Feature/dicom annotator

label_studio/annotation_templates/computer-vision/dicom-annotation/config.yml

@@ -0,0 +1,39 @@
+title: DICOM Medical Image Annotation
+type: community
+group: Computer Vision
+image: /static/templates/dicom-annotation.png
+details: |
+  <h1>Annotate DICOM medical images with multi-frame support</h1>
+  <dl>
+    <dt>Industry Applications</dt>
+    <dd>radiology, pathology, oncology, diagnostic imaging, medical diagnosis, clinical decision support, medical AI, healthcare AI, CT scan, MRI, X-ray, ultrasound, mammography, PET scan, nuclear medicine, interventional radiology, cardiac imaging, neuroimaging, musculoskeletal imaging</dd>
+    <dt>Domain Terminology</dt>
+    <dd>DICOM, PACS, RIS, windowing, window level, window width, Hounsfield units, slice thickness, multi-planar reconstruction, segmentation, contouring, ROI, region of interest, lesion detection, tumor segmentation</dd>
+    <dt>Regulatory</dt>
+    <dd>FDA approval, medical device, clinical validation, HIPAA compliance, patient privacy, de-identification, anonymization</dd>
+  </dl>
+config: |
+  <View>
+    <Header value="DICOM Medical Image Annotation"/>
+
+    <Dicom name="dicom" value="$dicom_url" 
+           brightnessControl="true" 
+           contrastControl="true"/>
+
+    <DicomRectangleLabels name="bbox" toName="dicom">
+      <Label value="Tumor" background="#FF0000"/>
+      <Label value="Lesion" background="#FFA500"/>
+      <Label value="Nodule" background="#FFFF00"/>
+      <Label value="Normal" background="#00FF00"/>
+    </DicomRectangleLabels>
+
+    <Choices name="finding" toName="dicom" choice="single">
+      <Choice value="Abnormal"/>
+      <Choice value="Normal"/>
+      <Choice value="Indeterminate"/>
+    </Choices>
+
+    <TextArea name="notes" toName="dicom" 
+              placeholder="Clinical notes and observations..."
+              rows="3"/>
+  </View>

label_studio/annotation_templates/computer-vision/dicom-segmentation/config.yml

@@ -0,0 +1,37 @@
+title: DICOM Multi-Frame Segmentation
+type: community
+group: Computer Vision
+image: /static/templates/dicom-segmentation.png
+details: |
+  <h1>Segment DICOM medical images across multiple frames/slices</h1>
+  <dl>
+    <dt>Industry Applications</dt>
+    <dd>radiology, radiation oncology, surgical planning, organ segmentation, tumor volumetrics, 3D reconstruction, treatment planning, dose calculation, CT colonography, cardiac CT, brain MRI, liver segmentation, lung nodule analysis</dd>
+    <dt>Domain Terminology</dt>
+    <dd>volumetric segmentation, contour propagation, slice-by-slice annotation, organ delineation, gross tumor volume, clinical target volume, planning target volume, isodose curves</dd>
+    <dt>Regulatory</dt>
+    <dd>FDA 510(k), CE marking, medical device software, clinical validation, HIPAA compliance, patient data protection</dd>
+  </dl>
+config: |
+  <View>
+    <Header value="DICOM Multi-Frame Segmentation"/>
+
+    <Dicom name="dicom" value="$dicom_url" 
+           brightnessControl="true" 
+           contrastControl="true"
+           defaultWindowCenter="40"
+           defaultWindowWidth="400"/>
+
+    <DicomBrushLabels name="segmentation" toName="dicom">
+      <Label value="Liver" background="#8B4513"/>
+      <Label value="Kidney" background="#DC143C"/>
+      <Label value="Spleen" background="#9370DB"/>
+      <Label value="Tumor" background="#FF6347"/>
+      <Label value="Vessel" background="#4169E1"/>
+    </DicomBrushLabels>
+
+    <DicomPolygonLabels name="outline" toName="dicom">
+      <Label value="Organ Boundary" background="#00CED1"/>
+      <Label value="Lesion Boundary" background="#FF4500"/>
+    </DicomPolygonLabels>
+  </View>

