From 34acfe9f9ea9fa6a9f5ecf5a8c81d902826b29ff Mon Sep 17 00:00:00 2001
From: Paul Elliott <paul.elliott@kitware.com>
Date: Wed, 25 Sep 2024 15:46:09 -0400
Subject: [PATCH] wip feat(dicom): run readOverlappingSegmentation for SEG

---
 src/io/dicom.ts             | 16 +++++++++++++---
 src/store/datasets-dicom.ts | 12 ++++++++----
 2 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/src/io/dicom.ts b/src/io/dicom.ts
index fed1a7b5..125858a4 100644
--- a/src/io/dicom.ts
+++ b/src/io/dicom.ts
@@ -1,6 +1,10 @@
 import { runPipeline, TextStream, InterfaceTypes, Image } from 'itk-wasm';
 
-import { readDicomTags, readImageDicomFileSeries } from '@itk-wasm/dicom';
+import {
+  readDicomTags,
+  readImageDicomFileSeries,
+  readOverlappingSegmentation,
+} from '@itk-wasm/dicom';
 
 import itkConfig from '@/src/io/itk/itkConfig';
 import { getDicomSeriesWorkerPool, getWorker } from '@/src/io/itk/worker';
@@ -176,13 +180,19 @@ export async function readVolumeSlice(
  * @param {File[]} seriesFiles the set of files to build volume from
  * @returns ItkImage
  */
-export async function buildImage(seriesFiles: File[]) {
+export async function buildImage(seriesFiles: File[], modality: string) {
   const inputImages = seriesFiles.map((file) => sanitizeFile(file));
+  if (modality === 'SEG') {
+    const result = await readOverlappingSegmentation(inputImages[0], {
+      webWorker: getWorker(),
+    });
+    console.log(result.metaInfo);
+    return result.segImage;
+  }
   const result = await readImageDicomFileSeries({
     webWorkerPool: getDicomSeriesWorkerPool(),
     inputImages,
     singleSortedSeries: false,
   });
-
   return result.outputImage;
 }
diff --git a/src/store/datasets-dicom.ts b/src/store/datasets-dicom.ts
index 41da3478..341708d4 100644
--- a/src/store/datasets-dicom.ts
+++ b/src/store/datasets-dicom.ts
@@ -143,12 +143,12 @@ export const getWindowLevels = (info: VolumeInfo) => {
   return widths.map((width, i) => ({ width, level: levels[i] }));
 };
 
-const constructImage = async (volumeKey: string) => {
+const constructImage = async (volumeKey: string, volumeInfo: VolumeInfo) => {
   const fileStore = useFileStore();
   const files = fileStore.getFiles(volumeKey);
   if (!files) throw new Error('No files for volume key');
   const image = vtkITKHelper.convertItkToVtkImage(
-    await DICOM.buildImage(files)
+    await DICOM.buildImage(files, volumeInfo.Modality)
   );
   return image;
 };
@@ -196,7 +196,11 @@ export const useDICOMStore = defineStore('dicom', {
         Object.entries(volumeToFiles).map(async ([volumeKey, files]) => {
           // Read tags of first file
           if (!(volumeKey in this.volumeInfo)) {
-            const tags = await readDicomTags(files[0]);
+            const rawTags = await readDicomTags(files[0]);
+            // trim whitespace from all values
+            const tags = Object.fromEntries(
+              Object.entries(rawTags).map(([key, value]) => [key, value.trim()])
+            );
             // TODO parse the raw string values
             const patient = {
               PatientID: tags.PatientID || ANONYMOUS_PATIENT_ID,
@@ -398,7 +402,7 @@ export const useDICOMStore = defineStore('dicom', {
         : [];
       // actually build volume or wait for existing build?
       const newImagePromise = buildNeeded
-        ? constructImage(volumeKey)
+        ? constructImage(volumeKey, this.volumeInfo[volumeKey])
         : this.volumeImageData[volumeKey];
       // let other calls to buildVolume reuse this constructImage work
       this.volumeImageData[volumeKey] = newImagePromise;