FIX pixel spacing in grid tool, now retrieved from larvitar manager (#…

…405)

* FIX pixel spacing in grid tool, now retrieved from larvitar manager

* Update docs

* new version

* Update docs

---------

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

dist/imaging/loaders/commonLoader.d.ts

@@ -92,6 +92,14 @@ export declare const removeSeriesFromLarvitarManager: (seriesId: string) => void
  * @return {Object} larvitar manager data
  */
 export declare const getSeriesDataFromLarvitarManager: (seriesId: string) => Series | import("../types").NrrdSeries | null;
+/**
+ * Return the metadata of a specific imageId stored in the Larvitar Manager
+ * @instance
+ * @function getImageDataFromLarvitarManager
+ * @param {String} imageId The Id of the image
+ * @return {MetaData | null} Image metadata
+ */
+export declare const getImageDataFromLarvitarManager: (imageId: string) => MetaData | null;
 /**
  * Compute and return image frame
  * @instance

dist/index.d.ts

@@ -26,7 +26,7 @@ import { addDiameterTool, addContoursTool, addMaskEditingTool, getCurrentMaskDat
 import { csToolsCreateStack, csToolsUpdateImageIds, csToolsUpdateImageIndex, initializeCSTools, setToolsStyle, addDefaultTools, addTool, setToolActive, setToolDisabled, setToolEnabled, setToolPassive, exportAnnotations } from "./imaging/tools/main";
 import { DEFAULT_TOOLS, dvTools, getDefaultToolsByType, setDefaultToolsProps, registerExternalTool } from "./imaging/tools/default";
 import { initSegmentationModule, addSegmentationMask, clearSegmentationState, deleteMask, setActiveLabelmap, setActiveSegment, enableBrushTool, disableBrushTool, undoLastStroke, redoLastStroke, setBrushProps, toggleContourMode, toggleVisibility, hexToRgb, rgbToHex, getActiveLabelmapBuffer } from "./imaging/tools/segmentation";
-import { updateLarvitarManager, populateLarvitarManager, populateInstanceGSPSDict, getLarvitarManager, getInstanceGSPSDict, getLarvitarImageTracker, resetLarvitarManager, resetInstanceGSPSDict, removeSeriesFromLarvitarManager, getSeriesDataFromLarvitarManager, getImageFrame, getSopInstanceUIDFromLarvitarManager } from "./imaging/loaders/commonLoader";
+import { updateLarvitarManager, populateLarvitarManager, populateInstanceGSPSDict, getLarvitarManager, getInstanceGSPSDict, getLarvitarImageTracker, resetLarvitarManager, resetInstanceGSPSDict, removeSeriesFromLarvitarManager, getSeriesDataFromLarvitarManager, getImageDataFromLarvitarManager, getImageFrame, getSopInstanceUIDFromLarvitarManager } from "./imaging/loaders/commonLoader";
 import { buildNrrdImage, getNrrdImageId, loadNrrdImage, getImageIdFromSlice, getSliceNumberFromImageId, getNrrdSerieDimensions } from "./imaging/loaders/nrrdLoader";
 import { getDicomImageId, cacheImage, cacheImages, loadAndCacheImageStack, loadAndCacheDsaImageStack } from "./imaging/loaders/dicomLoader";
 import { loadReslicedImage } from "./imaging/loaders/resliceLoader";
@@ -37,4 +37,4 @@ import { getColormapsList, applyColorMap, addColorMap, fillPixelData, HSVToRGB }
 import { applyDSAShift } from "./imaging/postProcessing/applyDSA";
 import { saveAnnotations, loadAnnotations } from "./imaging/tools/io";
 import { addMouseKeyHandlers, removeMouseKeyHandlers, toggleMouseToolsListeners } from "./imaging/tools/interaction";
