From b089616434dcce4d70061a2bdca209bc02923600 Mon Sep 17 00:00:00 2001
From: Paul Elliott <paul.elliott@kitware.com>
Date: Thu, 11 Apr 2024 14:48:10 -0400
Subject: [PATCH] feat(segmentGroups): create segments from converted image

---
 src/io/dicom.ts            | 30 --------------------------
 src/store/segmentGroups.ts | 43 ++++++++++++++++++++++++++++++++++----
 2 files changed, 39 insertions(+), 34 deletions(-)

diff --git a/src/io/dicom.ts b/src/io/dicom.ts
index af54476da..1dc91a36d 100644
--- a/src/io/dicom.ts
+++ b/src/io/dicom.ts
@@ -219,36 +219,6 @@ export class DICOMIO {
     return result.outputs[0].data as Image;
   }
 
-  async resample(fixed: SpatialParameters, moving: Image) {
-    await this.initialize();
-
-    const { size, spacing, origin, direction } = fixed;
-    const args = [
-      '--action',
-      'resample',
-      '0', // space for input image
-
-      '--size',
-      size.join(','),
-      '--spacing',
-      spacing.join(','),
-      '--origin',
-      origin.join(','),
-      '--direction',
-      direction.join(','),
-
-      '--memory-io',
-      '0',
-    ];
-
-    const inputs = [{ type: InterfaceTypes.Image, data: moving }];
-    const outputs = [{ type: InterfaceTypes.Image }];
-
-    const result = await this.runTask('dicom', args, inputs, outputs);
-    const image = result.outputs[0].data as Image;
-    return image;
-  }
-
   /**
    * Builds a volume for a set of files.
    * @async
diff --git a/src/store/segmentGroups.ts b/src/store/segmentGroups.ts
index 4b89b47b5..dc1f3c73b 100644
--- a/src/store/segmentGroups.ts
+++ b/src/store/segmentGroups.ts
@@ -28,6 +28,7 @@ import {
   selectionEquals,
 } from './datasets';
 import { ensureSameSpace } from '../io/resample/resample';
+import { useDICOMStore } from './datasets-dicom';
 
 const LabelmapArrayType = Uint8Array;
 export type LabelmapArrayType = Uint8Array;
@@ -205,6 +206,41 @@ export const useSegmentGroupStore = defineStore('segmentGroup', () => {
     delete metadataByID[id];
   }
 
+  let lastColorIndex = 0;
+  function getNextColor() {
+    const color = DEFAULT_SEGMENT_MASKS[lastColorIndex].color;
+    lastColorIndex = (lastColorIndex + 1) % DEFAULT_SEGMENT_MASKS.length;
+    return color;
+  }
+
+  function decodeSegments(image: DataSelection) {
+    if (image.type === 'image') {
+      return structuredClone(DEFAULT_SEGMENT_MASKS);
+    }
+
+    const dicomStore = useDICOMStore();
+    const volumeInfo = dicomStore.volumeInfo[image.volumeKey];
+    const segmentSequence = undefined; // volumeInfo.SegmentSequence;
+    if (!segmentSequence) {
+      return [
+        {
+          value: 255,
+          name: volumeInfo.SeriesDescription || 'Unknown Segment',
+          color: getNextColor(),
+        },
+      ];
+    }
+    // TODO convert Recommended Display CIELab Value (0062,000D) tag to a segment color
+    // TODO convert SegmentDescription (0062,0006) tag to a segment name
+    return [
+      {
+        value: 255,
+        name: volumeInfo.SeriesDescription || 'Unknown Segment',
+        color: [255, 0, 255, 255],
+      },
+    ];
+  }
+
   /**
    * Converts an image to a labelmap.
    */
@@ -241,10 +277,9 @@ export const useSegmentGroupStore = defineStore('segmentGroup', () => {
     const resampled = await ensureSameSpace(parentImage, childImage, true);
     const labelmapImage = toLabelMap(resampled);
 
-    const { order, byKey } = normalizeForStore(
-      structuredClone(DEFAULT_SEGMENT_MASKS),
-      'value'
-    );
+    const segments = decodeSegments(image);
+
+    const { order, byKey } = normalizeForStore(segments, 'value');
     const segmentGroupStore = useSegmentGroupStore();
     segmentGroupStore.addLabelmap(labelmapImage, {
       name: imageStore.metadata[imageID].name,