@cornerstonejs/tools 2.0.0-beta.1 → 2.0.0-beta.3

package/src/tools/annotation/PlanarFreehandROITool.ts

@@ -44,14 +44,13 @@ import {
   AnnotationStyle,
   PublicToolProps,
   ToolProps,
-  InteractionTypes,
   SVGDrawingHelper,
 } from '../../types';
-import { drawLine, drawCircle, drawLinkedTextBox } from '../../drawingSvg';
+import { drawLinkedTextBox } from '../../drawingSvg';
 import { PlanarFreehandROIAnnotation } from '../../types/ToolSpecificAnnotationTypes';
 import { getTextBoxCoordsCanvas } from '../../utilities/drawing';
 import { PlanarFreehandROICommonData } from '../../utilities/math/polyline/planarFreehandROIInternalTypes';
-import pointInPolyline from '../../utilities/math/polyline/pointInPolyline';
+
 import { getIntersectionCoordinatesWithPolyline } from '../../utilities/math/polyline/getIntersectionWithPolyline';
 import pointInShapeCallback from '../../utilities/pointInShapeCallback';
 import { isViewportPreScaled } from '../../utilities/viewport/isViewportPreScaled';
@@ -59,6 +58,7 @@ import {
   ModalityUnitOptions,
   getModalityUnit,
 } from '../../utilities/getModalityUnit';
+import { BasicStatsCalculator } from '../../utilities/math/basic';
 
 const { pointCanProjectOnLine } = polyline;
 const { EPSILON } = CONSTANTS;
@@ -124,6 +124,7 @@ const PARALLEL_THRESHOLD = 1 - EPSILON;
  *
  * Read more in the Docs section of the website.
  */
+
 class PlanarFreehandROITool extends AnnotationTool {
   static toolName;
 
@@ -215,6 +216,8 @@ class PlanarFreehandROITool extends AnnotationTool {
           knotsRatioPercentageOnEdit: 40,
         },
         calculateStats: false,
+        getTextLines: defaultGetTextLines,
+        statsCalculator: BasicStatsCalculator,
       },
     }
   ) {
@@ -662,30 +665,24 @@ class PlanarFreehandROITool extends AnnotationTool {
       renderStatus = true;
     }
 
-    if (!this.configuration.calculateStats) return;
+    if (!this.configuration.calculateStats) {
+      return;
+    }
 
     annotations.forEach((annotation) => {
       const activeAnnotationUID = this.commonData?.annotation.annotationUID;
       if (
         annotation.annotationUID === activeAnnotationUID &&
         !this.commonData?.movingTextBox
-      )
+      ) {
         return;
-
-      const modalityUnitOptions = {
-        isPreScaled: isViewportPreScaled(viewport, targetId),
-        isSuvScaled: this.isSuvScaled(
-          viewport,
-          targetId,
-          annotation.metadata.referencedImageId
-        ),
-      };
+      }
 
       if (!this.commonData?.movingTextBox) {
         const { data } = annotation;
         if (
           !data.cachedStats[targetId] ||
-          data.cachedStats[targetId].areaUnit === undefined
+          data.cachedStats[targetId].areaUnit == null
         ) {
           data.cachedStats[targetId] = {
             Modality: null,
@@ -700,16 +697,14 @@ class PlanarFreehandROITool extends AnnotationTool {
             annotation,
             viewport,
             renderingEngine,
-            enabledElement,
-            modalityUnitOptions
+            enabledElement
           );
         } else if (annotation.invalidated) {
           this._throttledCalculateCachedStats(
             annotation,
             viewport,
             renderingEngine,
-            enabledElement,
-            modalityUnitOptions
+            enabledElement
           );
         }
       }
@@ -724,8 +719,7 @@ class PlanarFreehandROITool extends AnnotationTool {
     annotation,
     viewport,
     renderingEngine,
-    enabledElement,
-    modalityUnitOptions: ModalityUnitOptions
+    enabledElement
   ) => {
     const data = annotation.data;
     const { cachedStats, polyline: points } = data;
@@ -745,9 +739,28 @@ class PlanarFreehandROITool extends AnnotationTool {
 
