualValue, allocator);
+  imageSetsJson.AddMember("", almostEqualValue, allocator);
 
   rapidjson::StringBuffer stringBuffer;
   rapidjson::Writer<rapidjson::StringBuffer> writer(stringBuffer);
-  volumesJson.Accept(writer);
-  volumes.Get() << stringBuffer.GetString();
+  imageSetsJson.Accept(writer);
+  imageSetsMetadata.Get() << stringBuffer.GetString();
 
   return EXIT_SUCCESS;
 }

packages/dicom/python/itkwasm-dicom-wasi/test/test_sort_dicom_series.py

@@ -0,0 +1,16 @@
+# Generated file. To retain edits, remove this comment.
+
+from itkwasm_dicom_wasi import image
+
+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"
+
+    assert test_file_path.exists()
+
+    output_text = image_sets_normalization([test_file_path])
+    assert output_text
+    

packages/dicom/python/itkwasm-dicom-wasi/tests/test_image_sets_normalization.py

@@ -0,0 +1,11 @@
+// Generated file. To retain edits, remove this comment.
+
+import { BinaryFile } from 'itk-wasm'
+
+interface ImageSetsNormalizationNodeOptions {
+  /** DICOM files */
+  files: string[] | File[] | BinaryFile[]
+
+}
+
+export default ImageSetsNormalizationNodeOptions

packages/dicom/sort-dicom-series/CMakeLists.txt

@@ -0,0 +1,11 @@
+// Generated file. To retain edits, remove this comment.
+
+import { JsonCompatible } from 'itk-wasm'
+
+interface ImageSetsNormalizationNodeResult {
+  /** Image sets JSON */
+  imageSetsMetadata: JsonCompatible
+
+}
+
+export default ImageSetsNormalizationNodeResult

packages/dicom/typescript/src/image-sets-normalization-node-options.ts

@@ -0,0 +1,74 @@
+// Generated file. To retain edits, remove this comment.
+
+import {
+  JsonCompatible,
+  InterfaceTypes,
+  PipelineOutput,
+  PipelineInput,
+  runPipelineNode
+} from 'itk-wasm'
+
+import ImageSetsNormalizationNodeOptions from './image-sets-normalization-node-options.js'
+import ImageSetsNormalizationNodeResult from './image-sets-normalization-node-result.js'
+
+import path from 'path'
+import { fileURLToPath } from 'url'
+
+/**
+ * Group DICOM files into image sets
+ *
+ * @param {ImageSetsNormalizationNodeOptions} options - options object
+ *
+ * @returns {Promise<ImageSetsNormalizationNodeResult>} - result object
+ */
+async function imageSetsNormalizationNode(
+  options: ImageSetsNormalizationNodeOptions = { files: [] as string[], }
+) : Promise<ImageSetsNormalizationNodeResult> {
+
+  const mountDirs: Set<string> = new Set()
+
+  const desiredOutputs: Array<PipelineOutput> = [
+    { type: InterfaceTypes.JsonCompatible },
+  ]
+
+  const inputs: Array<PipelineInput> = [
+  ]
+
+  const args = []
+  // Inputs
+  // Outputs
+  const imageSetsMetadataName = '0'
+  args.push(imageSetsMetadataName)
+
+  // Options
+  args.push('--memory-io')
+  if (options.files) {
+    if(options.files.length < 1) {
+      throw new Error('"files" option must have a length > 1')
+    }
+    args.push('--files')
+
+    options.files.forEach((value) => {
+      mountDirs.add(path.dirname(value as string))
+      args.push(value as string)
+    })
+  }
+
+  const pipelinePath = path.join(path.dirname(fileURLToPath(import.meta.url)), 'pipelines', 'image-sets-normalization')
+
+  const {
+    returnValue,
+    stderr,
+    outputs
+  } = await runPipelineNode(pipelinePath, args, desiredOutputs, inputs, mountDirs)
+  if (returnValue !== 0 && stderr !== "") {
+    throw new Error(stderr)
+  }
+
+  const result = {
+    imageSetsMetadata: outputs[0]?.data as JsonCompatible,
+  }
+  return result
+}
+
+export default imageSetsNormalizationNode

packages/dicom/typescript/src/image-sets-normalization-node-result.ts

@@ -0,0 +1,11 @@
+// Generated file. To retain edits, remove this comment.
+
+import { BinaryFile, WorkerPoolFunctionOption } from 'itk-wasm'
+
+interface ImageSetsNormalizationOptions extends WorkerPoolFunctionOption {
+  /** DICOM files */
+  files: string[] | File[] | BinaryFile[]
+
+}
+
+export default ImageSetsNormalizationOptions

packages/dicom/typescript/src/image-sets-normalization-node.ts

@@ -0,0 +1,11 @@
+// Generated file. To retain edits, remove this comment.
+
+import { JsonCompatible, WorkerPoolFunctionResult } from 'itk-wasm'
+
+interface ImageSetsNormalizationResult extends WorkerPoolFunctionResult {
+  /** Image sets JSON */
+  imageSetsMetadata: JsonCompatible
+
+}
+
+export default ImageSetsNormalizationResult

