WIP: change pipeline interface

Author: PaulHax

packages/dicom/CMakeLists.txt

@@ -5,13 +5,4 @@ set(CMAKE_CXX_STANDARD 17)
 
 add_subdirectory(gdcm)
 add_subdirectory(dcmtk)
-
-find_package(ITK REQUIRED
-  COMPONENTS ITKCommon
-    ITKGDCM
-    WebAssemblyInterface
-  )
-include(${ITK_USE_FILE})
-
-add_executable(sort-dicom-series sort-dicom-series.cxx)
-target_link_libraries(sort-dicom-series PUBLIC ${ITK_LIBRARIES})
+add_subdirectory(sort-dicom-series)

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

@@ -0,0 +1,15 @@
+from pathlib import Path
+
+
+def test_sort_dicom_series():
+    from itkwasm_dicom_wasi import sort_dicom_series
+
+    file_name = "ImageOrientation.1.dcm"
+    test_file_path = Path(
+        "..", "..", "test", "data", "input", "DicomImageOrientationTest", file_name
+    )
+
+    assert test_file_path.exists()
+
+    output_text = sort_dicom_series([test_file_path])
+    assert output_text

packages/dicom/sort-dicom-series.cxx

@@ -0,0 +1,20 @@
+find_package(ITK REQUIRED
+  COMPONENTS ITKCommon
+    ITKGDCM
+    WebAssemblyInterface
+)
+include(${ITK_USE_FILE})
+
+add_executable(sort-dicom-series sort-dicom-series.cxx)
+target_link_libraries(sort-dicom-series PUBLIC ${ITK_LIBRARIES})
+
+enable_testing()
+
+add_test(NAME sort-dicom-series-help COMMAND sort-dicom-series --help)
+
+add_test(NAME sort-dicom-series-smoke
+  COMMAND sort-dicom-series --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/sort-dicom-series/CMakeLists.txt

@@ -0,0 +1,52 @@
+/*=========================================================================
+
+ *  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 "itkPipeline.h"
+#include "itkOutputTextStream.h"
+
+#include "rapidjson/document.h"
+#include "rapidjson/stringbuffer.h"
+#include "rapidjson/writer.h"
+
+int main(int argc, char *argv[])
+{
+  itk::wasm::Pipeline pipeline("sort-dicom-series", "Group DICOM files into volumes", 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");
+
+  itk::wasm::OutputTextStream volumes;
+  pipeline.add_option("volumes", volumes, "Files grouped into volumes")->required()->type_name("OUTPUT_JSON");
+
+  ITK_WASM_PARSE(pipeline);
+
+  rapidjson::Document volumesJson;
+  volumesJson.SetObject();
+  rapidjson::Document::AllocatorType &allocator = volumesJson.GetAllocator();
+
+  rapidjson::Value almostEqualValue;
+  almostEqualValue.SetBool(false);
+  volumesJson.AddMember("almostEqual", almostEqualValue, allocator);
+
+  rapidjson::StringBuffer stringBuffer;
+  rapidjson::Writer<rapidjson::StringBuffer> writer(stringBuffer);
+  volumesJson.Accept(writer);
+  volumes.Get() << stringBuffer.GetString();
+
+  return EXIT_SUCCESS;
+}

packages/dicom/sort-dicom-series/sort-dicom-series.cxx

@@ -60,3 +60,13 @@ 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/index-node-only.ts

@@ -66,3 +66,13 @@ export { readImageDicomFileSeries }
 
 import readImageDicomFileSeriesWorkerFunction from './read-image-dicom-file-series-worker-function.js'
 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 sortDicomSeries from "./sort-dicom-series.js";
+export { sortDicomSeries };

packages/dicom/typescript/src/index-only.ts

@@ -0,0 +1,19 @@
+import test from "ava";
+import path from "path";
+import glob from "glob";
+
+import { sortDicomSeriesNode } from "../../dist/index-node.js";
+
+const testDataInputDirectory = path.resolve("..", "test", "data", "input");
+const testSeriesDirectory = path.resolve(
+  testDataInputDirectory,
+  "DicomImageOrientationTest",
+);
+const testDicomSeriesFiles = glob.sync(`${testSeriesDirectory}/*.dcm`);
+
+test("Test reading a DICOM file", async (t) => {
+  const { volumes } = await sortDicomSeriesNode({
+    files: testDicomSeriesFiles,
+  });
+  t.assert(!!volumes);
+});