       const { imageData, metadata } = image;
       const canvasCoordinates = points.map((p) => viewport.worldToCanvas(p));
+
+      // Using an arbitrary start point (canvasPoint), calculate the
+      // mm spacing for the canvas in the X and Y directions.
+      const canvasPoint = canvasCoordinates[0];
+      const originalWorldPoint = viewport.canvasToWorld(canvasPoint);
+      const deltaXPoint = viewport.canvasToWorld([
+        canvasPoint[0] + 1,
+        canvasPoint[1],
+      ]);
+      const deltaYPoint = viewport.canvasToWorld([
+        canvasPoint[0],
+        canvasPoint[1] + 1,
+      ]);
+
+      const deltaInX = vec3.distance(originalWorldPoint, deltaXPoint);
+      const deltaInY = vec3.distance(originalWorldPoint, deltaYPoint);
+
       const scale = getCalibratedScale(image);
-      const area =
+      let area =
         polyline.calculateAreaOfPoints(canvasCoordinates) / scale / scale;
+      // Convert from canvas_pixels ^2 to mm^2
+      area *= deltaInX * deltaInY;
 
       const worldPosIndex = csUtils.transformWorldToIndex(imageData, points[0]);
       worldPosIndex[0] = Math.floor(worldPosIndex[0]);
@@ -802,25 +815,10 @@ class PlanarFreehandROITool extends AnnotationTool {
       const worldPosEnd = imageData.indexToWorld([iMax, jMax, kMax]);
       const canvasPosEnd = viewport.worldToCanvas(worldPosEnd);
 
-      let count = 0;
-      let sum = 0;
-      let sumSquares = 0;
-      let max = -Infinity;
-
-      const statCalculator = ({ value: newValue }) => {
-        if (newValue > max) {
-          max = newValue;
-        }
-
-        sum += newValue;
-        sumSquares += newValue ** 2;
-        count += 1;
-      };
-
       let curRow = 0;
       let intersections = [];
       let intersectionCounter = 0;
-      pointInShapeCallback(
+      const pointsInShape = pointInShapeCallback(
         imageData,
         (pointLPS, pointIJK) => {
           let result = true;
@@ -854,15 +852,18 @@ class PlanarFreehandROITool extends AnnotationTool {
           }
           return result;
         },
-        statCalculator,
+        this.configuration.statsCalculator.statsCallback,
         boundsIJK
       );
 
-      const mean = sum / count;
-
-      // https://www.strchr.com/standard_deviation_in_one_pass?allcomments=1
-      let stdDev = sumSquares / count - mean ** 2;
-      stdDev = Math.sqrt(stdDev);
+      const modalityUnitOptions = {
+        isPreScaled: isViewportPreScaled(viewport, targetId),
+        isSuvScaled: this.isSuvScaled(
+          viewport,
+          targetId,
+          annotation.metadata.referencedImageId
+        ),
+      };
 
       const modalityUnit = getModalityUnit(
         metadata.Modality,
@@ -870,12 +871,16 @@ class PlanarFreehandROITool extends AnnotationTool {
         modalityUnitOptions
       );
 
+      const stats = this.configuration.statsCalculator.getStatistics();
+
       cachedStats[targetId] = {
         Modality: metadata.Modality,
         area,
-        mean,
-        max,
-        stdDev,
+        mean: stats[1]?.value,
+        max: stats[0]?.value,
+        stdDev: stats[3]?.value,
+        statsArray: stats,
+        pointsInShape: pointsInShape,
         areaUnit: getCalibratedAreaUnits(null, image),
         modalityUnit,
       };
@@ -892,8 +897,21 @@ class PlanarFreehandROITool extends AnnotationTool {
     const data = annotation.data;
     const targetId = this.getTargetId(viewport);
 