-export { VERSION, cornerstone, cornerstoneTools, parseDicom, cornerstoneFileImageLoader, segModule, cornerstoneDICOMImageLoader, checkAndClearMemory, checkMemoryAllocation, getUsedMemory, getAvailableMemory, getPerformanceMonitor, activatePerformanceMonitor, deactivatePerformanceMonitor, store, parseECG, renderECG, unrenderECG, syncECGFrame, updateECGFrame, getDefaultECGLayout, getImagePresets, setImagePreset, setImageCustomPreset, getNormalOrientation, getMinPixelValue, getMaxPixelValue, getPixelRepresentation, getTypedArrayFromDataType, getSortedStack, randomId, getMeanValue, getReslicedMetadata, getReslicedPixeldata, getDistanceBetweenSlices, getImageMetadata, buildHeader, getCachedPixelData, buildData, buildDataAsync, importNRRDImage, exportImageToBase64, exportImageToBase64OriginalSizes, anonymize, customizeByteArray, buildLayer, updateLayer, getActiveLayer, setActiveLayer, initializeImageLoader, initializeWebImageLoader, initializeFileImageLoader, registerNRRDImageLoader, registerResliceLoader, registerMultiFrameImageLoader, registerDsaImageLoader, updateLoadedStack, readFile, readFiles, parseDataSet, clearImageParsing, clearImageCache, loadAndCacheImages, renderFileImage, renderDICOMPDF, renderWebImage, disableViewport, unloadViewport, resizeViewport, renderImage, updateImage, redrawImage, resetViewports, updateViewportData, toggleMouseToolsListeners, storeViewportData, invertImage, flipImageHorizontal, flipImageVertical, rotateImageLeft, rotateImageRight, resliceSeries, getColormapsList, applyColorMap, addColorMap, fillPixelData, HSVToRGB, parseContours, updateLarvitarManager, populateLarvitarManager, populateInstanceGSPSDict, getLarvitarManager, getInstanceGSPSDict, getLarvitarImageTracker, resetLarvitarManager, resetInstanceGSPSDict, removeSeriesFromLarvitarManager, getSeriesDataFromLarvitarManager, getImageFrame, getSopInstanceUIDFromLarvitarManager, buildNrrdImage, getNrrdImageId, loadNrrdImage, getImageIdFromSlice, getSliceNumberFromImageId, getNrrdSerieDimensions, loadReslicedImage, getDicomImageId, cacheImage, cacheImages, loadAndCacheImageStack, loadAndCacheDsaImageStack, loadMultiFrameImage, buildMultiFrameImage, getMultiFrameImageId, clearMultiFrameCache, populateDsaImageIds, getFileManager, resetFileLoader, resetFileManager, populateFileManager, getFileImageId, applyDSAShift, addDiameterTool, addContoursTool, addMaskEditingTool, getCurrentMaskData, addStackStateToElement, addSeedsTool, clearMeasurements, getToolState, clearToolStateByName, updateDiameterTool, addToolStateSingleSlice, clearCornerstoneElements, syncToolStack, updateStackToolState, setSegmentationConfig, csToolsCreateStack, csToolsUpdateImageIds, csToolsUpdateImageIndex, initializeCSTools, setToolsStyle, addDefaultTools, addTool, setToolActive, setToolDisabled, setToolEnabled, setToolPassive, exportAnnotations, DEFAULT_TOOLS, dvTools, getDefaultToolsByType, setDefaultToolsProps, registerExternalTool, saveAnnotations, loadAnnotations, addMouseKeyHandlers, removeMouseKeyHandlers, initSegmentationModule, addSegmentationMask, setActiveLabelmap, setActiveSegment, undoLastStroke, redoLastStroke, setBrushProps, hexToRgb, rgbToHex, clearSegmentationState, deleteMask, enableBrushTool, disableBrushTool, toggleContourMode, toggleVisibility, getActiveLabelmapBuffer, updateTemporalViewportData };