packages/dicom/typescript/src/image-sets-normalization-options.ts

@@ -0,0 +1,87 @@
+// Generated file. To retain edits, remove this comment.
+
+import {
+  JsonCompatible,
+  BinaryFile,
+  InterfaceTypes,
+  PipelineOutput,
+  PipelineInput,
+  runPipeline
+} from 'itk-wasm'
+
+import ImageSetsNormalizationOptions from './image-sets-normalization-options.js'
+import ImageSetsNormalizationResult from './image-sets-normalization-result.js'
+
+import { getPipelinesBaseUrl } from './pipelines-base-url.js'
+import { getPipelineWorkerUrl } from './pipeline-worker-url.js'
+
+import { getDefaultWebWorker } from './default-web-worker.js'
+
+/**
+ * Group DICOM files into image sets
+ *
+ * @param {ImageSetsNormalizationOptions} options - options object
+ *
+ * @returns {Promise<ImageSetsNormalizationResult>} - result object
+ */
+async function imageSetsNormalization(
+  options: ImageSetsNormalizationOptions = { files: [] as BinaryFile[] | File[] | string[], }
+) : Promise<ImageSetsNormalizationResult> {
+
+  const desiredOutputs: Array<PipelineOutput> = [
+    { type: InterfaceTypes.JsonCompatible },
+  ]
+
+  const inputs: Array<PipelineInput> = [
+  ]
+
+  const args = []
+  // Inputs
+  // Outputs
+  const imageSetsMetadataName = '0'
+  args.push(imageSetsMetadataName)
+
+  // Options
+  args.push('--memory-io')
+  if (options.files) {
+    if(options.files.length < 1) {
+      throw new Error('"files" option must have a length > 1')
+    }
+    args.push('--files')
+
+    await Promise.all(options.files.map(async (value) => {
+      let valueFile = value
+      if (value instanceof File) {
+        const valueBuffer = await value.arrayBuffer()
+        valueFile = { path: value.name, data: new Uint8Array(valueBuffer) }
+      }
+      inputs.push({ type: InterfaceTypes.BinaryFile, data: valueFile as BinaryFile })
+      const name = value instanceof File ? value.name : (valueFile as BinaryFile).path
+      args.push(name)
+    }))
+  }
+
+  const pipelinePath = 'image-sets-normalization'
+
+  let workerToUse = options?.webWorker
+  if (workerToUse === undefined) {
+    workerToUse = await getDefaultWebWorker()
+  }
+  const {
+    webWorker: usedWebWorker,
+    returnValue,
+    stderr,
+    outputs
+  } = await runPipeline(pipelinePath, args, desiredOutputs, inputs, { pipelineBaseUrl: getPipelinesBaseUrl(), pipelineWorkerUrl: getPipelineWorkerUrl(), webWorker: workerToUse, noCopy: options?.noCopy })
+  if (returnValue !== 0 && stderr !== "") {
+    throw new Error(stderr)
+  }
+
+  const result = {
+    webWorker: usedWebWorker as Worker,
+    imageSetsMetadata: outputs[0]?.data as JsonCompatible,
+  }
+  return result
+}
+
+export default imageSetsNormalization

packages/dicom/typescript/src/image-sets-normalization-result.ts

@@ -42,6 +42,16 @@ import structuredReportToTextNode from './structured-report-to-text-node.js'
 export { structuredReportToTextNode }
 
 
+import ImageSetsNormalizationNodeResult from './image-sets-normalization-node-result.js'
+export type { ImageSetsNormalizationNodeResult }
+
+import ImageSetsNormalizationNodeOptions from './image-sets-normalization-node-options.js'
+export type { ImageSetsNormalizationNodeOptions }
+
+import imageSetsNormalizationNode from './image-sets-normalization-node.js'
+export { imageSetsNormalizationNode }
+
+
 import ReadDicomTagsNodeResult from './read-dicom-tags-node-result.js'
 export type { ReadDicomTagsNodeResult }
 
@@ -60,13 +70,3 @@ export type { ReadImageDicomFileSeriesNodeOptions }
 
 import readImageDicomFileSeriesNode from './read-image-dicom-file-series-node.js'
 export { readImageDicomFileSeriesNode }
-
-
-import SortDicomSeriesNodeResult from './sort-dicom-series-node-result.js'
-export type { SortDicomSeriesNodeResult }
-
-import SortDicomSeriesNodeOptions from './sort-dicom-series-node-options.js'
-export type { SortDicomSeriesNodeOptions }
-
-import sortDicomSeriesNode from './sort-dicom-series-node.js'
-export { sortDicomSeriesNode }

packages/dicom/typescript/src/image-sets-normalization.ts

@@ -68,11 +68,12 @@ import readImageDicomFileSeriesWorkerFunction from './read-image-dicom-file-seri
 export { readImageDicomFileSeriesWorkerFunction }
 
 
-import SortDicomSeriesResult from "./sort-dicom-series-result.js";
-export type { SortDicomSeriesResult };
 
-import SortDicomSeriesOptions from "./sort-dicom-series-options.js";
-export type { SortDicomSeriesOptions };
+import ImageSetsNormalizationResult from './image-sets-normalization-result.js'
+export type { ImageSetsNormalizationResult }
 
-import sortDicomSeries from "./sort-dicom-series.js";
-export { sortDicomSeries };
+import ImageSetsNormalizationOptions from './image-sets-normalization-options.js'
+export type { ImageSetsNormalizationOptions }
+
+import imageSetsNormalization from './image-sets-normalization.js'
+export { imageSetsNormalization }