label_studio/core/settings/base.py

@@ -486,6 +486,8 @@
     [
         '.bmp',
         '.csv',
+        '.dcm',
+        '.dicom',
         '.flac',
         '.gif',
         '.htm',

web/libs/editor/package.json

@@ -13,6 +13,8 @@
     "colormap": "^2.3.2",
     "d3": "^5.16.0",
     "date-fns": "^2.20.1",
+    "dwv": "^0.33.0",
+    "dwv-react": "^0.15.0",
     "emoji-regex": "^7.0.3",
     "insert-after": "^0.1.4",
     "keymaster": "^1.6.2",
@@ -35,12 +37,11 @@
     "react-virtualized-auto-sizer": "^1.0.20",
     "react-window": "^1.8.9",
     "sanitize-html": "^2.12.1",
-
     "webfft": "^1.0.3",
     "xpath-range": "^1.1.1"
   },
   "main": "src/index.js",
   "devDependencies": {
     "babel-plugin-istanbul": "^7.0.0"
   }
-}
+}

web/libs/editor/src/regions/DicomBrushRegion.js

@@ -0,0 +1,105 @@
+import { types } from "mobx-state-tree";
+
+import NormalizationMixin from "../mixins/Normalization";
+import RegionsMixin from "../mixins/Regions";
+import Registry from "../core/Registry";
+import { AreaMixin } from "../mixins/AreaMixin";
+import { DicomRegion, onlyProps } from "./DicomRegion";
+
+/**
+ * DicomBrushRegion - Brush/segmentation region with DICOM frame support
+ * Stores brush strokes per frame
+ */
+const Model = types
+  .model("DicomBrushRegionModel", {
+    type: "dicombrushregion",
+
+    // Brush data (RLE encoded or raw)
+    rle: types.maybeNull(types.frozen()),
+    touches: types.maybeNull(types.frozen()),
+
+    // Brush properties
+    strokeWidth: types.optional(types.number, 15),
+    opacity: types.optional(types.number, 1),
+  })
+  .volatile(() => ({
+    props: ["rle", "touches", "strokeWidth", "opacity"],
+    // Canvas for brush rendering
+    canvas: null,
+    imageData: null,
+  }))
+  .views((self) => ({
+    get bboxCoords() {
+      // For brush regions, we need to calculate from the mask
+      if (!self.rle && !self.touches) return null;
+      // This would be calculated from the actual brush data
+      return null;
+    },
+
+    /**
+     * Check if this brush region has any data
+     */
+    get hasData() {
+      return !!(self.rle || self.touches);
+    },
+  }))
+  .actions((self) => ({
+    setCanvas(canvas) {
+      self.canvas = canvas;
+    },
+
+    setRle(rle) {
+      self.rle = rle;
+
+      if (self.isMultiFrame) {
+        self.updateShape({ rle }, self.currentFrame);
+      }
+    },
+
+    setTouches(touches) {
+      self.touches = touches;
+
+      if (self.isMultiFrame) {
+        self.updateShape({ touches }, self.currentFrame);
+      }
+    },
+
+    setStrokeWidth(width) {
+      self.strokeWidth = width;
+    },
+
+    setOpacity(opacity) {
+      self.opacity = opacity;
+    },
+
+    /**
+     * Add a brush stroke point
+     */
+    addStrokePoint(point) {
+      const touches = self.touches ? [...self.touches] : [];
+      touches.push(point);
+      self.setTouches(touches);
+    },
+
+    /**
+     * Clear the brush data
+     */
+    clear() {
+      self.rle = null;
+      self.touches = null;
+      self.imageData = null;
+    },
+  }));
+
+const DicomBrushRegionModel = types.compose(
+  "DicomBrushRegionModel",
+  RegionsMixin,
+  DicomRegion,
+  AreaMixin,
+  NormalizationMixin,
+  Model,
+);
+
+Registry.addRegionType(DicomBrushRegionModel, "dicom");
+
+export { DicomBrushRegionModel };