-    const textLines = this._getTextLines(data, targetId);
-    if (!textLines || textLines.length === 0) return;
+    const styleSpecifier: AnnotationStyle.StyleSpecifier = {
+      toolGroupId: this.toolGroupId,
+      toolName: this.getToolName(),
+      viewportId: enabledElement.viewport.id,
+    };
+
+    const options = this.getLinkedTextBoxStyle(styleSpecifier, annotation);
+    if (!options.visibility) {
+      return;
+    }
+
+    const textLines = this.configuration.getTextLines(data, targetId);
+    if (!textLines || textLines.length === 0) {
+      return;
+    }
 
     const canvasCoordinates = data.polyline.map((p) =>
       viewport.worldToCanvas(p)
@@ -909,12 +927,6 @@ class PlanarFreehandROITool extends AnnotationTool {
       data.handles.textBox.worldPosition
     );
 
-    const styleSpecifier: AnnotationStyle.StyleSpecifier = {
-      toolGroupId: this.toolGroupId,
-      toolName: this.getToolName(),
-      viewportId: enabledElement.viewport.id,
-    };
-
     const textBoxUID = '1';
     const boundingBox = drawLinkedTextBox(
       svgDrawingHelper,
@@ -924,7 +936,7 @@ class PlanarFreehandROITool extends AnnotationTool {
       textBoxPosition,
       canvasCoordinates,
       {},
-      this.getLinkedTextBoxStyle(styleSpecifier, annotation)
+      options
     );
 
     const { x: left, y: top, width, height } = boundingBox;
@@ -936,35 +948,35 @@ class PlanarFreehandROITool extends AnnotationTool {
       bottomRight: viewport.canvasToWorld([left + width, top + height]),
     };
   };
+}
 
-  _getTextLines = (data, targetId: string): string[] => {
-    const cachedVolumeStats = data.cachedStats[targetId];
-    const { area, mean, stdDev, max, isEmptyArea, areaUnit, modalityUnit } =
-      cachedVolumeStats;
+function defaultGetTextLines(data, targetId): string[] {
+  const cachedVolumeStats = data.cachedStats[targetId];
+  const { area, mean, stdDev, max, isEmptyArea, areaUnit, modalityUnit } =
+    cachedVolumeStats;
 
-    const textLines: string[] = [];
+  const textLines: string[] = [];
 
-    if (area) {
-      const areaLine = isEmptyArea
-        ? `Area: Oblique not supported`
-        : `Area: ${roundNumber(area)} ${areaUnit}`;
-      textLines.push(areaLine);
-    }
+  if (area) {
+    const areaLine = isEmptyArea
+      ? `Area: Oblique not supported`
+      : `Area: ${roundNumber(area)} ${areaUnit}`;
+    textLines.push(areaLine);
+  }
 
-    if (mean) {
-      textLines.push(`Mean: ${roundNumber(mean)} ${modalityUnit}`);
-    }
+  if (mean) {
+    textLines.push(`Mean: ${roundNumber(mean)} ${modalityUnit}`);
+  }
 
-    if (max) {
-      textLines.push(`Max: ${roundNumber(max)} ${modalityUnit}`);
-    }
+  if (max) {
+    textLines.push(`Max: ${roundNumber(max)} ${modalityUnit}`);
+  }
 
-    if (stdDev) {
-      textLines.push(`Std Dev: ${roundNumber(stdDev)} ${modalityUnit}`);
-    }
+  if (stdDev) {
+    textLines.push(`Std Dev: ${roundNumber(stdDev)} ${modalityUnit}`);
+  }
 
-    return textLines;
-  };
+  return textLines;
 }
 
 PlanarFreehandROITool.toolName = 'PlanarFreehandROI';

package/src/tools/annotation/ProbeTool.ts

@@ -94,6 +94,7 @@ const { transformWorldToIndex } = csUtils;
  * Read more in the Docs section of the website.
  *
  */
+
 class ProbeTool extends AnnotationTool {
   static toolName;
 
@@ -118,6 +119,7 @@ class ProbeTool extends AnnotationTool {
       configuration: {
         shadow: true,
         preventHandleOutsideImage: false,
+        getTextLines: defaultGetTextLines,
       },
     }
   ) {
@@ -440,36 +442,19 @@ class ProbeTool extends AnnotationTool {
 
       const color = this.getStyle('color', styleSpecifier, annotation);
 