+export { VERSION, cornerstone, cornerstoneTools, parseDicom, cornerstoneFileImageLoader, segModule, cornerstoneDICOMImageLoader, checkAndClearMemory, checkMemoryAllocation, getUsedMemory, getAvailableMemory, getPerformanceMonitor, activatePerformanceMonitor, deactivatePerformanceMonitor, store, parseECG, renderECG, unrenderECG, syncECGFrame, updateECGFrame, getDefaultECGLayout, getImagePresets, setImagePreset, setImageCustomPreset, getNormalOrientation, getMinPixelValue, getMaxPixelValue, getPixelRepresentation, getTypedArrayFromDataType, getSortedStack, randomId, getMeanValue, getReslicedMetadata, getReslicedPixeldata, getDistanceBetweenSlices, getImageMetadata, buildHeader, getCachedPixelData, buildData, buildDataAsync, importNRRDImage, exportImageToBase64, exportImageToBase64OriginalSizes, anonymize, customizeByteArray, buildLayer, updateLayer, getActiveLayer, setActiveLayer, initializeImageLoader, initializeWebImageLoader, initializeFileImageLoader, registerNRRDImageLoader, registerResliceLoader, registerMultiFrameImageLoader, registerDsaImageLoader, updateLoadedStack, readFile, readFiles, parseDataSet, clearImageParsing, clearImageCache, loadAndCacheImages, renderFileImage, renderDICOMPDF, renderWebImage, disableViewport, unloadViewport, resizeViewport, renderImage, updateImage, redrawImage, resetViewports, updateViewportData, toggleMouseToolsListeners, storeViewportData, invertImage, flipImageHorizontal, flipImageVertical, rotateImageLeft, rotateImageRight, resliceSeries, getColormapsList, applyColorMap, addColorMap, fillPixelData, HSVToRGB, parseContours, updateLarvitarManager, populateLarvitarManager, populateInstanceGSPSDict, getLarvitarManager, getInstanceGSPSDict, getLarvitarImageTracker, resetLarvitarManager, resetInstanceGSPSDict, removeSeriesFromLarvitarManager, getSeriesDataFromLarvitarManager, getImageDataFromLarvitarManager, getImageFrame, getSopInstanceUIDFromLarvitarManager, buildNrrdImage, getNrrdImageId, loadNrrdImage, getImageIdFromSlice, getSliceNumberFromImageId, getNrrdSerieDimensions, loadReslicedImage, getDicomImageId, cacheImage, cacheImages, loadAndCacheImageStack, loadAndCacheDsaImageStack, loadMultiFrameImage, buildMultiFrameImage, getMultiFrameImageId, clearMultiFrameCache, populateDsaImageIds, getFileManager, resetFileLoader, resetFileManager, populateFileManager, getFileImageId, applyDSAShift, addDiameterTool, addContoursTool, addMaskEditingTool, getCurrentMaskData, addStackStateToElement, addSeedsTool, clearMeasurements, getToolState, clearToolStateByName, updateDiameterTool, addToolStateSingleSlice, clearCornerstoneElements, syncToolStack, updateStackToolState, setSegmentationConfig, csToolsCreateStack, csToolsUpdateImageIds, csToolsUpdateImageIndex, initializeCSTools, setToolsStyle, addDefaultTools, addTool, setToolActive, setToolDisabled, setToolEnabled, setToolPassive, exportAnnotations, DEFAULT_TOOLS, dvTools, getDefaultToolsByType, setDefaultToolsProps, registerExternalTool, saveAnnotations, loadAnnotations, addMouseKeyHandlers, removeMouseKeyHandlers, initSegmentationModule, addSegmentationMask, setActiveLabelmap, setActiveSegment, undoLastStroke, redoLastStroke, setBrushProps, hexToRgb, rgbToHex, clearSegmentationState, deleteMask, enableBrushTool, disableBrushTool, toggleContourMode, toggleVisibility, getActiveLabelmapBuffer, updateTemporalViewportData };