web/libs/editor/src/regions/DicomPolygonRegion.js

@@ -0,0 +1,125 @@
+import { types } from "mobx-state-tree";
+
+import NormalizationMixin from "../mixins/Normalization";
+import RegionsMixin from "../mixins/Regions";
+import Registry from "../core/Registry";
+import { AreaMixin } from "../mixins/AreaMixin";
+import { DicomRegion, onlyProps } from "./DicomRegion";
+
+/**
+ * DicomPolygonRegion - Polygon region with DICOM frame support
+ * Stores polygon points per frame for multi-frame interpolation
+ */
+const Model = types
+  .model("DicomPolygonRegionModel", {
+    type: "dicompolygonregion",
+
+    // Polygon points as array of {x, y}
+    points: types.optional(types.frozen([]), []),
+
+    // Whether the polygon is closed
+    closed: types.optional(types.boolean, true),
+  })
+  .volatile(() => ({
+    props: ["points", "closed"],
+  }))
+  .views((self) => ({
+    get bboxCoords() {
+      const pts = self.isMultiFrame
+        ? self.getShape(self.currentFrame)?.points
+        : self.points;
+
+      if (!pts || pts.length === 0) return null;
+
+      let minX = Infinity,
+        minY = Infinity;
+      let maxX = -Infinity,
+        maxY = -Infinity;
+
+      for (const pt of pts) {
+        minX = Math.min(minX, pt.x);
+        minY = Math.min(minY, pt.y);
+        maxX = Math.max(maxX, pt.x);
+        maxY = Math.max(maxY, pt.y);
+      }
+
+      return {
+        left: minX,
+        top: minY,
+        right: maxX,
+        bottom: maxY,
+      };
+    },
+
+    get pointsArray() {
+      const pts = self.isMultiFrame
+        ? self.getShape(self.currentFrame)?.points
+        : self.points;
+      return pts || [];
+    },
+
+    get flatPoints() {
+      const pts = self.pointsArray;
+      const flat = [];
+      for (const pt of pts) {
+        flat.push(pt.x, pt.y);
+      }
+      return flat;
+    },
+  }))
+  .actions((self) => ({
+    setPoints(points) {
+      self.points = points;
+
+      if (self.isMultiFrame) {
+        self.updateShape({ points }, self.currentFrame);
+      }
+    },
+
+    addPoint(point) {
+      const points = [...self.points, point];
+      self.setPoints(points);
+    },
+
+    removePoint(index) {
+      const points = self.points.filter((_, i) => i !== index);
+      self.setPoints(points);
+    },
+
+    updatePoint(index, point) {
+      const points = self.points.map((p, i) => (i === index ? point : p));
+      self.setPoints(points);
+    },
+
+    setClosed(closed) {
+      self.closed = closed;
+
+      if (self.isMultiFrame) {
+        self.updateShape({ closed }, self.currentFrame);
+      }
+    },
+
+    /**
+     * Move the entire polygon by offset
+     */
+    moveBy(dx, dy) {
+      const points = self.points.map((pt) => ({
+        x: pt.x + dx,
+        y: pt.y + dy,
+      }));
+      self.setPoints(points);
+    },
+  }));
+
+const DicomPolygonRegionModel = types.compose(
+  "DicomPolygonRegionModel",
+  RegionsMixin,
+  DicomRegion,
+  AreaMixin,
+  NormalizationMixin,
+  Model,
+);
+
+Registry.addRegionType(DicomPolygonRegionModel, "dicom");
+
+export { DicomPolygonRegionModel };