-      const modalityUnitOptions = {
-        isPreScaled: isViewportPreScaled(viewport, targetId),
-
-        isSuvScaled: this.isSuvScaled(
-          viewport,
-          targetId,
-          annotation.metadata.referencedImageId
-        ),
-      };
-
-      if (!data.cachedStats[targetId]) {
+      if (
+        !data.cachedStats[targetId] ||
+        data.cachedStats[targetId].value == null
+      ) {
         data.cachedStats[targetId] = {
           Modality: null,
           index: null,
           value: null,
         };
 
-        this._calculateCachedStats(
-          annotation,
-          renderingEngine,
-          enabledElement,
-          modalityUnitOptions
-        );
+        this._calculateCachedStats(annotation, renderingEngine, enabledElement);
       } else if (annotation.invalidated) {
-        this._calculateCachedStats(
-          annotation,
-          renderingEngine,
-          enabledElement,
-          modalityUnitOptions
-        );
+        this._calculateCachedStats(annotation, renderingEngine, enabledElement);
 
         // If the invalidated data is as a result of volumeViewport manipulation
         // of the tools, we need to invalidate the related stackViewports data if
@@ -525,7 +510,12 @@ class ProbeTool extends AnnotationTool {
 
       renderStatus = true;
 
-      const textLines = this._getTextLines(data, targetId);
+      const options = this.getLinkedTextBoxStyle(styleSpecifier, annotation);
+      if (!options.visibility) {
+        continue;
+      }
+
+      const textLines = this.configuration.getTextLines(data, targetId);
       if (textLines) {
         const textCanvasCoordinates = [
           canvasCoordinates[0] + 6,
@@ -539,7 +529,7 @@ class ProbeTool extends AnnotationTool {
           textUID,
           textLines,
           [textCanvasCoordinates[0], textCanvasCoordinates[1]],
-          this.getLinkedTextBoxStyle(styleSpecifier, annotation)
+          options
         );
       }
     }
@@ -547,31 +537,9 @@ class ProbeTool extends AnnotationTool {
     return renderStatus;
   };
 
-  _getTextLines(data, targetId: string): string[] | undefined {
-    const cachedVolumeStats = data.cachedStats[targetId];
-    const { index, value, modalityUnit } = cachedVolumeStats;
-
-    if (value === undefined) {
-      return;
-    }
-
-    const textLines = [];
-
-    textLines.push(`(${index[0]}, ${index[1]}, ${index[2]})`);
-
-    textLines.push(`${value.toFixed(2)} ${modalityUnit}`);
-
-    return textLines;
-  }
-
-  _calculateCachedStats(
-    annotation,
-    renderingEngine,
-    enabledElement,
-    modalityUnitOptions: ModalityUnitOptions
-  ) {
+  _calculateCachedStats(annotation, renderingEngine, enabledElement) {
     const data = annotation.data;
-    const { viewportId, renderingEngineId } = enabledElement;
+    const { viewportId, renderingEngineId, viewport } = enabledElement;
 
     const worldPos = data.handles.points[0];
     const { cachedStats } = data;
@@ -581,6 +549,15 @@ class ProbeTool extends AnnotationTool {
     for (let i = 0; i < targetIds.length; i++) {
       const targetId = targetIds[i];
 
+      const modalityUnitOptions = {
+        isPreScaled: isViewportPreScaled(viewport, targetId),
+        isSuvScaled: this.isSuvScaled(
+          viewport,
+          targetId,
+          annotation.metadata.referencedImageId
+        ),
+      };
+
       const image = this.getTargetIdImage(targetId, renderingEngine);
 
       // If image does not exists for the targetId, skip. This can be due
@@ -662,5 +639,22 @@ class ProbeTool extends AnnotationTool {
   }
 }
 
+function defaultGetTextLines(data, targetId): string[] {
+  const cachedVolumeStats = data.cachedStats[targetId];
+  const { index, value, modalityUnit } = cachedVolumeStats;
+
+  if (value === undefined) {
+    return;
+  }
+
+  const textLines = [];
+
+  textLines.push(`(${index[0]}, ${index[1]}, ${index[2]})`);
+
+  textLines.push(`${value.toFixed(2)} ${modalityUnit}`);
+
+  return textLines;
+}
+
 ProbeTool.toolName = 'Probe';
 export default ProbeTool;