imaging/loaders/commonLoader.ts

@@ -260,6 +260,25 @@ export const getSeriesDataFromLarvitarManager = function (seriesId: string) {
   return larvitarManager ? larvitarManager[seriesId] : null;
 };
 
+/**
+ * Return the metadata of a specific imageId stored in the Larvitar Manager
+ * @instance
+ * @function getImageDataFromLarvitarManager
+ * @param {String} imageId The Id of the image
+ * @return {MetaData | null} Image metadata
+ */
+export const getImageDataFromLarvitarManager = function (imageId: string) {
+  if (larvitarManager) {
+    for (const [seriesId, seriesObj] of Object.entries(larvitarManager)) {
+      if (seriesObj.imageIds && seriesObj.imageIds.includes(imageId)) {
+        const imageData = seriesObj.instances[imageId].metadata;
+        return imageData;
+      }
+    }
+  }
+  return null;
+};
+
 /**
  * Compute and return image frame
  * @instance

imaging/tools/custom/gridTool.ts

@@ -23,6 +23,7 @@ import {
 import { handleElement } from "./utils/gridToolUtils/gridToolUtils";
 import { Coords, GridConfig, MeasurementMouseEvent } from "../types";
 import { DEFAULT_TOOLS } from "../default";
+import { getImageDataFromLarvitarManager } from "../../loaders/commonLoader";
 
 /**
  * @public
@@ -148,15 +149,12 @@ export class GridTool extends BaseTool {
     if (newSetup) this.configuration.setup = newSetup;
 
     const image = enabledElement.image as Image;
-    const pixelSpacing = {
-      x: image.columnPixelSpacing,
-      y: image.rowPixelSpacing
-    };
-
+    const imageMetadata = getImageDataFromLarvitarManager(image.imageId);
+    const pixelSpacing = imageMetadata!.pixelSpacing!;
     try {
       validatePixelSpacing(
-        pixelSpacing.x,
-        pixelSpacing.y,
+        pixelSpacing[0],
+        pixelSpacing[1],
         this.configuration.setup.minPixelSpacing
       );
     } catch (error: any) {
@@ -178,11 +176,11 @@ export class GridTool extends BaseTool {
     );
 
     let patternHeight = this.configuration.setup.gridDimensionMM
-      ? mmToPixels(this.configuration.setup.gridDimensionMM, pixelSpacing.y)
-      : mmToPixels(this.configuration.setup.gridDimensionMM, pixelSpacing.y);
+      ? mmToPixels(this.configuration.setup.gridDimensionMM, pixelSpacing[1])
+      : mmToPixels(this.configuration.setup.gridDimensionMM, pixelSpacing[1]);
     let patternWidth = this.configuration.setup.gridDimensionMM
-      ? mmToPixels(this.configuration.setup.gridDimensionMM, pixelSpacing.x)
-      : mmToPixels(this.configuration.setup.gridDimensionMM, pixelSpacing.x);
+      ? mmToPixels(this.configuration.setup.gridDimensionMM, pixelSpacing[0])
+      : mmToPixels(this.configuration.setup.gridDimensionMM, pixelSpacing[0]);
     const patternCanvasDimensions = convertDimensionsToCanvas(
       element,
       patternWidth,
@@ -192,11 +190,11 @@ export class GridTool extends BaseTool {
     //dash dimension
     let dashHeight = mmToPixels(
       this.configuration.setup.dashHeightMM,
-      pixelSpacing.y
+      pixelSpacing[1]
     );
     let dashWidth = mmToPixels(
       this.configuration.setup.dashWidthMM,
-      pixelSpacing.x
+      pixelSpacing[0]
     );
     const dashCanvasDimensions = convertDimensionsToCanvas(
       element,

index.ts

@@ -199,6 +199,7 @@ import {
   resetInstanceGSPSDict,
   removeSeriesFromLarvitarManager,
   getSeriesDataFromLarvitarManager,
+  getImageDataFromLarvitarManager,
   getImageFrame,
   getSopInstanceUIDFromLarvitarManager
 } from "./imaging/loaders/commonLoader";
@@ -375,6 +376,7 @@ export {
   resetInstanceGSPSDict,
   removeSeriesFromLarvitarManager,
   getSeriesDataFromLarvitarManager,
+  getImageDataFromLarvitarManager,
   getImageFrame,
   getSopInstanceUIDFromLarvitarManager,
   // loaders/nrrdLoader

package.json

@@ -6,7 +6,7 @@
     "medical",
     "cornerstone"
   ],
-  "version": "2.6.2-beta.0",
+  "version": "2.6.2-beta.1",
   "description": "typescript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",